Re: Building Namd on a linux cluster.

From: Khaled Barakat (kbarakat_at_phys.ualberta.ca)
Date: Fri May 30 2008 - 19:30:23 CDT

Thank you for your help.
 
Now I continued to build NAMD. I did the following steps:

1- I edited the files Make.charm, arch/Linux-amd64.fftw , arch/Linux-amd64.tcl
Linux-amd64- MPI.arch to include the appropriate directories of charm, fftw and tcl

2- then I initiated ./config tcl fftw Linux-amd64-MPI

3- cd Linux-amd64-MPI
      make

the compilation process continued and at the final step I got this error:
 
pgCC-Warning-Unknown switch: --instantiate=used
pgCC-Warning-Unknown switch: -rdynamic
pgCC-Warning-Unknown switch: -m64
pgCC-Warning-Unknown switch: -fexpensive-optimizations
pgCC-Warning-Unknown switch: -ffast-math
/usr/bin/ld: skipping incompatible /home/kbarakat/tcl/linux/lib/libtcl8.3.a when searching for -
ltcl8.3
/usr/bin/ld: skipping incompatible /home/kbarakat/tcl/linux/lib/libtcl8.3.a when searching for -
ltcl8.3
/usr/bin/ld: cannot find -ltcl8.3
Fatal Error by charmc in directory /home/kbarakat/NAMD_2.6_Source/Linux-amd64-MPI

Command pgCC --instantiate=used -rdynamic -L/home/kbarakat/tcl/linux/lib -
L/home/kbarakat/tcl/linux/lib -L/home/kbarakat/fftw/linux//lib -L/home/kbarakat/fftw/linux/lib
-L/usr/local/mpich2/lib -I/home/kbarakat/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64-
pthreads-pgcc/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -m64 -fexpensive-optimizations -
ffast-math -L/usr/local/mpich2/lib -o namd2 -L/home/kbarakat/NAMD_2.6_Source/charm-
5.9/mpi-linux-amd64-pthreads-pgcc/bin/../lib -I/home/kbarakat/NAMD_2.6_Source/charm-
5.9/mpi-linux-amd64-pthreads-pgcc/bin/../include /home/kbarakat/NAMD_2.6_Source/charm-
5.9/mpi-linux-amd64-pthreads-pgcc/bin/../lib/libldb-rand.o obj/buildinfo.o obj/common.o
obj/dcdlib.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/ComputeBonds.o
obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o obj/ComputeCrossterms.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/ComputeFullDirect.o obj/ComputeHomePatch.o obj/ComputeHomePatches.o
obj/ComputeImpropers.o obj/ComputeGlobal.o obj/ComputeGlobalMsgs.o obj/ComputeMap.o
obj/ComputeMgr.o obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o
obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o obj/ComputeNonbondedFEP.o
obj/ComputeNonbondedLES.o obj/ComputeNonbondedPProf.o obj/ComputePatch.o
obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o
obj/ComputeStir.o obj/ComputeTclBC.o obj/ConfigList.o obj/Controller.o obj/ccsinterface.o
obj/DataStream.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/GlobalMaster.o
obj/GlobalMasterServer.o obj/GlobalMasterTest.o obj/GlobalMasterIMD.o obj/GlobalMasterTcl.o
obj/GlobalMasterSMD.o obj/GlobalMasterTMD.o obj/GlobalMasterFreeEnergy.o
obj/GlobalMasterEasy.o obj/GlobalMasterMisc.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/MStream.o obj/MigrateAtomsMsg.o obj/Molecule.o obj/NamdCentLB.o obj/NamdNborLB.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/PmeBase.o obj/PmeKSpace.o obj/PmeRealSpace.o obj/ProcessorPrivate.o obj/ProxyMgr.o
obj/ProxyPatch.o obj/Rebalancer.o obj/RecBisection.o obj/ReductionMgr.o obj/RefineOnly.o
obj/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o obj/SimParameters.o obj/Sync.o
obj/TclCommands.o obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o
obj/dcdplugin.o moduleinit19862.o -lmoduleNeighborLB -lmodulecommlib
/home/kbarakat/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64-pthreads-
pgcc/bin/../lib/libmemory-default.o /home/kbarakat/NAMD_2.6_Source/charm-5.9/mpi-linux-
amd64-pthreads-pgcc/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util
-lckqt -lmpich -lpthread -Wl,-ldl -ltcl8.3 -ldl -lsrfftw -lsfftw -lm -lmoduleNeighborLB -
lmodulecommlib -lmpich -lm returned error code 2
charmc exiting...
rm -f moduleinit19862.C moduleinit19862.o
make: *** [namd2] Error 1

khaled

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