[package - 113i386-default][science/plumed] Failed for plumed-2.6.0 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sat May 9 14:05:25 UTC 2020
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri at FreeBSD.org
Last committer: linimon at FreeBSD.org
Ident: $FreeBSD: head/science/plumed/Makefile 534167 2020-05-06 12:00:53Z linimon $
Log URL: http://beefy10.nyi.freebsd.org/data/113i386-default/534700/logs/plumed-2.6.0.log
Build URL: http://beefy10.nyi.freebsd.org/build.html?mastername=113i386-default&build=534700
Log:
=>> Building science/plumed
build started at Sat May 9 13:49:42 UTC 2020
port directory: /usr/ports/science/plumed
package name: plumed-2.6.0
building for: FreeBSD 113i386-default-job-05 11.3-RELEASE-p8 FreeBSD 11.3-RELEASE-p8 i386
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/science/plumed/Makefile 534167 2020-05-06 12:00:53Z linimon $
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=======================<phase: check-sanity >============================
===> License LGPL3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> plumed-2.6.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.14.4.txz
[113i386-default-job-05] Installing pkg-1.14.4...
[113i386-default-job-05] Extracting pkg-1.14.4: .......... done
===> plumed-2.6.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of plumed-2.6.0
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by plumed-2.6.0 for building
===========================================================================
=======================<phase: checksum >============================
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by plumed-2.6.0 for building
=> SHA256 Checksum OK for plumed-plumed2-v2.6.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by plumed-2.6.0 for building
===> Extracting for plumed-2.6.0
=> SHA256 Checksum OK for plumed-plumed2-v2.6.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for plumed-2.6.0
===> Applying FreeBSD patches for plumed-2.6.0
===> Cleanly applied FreeBSD patch(es) patch-configure.ac
===========================================================================
=======================<phase: build-depends >============================
===> plumed-2.6.0 depends on executable: bash - not found
===> Installing existing package /packages/All/bash-5.0.17.txz
[113i386-default-job-05] Installing bash-5.0.17...
[113i386-default-job-05] `-- Installing gettext-runtime-0.20.2...
[113i386-default-job-05] | `-- Installing indexinfo-0.3.1...
[113i386-default-job-05] | `-- Extracting indexinfo-0.3.1: .... done
[113i386-default-job-05] `-- Extracting gettext-runtime-0.20.2: .......... done
[113i386-default-job-05] Extracting bash-5.0.17: .......... done
===> plumed-2.6.0 depends on executable: bash - found
===> Returning to build of plumed-2.6.0
===> plumed-2.6.0 depends on executable: xxd - not found
===> Installing existing package /packages/All/vim-console-8.2.0491_1.txz
[113i386-default-job-05] Installing vim-console-8.2.0491_1...
[113i386-default-job-05] Extracting vim-console-8.2.0491_1: .......... done
<snip>
compiling VolumeCavity.cpp
compiling CoordinationNumbers.cpp
compiling DistanceFromContour.cpp
compiling Angles.cpp
compiling AtomValuePack.cpp
compiling CatomPack.cpp
compiling CenterOfMultiColvar.cpp
compiling InPlaneDistances.cpp
compiling XAngle.cpp
compiling VolumeBetweenContours.cpp
compiling VolumeInSphere.cpp
compiling AlphaBeta.cpp
compiling Torsions.cpp
compiling BridgedMultiColvarFunction.cpp
compiling MultiColvarBase.cpp
gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/multicolvar'
gmake -C ../reference obj
gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/reference'
compiling NormalizedEuclideanDistance.cpp
compiling DotProductDistance.cpp
compiling ReferenceAtoms.cpp
compiling MetricRegister.cpp
compiling OptimalRMSD.cpp
compiling ReferenceArguments.cpp
compiling SingleDomainRMSD.cpp
compiling ReferenceValuePack.cpp
compiling RMSDBase.cpp
compiling SimpleRMSD.cpp
compiling MultiDomainRMSD.cpp
compiling IntermolecularDRMSD.cpp
compiling ArgumentOnlyDistance.cpp
compiling MahalanobisDistance.cpp
compiling DRMSD.cpp
compiling EuclideanDistance.cpp
compiling ReferenceConfiguration.cpp
compiling Direction.cpp
compiling IntramolecularDRMSD.cpp
compiling FakeFrame.cpp
gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/reference'
gmake -C ../secondarystructure obj
gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/secondarystructure'
compiling SecondaryStructureRMSD.cpp
compiling AlphaRMSD.cpp
compiling AntibetaRMSD.cpp
compiling ParabetaRMSD.cpp
gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/secondarystructure'
gmake -C ../setup obj
gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/setup'
compiling Load.cpp
compiling MolInfo.cpp
compiling Restart.cpp
compiling Units.cpp
gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/setup'
gmake -C ../tools obj
gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/tools'
compiling DynamicList.cpp
compiling Exception.cpp
compiling SwitchingFunction.cpp
compiling Angle.cpp
compiling Vector.cpp
compiling Communicator.cpp
compiling Pbc.cpp
compiling AtomNumber.cpp
compiling Keywords.cpp
compiling OFile.cpp
compiling PlumedHandle.cpp
compiling MolDataClass.cpp
compiling Subprocess.cpp
compiling Torsion.cpp
compiling Log.cpp
compiling RootFindingBase.cpp
compiling Citations.cpp
compiling Matrix.cpp
compiling Brent1DRootSearch.cpp
compiling FileBase.cpp
compiling DLLoader.cpp
compiling KernelFunctions.cpp
compiling LatticeReduction.cpp
compiling ConjugateGradient.cpp
compiling PDB.cpp
compiling Minimise1DBrent.cpp
compiling RMSD.cpp
RMSD.cpp:93:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
void RMSD::setReference(const vector<Vector> & reference) {
^
RMSD.cpp:112:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
void RMSD::setAlign(const vector<double> & align, bool normalize_weights, bool remove_center) {
^
RMSD.cpp:112:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
RMSD.cpp:147:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
void RMSD::setDisplace(const vector<double> & displace, bool normalize_weights) {
^
RMSD.cpp:147:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
RMSD.cpp:958:20: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
void RMSDCoreData::doCoreCalc(bool safe,bool alEqDis, bool only_rotation) {
^
RMSD.cpp:1106:22: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
double RMSDCoreData::getDistance( bool squared) {
^
RMSD.cpp:1134:20: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
void RMSDCoreData::doCoreCalcWithCloseStructure(bool safe,bool alEqDis, Tensor & rotationPosClose, Tensor & rotationRefClose, std::array<std::array<Tensor,3>,3> & drotationPosCloseDrr01) {
^
RMSD.cpp:1169:35: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
std::vector<Vector> RMSDCoreData::getDDistanceDPositions() {
^
RMSD.cpp:1205:36: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
std::vector<Vector> RMSDCoreData::getDDistanceDReference() {
^
10 warnings generated.
compiling h36.cpp
compiling Random.cpp
compiling OpenMP.cpp
compiling Tools.cpp
compiling LinkCells.cpp
compiling MinimiseBase.cpp
compiling BiasRepresentation.cpp
compiling ERMSD.cpp
compiling Units.cpp
compiling MatrixSquareBracketsAccess.cpp
compiling Grid.cpp
compiling ForwardDecl.cpp
compiling MultiValue.cpp
compiling LoopUnroller.cpp
compiling Stopwatch.cpp
compiling IFile.cpp
compiling NeighborList.cpp
compiling HistogramBead.cpp
compiling Tensor.cpp
gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/tools'
gmake -C ../vatom obj
gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/vatom'
compiling Center.cpp
compiling ActionWithVirtualAtom.cpp
compiling FixedAtom.cpp
compiling Ghost.cpp
gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/vatom'
gmake -C ../vesselbase obj
gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/vesselbase'
compiling Highest.cpp
compiling VesselRegister.cpp
compiling Sum.cpp
compiling ActionWithInputVessel.cpp
compiling AveragingVessel.cpp
compiling ActionWithAveraging.cpp
compiling ValueVessel.cpp
compiling Histogram.cpp
compiling MoreThan.cpp
compiling Min.cpp
compiling ShortcutVessel.cpp
compiling OrderingVessel.cpp
compiling Between.cpp
compiling BridgeVessel.cpp
compiling Max.cpp
compiling StoreDataVessel.cpp
compiling AltMin.cpp
compiling Moments.cpp
compiling Mean.cpp
compiling ActionWithVessel.cpp
compiling Lowest.cpp
compiling FunctionVessel.cpp
compiling Vessel.cpp
compiling LessThan.cpp
gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/vesselbase'
gmake -C ../wrapper obj
gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/wrapper'
compiling PlumedStatic.cpp
compiling Plumed.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/wrapper'
gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/lib'
gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/lib'
gmake lib
gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/lib'
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -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/ope
rand.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/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.
o ../cltools/kT.o ../cltools/pesmd.o ../colv!
ar/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/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.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/Exchan
gePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.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/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/Actio
nWithInputGrid.o ../gridtools/ActionWithInte!
gral.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 ../mul
ticolvar/MultiColvarFilter.o ../multicolvar/!
MultiColv!
arProduct.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/Sim
pleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.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/Ra!
ndom.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.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 ../config/Config.o ../wrapper/PlumedStatic.o -o
plumed-static -ldl -lstdc++ -lz -ldl -fstack-protector-strong -rdynamic -Wl,-Bsymbolic -fopenmp
./colvar/CoordinationBase.o: In function `.omp_outlined.':
CoordinationBase.cpp:(.text+0x2191): undefined reference to `__atomic_load'
./colvar/EEFSolv.o: In function `.omp_outlined.':
EEFSolv.cpp:(.text+0x3b64): undefined reference to `__atomic_load'
./generic/EffectiveEnergyDrift.o: In function `.omp_outlined..27':
EffectiveEnergyDrift.cpp:(.text+0x3ed3): undefined reference to `__atomic_load'
./isdb/Metainference.o: In function `.omp_outlined.':
Metainference.cpp:(.text+0x16ed9): undefined reference to `__atomic_load'
./isdb/Metainference.o: In function `.omp_outlined..188':
Metainference.cpp:(.text+0x17383): undefined reference to `__atomic_load'
./isdb/Metainference.o:Metainference.cpp:(.text+0x1788e): more undefined references to `__atomic_load' follow
c++: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[5]: *** [Makefile:484: plumed-static] Error 1
gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/lib'
gmake[4]: *** [Makefile:112: all] Error 2
gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/lib'
gmake[3]: *** [Makefile:8: lib] Error 2
gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src'
gmake[2]: *** [Makefile:32: lib] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0'
gmake[1]: *** [Makefile:21: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0'
*** Error code 1
Stop.
make: stopped in /usr/ports/science/plumed
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