Re: compiling NAMD 2.13 make error

From: Priyanka Mondal (pmondal_at_udel.edu)
Date: Mon May 20 2019 - 13:22:17 CDT

Hi Kosar,
I am not sure how you are compiling the package or which version you
downloaded. As I mentioned earlier, I downloaded package :
"NAMD_Git-2019-05-20_Linux-x86_64-multicore"

Once you extract files from downloaded file.tar.gz, you have the executable
to use ( all of them including namd2, psfgen, charmrun etc ) and therefore
if you are in the same directory as the executable, you can run namd2.
Editing the bashrc is needed when you want to access the executable from
any other folder without specifying path every time you call namd2. Try
using the following line to add PATH variable for .bashrc :

export
PATH=/home/pmondal/Packages/NAMD/NAMD_Git-2019-05-20_Linux-x86_64-multicore:$PATH

replace the path here directing where you have executable, probably this :
/home/kosar/NAMD/NAMD_2.13_Source/Linux-x86_64-g++

and finally source it. It should work. The installation can be checked
using "which namd2" command which will show you where namd2 executables are
stored i.e. the PATH that you provided in .bashrc

Priyanka Mondal,
Department of Physics and Astronomy,
University of Delaware,
USA

On Sat, May 18, 2019 at 3:52 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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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