Re: Building Namd on a linux cluster.

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri May 30 2008 - 19:25:00 CDT

On Fri, 30 May 2008, Khaled Barakat wrote:

KB>
KB> Thank you for your help.
KB>
KB> Now I continued to build NAMD. I did the following steps:
KB>
KB> 1- I edited the files Make.charm, arch/Linux-amd64.fftw , arch/Linux-amd64.tcl
KB> Linux-amd64- MPI.arch to include the appropriate directories of charm, fftw and tcl

yes. but you didn't edit it _properly_!

- you are (still, despite my advice) using PGI but didn't change
  the GCC flags to equivalent PGI flags (your NAMD with be much slower!).
- you tcl library is 32-bit.

 you didn't read your output and didn't act accordingly.
 it is all fairly evident...

axel.

KB>
KB> 2- then I initiated ./config tcl fftw Linux-amd64-MPI
KB>
KB> 3- cd Linux-amd64-MPI
KB> make
KB>
KB> the compilation process continued and at the final step I got this error:
KB>
KB> pgCC-Warning-Unknown switch: --instantiate=used
KB> pgCC-Warning-Unknown switch: -rdynamic
KB> pgCC-Warning-Unknown switch: -m64
KB> pgCC-Warning-Unknown switch: -fexpensive-optimizations
KB> pgCC-Warning-Unknown switch: -ffast-math
KB> /usr/bin/ld: skipping incompatible /home/kbarakat/tcl/linux/lib/libtcl8.3.a when searching for -
KB> ltcl8.3
KB> /usr/bin/ld: skipping incompatible /home/kbarakat/tcl/linux/lib/libtcl8.3.a when searching for -
KB> ltcl8.3
KB> /usr/bin/ld: cannot find -ltcl8.3
KB> Fatal Error by charmc in directory /home/kbarakat/NAMD_2.6_Source/Linux-amd64-MPI
KB>
KB>
KB> Command pgCC --instantiate=used -rdynamic -L/home/kbarakat/tcl/linux/lib -
KB> L/home/kbarakat/tcl/linux/lib -L/home/kbarakat/fftw/linux//lib -L/home/kbarakat/fftw/linux/lib
KB> -L/usr/local/mpich2/lib -I/home/kbarakat/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64-
KB> pthreads-pgcc/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -m64 -fexpensive-optimizations -
KB> ffast-math -L/usr/local/mpich2/lib -o namd2 -L/home/kbarakat/NAMD_2.6_Source/charm-
KB> 5.9/mpi-linux-amd64-pthreads-pgcc/bin/../lib -I/home/kbarakat/NAMD_2.6_Source/charm-
KB> 5.9/mpi-linux-amd64-pthreads-pgcc/bin/../include /home/kbarakat/NAMD_2.6_Source/charm-
KB> 5.9/mpi-linux-amd64-pthreads-pgcc/bin/../lib/libldb-rand.o obj/buildinfo.o obj/common.o
KB> obj/dcdlib.o obj/erf.o obj/fitrms.o obj/main.o obj/mainfunc.o obj/memusage.o obj/strlib.o
KB> obj/AlgSeven.o obj/AlgRecBisection.o obj/AlgNbor.o obj/AtomMap.o obj/BackEnd.o
KB> obj/BroadcastMgr.o obj/BroadcastClient.o obj/CollectionMaster.o obj/CollectionMgr.o
KB> obj/Communicate.o obj/Compute.o obj/ComputeAngles.o obj/ComputeBonds.o
KB> obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o obj/ComputeCrossterms.o
KB> obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o
KB> obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.o obj/ComputeEwald.o
KB> obj/ComputeExt.o obj/ComputeFullDirect.o obj/ComputeHomePatch.o obj/ComputeHomePatches.o
KB> obj/ComputeImpropers.o obj/ComputeGlobal.o obj/ComputeGlobalMsgs.o obj/ComputeMap.o
KB> obj/ComputeMgr.o obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o
KB> obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o obj/ComputeNonbondedFEP.o
KB> obj/ComputeNonbondedLES.o obj/ComputeNonbondedPProf.o obj/ComputePatch.o
KB> obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o
KB> obj/ComputeStir.o obj/ComputeTclBC.o obj/ConfigList.o obj/Controller.o obj/ccsinterface.o
KB> obj/DataStream.o obj/DumpBench.o obj/FreeEnergyAssert.o obj/FreeEnergyGroup.o
KB> obj/FreeEnergyLambda.o obj/FreeEnergyLambdMgr.o obj/FreeEnergyParse.o
KB> obj/FreeEnergyRestrain.o obj/FreeEnergyRMgr.o obj/FreeEnergyVector.o obj/GlobalMaster.o
KB> obj/GlobalMasterServer.o obj/GlobalMasterTest.o obj/GlobalMasterIMD.o obj/GlobalMasterTcl.o
KB> obj/GlobalMasterSMD.o obj/GlobalMasterTMD.o obj/GlobalMasterFreeEnergy.o
KB> obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o obj/GromacsTopFile.o obj/heap.o obj/HomePatch.o
KB> obj/IMDOutput.o obj/InfoStream.o obj/LdbCoordinator.o obj/LJTable.o obj/Measure.o
KB> obj/MStream.o obj/MigrateAtomsMsg.o obj/Molecule.o obj/NamdCentLB.o obj/NamdNborLB.o
KB> obj/NamdState.o obj/NamdOneTools.o obj/Node.o obj/Output.o obj/Parameters.o
KB> obj/ParseOptions.o obj/Patch.o obj/PatchMgr.o obj/PatchMap.o obj/PDB.o obj/PDBData.o
KB> obj/PmeBase.o obj/PmeKSpace.o obj/PmeRealSpace.o obj/ProcessorPrivate.o obj/ProxyMgr.o
KB> obj/ProxyPatch.o obj/Rebalancer.o obj/RecBisection.o obj/ReductionMgr.o obj/RefineOnly.o
KB> obj/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o obj/SimParameters.o obj/Sync.o
KB> obj/TclCommands.o obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o
KB> obj/dcdplugin.o moduleinit19862.o -lmoduleNeighborLB -lmodulecommlib
KB> /home/kbarakat/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64-pthreads-
KB> pgcc/bin/../lib/libmemory-default.o /home/kbarakat/NAMD_2.6_Source/charm-5.9/mpi-linux-
KB> amd64-pthreads-pgcc/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util
KB> -lckqt -lmpich -lpthread -Wl,-ldl -ltcl8.3 -ldl -lsrfftw -lsfftw -lm -lmoduleNeighborLB -
KB> lmodulecommlib -lmpich -lm returned error code 2
KB> charmc exiting...
KB> rm -f moduleinit19862.C moduleinit19862.o
KB> make: *** [namd2] Error 1
KB>
KB>
KB> khaled
KB>
KB>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

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