Date: Sat, 9 May 2020 20:40:59 GMT From: pkg-fallout@FreeBSD.org To: yuri@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - head-i386-default][science/plumed] Failed for plumed-2.6.0 in build Message-ID: <202005092040.049KexCC094096@beefy17.nyi.freebsd.org>
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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@FreeBSD.org Last committer: linimon@FreeBSD.org Ident: $FreeBSD: head/science/plumed/Makefile 534167 2020-05-06 12:00:53Z linimon $ Log URL: http://beefy17.nyi.freebsd.org/data/head-i386-default/p534700_s360829/logs/plumed-2.6.0.log Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p534700_s360829 Log: =>> Building science/plumed build started at Sat May 9 20:32:09 UTC 2020 port directory: /usr/ports/science/plumed package name: plumed-2.6.0 building for: FreeBSD head-i386-default-job-12 13.0-CURRENT FreeBSD 13.0-CURRENT 1300094 i386 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/science/plumed/Makefile 534167 2020-05-06 12:00:53Z linimon $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300089 Jail OSVERSION: 1300094 Job Id: 12 !!! Jail is newer than host. (Jail: 1300094, Host: 1300089) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1300094 UNAME_v=FreeBSD 13.0-CURRENT 1300094 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-i386-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --enable-shared --disable-python --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/science/plumed/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/plumed/work HOME=/wrkdirs/usr/ports/science/plumed/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/plumed/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/plumed/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/plumed/work HOME=/wrkdirs/usr/ports/science/plumed/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/plumed/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/plumed" EXAMPLESDIR="share/examples/plumed" DATADIR="share/plumed" WWWDIR="www/plumed" ETCDIR="etc/plumed" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/plumed DOCSDIR=/usr/local/share/doc/plumed EXAMPLESDIR=/usr/local/share/examples/plumed WWWDIR=/usr/local/www/plumed ETCDIR=/usr/local/etc/plumed --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-m" "elf_i386_fbsd" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300094 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 524288 stack size (kbytes, -s) 65536 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<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 [head-i386-default-job-12] Installing pkg-1.14.4... [head-i386-default-job-12] Extracting pkg-1.14.4: .......... done ldconfig: aout support is deprecated ===> 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 [head-i386-default-job-12] Installing bash-5.0.17... [head-i386-default-job-12] `-- Installing gettext-runtime-0.20.2... <snip> compiling AlphaRMSD.cpp compiling MultiColvarDensity.cpp compiling AntibetaRMSD.cpp compiling MultiColvarCombine.cpp compiling ParabetaRMSD.cpp compiling VolumeCavity.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 CoordinationNumbers.cpp compiling MolInfo.cpp compiling Restart.cpp compiling DistanceFromContour.cpp compiling Units.cpp gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/setup' compiling Angles.cpp 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 AtomValuePack.cpp compiling SwitchingFunction.cpp compiling CatomPack.cpp compiling Angle.cpp compiling CenterOfMultiColvar.cpp compiling Vector.cpp compiling Communicator.cpp compiling Pbc.cpp compiling InPlaneDistances.cpp compiling AtomNumber.cpp compiling Keywords.cpp compiling XAngle.cpp compiling VolumeBetweenContours.cpp compiling OFile.cpp compiling VolumeInSphere.cpp compiling PlumedHandle.cpp compiling MolDataClass.cpp compiling AlphaBeta.cpp compiling Torsions.cpp compiling Subprocess.cpp compiling BridgedMultiColvarFunction.cpp compiling Torsion.cpp compiling Log.cpp compiling MultiColvarBase.cpp compiling RootFindingBase.cpp compiling Citations.cpp compiling Matrix.cpp compiling Brent1DRootSearch.cpp compiling FileBase.cpp compiling DLLoader.cpp compiling KernelFunctions.cpp gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/multicolvar' 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 LatticeReduction.cpp compiling FixedAtom.cpp compiling ConjugateGradient.cpp compiling PDB.cpp compiling Ghost.cpp gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/vatom' compiling Minimise1DBrent.cpp gmake -C ../vesselbase obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/vesselbase' compiling Highest.cpp compiling RMSD.cpp compiling VesselRegister.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() { ^ compiling Sum.cpp 10 warnings generated. compiling h36.cpp compiling ActionWithInputVessel.cpp compiling Random.cpp compiling AveragingVessel.cpp compiling OpenMP.cpp compiling Tools.cpp compiling ActionWithAveraging.cpp compiling LinkCells.cpp compiling ValueVessel.cpp compiling MinimiseBase.cpp compiling BiasRepresentation.cpp compiling Histogram.cpp compiling MoreThan.cpp compiling ERMSD.cpp compiling Min.cpp compiling Units.cpp compiling MatrixSquareBracketsAccess.cpp compiling Grid.cpp compiling ShortcutVessel.cpp compiling OrderingVessel.cpp compiling Between.cpp compiling BridgeVessel.cpp compiling ForwardDecl.cpp compiling Max.cpp compiling MultiValue.cpp compiling LoopUnroller.cpp compiling Stopwatch.cpp compiling StoreDataVessel.cpp compiling IFile.cpp compiling AltMin.cpp compiling NeighborList.cpp compiling Moments.cpp compiling HistogramBead.cpp compiling Mean.cpp compiling Tensor.cpp gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/tools' gmake -C ../wrapper obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/wrapper' compiling PlumedStatic.cpp compiling ActionWithVessel.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' 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[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 Building Plumed.inc chmod a+x plumed-config chmod a+x plumed-mklib chmod a+x plumed-newcv chmod a+x plumed-partial_tempering chmod a+x plumed-patch chmod a+x plumed-selector chmod a+x plumed-vim2html c++ -shared -o libplumedKernel.so ../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/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 ../co lvar/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/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/Pl umedMain.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/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid. o ../gridtools/ContourFindingBase.o ../gridt! ools/Conv! ertToFES..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 ../multicol var/NumberOfLinks.o ../multicolvar/Torsions.! o ../multi! colvar/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/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/Random.o ../tools/RootFind ingBase.o ../tools/Stopwatch.o ../tools/Subp! rocess.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 -Wl,-soname,"libplumedKernel.so" -lstdc++ -lz -ldl -fstack-protector-strong -rdynamic -Wl,-Bsymbolic -f openmp ld: error: undefined symbol: __atomic_load >>> referenced by CoordinationBase.cpp >>> ../colvar/CoordinationBase.o:(.omp_outlined.) >>> referenced by EEFSolv.cpp >>> ../colvar/EEFSolv.o:(.omp_outlined.) >>> referenced by EffectiveEnergyDrift.cpp >>> ../generic/EffectiveEnergyDrift.o:(.omp_outlined..27) >>> referenced by Metainference.cpp >>> ../isdb/Metainference.o:(.omp_outlined.) >>> referenced by Metainference.cpp >>> ../isdb/Metainference.o:(.omp_outlined..188) >>> referenced by Metainference.cpp >>> ../isdb/Metainference.o:(.omp_outlined..190) >>> referenced by Metainference.cpp >>> ../isdb/Metainference.o:(.omp_outlined..192) >>> referenced by Metainference.cpp >>> ../isdb/Metainference.o:(.omp_outlined..194) >>> referenced by Metainference.cpp >>> ../isdb/Metainference.o:(.omp_outlined..198) >>> referenced by Metainference.cpp >>> ../isdb/Metainference.o:(.omp_outlined..200) >>> referenced 9 more times c++: error: linker command failed with exit code 1 (use -v to see invocation) gmake[5]: *** [Makefile:484: plumed-static] Error 1 gmake[5]: *** Waiting for unfinished jobs.... 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' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/science/plumed
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