From: Do, Hung Nguyen (hungd238_at_ku.edu)
Date: Tue Apr 05 2022 - 22:15:30 CDT
Hello,
I followed the instructions in notes.txt and got the following error while trying to compile NAMD 2.15 Source Codes. Can someone please have a look and let me know how to fix this? I used the default charm-6.10.2 (and tcl-threaded and fftw) included in the NAMD folder.
Many thanks,
Hung
OpenMP support not enabled
charmc> ----------- Module dependency search ------------
charmc> ----------- Module dependency search complete ------------
charmc> All libraries are: -L.rootdir/charm-6.10.2/multicore-linux-x86_64/bin/../lib -lmoduleCkLoop -lmoduleCkMulticast -lckmain -lck -lmemory-default -lthreads-default -lconv-machine -lconv-core -ltmgr -lconv-util -lconv-partition -lhwloc_embedded -lm -lcudart -lmemory-default -lthreads-default -lldb-rand -lconv-ldb -lpthread -lckqt -ldl -ltcl8.5 -ldl -lpthread -lsrfftw -lsfftw -lm -lmoduleCkMulticast -lmoduleCkLoop -lmoduleNDMeshStreamer -lmodulecompletion -lz -lm .rootdir/charm-6.10.2/multicore-linux-x86_64/bin/../lib/conv-static.o
Adding registration for module CkMulticast
Adding registration for module CkLoop
charmc: Executing g++ -DCMK_GFORTRAN -D_REENTRANT -I.rootdir/charm-6.10.2/multicore-linux-x86_64/bin/../include -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -fexpensive-optimizations -ffast-math -U_FORTIFY_SOURCE -fno-stack-protector -fno-lifetime-dse -c moduleinit2681096.C -o moduleinit2681096.o
charmc: Executing g++ -rdynamic -D_REENTRANT -O3 -fexpensive-optimizations -ffast-math -I.rootdir/charm-6.10.2/multicore-linux-x86_64/include -L.rootdir/tcl-threaded/lib -L.rootdir/fftw/lib obj/buildinfo.o obj/AVXTiles.o obj/AVXTilesKernel.o obj/AVXTileLists.o obj/ComputeMoa.o obj/ComputeMsm.o obj/ComputeMsmMsa.o obj/ComputeMsmSerial.o obj/ComputeFmmSerial.o obj/msm.o obj/msm_longrng.o obj/msm_longrng_sprec.o obj/msm_setup.o obj/msm_shortrng.o obj/msm_shortrng_sprec.o obj/wkfutils.o obj/common.o obj/dcdlib.o obj/eabf1D.o obj/eabf2D.o obj/eabffunc.o obj/eabfTcl.o obj/erf.o obj/fitrms.o obj/main.o obj/mainfunc.o obj/memusage.o obj/strlib.o obj/AlgSeven.o obj/AlgRecBisection.o obj/AlgNbor.o obj/AtomMap.o obj/BackEnd.o obj/BroadcastMgr.o obj/BroadcastClient.o obj/CollectionMaster.o obj/CollectionMgr.o obj/Communicate.o obj/Compute.o obj/ComputeAngles.o obj/ComputeAniso.o obj/ComputeBonds.o obj/ComputeBondedCUDA.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o obj/ComputeCrossterms.o obj/ComputeCUDAMgr.o obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.o obj/ComputeEwald.o obj/ComputeExt.o obj/ComputeQM.o obj/ComputeGBISser.o obj/ComputeGBIS.o obj/ComputeGromacsPair.o obj/ComputeLCPO.o obj/ComputeFullDirect.o obj/ComputeHomePatch.o obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o obj/ComputeGlobalMsgs.o obj/ComputeGridForce.o obj/ComputeMap.o obj/ComputeMgr.o obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o obj/ComputeNonbondedFEP.o obj/ComputeNonbondedGo.o obj/ComputeNonbondedTI.o obj/ComputeNonbondedLES.o obj/ComputeNonbondedPProf.o obj/ComputeNonbondedTabEnergies.o obj/ComputeNonbondedCUDA.o obj/ComputeNonbondedCUDAExcl.o obj/ComputeNonbondedMIC.o obj/ComputeNonbondedMICKernel.o obj/ComputePatch.o obj/ComputePatchPair.o obj/ComputePme.o obj/ComputePmeCUDA.o obj/ComputePmeCUDAMgr.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o obj/ComputeStir.o obj/ComputeTclBC.o obj/ComputeThole.o obj/ConfigList.o obj/Controller.o obj/CudaComputeNonbonded.o obj/CudaNonbondedTables.o obj/CudaPmeSolver.o obj/CudaPmeSolverUtil.o obj/CudaUtils.o obj/ccsinterface.o obj/DataStream.o obj/DeviceCUDA.o obj/DumpBench.o obj/FreeEnergyAssert.o obj/FreeEnergyGroup.o obj/FreeEnergyLambda.o obj/FreeEnergyLambdMgr.o obj/FreeEnergyParse.o obj/FreeEnergyRestrain.o obj/FreeEnergyRMgr.o obj/FreeEnergyVector.o obj/fstream_namd.o obj/GlobalMaster.o obj/GlobalMasterServer.o obj/GlobalMasterTest.o obj/GlobalMasterIMD.o obj/GlobalMasterTcl.o obj/GlobalMasterSMD.o obj/GlobalMasterTMD.o obj/Matrix4Symmetry.o obj/GlobalMasterSymmetry.o obj/GlobalMasterFreeEnergy.o obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o obj/colvarproxy_namd.o obj/GridForceGrid.o obj/GromacsTopFile.o obj/heap.o obj/HomePatch.o obj/IMDOutput.o obj/InfoStream.o obj/LdbCoordinator.o obj/LJTable.o obj/Measure.o obj/MGridforceParams.o obj/MStream.o obj/MigrateAtomsMsg.o obj/Molecule.o obj/Molecule2.o obj/GoMolecule.o obj/MoleculeQM.o obj/NamdCentLB.o obj/NamdHybridLB.o obj/NamdDummyLB.o obj/NamdState.o obj/NamdOneTools.o obj/Node.o obj/Output.o obj/Parameters.o obj/ParseOptions.o obj/Patch.o obj/PatchMgr.o obj/PatchMap.o obj/PDB.o obj/PDBData.o obj/PmeKSpace.o obj/PmeRealSpace.o obj/PmeSolver.o obj/ProcessorPrivate.o obj/ProxyMgr.o obj/ProxyPatch.o obj/Rebalancer.o obj/RecBisection.o obj/ReductionMgr.o obj/RefineOnly.o obj/RefineTorusLB.o obj/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o obj/SimParameters.o obj/SortAtoms.o obj/Sync.o obj/TclCommands.o obj/TorusLB.o obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o obj/CompressPsf.o obj/PluginIOMgr.o obj/DataExchanger.o obj/ParallelIOMgr.o obj/dcdplugin.o obj/jsplugin.o obj/namdbinplugin.o obj/pdbplugin.o obj/psfplugin.o obj/tcl_psfgen.o obj/charmm_file.o obj/charmm_parse_topo_defs.o obj/extract_alias.o obj/hash.o obj/hasharray.o obj/memarena.o obj/pdb_file.o obj/pdb_file_extract.o obj/psf_file.o obj/psf_file_extract.o obj/topo_defs.o obj/topo_mol.o obj/topo_mol_output.o obj/topo_mol_pluginio.o obj/stringhash.o obj/colvar.o obj/colvaratoms.o obj/colvarbias.o obj/colvarbias_abf.o obj/colvarbias_alb.o obj/colvarbias_histogram.o obj/colvarbias_meta.o obj/colvarbias_restraint.o obj/colvarcomp.o obj/colvarcomp_angles.o obj/colvarcomp_apath.o obj/colvarcomp_coordnums.o obj/colvarcomp_distances.o obj/colvarcomp_gpath.o obj/colvarcomp_protein.o obj/colvarcomp_rotations.o obj/colvarcomp_volmaps.o obj/colvardeps.o obj/colvargrid.o obj/colvarmodule.o obj/colvarparams.o obj/colvarparse.o obj/colvarproxy.o obj/colvarproxy_volmaps.o obj/colvarproxy_replicas.o obj/colvarproxy_tcl.o obj/colvarscript.o obj/colvarscript_commands.o obj/colvarscript_commands_bias.o obj/colvarscript_commands_colvar.o obj/colvartypes.o obj/colvarvalue.o obj/CompiledExpression.o obj/ExpressionProgram.o obj/ExpressionTreeNode.o obj/Operation.o obj/ParsedExpression.o obj/Parser.o moduleinit2681096.o -L.rootdir/charm-6.10.2/multicore-linux-x86_64/bin/../lib -lmoduleCkLoop -lmoduleCkMulticast -lckmain -lck -lmemory-default -lthreads-default -lconv-machine -lconv-core -ltmgr -lconv-util -lconv-partition -lhwloc_embedded -lm -lcudart -lmemory-default -lthreads-default -lldb-rand -lconv-ldb -lpthread -lckqt -ldl -ltcl8.5 -ldl -lpthread -lsrfftw -lsfftw -lm -lmoduleCkMulticast -lmoduleCkLoop -lmoduleNDMeshStreamer -lmodulecompletion -lz -lm .rootdir/charm-6.10.2/multicore-linux-x86_64/bin/../lib/conv-static.o -o namd2
/usr/bin/ld: .rootdir/fftw/lib/libsrfftw.a(rfftwnd.o): relocation R_X86_64_32 against `.rodata.str1.32' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsrfftw.a(rplanner.o): relocation R_X86_64_32 against symbol `rfftw_config' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsrfftw.a(rexec.o): relocation R_X86_64_32 against `.rodata.str1.32' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(planner.o): relocation R_X86_64_32 against symbol `fftw_config' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(executor.o): relocation R_X86_64_32 against `.rodata.str1.32' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(fftwnd.o): relocation R_X86_64_32 against `.rodata.str1.32' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(malloc.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(wisdom.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(wisdomio.o): relocation R_X86_64_32 against `.text' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(putils.o): relocation R_X86_64_32S against `.rodata' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(rader.o): relocation R_X86_64_32 against symbol `fftw_twiddle_rader' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(twiddle.o): relocation R_X86_64_32 against `.bss' can not be used when making a PIE object; recompile with -fPIE
collect2: error: ld returned 1 exit status
Fatal Error by charmc in directory /data/hung/NAMD/NAMD_2.15alpha2_Source/Linux-x86_64-g++
Command g++ -rdynamic -D_REENTRANT -O3 -fexpensive-optimizations -ffast-math -I.rootdir/charm-6.10.2/multicore-linux-x86_64/include -L.rootdir/tcl-threaded/lib -L.rootdir/fftw/lib obj/buildinfo.o obj/AVXTiles.o obj/AVXTilesKernel.o obj/AVXTileLists.o obj/ComputeMoa.o obj/ComputeMsm.o obj/ComputeMsmMsa.o obj/ComputeMsmSerial.o obj/ComputeFmmSerial.o obj/msm.o obj/msm_longrng.o obj/msm_longrng_sprec.o obj/msm_setup.o obj/msm_shortrng.o obj/msm_shortrng_sprec.o obj/wkfutils.o obj/common.o obj/dcdlib.o obj/eabf1D.o obj/eabf2D.o obj/eabffunc.o obj/eabfTcl.o obj/erf.o obj/fitrms.o obj/main.o obj/mainfunc.o obj/memusage.o obj/strlib.o obj/AlgSeven.o obj/AlgRecBisection.o obj/AlgNbor.o obj/AtomMap.o obj/BackEnd.o obj/BroadcastMgr.o obj/BroadcastClient.o obj/CollectionMaster.o obj/CollectionMgr.o obj/Communicate.o obj/Compute.o obj/ComputeAngles.o obj/ComputeAniso.o obj/ComputeBonds.o obj/ComputeBondedCUDA.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o obj/ComputeCrossterms.o obj/ComputeCUDAMgr.o obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.o obj/ComputeEwald.o obj/ComputeExt.o obj/ComputeQM.o obj/ComputeGBISser.o obj/ComputeGBIS.o obj/ComputeGromacsPair.o obj/ComputeLCPO.o obj/ComputeFullDirect.o obj/ComputeHomePatch.o obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o obj/ComputeGlobalMsgs.o obj/ComputeGridForce.o obj/ComputeMap.o obj/ComputeMgr.o obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o obj/ComputeNonbondedFEP.o obj/ComputeNonbondedGo.o obj/ComputeNonbondedTI.o obj/ComputeNonbondedLES.o obj/ComputeNonbondedPProf.o obj/ComputeNonbondedTabEnergies.o obj/ComputeNonbondedCUDA.o obj/ComputeNonbondedCUDAExcl.o obj/ComputeNonbondedMIC.o obj/ComputeNonbondedMICKernel.o obj/ComputePatch.o obj/ComputePatchPair.o obj/ComputePme.o obj/ComputePmeCUDA.o obj/ComputePmeCUDAMgr.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o obj/ComputeStir.o obj/ComputeTclBC.o obj/ComputeThole.o obj/ConfigList.o obj/Controller.o obj/CudaComputeNonbonded.o obj/CudaNonbondedTables.o obj/CudaPmeSolver.o obj/CudaPmeSolverUtil.o obj/CudaUtils.o obj/ccsinterface.o obj/DataStream.o obj/DeviceCUDA.o obj/DumpBench.o obj/FreeEnergyAssert.o obj/FreeEnergyGroup.o obj/FreeEnergyLambda.o obj/FreeEnergyLambdMgr.o obj/FreeEnergyParse.o obj/FreeEnergyRestrain.o obj/FreeEnergyRMgr.o obj/FreeEnergyVector.o obj/fstream_namd.o obj/GlobalMaster.o obj/GlobalMasterServer.o obj/GlobalMasterTest.o obj/GlobalMasterIMD.o obj/GlobalMasterTcl.o obj/GlobalMasterSMD.o obj/GlobalMasterTMD.o obj/Matrix4Symmetry.o obj/GlobalMasterSymmetry.o obj/GlobalMasterFreeEnergy.o obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o obj/colvarproxy_namd.o obj/GridForceGrid.o obj/GromacsTopFile.o obj/heap.o obj/HomePatch.o obj/IMDOutput.o obj/InfoStream.o obj/LdbCoordinator.o obj/LJTable.o obj/Measure.o obj/MGridforceParams.o obj/MStream.o obj/MigrateAtomsMsg.o obj/Molecule.o obj/Molecule2.o obj/GoMolecule.o obj/MoleculeQM.o obj/NamdCentLB.o obj/NamdHybridLB.o obj/NamdDummyLB.o obj/NamdState.o obj/NamdOneTools.o obj/Node.o obj/Output.o obj/Parameters.o obj/ParseOptions.o obj/Patch.o obj/PatchMgr.o obj/PatchMap.o obj/PDB.o obj/PDBData.o obj/PmeKSpace.o obj/PmeRealSpace.o obj/PmeSolver.o obj/ProcessorPrivate.o obj/ProxyMgr.o obj/ProxyPatch.o obj/Rebalancer.o obj/RecBisection.o obj/ReductionMgr.o obj/RefineOnly.o obj/RefineTorusLB.o obj/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o obj/SimParameters.o obj/SortAtoms.o obj/Sync.o obj/TclCommands.o obj/TorusLB.o obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o obj/CompressPsf.o obj/PluginIOMgr.o obj/DataExchanger.o obj/ParallelIOMgr.o obj/dcdplugin.o obj/jsplugin.o obj/namdbinplugin.o obj/pdbplugin.o obj/psfplugin.o obj/tcl_psfgen.o obj/charmm_file.o obj/charmm_parse_topo_defs.o obj/extract_alias.o obj/hash.o obj/hasharray.o obj/memarena.o obj/pdb_file.o obj/pdb_file_extract.o obj/psf_file.o obj/psf_file_extract.o obj/topo_defs.o obj/topo_mol.o obj/topo_mol_output.o obj/topo_mol_pluginio.o obj/stringhash.o obj/colvar.o obj/colvaratoms.o obj/colvarbias.o obj/colvarbias_abf.o obj/colvarbias_alb.o obj/colvarbias_histogram.o obj/colvarbias_meta.o obj/colvarbias_restraint.o obj/colvarcomp.o obj/colvarcomp_angles.o obj/colvarcomp_apath.o obj/colvarcomp_coordnums.o obj/colvarcomp_distances.o obj/colvarcomp_gpath.o obj/colvarcomp_protein.o obj/colvarcomp_rotations.o obj/colvarcomp_volmaps.o obj/colvardeps.o obj/colvargrid.o obj/colvarmodule.o obj/colvarparams.o obj/colvarparse.o obj/colvarproxy.o obj/colvarproxy_volmaps.o obj/colvarproxy_replicas.o obj/colvarproxy_tcl.o obj/colvarscript.o obj/colvarscript_commands.o obj/colvarscript_commands_bias.o obj/colvarscript_commands_colvar.o obj/colvartypes.o obj/colvarvalue.o obj/CompiledExpression.o obj/ExpressionProgram.o obj/ExpressionTreeNode.o obj/Operation.o obj/ParsedExpression.o obj/Parser.o moduleinit2681096.o -L.rootdir/charm-6.10.2/multicore-linux-x86_64/bin/../lib -lmoduleCkLoop -lmoduleCkMulticast -lckmain -lck -lmemory-default -lthreads-default -lconv-machine -lconv-core -ltmgr -lconv-util -lconv-partition -lhwloc_embedded -lm -lcudart -lmemory-default -lthreads-default -lldb-rand -lconv-ldb -lpthread -lckqt -ldl -ltcl8.5 -ldl -lpthread -lsrfftw -lsfftw -lm -lmoduleCkMulticast -lmoduleCkLoop -lmoduleNDMeshStreamer -lmodulecompletion -lz -lm .rootdir/charm-6.10.2/multicore-linux-x86_64/bin/../lib/conv-static.o -o namd2 returned error code 1
charmc exiting...
rm -f moduleinit2681096.C moduleinit2681096.o
make: *** [Makefile:470: namd2] Error 1
This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST