Re: compiling NAMD 2.13 make error

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat May 18 2019 - 14:46:52 CDT

This message is probably what you want to look into.

*`.bss' can not be used when making a PIE object; recompile with -fPIC*

On Sat, May 18, 2019 at 5:39 AM Kosar Khajeh <khajeh.k.2005_at_gmail.com>
wrote:

> Hello dear NAMD users
> During compiling NAMD source code 13 on ubuntu 18.01 (64bit version) I
> received below error;
>
> `.bss' can not be used when making a PIE object; recompile with -fPIC
> /usr/bin/ld: final link failed: Nonrepresentable section on output
> collect2: error: ld returned 1 exit status
> Fatal Error by charmc in directory
> /home/kosar/NAMD/NAMD_2.13_Source/Linux-x86_64-g++
> Command g++ -rdynamic -D_REENTRANT -fexpensive-optimizations
> -ffast-math -L.rootdir/tcl-threaded/lib -L.rootdir/fftw/lib
> -I.rootdir/charm-6.8.2/multicore-linux-x86_64/include -o namd2
> -L.rootdir/charm-6.8.2/multicore-linux-x86_64/bin/../lib
> -I.rootdir/charm-6.8.2/multicore-linux-x86_64/bin/../include
> obj/buildinfo.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/OptPme.o
> obj/OptPmeRealSpace.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/NamdNborLB.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_coordnums.o
> obj/colvarcomp_distances.o obj/colvarcomp_protein.o
> obj/colvarcomp_rotations.o obj/colvardeps.o obj/colvargrid.o
> obj/colvarmodule.o obj/colvarparse.o obj/colvarproxy.o obj/colvarscript.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 moduleinit25210.o
> -lmoduleGreedyRefineLB -lmoduleCkLoop -lmoduleCkMulticast -lmoduleGreedyLB
> -lmoduleRefineLB -lmoduleHybridLB -lmoduleNeighborLB -lckmain -lck
> -lmemory-default -lthreads-default -lconv-cplus-y -lconv-core -ltmgr
> -lconv-util -lconv-partition -lmemory-default -lthreads-default -lldb-rand
> -lconv-ldb -lpthread -lckqt -ldl -ltcl8.5 -ldl -lpthread -lsrfftw -lsfftw
> -lm -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB
> -lmoduleCkMulticast -lmoduleCkLoop -lmoduleGreedyRefineLB
> -lmoduleNDMeshStreamer -lmodulecompletion -lm returned error code 1
> charmc exiting...
> rm -f moduleinit25210.C moduleinit25210.o
> Makefile:474: recipe for target 'namd2' failed
> make: *** [namd2] Error 1
>
>
> After googling this error and comment from "
> Priyanka Mondal <pmondal_at_udel.edu>
> ""I am using in linux 18.04. The method was just to download the package
> and update your ~/.bashrc with PATH of executable and source it .You can
> access it with
> ./namd2 file.namd "
>
> I added below comment to bashrc file in home directory and source it;
> export PATH=$PATH:/home/kosar/NAMD/NAMD_2.13_Source/Linux-x86_64-g++
>
> after that again I continued the compiling process. unfortunately i
> received previous error!!!
> I do not know what I should to do!
> Any assistance is appreciated
> Best regards
> Kosar
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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