Problem compiling NAMD on BlueGene

From: Jianhui Tian (jianhuitian_at_gmail.com)
Date: Tue Feb 06 2007 - 13:08:06 CST

Hi all,

I am compiling NAMD on BlueGene mahines. First, I compiled the
charm++; then went to NAMD directory, downloaded the precompiled
fftw-bluegene from
http://www.ks.uiuc.edu/Research/namd/libraries/, recompiled the hacked
tcl (tcl8.3.3-hacked), edited the Make.charm, ./arch/BlueGeneL.fftw
and ./arch/BlueGeneL.tcl; typed ./config tcl fftw BlueGeneL-MPI-xlC
and make, got the following error message:

/bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/bin/ld: cannot
find -ltcl8.3
Fatal Error by charmc in directory
/gpfs/gpfs0/home/herceh/namd/BlueGeneL-MPI-xlC

In full:

Adding registration for module NeighborLB
Adding registration for module commlib
charmc: Executing /opt/ibmcmp/vacpp/bg/8.0/bin/blrts_xlC
-D__CHARMC__=1 -I/bgl/BlueLight/ppcfloor/bglsys/include -c
moduleinit4288.C -o moduleinit4288.o
charmc: Executing /opt/ibmcmp/vacpp/bg/8.0/bin/blrts_xlC
-L/gpfs/gpfs0/home/herceh/namd/tcl-8.3.3/lib
-L/gpfs/gpfs0/home/herceh/namd/fftw-bluegene/lib
-L/bgl/BlueLight/ppcfloor/bglsys/lib
-I/gpfs/gpfs0/home/herceh/charm/mpi-bluegenel-xlc/include
-DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -Q -qarch=440 -qtune=440 -qhot
-DARCH_POWERPC -o namd2
-L/gpfs/gpfs0/home/herceh/charm/mpi-bluegenel-xlc/bin/../lib
-I/gpfs/gpfs0/home/herceh/charm/mpi-bluegenel-xlc/bin/../include
/gpfs/gpfs0/home/herceh/charm/mpi-bluegenel-xlc/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 moduleinit4288.o
-lmoduleNeighborLB -lmodulecommlib
/gpfs/gpfs0/home/herceh/charm/mpi-bluegenel-xlc/bin/../lib/libmemory-default.o
/gpfs/gpfs0/home/herceh/charm/mpi-bluegenel-xlc/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -lmpich.rts
-lmsglayer.rts -lrts.rts -ldevices.rts -lrts.rts -ltcl8.3 -lrfftw
-lfftw -lm -lmoduleNeighborLB -lmodulecommlib -lm
/bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/bin/ld: cannot
find -ltcl8.3
Fatal Error by charmc in directory
/gpfs/gpfs0/home/herceh/namd/BlueGeneL-MPI-xlC
   Command /opt/ibmcmp/vacpp/bg/8.0/bin/blrts_xlC
-L/gpfs/gpfs0/home/herceh/namd/tcl-8.3.3/lib
-L/gpfs/gpfs0/home/herceh/namd/fftw-bluegene/lib
-L/bgl/BlueLight/ppcfloor/bglsys/lib
-I/gpfs/gpfs0/home/herceh/charm/mpi-bluegenel-xlc/include
-DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -Q -qarch=440 -qtune=440 -qhot
-DARCH_POWERPC -o namd2
-L/gpfs/gpfs0/home/herceh/charm/mpi-bluegenel-xlc/bin/../lib
-I/gpfs/gpfs0/home/herceh/charm/mpi-bluegenel-xlc/bin/../include
/gpfs/gpfs0/home/herceh/charm/mpi-bluegenel-xlc/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 moduleinit4288.o
-lmoduleNeighborLB -lmodulecommlib
/gpfs/gpfs0/home/herceh/charm/mpi-bluegenel-xlc/bin/../lib/libmemory-default.o
/gpfs/gpfs0/home/herceh/charm/mpi-bluegenel-xlc/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -lmpich.rts
-lmsglayer.rts -lrts.rts -ldevices.rts -lrts.rts -ltcl8.3 -lrfftw
-lfftw -lm -lmoduleNeighborLB -lmodulecommlib -lm returned error code
1
charmc exiting...
rm -f moduleinit4288.C moduleinit4288.o
make: *** [namd2] Error 1

Any one has any suggestion? Thanks a lot in advance.

Justin

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