From: Tom Joseph (thomas.joseph_at_mssm.edu)
Date: Mon Nov 05 2007 - 13:18:25 CST
Looks like it's having trouble finding your MPI library. Is it
installed properly, and can you verify that the build command is
finding it?
--Tom
On Nov 5, 2007 11:18 AM, <hazards_at_musc.edu> wrote:
> Folks,
>
> I have compiled namd2 on a linux workstation and now I am trying to dupicate the
> process on a 16 node cluster.
>
> After some fumbling, I have gotten to a point where the compile process is
> stopping with an error saying "/usr/bin/ld: cannot find -lmpich"
>
>
>
> here is the full message
>
> charmc> ----------- Module dependency search ------------
> charmc> ----------- Module dependency search complete ------------
> Adding registration for module NeighborLB
> Adding registration for module commlib
> charmc: Executing mpiCC -m64 -fPIC -D__CHARMC__=1 -c moduleinit4630.C -o
> moduleinit4630.o
> charmc: Executing mpiCC -m64 -fPIC -rdynamic
> -L/home/hazards/COMPILE/NAMD_2.6_Source/linux-amd64/lib
> -L/home/hazards/fftw/lib
> -I/home/hazards/COMPILE/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/include
> -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -m64 -fexpensive-optimizations -ffast-math -o
> namd2
> -L/home/hazards/COMPILE/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib
> -I/home/hazards/COMPILE/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../include
> /home/hazards/COMPILE/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/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 moduleinit4630.o -lmoduleNeighborLB -lmodulecommlib
> /home/hazards/COMPILE/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> /home/hazards/COMPILE/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libthreads-default.o
> -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -lmpich -ldl -ltcl8.3 -ldl
> -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib -lmpich -lm
> /usr/bin/ld: cannot find -lmpich
> collect2: ld returned 1 exit status
> Fatal Error by charmc in directory
> /home/hazards/COMPILE/NAMD_2.6_Source/Linux-amd64-MPI
> Command mpiCC -m64 -fPIC -rdynamic
> -L/home/hazards/COMPILE/NAMD_2.6_Source/linux-amd64/lib
> -L/home/hazards/fftw/lib
> -I/home/hazards/COMPILE/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/include
> -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -m64 -fexpensive-optimizations -ffast-math -o
> namd2
> -L/home/hazards/COMPILE/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib
> -I/home/hazards/COMPILE/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../include
> /home/hazards/COMPILE/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/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 moduleinit4630.o -lmoduleNeighborLB -lmodulecommlib
> /home/hazards/COMPILE/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
> /home/hazards/COMPILE/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libthreads-default.o
> -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -lmpich -ldl -ltcl8.3 -ldl
> -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib -lmpich -lm returned
> error code 1
> charmc exiting...
> rm -f moduleinit4630.C moduleinit4630.o
> make: *** [namd2] Error 1
>
>
> How can I fix this?
>
> Starr
>
>
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