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[ 23%] Building CXX object CMakeFiles/gpu.dir/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/lib/gpu/lal_tersoff_zbl.cpp.o [ 23%] Building CXX object CMakeFiles/gpu.dir/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/lib/gpu/lal_tersoff_zbl_ext.cpp.o [ 24%] Building CXX object CMakeFiles/gpu.dir/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/lib/gpu/lal_ufm.cpp.o [ 24%] Building CXX object CMakeFiles/gpu.dir/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/lib/gpu/lal_ufm_ext.cpp.o [ 24%] Building CXX object CMakeFiles/gpu.dir/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/lib/gpu/lal_vashishta.cpp.o [ 24%] Building CXX object CMakeFiles/gpu.dir/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/lib/gpu/lal_vashishta_ext.cpp.o [ 24%] Building CXX object CMakeFiles/gpu.dir/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/lib/gpu/lal_yukawa.cpp.o [ 24%] Building CXX object CMakeFiles/gpu.dir/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/lib/gpu/lal_yukawa_colloid.cpp.o [ 24%] Building CXX object CMakeFiles/gpu.dir/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/lib/gpu/lal_yukawa_colloid_ext.cpp.o [ 24%] Building CXX object CMakeFiles/gpu.dir/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/lib/gpu/lal_yukawa_ext.cpp.o [ 24%] Building CXX object CMakeFiles/gpu.dir/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/lib/gpu/lal_zbl.cpp.o [ 24%] Building CXX object CMakeFiles/gpu.dir/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/lib/gpu/lal_zbl_ext.cpp.o yes configure: Regtest suite will use env var PLUMED_MPIRUN to run MPI tests (default: mpirun) configure: PLUMED seems to be configured properly! configure: ************************** checking whether C++ objects can be grouped with ld -r -o... yes checking whether static libraries can be created with ar cr... yes checking whether static-object constructors can be linked from a static archive... yes configure: I will now check if C++ objects can be linked by C/Fortran compilers configure: This is relevant if you want to use plumed patch --static on a non-C++ code checking whether C can link a C++ object... no checking whether C can link a C++ object with library -lstdc++... yes [ 24%] Linking CXX static library liblammps_gpu.a checking whether FORTRAN can link a C++ object... yes checking for pkg-config... /usr/bin/pkg-config configure: bash-completion is not installed or it is installed on a different prefix configure: bash completion for plumed will not be installed configure: **** PLUMED will be installed using the following paths: configure: **** prefix: /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix configure: **** exec_prefix: ${prefix} configure: **** bindir: ${exec_prefix}/bin configure: **** libdir: ${exec_prefix}/lib configure: **** includedir: ${prefix}/include configure: **** datarootdir: ${prefix}/share configure: **** datadir: ${datarootdir} configure: **** docdir: ${prefix}/share/doc/plumed configure: **** htmldir: ${docdir} configure: **** Executable will be named plumed configure: **** As of PLUMED 2.5, you cannot change paths anymore during "make install" configure: **** Please configure and make clean to change the prefix configure: **** PLUMED will be compiled using MPI configure: creating ./config.status config.status: creating Makefile.conf config.status: creating sourceme.sh config.status: creating stamp-h [ 24%] Built target gpu [ 24%] Performing build step for 'plumed_build' *** Updating links to used modules in all directories *** Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/annfunc Nothing to do in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/config Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/blas Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/fisst Verify modules and 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/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/cltools Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/main Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/bias Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/piv Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/manyrestraints Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/dimred Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/molfile Verify modules and create links in 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/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/colvar Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/core Nothing to do in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/wrapper Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/reference Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/multicolvar Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/vesselbase Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/ves Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/tools *** Compiling all directories *** compiling ANN.cpp compiling blas.cpp compiling EDS.cpp compiling legendre_rule_fast.cpp compiling FPS.cpp compiling LogMFD.cpp compiling drrtool.cpp compiling LWalls.cpp Updating ConfigInstall.inc compiling lapack.cpp compiling ExpressionTreeNode.cpp compiling TrigonometricPathVessel.cpp compiling PIV.cpp compiling main.cpp compiling HBPammMatrix.cpp compiling OPESmetad.cpp compiling dcdplugin.cpp compiling EuclideanDissimilarityMatrix.cpp compiling Manual.cpp compiling GridPrintingBase.cpp compiling ReweightBias.cpp compiling Stats.cpp compiling SketchMap.cpp compiling ClusterSize.cpp compiling ParabetaRMSD.cpp compiling Units.cpp compiling OrientationSphere.cpp compiling Value.cpp compiling Rescale.cpp compiling Steered_MD.cpp compiling WrapAround.cpp compiling utils.cpp compiling Torsion.cpp compiling MultiColvarBase.cpp compiling FakeFrame.cpp Updating Config.inc compiling Torsion.cpp Updating version.h Updating config.txt file compiling DynamicReferenceRestraining.cpp compiling assembler.cpp compiling Random_Walk.cpp compiling CLTool.cpp compiling x86operand.cpp compiling colvar_UIestimator.cpp compiling codeholder.cpp compiling zone.cpp Building compile_options.sh, a sourceable bash script with some compilation options compiling Config.cpp compiling arch.cpp compiling runtime.cpp compiling x86assembler.cpp compiling x86compiler.cpp compiling func.cpp compiling inst.cpp compiling codecompiler.cpp compiling codebuilder.cpp compiling string.cpp compiling FISST.cpp compiling codeemitter.cpp compiling ERMSD.cpp compiling crdplugin.cpp compiling constpool.cpp compiling ConfigInstall.cpp compiling vmem.cpp compiling x86builder.cpp compiling DRR.cpp compiling x86instimpl.cpp compiling gromacsplugin.cpp compiling pdbplugin.cpp compiling x86operand_regs.cpp compiling osutils.cpp compiling PathReparameterization.cpp compiling regalloc.cpp compiling x86inst.cpp compiling Parser.cpp compiling operand.cpp compiling Restraint.cpp compiling logging.cpp compiling x86logging.cpp compiling cpuinfo.cpp compiling globals.cpp compiling ExchangePatterns.cpp compiling x86regalloc.cpp compiling kT.cpp compiling x86internal.cpp compiling Driver.cpp compiling PathMSD.cpp compiling IntramolecularDRMSD.cpp compiling LocalEnsemble.cpp compiling Custom.cpp compiling FuncSumHills.cpp compiling Ensemble.cpp compiling Combine.cpp compiling ManyRestraintsBase.cpp compiling HistogramBead.cpp compiling Communicator.cpp compiling Restart.cpp compiling Simulated_Annealing.cpp compiling DataFetchingObject.cpp compiling DumpForces.cpp compiling Bias.cpp compiling SketchMapPointwise.cpp compiling SketchMapRead.cpp compiling PammObject.cpp compiling AntibetaRMSD.cpp compiling ActionWithInputGrid.cpp compiling PAMM.cpp compiling Tetrahedral.cpp compiling DFSClustering.cpp compiling GenTemplate.cpp compiling FourierTransform.cpp compiling DataCollectionObject.cpp compiling Funnel.cpp compiling ParsedExpression.cpp compiling PrintDissimilarityMatrix.cpp compiling FretEfficiency.cpp compiling Direction.cpp compiling ReadDissimilarityMatrix.cpp compiling PathMSDBase.cpp compiling Load.cpp compiling UWalls.cpp compiling MolDataClass.cpp compiling PBMetaD.cpp compiling Include.cpp compiling RandomExchanges.cpp compiling EndPlumed.cpp compiling SimpleMD.cpp [ 25%] Linking CXX static library liblammps_pace.a compiling DriverFloat.cpp compiling pesmd.cpp compiling CompiledExpression.cpp [ 25%] Built target pace compiling MetainferenceBase.cpp compiling PathBase.cpp compiling Path.cpp compiling SpathVessel.cpp compiling PlumedMainInitializer.cpp compiling Member.cpp compiling Optimizer.cpp compiling Loss.cpp compiling ExtendedLagrangian.cpp compiling ClusterWithSurface.cpp compiling BridgedMultiColvarFunction.cpp compiling LWalls.cpp compiling WholeMolecules.cpp compiling AlphaRMSD.cpp compiling Flush.cpp compiling HBPammHydrogens.cpp compiling HBPammObject.cpp compiling ReferenceConfiguration.cpp compiling VectorSum.cpp compiling ExpressionProgram.cpp compiling CLTool.cpp compiling ReferenceArguments.cpp compiling PathTools.cpp compiling DRMSD.cpp compiling Core.cpp compiling HistogramOnGrid.cpp compiling Optimizer_Bias.cpp compiling Tools.cpp compiling IntegrateGrid.cpp compiling DumpGrid.cpp compiling Stopwatch.cpp compiling Operation.cpp compiling FindContourSurface.cpp compiling ProjectNonLandmarkPoints.cpp compiling FindContour.cpp compiling GridVessel.cpp compiling SMACMatrix.cpp compiling SmacoffMDS.cpp compiling AnalysisBase.cpp compiling GridSearch.cpp compiling AverageOnGrid.cpp compiling ReweightMetad.cpp compiling ReweightTemperaturePressure.cpp compiling FlexibleBin.cpp compiling ContourFindingBase.cpp compiling Torsions.cpp compiling Q6.cpp compiling LoopUnroller.cpp compiling CenterOfMultiColvar.cpp compiling MaxEnt.cpp compiling ForwardDecl.cpp compiling PCA.cpp compiling ReferenceAtoms.cpp compiling FuncPathGeneral.cpp compiling SecondaryStructureRMSD.cpp compiling Random_Acceleration_MD.cpp compiling ArgumentOnlyDistance.cpp compiling Units.cpp compiling CLToolRegister.cpp compiling Action.cpp compiling TargetDist.cpp compiling Volume.cpp compiling ActionRegister.cpp compiling WithCmd.cpp compiling OutputPCAProjections.cpp compiling DumpProjections.cpp compiling Ghost.cpp compiling CoeffsMatrix.cpp compiling FixedAtom.cpp compiling ActionWithVirtualAtom.cpp compiling SketchMapSmacof.cpp compiling ClusterAnalysisBase.cpp compiling AdjacencyMatrixVessel.cpp compiling SelectWithStride.cpp compiling MatrixSquareBracketsAccess.cpp compiling ZpathVessel.cpp compiling BiasRepresentation.cpp compiling Info.cpp compiling GenExample.cpp compiling DriverDouble.cpp compiling SumHills.cpp compiling PdbRenumber.cpp compiling Select.cpp compiling MultiDomainRMSD.cpp compiling Metainference.cpp [ 26%] No install step for 'voro_build' [ 26%] Completed 'voro_build' [ 26%] Built target voro_build compiling Tools.cpp compiling RMSD.cpp compiling Print.cpp compiling Center.cpp compiling BF_Sine.cpp compiling Memetic.cpp compiling Read.cpp compiling InterpolateGrid.cpp compiling PCARMSD.cpp compiling ResetCell.cpp compiling AlphaBeta.cpp compiling Fccubic.cpp compiling VolumeInSphere.cpp compiling MatrixColumnSums.cpp [ 26%] Linking CXX static library liblammps_colvars.a compiling Sort.cpp compiling Function.cpp compiling SimpleRMSD.cpp compiling ActionWithArguments.cpp compiling FitToTemplate.cpp compiling EffectiveEnergyDrift.cpp compiling Target.cpp compiling PCAVars.cpp compiling RMSDBase.cpp compiling Mapping.cpp compiling MahalanobisDistance.cpp compiling SingleDomainRMSD.cpp compiling WhamHistogram.cpp compiling IntermolecularDRMSD.cpp compiling TD_ChiSquared.cpp compiling Opt_Dummy.cpp compiling ActionPilot.cpp [ 26%] Built target colvars compiling BF_Combined.cpp compiling SMACOF.cpp compiling Dimer.cpp compiling Distance.cpp compiling ClusterProperties.cpp compiling ClusterDistribution.cpp compiling AdjacencyMatrixBase.cpp compiling VectorMean.cpp compiling MoleculeOrientation.cpp compiling FileBase.cpp compiling SwitchingFunction.cpp compiling OpenMP.cpp compiling SelectRandomFrames.cpp compiling LinkCells.cpp compiling ActionWithIntegral.cpp compiling Random_MT.cpp compiling Minimise1DBrent.cpp compiling MultiValue.cpp compiling PDB.cpp compiling IFile.cpp compiling Exception.cpp compiling SketchMapBase.cpp compiling InterMolecularTorsions.cpp compiling Completion.cpp compiling Random.cpp compiling OptimalRMSD.cpp compiling EnvironmentSimilarity.cpp compiling VolumeBetweenContours.cpp compiling MolInfo.cpp compiling EuclideanDistance.cpp compiling ActionWithValue.cpp compiling MetricRegister.cpp compiling FuncPathMSD.cpp compiling DotProductDistance.cpp compiling ReweightWham.cpp compiling BF_Powers.cpp compiling NormalizedEuclideanDistance.cpp compiling ReferenceValuePack.cpp compiling External.cpp compiling MetaD.cpp compiling BiasValue.cpp compiling UWalls.cpp compiling XAngle.cpp compiling FilterBetween.cpp compiling ReweightBase.cpp compiling MovingRestraint.cpp compiling ActionWithGrid.cpp compiling GridToXYZ.cpp compiling ERMSD.cpp compiling FindSphericalContour.cpp compiling DumpCube.cpp compiling CatomPack.cpp compiling AtomValuePack.cpp compiling FarthestPointSampling.cpp compiling ActionAnyorder.cpp compiling TD_ProductDistribution.cpp compiling TD_Chi.cpp compiling OutputCluster.cpp compiling PropertyMap.cpp compiling DumpAtoms.cpp compiling Jcoupling.cpp compiling AdaptivePath.cpp compiling CS2Backbone.cpp compiling Time.cpp compiling PRE.cpp compiling Caliber.cpp compiling DumpMassCharge.cpp compiling Selector.cpp compiling RDC.cpp compiling DLLoader.cpp compiling h36.cpp compiling SketchMapConjGrad.cpp compiling ABMD.cpp compiling BF_Custom.cpp compiling Piecewise.cpp compiling GenericMolInfo.cpp compiling TD_MultithermalMultibaric.cpp compiling HbondMatrix.cpp compiling ClusteringBase.cpp compiling Brent1DRootSearch.cpp compiling Matrix.cpp compiling DRMSD.cpp compiling MultiRMSD.cpp compiling LessThan.cpp compiling RMSD.cpp compiling LatticeReduction.cpp compiling Citations.cpp compiling ConvertToFES.cpp compiling Angles.cpp compiling PlumedStatic.cpp compiling Plumed.c compiling Committor.cpp compiling LandmarkSelectionBase.cpp compiling BF_Cosine.cpp compiling Sprint.cpp compiling EEFSolv.cpp compiling OutputColvarFile.cpp compiling OutputPDBFile.cpp compiling RootFindingBase.cpp compiling TD_Multicanonical.cpp compiling ClassicalMultiDimensionalScaling.cpp compiling DimensionalityReductionBase.cpp compiling Histogram.cpp compiling OutputTargetDistribution.cpp compiling BF_Fourier.cpp compiling TD_GeneralizedExtremeValue.cpp compiling SMAC.cpp compiling NeighborList.cpp compiling MinimiseBase.cpp compiling Optimizer.cpp compiling Sum.cpp compiling Vessel.cpp compiling TD_WellTempered.cpp compiling FunctionVessel.cpp compiling TargetDistribution.cpp compiling VolumeCavity.cpp compiling ConjugateGradient.cpp compiling Grid.cpp compiling BondOrientation.cpp compiling MultiColvarCombine.cpp compiling BF_Chebyshev.cpp compiling OutputBasisFunctions.cpp compiling BF_Legendre.cpp compiling SimpleCubic.cpp compiling Q4.cpp compiling Position.cpp compiling MultiColvarDensity.cpp compiling SAXS.cpp compiling ContactAlignedMatrix.cpp compiling InPlaneDistances.cpp compiling Group.cpp compiling PolymerAngles.cpp compiling Q3.cpp compiling MoleculePlane.cpp compiling Atoms.cpp compiling Colvar.cpp compiling LandmarkStaged.cpp compiling AverageVessel.cpp compiling StoreDataVessel.cpp compiling ContactMatrix.cpp compiling LocalSteinhardt.cpp compiling TopologyMatrix.cpp compiling FilterLessThan.cpp compiling MultiColvarProduct.cpp compiling Lowest.cpp compiling ActionWithVessel.cpp compiling Subprocess.cpp compiling Tensor.cpp compiling Angle.cpp compiling NOE.cpp compiling ActionAtomistic.cpp compiling ActionWithVirtualAtom.cpp compiling EMMI.cpp compiling Plumed.cpp compiling VesBias.cpp compiling TD_LinearCombination.cpp compiling TD_Exponential.cpp compiling BasisFunctions.cpp compiling GridLinearInterpolation.cpp compiling TD_Uniform.cpp compiling CoeffsBase.cpp compiling VesDeltaF.cpp compiling TD_GeneralizedNormal.cpp compiling ClusterDiameter.cpp compiling Mean.cpp compiling AltMin.cpp compiling ActionWithInputMatrix.cpp compiling MatrixRowSums.cpp compiling AlignedMatrixBase.cpp compiling Angle.cpp compiling ProjectionOnAxis.cpp compiling MoreThan.cpp compiling GradientVessel.cpp compiling VectorMultiColvar.cpp compiling Log.cpp compiling DumpGraph.cpp compiling Coordination.cpp compiling Colvar.cpp compiling Average.cpp compiling DHEnergy.cpp compiling CoordinationBase.cpp compiling ContactMap.cpp compiling DumpMultiColvar.cpp compiling Dipole.cpp compiling DistanceFromContour.cpp compiling CoordinationNumbers.cpp compiling VolumeInCylinder.cpp compiling Steinhardt.cpp compiling KernelFunctions.cpp compiling Constant.cpp compiling ActionSet.cpp compiling PlumedHandle.cpp compiling Max.cpp compiling MD_LinearExpansionPES.cpp compiling ActionShortcut.cpp compiling UpdateIf.cpp compiling Gradient.cpp compiling DumpDerivatives.cpp compiling MDAtoms.cpp compiling CubicHarmonicBase.cpp compiling OFile.cpp compiling Keywords.cpp compiling AtomNumber.cpp compiling ActionSetup.cpp compiling Debug.cpp compiling BridgeVessel.cpp compiling PlumedMain.cpp compiling Between.cpp compiling ActionWithAveraging.cpp compiling ShortcutVessel.cpp compiling ReadAnalysisFrames.cpp compiling Min.cpp compiling OrderingVessel.cpp compiling Histogram.cpp compiling Density.cpp compiling Distances.cpp compiling Bridge.cpp compiling FilterMoreThan.cpp compiling VolumeGradientBase.cpp compiling Puckering.cpp compiling WhamWeights.cpp compiling GREX.cpp compiling CLToolMain.cpp compiling ExtraCV.cpp compiling Vector.cpp compiling Pbc.cpp compiling ReselectLandmarks.cpp compiling XDistances.cpp compiling ValueVessel.cpp compiling Cell.cpp compiling XYDistances.cpp compiling PropertyMap.cpp compiling DynamicList.cpp compiling AveragingVessel.cpp compiling ActionWithInputVessel.cpp compiling VesselRegister.cpp compiling Highest.cpp compiling VesTools.cpp compiling TD_Grid.cpp compiling OutputFesBias.cpp compiling GridIntegrationWeights.cpp compiling NumberOfLinks.cpp compiling Moments.cpp compiling VolumeAround.cpp compiling Gyration.cpp compiling XYTorsion.cpp compiling ActionVolume.cpp compiling VolumeTetrapore.cpp compiling Template.cpp compiling TD_Custom.cpp compiling Energy.cpp compiling Fake.cpp compiling FermiSwitchingFunction.cpp compiling LocalAverage.cpp compiling MultiColvarFilter.cpp compiling TD_ExponentiallyModifiedGaussian.cpp compiling LinearBasisSetExpansion.cpp compiling DihedralCorrelation.cpp compiling TD_ProductCombination.cpp compiling CoeffsVector.cpp compiling VesLinearExpansion.cpp compiling Opt_BachAveragedSGD.cpp compiling TD_VonMises.cpp compiling TD_Gaussian.cpp compiling GridProjWeights.cpp compiling TargetDistModifer.cpp Building Plumed.inc Building Plumed.inc, runtime-linking version Building Plumed.inc, shared version Building Plumed.inc, static version Building Plumed.cmake Building Plumed.cmake, static version Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared version *** Updating links to used modules in all directories *** Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/annfunc Nothing to do in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/config Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/blas Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/eds Verify modules and create links in 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/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/multicolvar *** Compiling all directories *** Updating ConfigInstall.inc Updating Config.inc Updating version.h Building Plumed.inc Building Plumed.inc, runtime-linking version Building Plumed.inc, shared version Building Plumed.inc, static version Building Plumed.cmake Building Plumed.cmake, static version Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared version Python support was not configured [ 26%] Performing install step for 'plumed_build' Updating ConfigInstall.inc Updating Config.inc Updating version.h *** Updating links to used modules in all directories *** Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/annfunc Nothing to do in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/config Verify modules and create links in 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/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/colvar Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/ves Verify modules and create links in /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/src/plumed_build/src/multicolvar *** Compiling all directories *** Updating ConfigInstall.inc Updating Config.inc Updating version.h Building Plumed.inc Building Plumed.inc, runtime-linking version Building Plumed.inc, shared version Building Plumed.inc, static version Building Plumed.cmake Building Plumed.cmake, static version Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared version *** PLUMED has been installed *** Install prefix : /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix Full name : plumed Setup your environment - Ensure this is in your execution path : /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/bin - Ensure this is in your include path : /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/include - Ensure this is in your library path : /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/lib - Ensure this is in your PKG_CONFIG_PATH path : /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/lib/pkgconfig For runtime binding: - Set this environment variable : PLUMED_KERNEL=/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/lib/libplumedKernel.so To create a tcl module that sets all the variables above, use this one as a starting point: /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/lib/plumed/modulefile To uninstall, remove the following files and directories: /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/lib/plumed /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/share/doc/plumed /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/include/plumed /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/bin/plumed /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/bin/plumed-patch /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/bin/plumed-config /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/lib/pkgconfig/plumed.pc /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/lib/libplumed.so /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/lib/libplumedKernel.so A vim plugin can be found here: /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/lib/plumed/vim/ Copy it to /home/cauchy/.vim/ directory Alternatively: - Set this environment variable : PLUMED_VIMPATH=/home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/plumed_build-prefix/lib/plumed/vim - Add the command 'let &runtimepath.=','.$PLUMED_VIMPATH' to your .vimrc file From vim, you can use :set syntax=plumed to enable it [ 26%] Completed 'plumed_build' [ 26%] Built target plumed_build CMake Error at /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/n2p2_build-prefix/src/n2p2_build-stamp/n2p2_build-build-RelWithDebInfo.cmake:49 (message): Command failed: 2 '/usr/bin/make' '-f' 'makefile' 'libnnpif' 'INTERFACES=LAMMPS' 'COMP=gnu' 'PROJECT_OPTIONS=' 'PROJECT_DEBUG=' 'PROJECT_CC=/usr/bin/c++' 'PROJECT_MPICC=/usr/bin/c++' 'PROJECT_CFLAGS=-fPIC -O2 -g -DNDEBUG -std=gnu++11' 'PROJECT_AR=/usr/bin/gcc-ar-9' 'APP_CORE=nnp-convert' 'APP_TRAIN=nnp-train' 'APP=nnp-convert' See also /home/cauchy/Desktop/LAMMPS/lammps-24Mar2022/build/n2p2_build-prefix/src/n2p2_build-stamp/n2p2_build-build-*.log make[2]: *** [CMakeFiles/n2p2_build.dir/build.make:115: n2p2_build-prefix/src/n2p2_build-stamp/n2p2_build-build] Error 1 make[1]: *** [CMakeFiles/Makefile2:1081: CMakeFiles/n2p2_build.dir/all] Error 2 make: *** [Makefile:130: all] Error 2