=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Building for plumed-2.8.0 /usr/pkg/bin/gmake lib gmake[1]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0' /usr/pkg/bin/gmake -C src gmake[2]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src' /usr/pkg/bin/gmake -C lib gmake[3]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' /usr/pkg/bin/gmake dirslinks gmake[4]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' *** Updating links to used modules in all directories *** /usr/pkg/bin/gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links ../xdrfile.links gmake[5]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' /usr/pkg/bin/gmake -C ../analysis links /usr/pkg/bin/gmake -C ../asmjit links /usr/pkg/bin/gmake -C ../bias links /usr/pkg/bin/gmake -C ../blas links gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/blas' gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/bias' gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/analysis' gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/asmjit' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/blas gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/blas' /usr/pkg/bin/gmake -C ../cltools links Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/bias Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/analysis Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/asmjit gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/asmjit' /usr/pkg/bin/gmake -C ../colvar links gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/cltools' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/cltools gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/colvar' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/colvar gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/bias' /usr/pkg/bin/gmake -C ../config links gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' Nothing to do in /tmp/math/plumed/work/plumed-2.8.0/src/config gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' /usr/pkg/bin/gmake -C ../core links gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/core' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/core gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/cltools' /usr/pkg/bin/gmake -C ../function links gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/colvar' /usr/pkg/bin/gmake -C ../generic links gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/function' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/function gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/generic' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/generic gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/core' /usr/pkg/bin/gmake -C ../gridtools links gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/analysis' /usr/pkg/bin/gmake -C ../isdb links gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/gridtools' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/gridtools gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/isdb' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/isdb gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/generic' /usr/pkg/bin/gmake -C ../lapack links gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lapack' gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/function' /usr/pkg/bin/gmake -C ../lepton links Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/lapack gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lepton' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/lepton gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/gridtools' /usr/pkg/bin/gmake -C ../main links gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lapack' gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/main' /usr/pkg/bin/gmake -C ../mapping links Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/main gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/mapping' gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lepton' /usr/pkg/bin/gmake -C ../molfile links Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/mapping gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/molfile' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/molfile gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/main' gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/molfile' /usr/pkg/bin/gmake -C ../multicolvar links /usr/pkg/bin/gmake -C ../reference links gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/reference' gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/multicolvar' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/reference Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/multicolvar gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/isdb' /usr/pkg/bin/gmake -C ../secondarystructure links gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/secondarystructure' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/secondarystructure gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/reference' /usr/pkg/bin/gmake -C ../setup links gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/setup' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/setup gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/mapping' /usr/pkg/bin/gmake -C ../tools links gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/multicolvar' /usr/pkg/bin/gmake -C ../vatom links gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/tools' gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/vatom' gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/setup' /usr/pkg/bin/gmake -C ../vesselbase links Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/tools gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/vesselbase' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/vatom gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/secondarystructure' /usr/pkg/bin/gmake -C ../wrapper links Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/vesselbase gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/wrapper' Nothing to do in /tmp/math/plumed/work/plumed-2.8.0/src/wrapper gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/wrapper' /usr/pkg/bin/gmake -C ../xdrfile links gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/xdrfile' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/xdrfile gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/xdrfile' gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/vatom' gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/tools' gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/vesselbase' gmake[5]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' gmake[4]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' /usr/pkg/bin/gmake dirs gmake[4]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' *** Compiling all directories *** /usr/pkg/bin/gmake ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper ../xdrfile gmake[5]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' /usr/pkg/bin/gmake -C ../analysis obj /usr/pkg/bin/gmake -C ../asmjit obj /usr/pkg/bin/gmake -C ../bias obj /usr/pkg/bin/gmake -C ../blas obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/blas' compiling blas.cpp gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/bias' gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/analysis' compiling ABMD.cpp compiling AnalysisBase.cpp gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/asmjit' compiling arch.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/blas' compiling Average.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling assembler.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling codebuilder.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling codecompiler.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Bias.cpp compiling codeemitter.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../cltools obj compiling AverageVessel.cpp gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/cltools' compiling CLTool.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling codeholder.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] { ../maketools/make-scripts-options.sh ; cat completion.sh ; }| ../maketools/xxd > completion.xxd compiling constpool.cpp ../../scripts/selector.sh: line 219: python: command not found compiling Driver.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling BiasValue.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] In file included from xdrfile/xdrfile_trr.h:1:0, from Driver.cpp:38: xdrfile/../../xdrfile/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile/../../xdrfile/xdrfile_trr.h:37:0, from xdrfile/xdrfile_trr.h:1, from Driver.cpp:38: xdrfile/../../xdrfile/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile/xdrfile_xtc.h:1:0, from Driver.cpp:39: xdrfile/../../xdrfile/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- compiling cpuinfo.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling func.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Committor.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ExtendedLagrangian.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DriverDouble.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] In file included from xdrfile/xdrfile_trr.h:1:0, from Driver.cpp:38, from DriverDouble.cpp:23: xdrfile/../../xdrfile/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile/../../xdrfile/xdrfile_trr.h:37:0, from xdrfile/xdrfile_trr.h:1, from Driver.cpp:38, from DriverDouble.cpp:23: xdrfile/../../xdrfile/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile/xdrfile_xtc.h:1:0, from Driver.cpp:39, from DriverDouble.cpp:23: xdrfile/../../xdrfile/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- compiling globals.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling inst.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling logging.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DataCollectionObject.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling External.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling operand.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling osutils.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling EuclideanDissimilarityMatrix.cpp compiling regalloc.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling runtime.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling string.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling LWalls.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling utils.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling vmem.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] vmem.cpp:284:13: warning: 'bool PLMD::asmjit::vMemMgrCheckTree(PLMD::asmjit::VMemMgr*)' defined but not used [-Wunused-function] static bool vMemMgrCheckTree(VMemMgr* self) noexcept { ^~~~~~~~~~~~~~~~ compiling DriverFloat.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling x86assembler.cpp In file included from xdrfile/xdrfile_trr.h:1:0, from Driver.cpp:38, from DriverFloat.cpp:23: xdrfile/../../xdrfile/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile/../../xdrfile/xdrfile_trr.h:37:0, from xdrfile/xdrfile_trr.h:1, from Driver.cpp:38, from DriverFloat.cpp:23: xdrfile/../../xdrfile/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile/xdrfile_xtc.h:1:0, from Driver.cpp:39, from DriverFloat.cpp:23: xdrfile/../../xdrfile/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MaxEnt.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling FarthestPointSampling.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Histogram.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling x86builder.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MetaD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling GenExample.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] MetaD.cpp: In constructor 'PLMD::bias::MetaD::MetaD(const PLMD::ActionOptions&)': MetaD.cpp:1232:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(result!=0&&result!=mpi_nw_) error("in this WALKERS_MPI run some replica have restarted from GRID while other do not!"); ~~~~~~^~~~~~~~~ MetaD.cpp:1297:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(result!=0&&result!=mpi_nw_) error("in this WALKERS_MPI run some replica have restarted from FILE while other do not!"); ~~~~~~^~~~~~~~~ compiling x86compiler.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling LandmarkSelectionBase.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling GenTemplate.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling LandmarkStaged.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Info.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling x86inst.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Manual.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling x86instimpl.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling OutputColvarFile.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling x86internal.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PdbRenumber.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling SimpleMD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling OutputPDBFile.cpp compiling x86logging.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling x86operand.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling x86operand_regs.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MovingRestraint.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling x86regalloc.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling SumHills.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PrintDissimilarityMatrix.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PBMetaD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ReadAnalysisFrames.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling kT.cpp compiling zone.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] zone.cpp:223:13: warning: 'bool PLMD::asmjit::ZoneHeap_hasDynamicBlock(PLMD::asmjit::ZoneHeap*, PLMD::asmjit::ZoneHeap::DynamicBlock*)' defined but not used [-Wunused-function] static bool ZoneHeap_hasDynamicBlock(ZoneHeap* self, ZoneHeap::DynamicBlock* block) noexcept { ^~~~~~~~~~~~~~~~~~~~~~~~ gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/asmjit' compiling Restraint.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling pesmd.cpp compiling ReadDissimilarityMatrix.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ReselectLandmarks.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Completion.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../colvar obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/colvar' compiling Angle.cpp compiling SelectRandomFrames.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/cltools' compiling ReweightBase.cpp compiling Cell.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../config obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' /usr/pkg/bin/gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[7]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' Updating ConfigInstall.inc cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc rm ConfigInstall.inc~ Updating Config.inc cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ Updating version.h Updating config.txt file gmake[7]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' /usr/pkg/bin/gmake Config.o ConfigInstall.o compile_options.sh gmake[7]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' cat ../../Makefile.conf | ../maketools/xxd > Makefile.conf.xxd Building compile_options.sh, a sourceable bash script with some compilation options compiling Config.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling SelectWithStride.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ConfigInstall.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ReweightBias.cpp compiling Colvar.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[7]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' compiling WhamHistogram.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ReweightMetad.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Constant.cpp compiling ContactMap.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling WhamWeights.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ReweightTemperaturePressure.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/analysis' compiling ReweightWham.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling UWalls.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../core obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/core' compiling Action.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Coordination.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../function obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/function' compiling Combine.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/bias' compiling CoordinationBase.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Custom.cpp compiling ActionAnyorder.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Ensemble.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DHEnergy.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ActionAtomistic.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../generic obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/generic' compiling Debug.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling FuncPathGeneral.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] ActionAtomistic.cpp: In member function 'void PLMD::ActionAtomistic::requestAtoms(const std::vector&, bool)': ActionAtomistic.cpp:71:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(indexes[i].index()>=n) { std::string num; Tools::convert( indexes[i].serial(),num ); error("atom " + num + " out of range"); } ~~~~~~~~~~~~~~~~~~^~~ ActionAtomistic.cpp: In member function 'void PLMD::ActionAtomistic::calculateAtomicNumericalDerivatives(PLMD::ActionWithValue*, const unsigned int&)': ActionAtomistic.cpp:109:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; igetOutputQuantity(j); ~^~~~~ ActionAtomistic.cpp:134:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int j=0; j >&, std::vector&)': ActionAtomistic.cpp:179:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(unsigned i=0; i] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DumpAtoms.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] In file included from xdrfile/xdrfile_xtc.h:1:0, from DumpAtoms.cpp:34: xdrfile/../../xdrfile/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile/../../xdrfile/xdrfile_xtc.h:37:0, from xdrfile/xdrfile_xtc.h:1, from DumpAtoms.cpp:34: xdrfile/../../xdrfile/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile/xdrfile_trr.h:1:0, from DumpAtoms.cpp:35: xdrfile/../../xdrfile/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- compiling ActionPilot.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling FuncPathMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ActionRegister.cpp compiling Dimer.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] Dimer.cpp: In constructor 'PLMD::colvar::Dimer::Dimer(const PLMD::ActionOptions&)': Dimer.cpp:212:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(unsigned int i=0; i] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ActionSet.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DumpDerivatives.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Dipole.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ActionSetup.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DumpForces.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ActionShortcut.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Distance.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DumpMassCharge.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ActionWithArguments.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling EEFSolv.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Function.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DumpProjections.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] ActionWithArguments.cpp: In member function 'virtual void PLMD::ActionWithArguments::calculateNumericalDerivatives(PLMD::ActionWithValue*)': ActionWithArguments.cpp:281:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; ihasDerivatives() ) for(int i=0; iaddDerivative(i,(value[i*nval+j]-a->getOutputQuantity(j))/sqrt(epsilon)); ~^~~~~ compiling LocalEnsemble.cpp compiling EffectiveEnergyDrift.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ActionWithValue.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Piecewise.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ActionWithVirtualAtom.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling EndPlumed.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Sort.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Atoms.cpp compiling FitToTemplate.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Stats.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ERMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] Atoms.cpp: In member function 'void PLMD::Atoms::wait()': Atoms.cpp:296:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; i] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Flush.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Energy.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling CLTool.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Group.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/function' compiling ExtraCV.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] ../maketools/makecmd map < CLToolMain.cpp > CLToolMainMap.inc compiling Fake.cpp ../maketools/makecmd enum < CLToolMain.cpp > CLToolMainEnum.inc fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling CLToolRegister.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Include.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Colvar.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling GHBFIX.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../gridtools obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/gridtools' compiling ActionWithGrid.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] Colvar.cpp: In member function 'virtual void PLMD::Colvar::apply()': Colvar.cpp:62:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ncp>4*comm.Get_size()) { ~~~^~~~~~~~~~~~~~~~~~ Colvar.cpp:102:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ncp>4*comm.Get_size()) { ~~~^~~~~~~~~~~~~~~~~~ compiling MolInfo.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DataFetchingObject.cpp GHBFIX.cpp: In constructor 'PLMD::colvar::GHBFIX::GHBFIX(const PLMD::ActionOptions&)': GHBFIX.cpp:165:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(auto i=0; i] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Plumed.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] DataFetchingObject.cpp: In static member function 'static void PLMD::DataFetchingObject::get_rank(const PLMD::ActionSet&, const string&, const string&, const PLMD::TypesafePtr&)': DataFetchingObject.cpp:78:10: warning: unused variable 'val' [-Wunused-variable] Value* val = myv->copyOutput( key ); ^~~ DataFetchingObject.cpp: In static member function 'static void PLMD::DataFetchingObject::get_shape(const PLMD::ActionSet&, const string&, const string&, const PLMD::TypesafePtr&)': DataFetchingObject.cpp:99:10: warning: unused variable 'val' [-Wunused-variable] Value* val = myv->copyOutput( key ); ^~~ compiling ActionWithInputGrid.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Gyration.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] Plumed.cpp: In member function 'virtual void PLMD::generic::Plumed::prepare()': Plumed.cpp:323:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bool redo=(index.size()!=n); ~~~~~~~~~~~~^~~ Plumed.cpp: In member function 'virtual void PLMD::generic::Plumed::calculate()': Plumed.cpp:364:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; i] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ActionWithIntegral.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Print.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MultiRMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling FlexibleBin.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling AverageOnGrid.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling RandomExchanges.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] ../maketools/makecmd map < GREX.cpp > GREXMap.inc ../maketools/makecmd enum < GREX.cpp > GREXEnum.inc compiling GenericMolInfo.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ContourFindingBase.cpp compiling PCARMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Read.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ConvertToFES.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ResetCell.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MDAtoms.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PathMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DumpCube.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Time.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PathMSDBase.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling UpdateIf.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DumpGrid.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] ../maketools/makecmd map < PlumedMain.cpp > PlumedMainMap.inc ../maketools/makecmd enum < PlumedMain.cpp > PlumedMainEnum.inc compiling PlumedMainInitializer.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling FindContour.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling WholeMolecules.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling TargetDist.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Value.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Position.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling WrapAround.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] In file included from tools/../../tools/RootFindingBase.h:26:0, from tools/RootFindingBase.h:1, from ContourFindingBase.h:26, from FindContour.cpp:24: tools/../../tools/Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': tools/../../tools/Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ compiling WithCmd.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling FindContourSurface.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ProjectionOnAxis.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling CLToolMain.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/generic' compiling FindSphericalContour.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PropertyMap.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] In file included from tools/../../tools/RootFindingBase.h:26:0, from tools/RootFindingBase.h:1, from ContourFindingBase.h:26, from FindContourSurface.cpp:23: tools/../../tools/Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': tools/../../tools/Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ compiling GREX.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] In file included from tools/../../tools/RootFindingBase.h:26:0, from tools/RootFindingBase.h:1, from ContourFindingBase.h:26, from FindSphericalContour.cpp:23: tools/../../tools/Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': tools/../../tools/Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ /usr/pkg/bin/gmake -C ../isdb obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/isdb' compiling CS2Backbone.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling FourierTransform.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Puckering.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PlumedMain.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling GridPrintingBase.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling RMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling GridSearch.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Template.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling GridToXYZ.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Caliber.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Torsion.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] Caliber.cpp: In member function 'double PLMD::isdb::Caliber::getSpline(unsigned int)': Caliber.cpp:273:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(tindex+1] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Volume.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling EMMI.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] GridVessel.cpp: In member function 'void PLMD::gridtools::GridVessel::getNeighbors(const std::vector&, const std::vector&, unsigned int&, std::vector&) const': GridVessel.cpp:419:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(!pbc[i] && i0>=nbin[i]) found=false; GridVessel.cpp:421:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if( pbc[i] && i0>=nbin[i]) i0%=nbin[i]; gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/core' compiling FretEfficiency.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/colvar' compiling Jcoupling.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] EMMI.cpp: In member function 'void PLMD::isdb::EMMI::write_model_overlap(long int)': EMMI.cpp:770:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; i PLMD::isdb::EMMI::read_exp_errors(std::__cxx11::string)': EMMI.cpp:954:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(unsigned i=0; i=GMM_d_grps_.size()) error("Check Beta values"); compiling HistogramOnGrid.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling IntegrateGrid.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../lapack obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lapack' compiling lapack.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lapack' compiling InterpolateGrid.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../lepton obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lepton' compiling CompiledExpression.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../main obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/main' compiling main.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/main' compiling ExpressionProgram.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Metainference.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../mapping obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/mapping' compiling AdaptivePath.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/gridtools' compiling Mapping.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] CompiledExpression.cpp: In member function 'void PLMD::lepton::CompiledExpression::compileExpression(const PLMD::lepton::ExpressionTreeNode&, std::vector >&)': CompiledExpression.cpp:157:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < node.getChildren().size(); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CompiledExpression.cpp:179:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 1; i < args.size(); i++) ~~^~~~~~~~~~~~~ CompiledExpression.cpp: In member function 'double PLMD::lepton::CompiledExpression::evaluate() const': CompiledExpression.cpp:240:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < variablesToCopy.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ CompiledExpression.cpp:245:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int step = 0; step < operation.size(); step++) { ~~~~~^~~~~~~~~~~~~~~~~~ CompiledExpression.cpp:250:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < args.size(); i++) ~~^~~~~~~~~~~~~ AdaptivePath.cpp: In constructor 'PLMD::mapping::AdaptivePath::AdaptivePath(const PLMD::ActionOptions&)': AdaptivePath.cpp:154:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; i] [-m|w ] [..] fmt [-Cr] [] [] [] ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*, const std::vector&)': ExpressionTreeNode.cpp:74:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (operation->getNumArguments() != children.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*, const PLMD::lepton::ExpressionTreeNode&, const PLMD::lepton::ExpressionTreeNode&)': ExpressionTreeNode.cpp:81:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (operation->getNumArguments() != children.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*, const PLMD::lepton::ExpressionTreeNode&)': ExpressionTreeNode.cpp:87:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (operation->getNumArguments() != children.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*)': ExpressionTreeNode.cpp:92:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (operation->getNumArguments() != children.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp: In member function 'void PLMD::lepton::ExpressionTreeNode::assignTags(std::vector&) const': ExpressionTreeNode.cpp:166:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (numTags == examples.size()) { ~~~~~~~~^~~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp:169:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < examples.size(); i++) { ~~^~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp:172:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j = 0; matches && j < getChildren().size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ compiling MetainferenceBase.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PCAVars.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Operation.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../molfile obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/molfile' compiling crdplugin.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling dcdplugin.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ParsedExpression.cpp dcdplugin.cpp: In function 'int PLMD::molfile::read_dcdheader(PLMD::molfile::fio_fd, int*, int*, int*, int*, double*, int*, int**, float**, int*, int*)': dcdplugin.cpp:226:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ dcdplugin.cpp:239:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ dcdplugin.cpp:257:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (input_integer[0] != dcdcordmagic) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ dcdplugin.cpp:434:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ dcdplugin.cpp:451:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ dcdplugin.cpp: In function 'int PLMD::molfile::read_dcdstep(PLMD::molfile::fio_fd, int, float*, float*, float*, float*, int, int, int*, float*, int, int)': dcdplugin.cpp:656:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ dcdplugin.cpp:660:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ dcdplugin.cpp:581:16: warning: variable 'readlen' set but not used [-Wunused-but-set-variable] fio_size_t readlen; /* number of bytes actually read */ ^~~~~~~ fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] In file included from dcdplugin.cpp:92:0: endianswap.h: At global scope: endianswap.h:136:13: warning: 'void PLMD::molfile::swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ endianswap.h:72:13: warning: 'void PLMD::molfile::swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ In file included from dcdplugin.cpp:83:0: fastio.h:676:12: warning: 'int PLMD::molfile::fio_write_str(PLMD::molfile::fio_fd, const char*)' defined but not used [-Wunused-function] static int fio_write_str(fio_fd fd, const char *str) { ^~~~~~~~~~~~~ fastio.h:672:12: warning: 'int PLMD::molfile::fio_read_int32(PLMD::molfile::fio_fd, int*)' defined but not used [-Wunused-function] static int fio_read_int32(fio_fd fd, int *i) { ^~~~~~~~~~~~~~ fastio.h:520:19: warning: 'PLMD::molfile::fio_size_t PLMD::molfile::fio_readv(PLMD::molfile::fio_fd, const PLMD::molfile::fio_iovec*, int)' defined but not used [-Wunused-function] static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { ^~~~~~~~~ compiling gromacsplugin.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] In file included from Gromacs.h:86:0, from gromacsplugin.cpp:62: endianswap.h:136:13: warning: 'void PLMD::molfile::swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ endianswap.h:105:13: warning: 'void PLMD::molfile::swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ endianswap.h:86:13: warning: 'void PLMD::molfile::swap4_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ endianswap.h:72:13: warning: 'void PLMD::molfile::swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ compiling pdbplugin.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] In file included from pdbplugin.cpp:64:0: periodic_table.h:173:12: warning: 'int PLMD::molfile::get_pte_idx(const char*)' defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^~~~~~~~~~~ gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/molfile' compiling Path.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] ParsedExpression.cpp: In static member function 'static PLMD::lepton::ExpressionTreeNode PLMD::lepton::ParsedExpression::substituteSimplerExpression(const PLMD::lepton::ExpressionTreeNode&, std::map&)': ParsedExpression.cpp:243:29: warning: 'first' may be used uninitialized in this function [-Wmaybe-uninitialized] if (first_const && first == 1.0) // Multiply by 1 ~~~~~~~~~~~~^~~~~~~~~~~~~~~ ParsedExpression.cpp:245:30: warning: 'second' may be used uninitialized in this function [-Wmaybe-uninitialized] if (second_const && second == 1.0) // Multiply by 1 ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ compiling NOE.cpp compiling Parser.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] Parser.cpp: In static member function 'static PLMD::lepton::ParsedExpression PLMD::lepton::Parser::parse(const string&, const std::map, PLMD::lepton::CustomFunction*>&)': Parser.cpp:238:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (pos != tokens.size()) ~~~~^~~~~~~~~~~~~~~~ Parser.cpp:247:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (pos != tokens.size()) ~~~~^~~~~~~~~~~~~~~~ Parser.cpp: In static member function 'static PLMD::lepton::ExpressionTreeNode PLMD::lepton::Parser::parsePrecedence(const std::vector&, int&, const std::map, PLMD::lepton::CustomFunction*>&, const std::map, PLMD::lepton::ExpressionTreeNode>&, int)': Parser.cpp:258:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (pos == tokens.size()) ~~~~^~~~~~~~~~~~~~~~ Parser.cpp:284:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (pos == tokens.size() || tokens[pos].getType() != ParseToken::RightParen) ~~~~^~~~~~~~~~~~~~~~ Parser.cpp:298:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (pos == tokens.size() || tokens[pos].getType() != ParseToken::RightParen) ~~~~^~~~~~~~~~~~~~~~ compiling PathBase.cpp /usr/pkg/bin/gmake -C ../multicolvar obj fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/multicolvar' compiling ActionVolume.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lepton' compiling AlphaBeta.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PathReparameterization.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PRE.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PathTools.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] PathReparameterization.cpp: In member function 'void PLMD::mapping::PathReparameterization::reparameterizePart(const int&, const int&, const double&, const double&)': PathReparameterization.cpp:72:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(unsigned i=istart; i= iend+1 ) plumed_merror("path reparameterization error"); ~~~~^~~~~~ PathReparameterization.cpp:103:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] else if( cfin==(iend+1) && k>=iend ) { k=iend-1; break; } ~~~~^~~~~~~~~~ PathReparameterization.cpp:104:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] else if( cfin==(iend-1) && k<=iend ) { k=iend+1; break; } ~~~~^~~~~~~~~~ PathReparameterization.cpp: In member function 'void PLMD::mapping::PathReparameterization::reparameterize(const int&, const int&, const double&)': PathReparameterization.cpp:141:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if( ifix2<(mypath.size()-1) ) reparameterizePart( ifix2, mypath.size()-1, target, TOL ); ~~~~~^~~~~~~~~~~~~~~~~~ PathTools.cpp: In member function 'virtual int PLMD::mapping::PathTools::main(FILE*, FILE*, PLMD::Communicator&)': PathTools.cpp:266:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i=0; i] [-m|w ] [..] fmt [-Cr] [] [] [] compiling AtomValuePack.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PropertyMap.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling RDC.cpp compiling Rescale.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Bridge.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling SpathVessel.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling TrigonometricPathVessel.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../reference obj compiling BridgedMultiColvarFunction.cpp gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/reference' compiling ArgumentOnlyDistance.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling SAXS.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] TrigonometricPathVessel.cpp: In member function 'virtual void PLMD::mapping::TrigonometricPathVessel::finish(const std::vector&)': TrigonometricPathVessel.cpp:137:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if( iclose3<0 || iclose3>=mymap->getFullNumberOfTasks() ) { ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compiling DRMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling CatomPack.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ZpathVessel.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Direction.cpp compiling CenterOfMultiColvar.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/mapping' compiling CoordinationNumbers.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DotProductDistance.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Select.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling EuclideanDistance.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../secondarystructure obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/secondarystructure' compiling AlphaRMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Density.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling FakeFrame.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Selector.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling IntermolecularDRMSD.cpp compiling AntibetaRMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/isdb' compiling DihedralCorrelation.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling IntramolecularDRMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../setup obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/setup' compiling Load.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ParabetaRMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MahalanobisDistance.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DistanceFromContour.cpp compiling Restart.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MetricRegister.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling SecondaryStructureRMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Units.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MultiDomainRMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] In file included from tools/../../tools/RootFindingBase.h:26:0, from tools/RootFindingBase.h:1, from DistanceFromContour.cpp:26: tools/../../tools/Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': tools/../../tools/Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/setup' compiling NormalizedEuclideanDistance.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Distances.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DumpMultiColvar.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling OptimalRMSD.cpp gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/secondarystructure' compiling FilterBetween.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling RMSDBase.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../tools obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/tools' compiling Angle.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ReferenceArguments.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling AtomNumber.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../vatom obj compiling FilterLessThan.cpp gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/vatom' compiling ActionWithVirtualAtom.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling BiasRepresentation.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Center.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ReferenceAtoms.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Brent1DRootSearch.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling FilterMoreThan.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Citations.cpp compiling ReferenceConfiguration.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling FixedAtom.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Communicator.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ReferenceValuePack.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling InPlaneDistances.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Ghost.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ConjugateGradient.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling SimpleRMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DLLoader.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling DynamicList.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/vatom' compiling ERMSD.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling SingleDomainRMSD.cpp compiling LocalAverage.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../vesselbase obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/vesselbase' compiling ActionWithAveraging.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/reference' compiling Exception.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MultiColvarBase.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling FileBase.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ActionWithInputVessel.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] MultiColvarBase.cpp: In member function 'void PLMD::multicolvar::MultiColvarBase::setupActiveTaskSet(std::vector&, const string&)': MultiColvarBase.cpp:741:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if( atom_lab[itask].first==input_code ) active_tasks[ atom_lab[itask].second ]=1; compiling ActionWithVessel.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ForwardDecl.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Grid.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../wrapper obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/wrapper' compiling PlumedStatic.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Plumed.c fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/wrapper' compiling MultiColvarCombine.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling HistogramBead.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling AltMin.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] In file included from RootFindingBase.h:26:0, from Grid.cpp:29: Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ compiling MultiColvarDensity.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] /usr/pkg/bin/gmake -C ../xdrfile obj gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/xdrfile' compiling xdrfile.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling AveragingVessel.cpp xdrfile.cpp:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile.cpp:60:0: xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- xdrfile.cpp: In function 'int PLMD::xdrfile::sizeofint(int)': xdrfile.cpp:504:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (size >= num && num_of_bits < 32) ~~~~~^~~~~~ xdrfile.cpp: In function 'int PLMD::xdrfile::sizeofints(int, unsigned int*)': xdrfile.cpp:550:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (bytes[num_of_bytes] >= num) ~~~~~~~~~~~~~~~~~~~~^~~~~~ xdrfile.cpp: In function 'void PLMD::xdrfile::encodeints(int*, int, int, unsigned int*, unsigned int*)': xdrfile.cpp:659:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (num_of_bits >= num_of_bytes * 8) ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ xdrfile.cpp:661:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < num_of_bytes; i++) ~~^~~~~~~~~~~~~~ xdrfile.cpp:669:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < num_of_bytes-1; i++) ~~^~~~~~~~~~~~~~~~ xdrfile.cpp: In function 'int PLMD::xdrfile::decodebits(int*, int)': xdrfile.cpp:709:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (lastbits < num_of_bits) ~~~~~~~~~^~~~~~~~~~~~~ xdrfile.cpp: In function 'int PLMD::xdrfile::xdrfile_decompress_coord_float(float*, int*, float*, PLMD::xdrfile::XDRFILE*)': xdrfile.cpp:819:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(size3>xfp->buf1size) ~~~~~^~~~~~~~~~~~~~ xdrfile.cpp:871:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] maxidx = (LASTIDXxfp->buf1size) ~~~~~^~~~~~~~~~~~~~ xdrfile.cpp:1138:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (smallidx < LASTIDX && magicints[smallidx] < mindiff) ^ xdrfile.cpp:1144:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] maxidx = (LASTIDXxfp->buf1size) ~~~~~^~~~~~~~~~~~~~ xdrfile.cpp:1371:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] maxidx = (LASTIDXxfp->buf1size) { ~~~~~^~~~~~~~~~~~~~ fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] xdrfile.cpp:1622:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { ^ xdrfile.cpp:1627:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] maxidx = (LASTIDX] [-m|w ] [..] fmt [-Cr] [] [] [] compiling xdrfile_trr.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] xdrfile_trr.cpp:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile_trr.cpp:41:0: xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile_trr.cpp:42:0: xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- xdrfile_trr.cpp: In function 'int PLMD::xdrfile::do_trnheader(PLMD::xdrfile::XDRFILE*, PLMD::xdrfile::mybool, PLMD::xdrfile::t_trnheader*)': xdrfile_trr.cpp:111:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (slen != strlen(version)+1) ~~~~~^~~~~~~~~~~~~~~~~~~~ xdrfile_trr.cpp:121:65: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (xdrfile_write_string(const_cast(version),xd) != (strlen(version)+1) ) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ compiling xdrfile_xtc.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] In file included from xdrfile_xtc.cpp:31:0: xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- In file included from xdrfile_xtc.cpp:32:0: xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- xdrfile_xtc.cpp: In function 'int PLMD::xdrfile::xtc_coord(PLMD::xdrfile::XDRFILE*, int*, float (*)[3], float (*)[3], float*, PLMD::xdrfile::mybool)': xdrfile_xtc.cpp:69:6: warning: unused variable 'i' [-Wunused-variable] int i,j,result; ^ xdrfile_xtc.cpp:69:8: warning: unused variable 'j' [-Wunused-variable] int i,j,result; ^ gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/xdrfile' compiling Between.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MultiColvarFilter.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling KernelFunctions.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling BridgeVessel.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Keywords.cpp compiling MultiColvarProduct.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling FunctionVessel.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling NumberOfLinks.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling LatticeReduction.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Highest.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Histogram.cpp compiling LinkCells.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Torsions.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling VolumeAround.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Log.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling LessThan.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling LoopUnroller.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Matrix.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MatrixSquareBracketsAccess.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Minimise1DBrent.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MinimiseBase.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Lowest.cpp compiling Max.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling VolumeBetweenContours.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MolDataClass.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling VolumeCavity.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Mean.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Min.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MultiValue.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling NeighborList.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] NeighborList.cpp: In member function 'void PLMD::NeighborList::update(const std::vector >&)': NeighborList.cpp:158:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(unsigned i=0; i] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling OFile.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling VolumeInCylinder.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling OpenMP.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling MoreThan.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PDB.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling VolumeInSphere.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Pbc.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling OrderingVessel.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling VolumeTetrapore.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling PlumedHandle.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ShortcutVessel.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling StoreDataVessel.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] PlumedHandle.cpp: In member function 'virtual void PLMD::PlumedHandle::cmd(const string&, const PLMD::TypesafePtr&)': PlumedHandle.cpp:78:20: warning: 'safe.plumed_safeptr::opt' may be used uninitialized in this function [-Wmaybe-uninitialized] plumed_safeptr safe; ^~~~ compiling RMSD.cpp compiling XAngle.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Sum.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Random.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling ValueVessel.cpp compiling Vessel.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling XDistances.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling XYDistances.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling VesselRegister.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling RootFindingBase.cpp compiling XYTorsion.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Stopwatch.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Subprocess.cpp gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/vesselbase' compiling SwitchingFunction.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Tensor.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Tools.cpp compiling Torsion.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/multicolvar' compiling Tree.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling TypesafePtr.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Units.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling Vector.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] compiling h36.cpp fmt: unknown option -- 1 Usage: fmt [-Cr] [-g ] [-m|w ] [..] fmt [-Cr] [] [] [] h36.cpp: In function 'const char* PLMD::h36::decode_pure(const int*, unsigned int, const char*, unsigned int, int*)': h36.cpp:154:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (dv < 0 || dv >= digits_size) { ~~~^~~~~~~~~~~~~~ gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/tools' gmake[5]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' gmake[4]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' /usr/pkg/bin/gmake lib-static gmake[4]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' 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 Building Plumed.inc chmod a+x plumed-config chmod a+x plumed-mklib chmod a+x plumed-newcv chmod a+x plumed-patch chmod a+x plumed-partial_tempering chmod a+x plumed-selector chmod a+x plumed-vim2html Building Plumed.inc, static version Building Plumed.cmake Building Plumed.cmake, static version gmake[4]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' /usr/pkg/bin/gmake install-build gmake[4]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' mkdir -p install/ /usr/pkg/bin/gmake PLUMED_INSTALL=Install all gmake[5]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' /usr/pkg/bin/gmake dirslinks gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' *** Updating links to used modules in all directories *** /usr/pkg/bin/gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links ../xdrfile.links gmake[7]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' /usr/pkg/bin/gmake -C ../analysis links /usr/pkg/bin/gmake -C ../asmjit links /usr/pkg/bin/gmake -C ../bias links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/analysis' /usr/pkg/bin/gmake -C ../blas links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/blas' gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/bias' gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/asmjit' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/analysis Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/blas gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/blas' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/asmjit /usr/pkg/bin/gmake -C ../cltools links gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/asmjit' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/bias /usr/pkg/bin/gmake -C ../colvar links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/cltools' gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/colvar' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/cltools Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/colvar gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/bias' /usr/pkg/bin/gmake -C ../config links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' Nothing to do in /tmp/math/plumed/work/plumed-2.8.0/src/config gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' /usr/pkg/bin/gmake -C ../core links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/core' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/core gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/colvar' /usr/pkg/bin/gmake -C ../function links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/function' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/function gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/cltools' /usr/pkg/bin/gmake -C ../generic links gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/analysis' /usr/pkg/bin/gmake -C ../gridtools links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/generic' gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/gridtools' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/generic Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/gridtools gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/core' /usr/pkg/bin/gmake -C ../isdb links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/isdb' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/isdb gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/function' /usr/pkg/bin/gmake -C ../lapack links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lapack' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/generic' /usr/pkg/bin/gmake -C ../lepton links Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/lapack gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lepton' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/gridtools' /usr/pkg/bin/gmake -C ../main links Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/lepton gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/main' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lapack' /usr/pkg/bin/gmake -C ../mapping links Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/main gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/mapping' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/main' /usr/pkg/bin/gmake -C ../molfile links Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/mapping gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/molfile' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lepton' /usr/pkg/bin/gmake -C ../multicolvar links Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/molfile gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/isdb' /usr/pkg/bin/gmake -C ../reference links gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/molfile' /usr/pkg/bin/gmake -C ../secondarystructure links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/secondarystructure' gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/reference' gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/multicolvar' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/secondarystructure Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/multicolvar Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/reference gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/reference' /usr/pkg/bin/gmake -C ../setup links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/setup' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/setup gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/secondarystructure' /usr/pkg/bin/gmake -C ../tools links gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/mapping' /usr/pkg/bin/gmake -C ../vatom links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/tools' gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/vatom' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/tools Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/vatom gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/multicolvar' /usr/pkg/bin/gmake -C ../vesselbase links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/vesselbase' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/vesselbase gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/setup' /usr/pkg/bin/gmake -C ../wrapper links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/wrapper' Nothing to do in /tmp/math/plumed/work/plumed-2.8.0/src/wrapper gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/wrapper' /usr/pkg/bin/gmake -C ../xdrfile links gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/xdrfile' Verify modules and create links in /tmp/math/plumed/work/plumed-2.8.0/src/xdrfile gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/xdrfile' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/tools' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/vatom' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/vesselbase' gmake[7]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' /usr/pkg/bin/gmake dirs gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' *** Compiling all directories *** /usr/pkg/bin/gmake ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper ../xdrfile gmake[7]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' /usr/pkg/bin/gmake -C ../analysis obj /usr/pkg/bin/gmake -C ../asmjit obj /usr/pkg/bin/gmake -C ../bias obj /usr/pkg/bin/gmake -C ../blas obj gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/blas' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/blas' /usr/pkg/bin/gmake -C ../cltools obj gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/bias' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/asmjit' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/bias' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/asmjit' /usr/pkg/bin/gmake -C ../colvar obj /usr/pkg/bin/gmake -C ../config obj gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/analysis' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/cltools' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/analysis' gmake[8]: Nothing to be done for 'obj'. /usr/pkg/bin/gmake -C ../core obj gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/cltools' /usr/pkg/bin/gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt /usr/pkg/bin/gmake -C ../function obj gmake[9]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' Updating ConfigInstall.inc gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/colvar' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/core' cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/colvar' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/core' rm ConfigInstall.inc~ /usr/pkg/bin/gmake -C ../generic obj gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/function' Updating Config.inc gmake[8]: Nothing to be done for 'obj'. gmake[9]: 'config.txt' is up to date. gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/generic' Updating version.h gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/function' gmake[8]: Nothing to be done for 'obj'. cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc /usr/pkg/bin/gmake -C ../gridtools obj gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/generic' rm Config.inc~ /usr/pkg/bin/gmake -C ../isdb obj /usr/pkg/bin/gmake -C ../lapack obj gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lapack' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lapack' /usr/pkg/bin/gmake -C ../lepton obj gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/gridtools' gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/isdb' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/isdb' /usr/pkg/bin/gmake Config.o ConfigInstall.o compile_options.sh /usr/pkg/bin/gmake -C ../main obj gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lepton' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/gridtools' gmake[9]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' gmake[9]: 'Config.o' is up to date. /usr/pkg/bin/gmake -C ../mapping obj gmake[9]: 'ConfigInstall.o' is up to date. gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/main' gmake[9]: 'compile_options.sh' is up to date. gmake[8]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lepton' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/config' gmake[8]: Nothing to be done for 'obj'. /usr/pkg/bin/gmake -C ../molfile obj gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/main' /usr/pkg/bin/gmake -C ../multicolvar obj gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/mapping' /usr/pkg/bin/gmake -C ../reference obj gmake[8]: Nothing to be done for 'obj'. gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/molfile' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/mapping' gmake[8]: Nothing to be done for 'obj'. /usr/pkg/bin/gmake -C ../secondarystructure obj gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/molfile' /usr/pkg/bin/gmake -C ../setup obj gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/reference' gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/secondarystructure' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/multicolvar' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/secondarystructure' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/reference' gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/multicolvar' /usr/pkg/bin/gmake -C ../tools obj /usr/pkg/bin/gmake -C ../vatom obj /usr/pkg/bin/gmake -C ../vesselbase obj gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/setup' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/setup' /usr/pkg/bin/gmake -C ../wrapper obj gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/vatom' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/vatom' /usr/pkg/bin/gmake -C ../xdrfile obj gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/wrapper' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/wrapper' gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/xdrfile' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/xdrfile' gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/vesselbase' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/vesselbase' gmake[8]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/tools' gmake[8]: Nothing to be done for 'obj'. gmake[8]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/tools' gmake[7]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' /usr/pkg/bin/gmake lib-static gmake[6]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' 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 Building Plumed.inc chmod a+x install/plumed-mklib chmod a+x install/plumed-config chmod a+x install/plumed-newcv chmod a+x install/plumed-partial_tempering chmod a+x install/plumed-patch chmod a+x install/plumed-selector Building Plumed.inc, static version chmod a+x install/plumed-vim2html Building Plumed.cmake Building Plumed.cmake, static version gmake[6]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' gmake[5]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' /usr/pkg/bin/gmake PLUMED_INSTALL=Install install/kernel.o gmake[5]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' 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 gmake[5]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' /usr/pkg/bin/gmake PLUMED_INSTALL=Install install/libplumed.a gmake[5]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' rm -f install/libplumed.a ar cr install/libplumed.a install/kernel.o ../wrapper/PlumedStatic.o gmake[5]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' gmake[4]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' gmake[3]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src/lib' gmake[2]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/src' gmake[1]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0' /usr/pkg/bin/gmake -C vim gmake[1]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/vim' ./vimsyntax.sh gmake[1]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/vim' /usr/pkg/bin/gmake -C python gmake[1]: Entering directory '/tmp/math/plumed/work/plumed-2.8.0/python' Python support was not configured gmake[1]: Leaving directory '/tmp/math/plumed/work/plumed-2.8.0/python'