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[*] c++ --version <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro --version -fPIC -fstack-protector-strong -I/tmp/math/plumed/work/.buildlink/include -pie [*] c++ -v <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -v -fPIC -fstack-protector-strong -I/tmp/math/plumed/work/.buildlink/include -pie [*] c++ -V <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -V -fPIC -fstack-protector-strong -I/tmp/math/plumed/work/.buildlink/include -pie [*] c++ -qversion <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -qversion -fPIC -fstack-protector-strong -I/tmp/math/plumed/work/.buildlink/include -pie [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib conftest.cpp -llapack -lblas <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib conftest.cpp -llapack -lblas -fPIC -fstack-protector-strong -pie [*] c++ -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib conftest.cpp -llapack -lblas <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib conftest.cpp -llapack -lblas -fPIC -fstack-protector-strong -pie [*] c++ -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib conftest.cpp -llapack -lblas <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib conftest.cpp -llapack -lblas -fPIC -fstack-protector-strong -pie [*] c++ -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include conftest.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include conftest.cpp -fPIC -fstack-protector-strong [*] c++ -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include conftest.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include conftest.cpp -fPIC -fstack-protector-strong [*] c++ -c -g -I/usr/include -I/usr/pkg/include conftest.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -g -I/tmp/math/plumed/work/.buildlink/include conftest.cpp -fPIC -fstack-protector-strong [*] cc --version <.> /tmp/math/plumed/work/.gcc/bin/gcc -fcommon -Wl,-zrelro --version -fPIC -D_FORTIFY_SOURCE=2 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[*] c++ -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -I/usr/include -I/usr/pkg/include -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib conftest.cpp -llapack -lblas <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib conftest.cpp -llapack -lblas -fPIC -fstack-protector-strong -pie [*] c++ -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -I/usr/include -I/usr/pkg/include conftest.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -fPIC -fstack-protector-strong [*] c++ -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall 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-llapack -lblas -fPIC -fstack-protector-strong -pie [*] c++ -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -I/usr/include -I/usr/pkg/include -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib conftest.cpp -lgslcblas -lz -llapack -lblas <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib conftest.cpp -lgslcblas -lz -llapack -lblas -fPIC -fstack-protector-strong -pie [*] c++ -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -I/usr/include -I/usr/pkg/include conftest.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -fPIC -fstack-protector-strong [*] c++ -E -I/usr/include -I/usr/pkg/include conftest.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -E -I/tmp/math/plumed/work/.buildlink/include conftest.cpp -fPIC -fstack-protector-strong [*] c++ -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -I/usr/include -I/usr/pkg/include -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib conftest.cpp -lgslcblas -lz -llapack -lblas <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib conftest.cpp -lgslcblas -lz -llapack -lblas -fPIC -fstack-protector-strong -pie [*] c++ -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -I/usr/include -I/usr/pkg/include -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib conftest.cpp -lgsl -lgslcblas -lz -llapack -lblas <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib conftest.cpp -lgsl -lgslcblas -lz -llapack -lblas -fPIC -fstack-protector-strong -pie [*] c++ -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -I/usr/include -I/usr/pkg/include conftest.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -fPIC -fstack-protector-strong [*] c++ -E -I/usr/include -I/usr/pkg/include conftest.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -E -I/tmp/math/plumed/work/.buildlink/include conftest.cpp -fPIC -fstack-protector-strong [*] c++ -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -I/usr/include -I/usr/pkg/include -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib conftest.cpp -lgsl -lgslcblas -lz -llapack -lblas <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib conftest.cpp -lgsl -lgslcblas -lz -llapack -lblas -fPIC -fstack-protector-strong -pie [*] c++ -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -I/usr/include -I/usr/pkg/include -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib conftest.cpp -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib conftest.cpp -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas -fPIC -fstack-protector-strong -pie [*] c++ -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -I/usr/include -I/usr/pkg/include -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib conftest.cpp -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -o conftest -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib conftest.cpp -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas -fPIC -fstack-protector-strong -pie [*] c++ --print-prog-name=ld <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro --print-prog-name=ld -fPIC -fstack-protector-strong -I/tmp/math/plumed/work/.buildlink/include -pie [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -c conftest-main.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-main.cpp -fPIC -fstack-protector-strong [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -c conftest-f.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-f.cpp -fPIC -fstack-protector-strong [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -c conftest-g.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-g.cpp -fPIC -fstack-protector-strong [*] ld -r -o conftest-both.o conftest-f.o conftest-g.o <.> ld -r -o conftest-both.o conftest-f.o conftest-g.o [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -o conftest.exe conftest-main.o conftest-both.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -o conftest.exe conftest-main.o conftest-both.o -fPIC -fstack-protector-strong -pie [*] c++ --print-prog-name=ar <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro --print-prog-name=ar -fPIC -fstack-protector-strong -I/tmp/math/plumed/work/.buildlink/include -pie [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -c conftest-main.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-main.cpp -fPIC -fstack-protector-strong [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -c conftest-f.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-f.cpp -fPIC -fstack-protector-strong [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -c conftest-g.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-g.cpp -fPIC -fstack-protector-strong [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -o conftest.exe conftest-main.o conftest-both.a <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -o conftest.exe conftest-main.o conftest-both.a -fPIC -fstack-protector-strong -pie [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -c conftest-main.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-main.cpp -fPIC -fstack-protector-strong [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -c conftest-f.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-f.cpp -fPIC -fstack-protector-strong [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -c conftest-g.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-g.cpp -fPIC -fstack-protector-strong [*] ld -r -o conftest-both.o conftest-f.o conftest-g.o <.> ld -r -o conftest-both.o conftest-f.o conftest-g.o [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -o conftest.exe conftest-main.o conftest-both.a <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -o conftest.exe conftest-main.o conftest-both.a -fPIC -fstack-protector-strong -pie [*] cc -c conftest-main.c <.> /tmp/math/plumed/work/.gcc/bin/gcc -fcommon -Wl,-zrelro -c conftest-main.c -fPIC -D_FORTIFY_SOURCE=2 -fstack-protector-strong -I/tmp/math/plumed/work/.buildlink/include [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -c conftest.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest.cpp -fPIC -fstack-protector-strong [*] cc conftest.o conftest-main.o -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas -o conftest.exe <.> /tmp/math/plumed/work/.gcc/bin/gcc -fcommon -Wl,-zrelro conftest.o conftest-main.o -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas -o conftest.exe -fPIC -D_FORTIFY_SOURCE=2 -fstack-protector-strong -I/tmp/math/plumed/work/.buildlink/include -pie [*] cc conftest.o conftest-main.o -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas -o conftest.exe <.> /tmp/math/plumed/work/.gcc/bin/gcc -fcommon -Wl,-zrelro conftest.o conftest-main.o -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas -o conftest.exe -fPIC -D_FORTIFY_SOURCE=2 -fstack-protector-strong -I/tmp/math/plumed/work/.buildlink/include -pie [*] f77 -c conftest-main.f90 <.> /tmp/math/plumed/work/.gfortran/bin/gfortran -c conftest-main.f90 -fPIC -fstack-protector-strong [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -c conftest.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest.cpp -fPIC -fstack-protector-strong [*] f77 conftest.o conftest-main.o -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas -o conftest.exe <.> /tmp/math/plumed/work/.gfortran/bin/gfortran conftest.o conftest-main.o -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas -o conftest.exe -fPIC -fstack-protector-strong -pie [*] /tmp/math/plumed/work/.tools/bin/mkdir conf17164.dir <.> /bin/mkdir -p conf17164.dir [*] /tmp/math/plumed/work/.tools/bin/mkdir -p . <.> /bin/mkdir -p -p . [*] /tmp/math/plumed/work/.tools/bin/true <.> true [*] /tmp/math/plumed/work/.tools/bin/true <.> true [*] /tmp/math/plumed/work/.tools/bin/true <.> true [*] /tmp/math/plumed/work/.tools/bin/true <.> true [*] /tmp/math/plumed/work/.tools/bin/true <.> true [*] /tmp/math/plumed/work/.tools/bin/true <.> true [*] /tmp/math/plumed/work/.tools/bin/true <.> true [*] /tmp/math/plumed/work/.tools/bin/true <.> true [*] /tmp/math/plumed/work/.tools/bin/true <.> true [*] /tmp/math/plumed/work/.tools/bin/true <.> true [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/blas <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/blas [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/bias [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/analysis <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/bias <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/analysis [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/cltools [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/asmjit <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/asmjit <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/cltools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/colvar <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/colvar [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p config [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> /bin/mkdir -p -p tools <.> /bin/mkdir -p -p config [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/echo Nothing to do in /tmp/math/plumed/work/plumed-2.8.0/src/config [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> echo Nothing to do in /tmp/math/plumed/work/plumed-2.8.0/src/config [*] /tmp/math/plumed/work/.tools/bin/mkdir -p reference [*] /tmp/math/plumed/work/.tools/bin/mkdir -p reference <.> /bin/mkdir -p -p reference <.> /bin/mkdir -p -p tools <.> /bin/mkdir -p -p reference [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/core <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p vesselbase <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p molfile <.> /bin/mkdir -p -p vesselbase <.> /bin/mkdir -p -p molfile [*] /tmp/math/plumed/work/.tools/bin/mkdir -p config <.> /bin/mkdir -p -p config [*] /tmp/math/plumed/work/.tools/bin/mkdir -p xdrfile <.> /bin/mkdir -p -p xdrfile [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/function <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p gridtools <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/function <.> /bin/mkdir -p -p gridtools [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/generic [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p lepton <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/generic [*] /tmp/math/plumed/work/.tools/bin/mkdir -p multicolvar <.> /bin/mkdir -p -p lepton <.> /bin/mkdir -p -p multicolvar <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p bias <.> /bin/mkdir -p -p core <.> /bin/mkdir -p -p bias [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/gridtools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p reference <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/gridtools <.> /bin/mkdir -p -p reference [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/isdb <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/isdb <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p bias <.> /bin/mkdir -p -p bias [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p xdrfile [*] /tmp/math/plumed/work/.tools/bin/mkdir -p lepton <.> /bin/mkdir -p -p xdrfile <.> /bin/mkdir -p -p tools <.> /bin/mkdir -p -p lepton [*] /tmp/math/plumed/work/.tools/bin/mkdir -p colvar <.> /bin/mkdir -p -p colvar [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/lapack <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/lapack [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/lepton <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/lepton [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p vesselbase [*] /tmp/math/plumed/work/.tools/bin/mkdir -p blas <.> /bin/mkdir -p -p vesselbase <.> /bin/mkdir -p -p blas [*] /tmp/math/plumed/work/.tools/bin/mkdir -p asmjit <.> /bin/mkdir -p -p asmjit [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/main <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/main [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/mapping <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/mapping [*] /tmp/math/plumed/work/.tools/bin/mkdir -p reference <.> /bin/mkdir -p -p reference [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/molfile <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/molfile [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p wrapper <.> /bin/mkdir -p -p core <.> /bin/mkdir -p -p wrapper [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/multicolvar <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/multicolvar [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/reference <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/reference [*] /tmp/math/plumed/work/.tools/bin/mkdir -p function <.> /bin/mkdir -p -p function [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p cltools <.> /bin/mkdir -p -p cltools [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/secondarystructure <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/secondarystructure [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p reference [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p reference [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> /bin/mkdir -p -p core <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p vesselbase <.> /bin/mkdir -p -p vesselbase [*] /tmp/math/plumed/work/.tools/bin/mkdir -p vesselbase <.> /bin/mkdir -p -p vesselbase [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/setup [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/setup <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p gridtools <.> /bin/mkdir -p -p gridtools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p reference <.> /bin/mkdir -p -p reference [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/vatom <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/vatom [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/tools <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p vesselbase <.> /bin/mkdir -p -p vesselbase [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/echo Nothing to do in /tmp/math/plumed/work/plumed-2.8.0/src/wrapper <.> echo Nothing to do in /tmp/math/plumed/work/plumed-2.8.0/src/wrapper [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/vesselbase <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/vesselbase [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p lapack <.> /bin/mkdir -p -p lapack [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/xdrfile <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/xdrfile [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p lepton <.> /bin/mkdir -p -p lepton [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p bias <.> /bin/mkdir -p -p bias [*] /tmp/math/plumed/work/.tools/bin/mkdir -p analysis <.> /bin/mkdir -p -p analysis [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] /tmp/math/plumed/work/.tools/bin/mkdir deps [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFblas.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp blas.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFblas.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp blas.cpp -fPIC -fstack-protector-strong <.> /bin/mkdir -p deps [*] c++ -c -MM -MFABMD.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ABMD.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFABMD.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ABMD.cpp -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFAnalysisBase.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AnalysisBase.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFAnalysisBase.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp AnalysisBase.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFarch.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp arch.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFarch.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp arch.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 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'-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp codebuilder.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFcodebuilder.d -I/tmp/math/plumed/work/.buildlink/include 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ExtendedLagrangian.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ExtendedLagrangian.cpp -o ExtendedLagrangian.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ExtendedLagrangian.cpp -o ExtendedLagrangian.o -fPIC 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-D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp osutils.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp osutils.cpp -o osutils.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp osutils.cpp -o osutils.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFregalloc.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp regalloc.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFregalloc.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp regalloc.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFEuclideanDissimilarityMatrix.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp EuclideanDissimilarityMatrix.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFEuclideanDissimilarityMatrix.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp EuclideanDissimilarityMatrix.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp regalloc.cpp -o regalloc.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp regalloc.cpp -o regalloc.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp EuclideanDissimilarityMatrix.cpp -o EuclideanDissimilarityMatrix.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp EuclideanDissimilarityMatrix.cpp -o EuclideanDissimilarityMatrix.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFruntime.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp runtime.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFruntime.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp runtime.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp runtime.cpp -o runtime.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' 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x86assembler.cpp -o x86assembler.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDriverFloat.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DriverFloat.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFDriverFloat.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DriverFloat.cpp -fPIC 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-I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MaxEnt.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFMaxEnt.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MaxEnt.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MaxEnt.cpp -o MaxEnt.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MaxEnt.cpp -o MaxEnt.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFFarthestPointSampling.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' 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-D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MetaD.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 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-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MetaD.cpp -o MetaD.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFGenExample.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp GenExample.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFGenExample.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp GenExample.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp GenExample.cpp -o GenExample.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp GenExample.cpp -o GenExample.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFx86compiler.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86compiler.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFx86compiler.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp x86compiler.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86compiler.cpp -o x86compiler.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp x86compiler.cpp -o x86compiler.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFLandmarkSelectionBase.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkSelectionBase.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFLandmarkSelectionBase.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkSelectionBase.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkSelectionBase.cpp -o LandmarkSelectionBase.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkSelectionBase.cpp -o LandmarkSelectionBase.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFGenTemplate.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp GenTemplate.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFGenTemplate.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp GenTemplate.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp GenTemplate.cpp -o GenTemplate.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp GenTemplate.cpp -o GenTemplate.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFLandmarkStaged.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkStaged.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFLandmarkStaged.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkStaged.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkStaged.cpp -o LandmarkStaged.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkStaged.cpp -o LandmarkStaged.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFx86inst.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86inst.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFx86inst.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp x86inst.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86inst.cpp -o x86inst.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 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-I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Manual.cpp -o Manual.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic 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OutputColvarFile.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp OutputColvarFile.cpp -o OutputColvarFile.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPdbRenumber.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PdbRenumber.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPdbRenumber.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PdbRenumber.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PdbRenumber.cpp -o PdbRenumber.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PdbRenumber.cpp -o PdbRenumber.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFx86logging.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86logging.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFx86logging.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp x86logging.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86logging.cpp -o x86logging.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp x86logging.cpp -o x86logging.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFOutputPDBFile.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp OutputPDBFile.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFOutputPDBFile.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp OutputPDBFile.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 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-D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp x86regalloc.cpp -o x86regalloc.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFMovingRestraint.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MovingRestraint.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFMovingRestraint.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MovingRestraint.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MovingRestraint.cpp -o MovingRestraint.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MovingRestraint.cpp -o MovingRestraint.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPrintDissimilarityMatrix.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PrintDissimilarityMatrix.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPrintDissimilarityMatrix.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PrintDissimilarityMatrix.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PrintDissimilarityMatrix.cpp -o PrintDissimilarityMatrix.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PrintDissimilarityMatrix.cpp -o PrintDissimilarityMatrix.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFSumHills.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp SumHills.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFSumHills.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SumHills.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp SumHills.cpp -o SumHills.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SumHills.cpp -o SumHills.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPBMetaD.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PBMetaD.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPBMetaD.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PBMetaD.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' 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-D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp kT.cpp -o kT.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFpesmd.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp pesmd.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFpesmd.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 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-D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp pesmd.cpp -o pesmd.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp pesmd.cpp -o pesmd.o -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFAngle.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Angle.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFAngle.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Angle.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Angle.cpp -o Angle.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Angle.cpp -o Angle.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFReselectLandmarks.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReselectLandmarks.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFReselectLandmarks.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ReselectLandmarks.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReselectLandmarks.cpp -o ReselectLandmarks.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ReselectLandmarks.cpp -o ReselectLandmarks.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFCell.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Cell.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFCell.d 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-pedantic -std=c++11 -fopenmp ReweightBase.cpp -o ReweightBase.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFSelectWithStride.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp SelectWithStride.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFSelectWithStride.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SelectWithStride.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFWhamHistogram.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp WhamHistogram.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFWhamHistogram.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp WhamHistogram.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp SelectWithStride.cpp -o SelectWithStride.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SelectWithStride.cpp -o SelectWithStride.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp WhamHistogram.cpp -o WhamHistogram.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp WhamHistogram.cpp -o WhamHistogram.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFContactMap.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ContactMap.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFContactMap.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' 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'-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ContactMap.cpp -o ContactMap.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ContactMap.cpp -o ContactMap.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFReweightBias.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightBias.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFReweightBias.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightBias.cpp -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/echo Building compile_options.sh, a sourceable bash script with some compilation options <.> echo Building compile_options.sh, a sourceable bash script with some compilation options [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFConfig.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Config.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFConfig.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Config.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightBias.cpp -o ReweightBias.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightBias.cpp -o ReweightBias.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Config.cpp -o Config.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Config.cpp -o Config.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFWhamWeights.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp WhamWeights.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFWhamWeights.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp WhamWeights.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp WhamWeights.cpp -o WhamWeights.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp WhamWeights.cpp -o WhamWeights.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFConfigInstall.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ConfigInstall.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFConfigInstall.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ConfigInstall.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ConfigInstall.cpp -o ConfigInstall.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 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-D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightTemperaturePressure.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFReweightTemperaturePressure.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 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-D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightTemperaturePressure.cpp -o ReweightTemperaturePressure.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightTemperaturePressure.cpp -o ReweightTemperaturePressure.o -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFAction.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Action.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFAction.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Action.cpp -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFCombine.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Combine.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFCombine.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Combine.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Action.cpp -o Action.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Action.cpp -o Action.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Combine.cpp -o Combine.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Combine.cpp -o Combine.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDHEnergy.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DHEnergy.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFDHEnergy.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DHEnergy.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DHEnergy.cpp -o DHEnergy.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DHEnergy.cpp -o DHEnergy.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFReweightWham.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightWham.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFReweightWham.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightWham.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightWham.cpp -o ReweightWham.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightWham.cpp -o ReweightWham.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFCustom.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Custom.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFCustom.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Custom.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Custom.cpp -o Custom.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Custom.cpp -o Custom.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionAnyorder.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionAnyorder.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFActionAnyorder.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionAnyorder.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDRMSD.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 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-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DRMSD.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionAnyorder.cpp -o ActionAnyorder.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionAnyorder.cpp -o ActionAnyorder.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 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-D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DRMSD.cpp -o DRMSD.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFUWalls.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp UWalls.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFUWalls.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp UWalls.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp UWalls.cpp -o UWalls.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp UWalls.cpp -o UWalls.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionAtomistic.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionAtomistic.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFActionAtomistic.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 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-D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionAtomistic.cpp -o ActionAtomistic.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionAtomistic.cpp -o ActionAtomistic.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFEnsemble.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Ensemble.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFEnsemble.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Ensemble.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Ensemble.cpp -o Ensemble.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Ensemble.cpp -o Ensemble.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionPilot.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionPilot.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFActionPilot.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionPilot.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionPilot.cpp -o ActionPilot.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionPilot.cpp -o ActionPilot.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDimer.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Dimer.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFDimer.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Dimer.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Dimer.cpp -o Dimer.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Dimer.cpp -o Dimer.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDipole.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Dipole.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFDipole.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Dipole.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Dipole.cpp -o Dipole.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Dipole.cpp -o Dipole.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFFuncPathGeneral.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FuncPathGeneral.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFFuncPathGeneral.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FuncPathGeneral.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FuncPathGeneral.cpp -o FuncPathGeneral.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FuncPathGeneral.cpp -o FuncPathGeneral.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionRegister.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 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-I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Debug.cpp -o Debug.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Debug.cpp -o Debug.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionSet.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionSet.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFActionSet.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionSet.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionSet.cpp -o ActionSet.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionSet.cpp -o ActionSet.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFFuncSumHills.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FuncSumHills.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFFuncSumHills.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FuncSumHills.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FuncSumHills.cpp -o FuncSumHills.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FuncSumHills.cpp -o FuncSumHills.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFEEFSolv.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp EEFSolv.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFEEFSolv.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp EEFSolv.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 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-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp EEFSolv.cpp -o EEFSolv.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionSetup.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 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-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionSetup.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 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-DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionSetup.cpp -o ActionSetup.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDumpAtoms.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpAtoms.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFDumpAtoms.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpAtoms.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpAtoms.cpp -o DumpAtoms.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpAtoms.cpp -o DumpAtoms.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionShortcut.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 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-D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionShortcut.cpp -o ActionShortcut.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionWithArguments.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 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-D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithArguments.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithArguments.cpp -o ActionWithArguments.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithArguments.cpp -o ActionWithArguments.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDumpDerivatives.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpDerivatives.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFDumpDerivatives.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpDerivatives.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpDerivatives.cpp -o DumpDerivatives.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 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-D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Function.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFFunction.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Function.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Function.cpp -o Function.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Function.cpp -o Function.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDumpForces.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpForces.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFDumpForces.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpForces.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpForces.cpp -o DumpForces.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpForces.cpp -o DumpForces.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionWithValue.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithValue.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFActionWithValue.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' 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'-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithValue.cpp -o ActionWithValue.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithValue.cpp -o ActionWithValue.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFLocalEnsemble.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LocalEnsemble.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFLocalEnsemble.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp LocalEnsemble.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 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-D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpMassCharge.cpp -o DumpMassCharge.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpMassCharge.cpp -o DumpMassCharge.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionWithVirtualAtom.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 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-D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Piecewise.cpp -o Piecewise.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDumpProjections.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 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-D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpProjections.cpp -o DumpProjections.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFEnergy.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 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-pedantic -std=c++11 -fopenmp EndPlumed.cpp -o EndPlumed.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFFake.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 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-c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Fake.cpp -o Fake.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Fake.cpp -o Fake.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFCLTool.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp CLTool.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFCLTool.d -I/tmp/math/plumed/work/.buildlink/include 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'-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp CLTool.cpp -o CLTool.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp CLTool.cpp -o CLTool.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFFitToTemplate.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FitToTemplate.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFFitToTemplate.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FitToTemplate.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 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-I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Group.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFGroup.d 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-DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DataFetchingObject.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 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-D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithGrid.cpp -o ActionWithGrid.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFExchangePatterns.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 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-D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ExchangePatterns.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFMolInfo.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MolInfo.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFMolInfo.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MolInfo.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ExchangePatterns.cpp -o ExchangePatterns.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ExchangePatterns.cpp -o ExchangePatterns.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MolInfo.cpp -o MolInfo.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MolInfo.cpp -o MolInfo.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPathMSD.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PathMSD.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPathMSD.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PathMSD.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PathMSD.cpp -o PathMSD.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PathMSD.cpp -o PathMSD.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionWithInputGrid.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithInputGrid.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFActionWithInputGrid.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithInputGrid.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithInputGrid.cpp -o ActionWithInputGrid.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithInputGrid.cpp -o ActionWithInputGrid.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFFlexibleBin.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FlexibleBin.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFFlexibleBin.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FlexibleBin.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FlexibleBin.cpp -o FlexibleBin.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FlexibleBin.cpp -o FlexibleBin.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPlumed.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Plumed.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPlumed.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Plumed.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Plumed.cpp -o Plumed.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Plumed.cpp -o Plumed.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPathMSDBase.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PathMSDBase.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPathMSDBase.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PathMSDBase.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PathMSDBase.cpp -o PathMSDBase.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PathMSDBase.cpp -o PathMSDBase.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionWithIntegral.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithIntegral.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFActionWithIntegral.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithIntegral.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFGenericMolInfo.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 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-D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp GenericMolInfo.cpp -o GenericMolInfo.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp GenericMolInfo.cpp -o GenericMolInfo.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPrint.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 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-D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Print.cpp -o Print.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Print.cpp -o Print.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFAverageOnGrid.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AverageOnGrid.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFAverageOnGrid.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp AverageOnGrid.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AverageOnGrid.cpp -o AverageOnGrid.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp AverageOnGrid.cpp -o AverageOnGrid.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFRandomExchanges.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp RandomExchanges.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFRandomExchanges.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp RandomExchanges.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp RandomExchanges.cpp -o RandomExchanges.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp RandomExchanges.cpp -o RandomExchanges.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFContourFindingBase.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ContourFindingBase.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFContourFindingBase.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ContourFindingBase.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ContourFindingBase.cpp -o ContourFindingBase.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ContourFindingBase.cpp -o ContourFindingBase.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPosition.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Position.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPosition.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Position.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Position.cpp -o Position.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Position.cpp -o Position.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFMDAtoms.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MDAtoms.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFMDAtoms.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MDAtoms.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 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-D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ProjectionOnAxis.cpp -o ProjectionOnAxis.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPlumedMainInitializer.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PlumedMainInitializer.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPlumedMainInitializer.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PlumedMainInitializer.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PlumedMainInitializer.cpp -o PlumedMainInitializer.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PlumedMainInitializer.cpp -o PlumedMainInitializer.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPropertyMap.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PropertyMap.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPropertyMap.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PropertyMap.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PropertyMap.cpp -o PropertyMap.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PropertyMap.cpp -o PropertyMap.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDumpCube.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpCube.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFDumpCube.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpCube.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFResetCell.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ResetCell.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFResetCell.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ResetCell.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpCube.cpp -o DumpCube.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DumpCube.cpp -o DumpCube.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ResetCell.cpp -o ResetCell.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ResetCell.cpp -o ResetCell.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFTargetDist.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' 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-D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Value.cpp -o Value.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 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-I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp UpdateIf.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFUpdateIf.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp UpdateIf.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp UpdateIf.cpp -o UpdateIf.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp UpdateIf.cpp -o UpdateIf.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFFindContour.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FindContour.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM 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'-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FindContour.cpp -o FindContour.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FindContour.cpp -o FindContour.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFWithCmd.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp WithCmd.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFWithCmd.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp WithCmd.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp WithCmd.cpp -o WithCmd.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 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-fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Template.cpp -o Template.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFWrapAround.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include 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<.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp WrapAround.cpp -o WrapAround.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFGREX.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp GREX.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFGREX.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp GREX.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp GREX.cpp -o GREX.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp GREX.cpp -o GREX.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFTorsion.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Torsion.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFTorsion.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Torsion.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Torsion.cpp -o Torsion.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 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-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PlumedMain.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPlumedMain.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 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-D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FindSphericalContour.cpp -o FindSphericalContour.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 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-D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Caliber.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFCaliber.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Caliber.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Caliber.cpp -o Caliber.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Caliber.cpp -o Caliber.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFGridPrintingBase.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp GridPrintingBase.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFGridPrintingBase.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp GridPrintingBase.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp GridPrintingBase.cpp -o GridPrintingBase.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp GridPrintingBase.cpp -o GridPrintingBase.o -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFlapack.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp lapack.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFlapack.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp lapack.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp lapack.cpp -o lapack.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp lapack.cpp -o lapack.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFGridSearch.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp GridSearch.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFGridSearch.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp GridSearch.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp GridSearch.cpp -o GridSearch.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp GridSearch.cpp -o GridSearch.o -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFCompiledExpression.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp CompiledExpression.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFCompiledExpression.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp CompiledExpression.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFGridToXYZ.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp GridToXYZ.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFGridToXYZ.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp GridToXYZ.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp GridToXYZ.cpp -o GridToXYZ.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 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-D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp GridVessel.cpp -o GridVessel.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFEMMI.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 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-D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp EMMI.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 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-D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FretEfficiency.cpp -o FretEfficiency.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFExpressionProgram.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 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-D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ExpressionProgram.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 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-D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp HistogramOnGrid.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFHistogramOnGrid.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp HistogramOnGrid.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp HistogramOnGrid.cpp -o HistogramOnGrid.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp HistogramOnGrid.cpp -o HistogramOnGrid.o -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFmain.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 main.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFmain.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 main.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 main.cpp -o main.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 main.cpp -o main.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFExpressionTreeNode.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ExpressionTreeNode.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFExpressionTreeNode.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ExpressionTreeNode.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFJcoupling.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Jcoupling.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFJcoupling.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Jcoupling.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ExpressionTreeNode.cpp -o ExpressionTreeNode.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ExpressionTreeNode.cpp -o ExpressionTreeNode.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Jcoupling.cpp -o Jcoupling.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Jcoupling.cpp -o Jcoupling.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFOperation.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 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'-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MetainferenceBase.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFMetainferenceBase.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' 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2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MetainferenceBase.cpp -o MetainferenceBase.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MetainferenceBase.cpp -o MetainferenceBase.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFNOE.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' 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-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_crdplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp crdplugin.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_crdplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp crdplugin.cpp -o crdplugin.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_crdplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp crdplugin.cpp -o crdplugin.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFdcdplugin.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_dcdplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp dcdplugin.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFdcdplugin.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_dcdplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp dcdplugin.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_dcdplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp dcdplugin.cpp -o dcdplugin.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_dcdplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp dcdplugin.cpp -o dcdplugin.o -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFActionVolume.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionVolume.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFActionVolume.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionVolume.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionVolume.cpp -o ActionVolume.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionVolume.cpp -o ActionVolume.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFgromacsplugin.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_gromacsplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp gromacsplugin.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFgromacsplugin.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_gromacsplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp gromacsplugin.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_gromacsplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp gromacsplugin.cpp -o gromacsplugin.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_gromacsplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp gromacsplugin.cpp -o gromacsplugin.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFpdbplugin.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_pdbplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp pdbplugin.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFpdbplugin.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_pdbplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp pdbplugin.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_pdbplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp pdbplugin.cpp -o pdbplugin.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -DSTATIC_PLUGIN -DVMDPLUGIN=molfile_pdbplugin -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp pdbplugin.cpp -o pdbplugin.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPRE.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 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-DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PRE.cpp -o PRE.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFAlphaBeta.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 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-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Path.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 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-D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Path.cpp -o Path.o -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFArgumentOnlyDistance.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ArgumentOnlyDistance.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFArgumentOnlyDistance.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ArgumentOnlyDistance.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ArgumentOnlyDistance.cpp -o ArgumentOnlyDistance.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ArgumentOnlyDistance.cpp -o ArgumentOnlyDistance.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDRMSD.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DRMSD.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFDRMSD.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DRMSD.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DRMSD.cpp -o DRMSD.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DRMSD.cpp -o DRMSD.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPathBase.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PathBase.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPathBase.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PathBase.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFAngles.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Angles.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFAngles.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Angles.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PathBase.cpp -o PathBase.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include 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-I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp EuclideanDistance.cpp -o EuclideanDistance.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp EuclideanDistance.cpp -o EuclideanDistance.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PathTools.cpp -o PathTools.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PathTools.cpp -o PathTools.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Bridge.cpp -o Bridge.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Bridge.cpp -o Bridge.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFRescale.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Rescale.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFRescale.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Rescale.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Rescale.cpp -o Rescale.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Rescale.cpp -o Rescale.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFFakeFrame.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FakeFrame.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFFakeFrame.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FakeFrame.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 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-D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SAXS.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 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-D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SAXS.cpp -o SAXS.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFIntramolecularDRMSD.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp IntramolecularDRMSD.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFIntramolecularDRMSD.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp IntramolecularDRMSD.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp IntramolecularDRMSD.cpp -o IntramolecularDRMSD.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp IntramolecularDRMSD.cpp -o IntramolecularDRMSD.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFSpathVessel.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp SpathVessel.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFSpathVessel.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SpathVessel.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp SpathVessel.cpp -o SpathVessel.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SpathVessel.cpp -o SpathVessel.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFCatomPack.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp CatomPack.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFCatomPack.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp CatomPack.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp CatomPack.cpp -o CatomPack.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp CatomPack.cpp -o CatomPack.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFMahalanobisDistance.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MahalanobisDistance.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFMahalanobisDistance.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MahalanobisDistance.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MahalanobisDistance.cpp -o MahalanobisDistance.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MahalanobisDistance.cpp -o MahalanobisDistance.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFCenterOfMultiColvar.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp CenterOfMultiColvar.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFCenterOfMultiColvar.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp CenterOfMultiColvar.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp CenterOfMultiColvar.cpp -o CenterOfMultiColvar.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp CenterOfMultiColvar.cpp -o CenterOfMultiColvar.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFTrigonometricPathVessel.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp TrigonometricPathVessel.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFTrigonometricPathVessel.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp TrigonometricPathVessel.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFMetricRegister.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MetricRegister.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFMetricRegister.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MetricRegister.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp TrigonometricPathVessel.cpp -o TrigonometricPathVessel.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp TrigonometricPathVessel.cpp -o TrigonometricPathVessel.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MetricRegister.cpp -o MetricRegister.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MetricRegister.cpp -o MetricRegister.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFCoordinationNumbers.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp CoordinationNumbers.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFCoordinationNumbers.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp CoordinationNumbers.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp CoordinationNumbers.cpp -o CoordinationNumbers.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp CoordinationNumbers.cpp -o CoordinationNumbers.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFMultiDomainRMSD.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiDomainRMSD.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFMultiDomainRMSD.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiDomainRMSD.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiDomainRMSD.cpp -o MultiDomainRMSD.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiDomainRMSD.cpp -o MultiDomainRMSD.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFZpathVessel.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ZpathVessel.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFZpathVessel.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ZpathVessel.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ZpathVessel.cpp -o ZpathVessel.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ZpathVessel.cpp -o ZpathVessel.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFSelect.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 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-D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Selector.cpp -o Selector.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Selector.cpp -o Selector.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFOptimalRMSD.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp OptimalRMSD.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFOptimalRMSD.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp OptimalRMSD.cpp -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFAlphaRMSD.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AlphaRMSD.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFAlphaRMSD.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp AlphaRMSD.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp OptimalRMSD.cpp -o OptimalRMSD.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp OptimalRMSD.cpp -o OptimalRMSD.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AlphaRMSD.cpp -o AlphaRMSD.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp AlphaRMSD.cpp -o AlphaRMSD.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDihedralCorrelation.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DihedralCorrelation.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFDihedralCorrelation.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DihedralCorrelation.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDistanceFromContour.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DistanceFromContour.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFDistanceFromContour.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DistanceFromContour.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DihedralCorrelation.cpp -o DihedralCorrelation.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DihedralCorrelation.cpp -o DihedralCorrelation.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DistanceFromContour.cpp -o DistanceFromContour.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DistanceFromContour.cpp -o DistanceFromContour.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFRMSDBase.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp RMSDBase.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFRMSDBase.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp RMSDBase.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp RMSDBase.cpp -o RMSDBase.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp RMSDBase.cpp -o RMSDBase.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFAntibetaRMSD.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AntibetaRMSD.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFAntibetaRMSD.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp AntibetaRMSD.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AntibetaRMSD.cpp -o AntibetaRMSD.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 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-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ReferenceArguments.cpp -o ReferenceArguments.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFReferenceAtoms.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 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-D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Load.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Load.cpp -o Load.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Load.cpp -o Load.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFReferenceConfiguration.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReferenceConfiguration.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFReferenceConfiguration.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ReferenceConfiguration.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReferenceConfiguration.cpp -o ReferenceConfiguration.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ReferenceConfiguration.cpp -o ReferenceConfiguration.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFSecondaryStructureRMSD.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp SecondaryStructureRMSD.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFSecondaryStructureRMSD.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SecondaryStructureRMSD.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFRestart.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Restart.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFRestart.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Restart.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp SecondaryStructureRMSD.cpp -o SecondaryStructureRMSD.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SecondaryStructureRMSD.cpp -o SecondaryStructureRMSD.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Restart.cpp -o Restart.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Restart.cpp -o Restart.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFReferenceValuePack.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReferenceValuePack.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFReferenceValuePack.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ReferenceValuePack.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' 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-D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Units.cpp -o Units.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 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-D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp SingleDomainRMSD.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFSingleDomainRMSD.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SingleDomainRMSD.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp SingleDomainRMSD.cpp -o SingleDomainRMSD.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SingleDomainRMSD.cpp -o SingleDomainRMSD.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFFilterBetween.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FilterBetween.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFFilterBetween.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FilterBetween.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFFilterLessThan.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FilterLessThan.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFFilterLessThan.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FilterLessThan.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FilterBetween.cpp -o FilterBetween.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FilterBetween.cpp -o FilterBetween.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FilterLessThan.cpp -o FilterLessThan.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FilterLessThan.cpp -o FilterLessThan.o -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFAngle.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Angle.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFAngle.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Angle.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Angle.cpp -o Angle.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Angle.cpp -o Angle.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFAtomNumber.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AtomNumber.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFAtomNumber.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp AtomNumber.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AtomNumber.cpp -o AtomNumber.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp AtomNumber.cpp -o AtomNumber.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFFilterMoreThan.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FilterMoreThan.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFFilterMoreThan.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FilterMoreThan.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FilterMoreThan.cpp -o FilterMoreThan.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FilterMoreThan.cpp -o FilterMoreThan.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFBiasRepresentation.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp BiasRepresentation.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFBiasRepresentation.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp BiasRepresentation.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 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-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp BiasRepresentation.cpp -o BiasRepresentation.o -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFActionWithVirtualAtom.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithVirtualAtom.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFActionWithVirtualAtom.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithVirtualAtom.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithVirtualAtom.cpp -o ActionWithVirtualAtom.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithVirtualAtom.cpp -o ActionWithVirtualAtom.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFBrent1DRootSearch.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Brent1DRootSearch.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFBrent1DRootSearch.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Brent1DRootSearch.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Brent1DRootSearch.cpp -o Brent1DRootSearch.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Brent1DRootSearch.cpp -o Brent1DRootSearch.o -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFActionWithAveraging.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithAveraging.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFActionWithAveraging.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithAveraging.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFCitations.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Citations.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFCitations.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Citations.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithAveraging.cpp -o ActionWithAveraging.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithAveraging.cpp -o ActionWithAveraging.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFInPlaneDistances.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 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-D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Communicator.cpp -o Communicator.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFLocalAverage.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LocalAverage.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFLocalAverage.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp LocalAverage.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFConjugateGradient.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ConjugateGradient.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFConjugateGradient.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ConjugateGradient.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ConjugateGradient.cpp -o ConjugateGradient.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ConjugateGradient.cpp -o ConjugateGradient.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LocalAverage.cpp -o LocalAverage.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp LocalAverage.cpp -o LocalAverage.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionWithInputVessel.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithInputVessel.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFActionWithInputVessel.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithInputVessel.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFFixedAtom.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FixedAtom.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFFixedAtom.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FixedAtom.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithInputVessel.cpp -o ActionWithInputVessel.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ActionWithInputVessel.cpp -o ActionWithInputVessel.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FixedAtom.cpp -o FixedAtom.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FixedAtom.cpp -o FixedAtom.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDLLoader.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DLLoader.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFDLLoader.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DLLoader.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DLLoader.cpp -o DLLoader.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DLLoader.cpp -o DLLoader.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFDynamicList.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 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-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp DynamicList.cpp -o DynamicList.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFActionWithVessel.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 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Exception.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFException.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Exception.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Exception.cpp -o Exception.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c 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-D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ForwardDecl.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 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-D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp ForwardDecl.cpp -o ForwardDecl.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFGrid.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Grid.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFGrid.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Grid.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Grid.cpp -o Grid.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Grid.cpp -o Grid.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFAveragingVessel.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AveragingVessel.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFAveragingVessel.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp AveragingVessel.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AveragingVessel.cpp -o AveragingVessel.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp AveragingVessel.cpp -o AveragingVessel.o -fPIC -fstack-protector-strong [*] /tmp/math/plumed/work/.tools/bin/mkdir deps <.> /bin/mkdir -p deps [*] c++ -c -MM -MFPlumedStatic.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 PlumedStatic.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPlumedStatic.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 PlumedStatic.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 PlumedStatic.cpp -o PlumedStatic.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 PlumedStatic.cpp -o PlumedStatic.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPlumed.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC Plumed.c -o Plumed.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPlumed.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC Plumed.c -o Plumed.o -fPIC -fstack-protector-strong [*] cc -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC Plumed.c -o Plumed.o <.> /tmp/math/plumed/work/.gcc/bin/gcc -fcommon -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC Plumed.c -o Plumed.o -fPIC -D_FORTIFY_SOURCE=2 -fstack-protector-strong [*] c++ -c -MM -MFMultiColvarDensity.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiColvarDensity.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFMultiColvarDensity.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiColvarDensity.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiColvarDensity.cpp -o MultiColvarDensity.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiColvarDensity.cpp -o MultiColvarDensity.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFHistogramBead.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp HistogramBead.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFHistogramBead.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp HistogramBead.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 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-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp HistogramBead.cpp -o HistogramBead.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFBetween.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 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-D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp xdrfile_xtc.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp xdrfile_xtc.cpp -o xdrfile_xtc.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp xdrfile_xtc.cpp -o xdrfile_xtc.o -fPIC 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-I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp IFile.cpp -o IFile.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFMultiColvarFilter.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiColvarFilter.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFMultiColvarFilter.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiColvarFilter.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiColvarFilter.cpp -o MultiColvarFilter.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiColvarFilter.cpp -o MultiColvarFilter.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFFunctionVessel.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FunctionVessel.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFFunctionVessel.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp FunctionVessel.cpp -fPIC -fstack-protector-strong [*] c++ -c -MM -MFMultiColvarProduct.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiColvarProduct.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFMultiColvarProduct.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MultiColvarProduct.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 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-D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Keywords.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 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-D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Histogram.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC 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-D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Histogram.cpp -o Histogram.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFLessThan.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LessThan.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFLessThan.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp LessThan.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LessThan.cpp -o LessThan.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp LessThan.cpp -o LessThan.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFTorsions.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Torsions.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFTorsions.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Torsions.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Torsions.cpp -o Torsions.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' 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-D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeAround.cpp -o VolumeAround.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' 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2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeBetweenContours.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFVolumeBetweenContours.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' 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-D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeBetweenContours.cpp -o VolumeBetweenContours.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' 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-D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LoopUnroller.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFLoopUnroller.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' 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-fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Min.cpp -o Min.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFMinimiseBase.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MinimiseBase.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFMinimiseBase.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MinimiseBase.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MinimiseBase.cpp -o MinimiseBase.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MinimiseBase.cpp -o MinimiseBase.o -fPIC -fstack-protector-strong [*] c++ -c -MM 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-I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp MolDataClass.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MolDataClass.cpp -o MolDataClass.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' 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'-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Moments.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFMoments.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Moments.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Moments.cpp -o Moments.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Moments.cpp -o Moments.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFMultiValue.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 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-D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp NeighborList.cpp -o NeighborList.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 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-D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp OFile.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFOFile.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp OFile.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp OFile.cpp -o OFile.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp OFile.cpp -o OFile.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFOrderingVessel.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp OrderingVessel.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFOrderingVessel.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp OrderingVessel.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp OrderingVessel.cpp -o OrderingVessel.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp OrderingVessel.cpp -o OrderingVessel.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFVolumeInCylinder.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeInCylinder.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFVolumeInCylinder.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeInCylinder.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeInCylinder.cpp -o VolumeInCylinder.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeInCylinder.cpp -o VolumeInCylinder.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFVolumeInSphere.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeInSphere.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFVolumeInSphere.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeInSphere.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeInSphere.cpp -o VolumeInSphere.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' 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-D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PDB.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 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-D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp StoreDataVessel.cpp -o StoreDataVessel.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFSum.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Sum.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFSum.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Sum.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PDB.cpp -o PDB.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PDB.cpp -o PDB.o -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Sum.cpp -o Sum.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Sum.cpp -o Sum.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFVolumeTetrapore.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeTetrapore.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFVolumeTetrapore.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeTetrapore.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeTetrapore.cpp -o VolumeTetrapore.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp VolumeTetrapore.cpp -o VolumeTetrapore.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFPbc.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Pbc.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPbc.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Pbc.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Pbc.cpp -o Pbc.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Pbc.cpp -o Pbc.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFValueVessel.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' 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-D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PlumedHandle.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFPlumedHandle.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PlumedHandle.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PlumedHandle.cpp -o PlumedHandle.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp PlumedHandle.cpp -o PlumedHandle.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFXDistances.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp XDistances.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFXDistances.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp XDistances.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp XDistances.cpp -o XDistances.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp XDistances.cpp -o XDistances.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFVesselRegister.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp VesselRegister.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFVesselRegister.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp VesselRegister.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp VesselRegister.cpp -o VesselRegister.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp VesselRegister.cpp -o VesselRegister.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFRMSD.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp RMSD.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFRMSD.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp RMSD.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp RMSD.cpp -o RMSD.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp RMSD.cpp -o RMSD.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFRandom.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Random.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFRandom.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' 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-D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Stopwatch.cpp -o Stopwatch.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFXYTorsion.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 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-D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp XYTorsion.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp XYTorsion.cpp -o XYTorsion.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp XYTorsion.cpp -o XYTorsion.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFSubprocess.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 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-D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Subprocess.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Subprocess.cpp -o Subprocess.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp Subprocess.cpp -o Subprocess.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFSwitchingFunction.d -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp SwitchingFunction.cpp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -MM -MFSwitchingFunction.d -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SwitchingFunction.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp SwitchingFunction.cpp -o SwitchingFunction.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp SwitchingFunction.cpp -o SwitchingFunction.o -fPIC -fstack-protector-strong [*] c++ -c -MM -MFTensor.d -I/usr/include 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'-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp h36.cpp -fPIC -fstack-protector-strong [*] c++ -c -I/usr/include -I/usr/pkg/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 -fopenmp h36.cpp -o h36.o <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -c -I/tmp/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -O2 -fPIC -D_FORTIFY_SOURCE=2 -fPIC -Wall -pedantic -std=c++11 -fopenmp h36.cpp -o h36.o -fPIC -fstack-protector-strong [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/Config.o ../wrapper/PlumedStatic.o -o plumed -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -fopenmp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/Config.o ../wrapper/PlumedStatic.o -o plumed -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib -fopenmp -fPIC -fstack-protector-strong -pie [*] /tmp/math/plumed/work/.tools/bin/echo Building Plumed.inc <.> echo Building Plumed.inc [*] /tmp/math/plumed/work/.tools/bin/echo Building Plumed.inc, static version <.> echo Building Plumed.inc, static version [*] /tmp/math/plumed/work/.tools/bin/echo Building Plumed.cmake <.> echo Building Plumed.cmake [*] /tmp/math/plumed/work/.tools/bin/echo Building Plumed.cmake, static version <.> echo Building Plumed.cmake, static version [*] /tmp/math/plumed/work/.tools/bin/mkdir -p install/ <.> /bin/mkdir -p -p install/ [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/blas <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/blas [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/bias <.> echo Verify modules and create links 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in /tmp/math/plumed/work/plumed-2.8.0/src/isdb [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/isdb <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p bias <.> /bin/mkdir -p -p bias [*] /tmp/math/plumed/work/.tools/bin/mkdir -p colvar <.> /bin/mkdir -p -p colvar [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p xdrfile <.> /bin/mkdir -p -p xdrfile [*] /tmp/math/plumed/work/.tools/bin/mkdir -p lepton <.> /bin/mkdir -p -p lepton [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/lapack <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/lapack [*] /tmp/math/plumed/work/.tools/bin/mkdir -p blas <.> /bin/mkdir -p -p blas [*] /tmp/math/plumed/work/.tools/bin/mkdir -p reference <.> /bin/mkdir -p -p reference [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/lepton <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/lepton [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/main <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/main [*] /tmp/math/plumed/work/.tools/bin/mkdir -p asmjit [*] /tmp/math/plumed/work/.tools/bin/mkdir -p wrapper <.> /bin/mkdir -p -p asmjit <.> /bin/mkdir -p -p wrapper [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p vesselbase <.> /bin/mkdir -p -p tools <.> /bin/mkdir -p -p vesselbase [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in 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-p vesselbase [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/setup <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/setup [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p vesselbase <.> /bin/mkdir -p -p vesselbase [*] /tmp/math/plumed/work/.tools/bin/mkdir -p reference <.> /bin/mkdir -p -p reference [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/tools <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p gridtools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p gridtools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p vesselbase <.> /bin/mkdir -p -p core <.> /bin/mkdir -p -p vesselbase [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/vatom <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/vatom [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/vesselbase <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/vesselbase [*] /tmp/math/plumed/work/.tools/bin/mkdir -p lapack [*] /tmp/math/plumed/work/.tools/bin/mkdir -p core <.> /bin/mkdir -p -p lapack <.> /bin/mkdir -p -p core [*] /tmp/math/plumed/work/.tools/bin/mkdir -p lepton <.> /bin/mkdir -p -p lepton [*] /tmp/math/plumed/work/.tools/bin/echo Nothing to do in /tmp/math/plumed/work/plumed-2.8.0/src/wrapper <.> echo Nothing to do in /tmp/math/plumed/work/plumed-2.8.0/src/wrapper [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools [*] /tmp/math/plumed/work/.tools/bin/echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/xdrfile <.> /bin/mkdir -p -p tools <.> echo Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/xdrfile [*] /tmp/math/plumed/work/.tools/bin/mkdir -p tools <.> /bin/mkdir -p -p tools [*] /tmp/math/plumed/work/.tools/bin/mkdir -p bias <.> /bin/mkdir -p -p bias [*] /tmp/math/plumed/work/.tools/bin/mkdir -p analysis <.> /bin/mkdir -p -p analysis [*] c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/ConfigInstall.o ../wrapper/PlumedStatic.o -o install/plumed -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -fopenmp <.> /tmp/math/plumed/work/.gcc/bin/g++ -Wl,-zrelro -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/tmp/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/ConfigInstall.o ../wrapper/PlumedStatic.o -o install/plumed -lstdc++ -lfftw3 -lgsl -lgslcblas -lz -llapack -lblas -Wl,-zrelro -L/tmp/math/plumed/work/.buildlink/lib -Wl,-rpath,/usr/pkg/lib -fopenmp -fPIC -fstack-protector-strong -pie [*] /tmp/math/plumed/work/.tools/bin/echo Building Plumed.inc <.> echo Building Plumed.inc [*] /tmp/math/plumed/work/.tools/bin/echo Building Plumed.inc, static version <.> echo Building Plumed.inc, static version [*] /tmp/math/plumed/work/.tools/bin/echo Building Plumed.cmake <.> echo Building Plumed.cmake [*] /tmp/math/plumed/work/.tools/bin/echo Building Plumed.cmake, static version <.> echo Building Plumed.cmake, static version [*] ld -r -o install/kernel.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/GenericMolInfo.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/ConfigInstall.o <.> ld -r -o install/kernel.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o 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