From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Thu Dec 16 2004 - 13:19:57 CST
Hi,
I don't know why this happened to you. Looks like your configure file
(of charm++) for mpi-linux chose to use a special timer (in assembly
code) instead of MPI timer. Could you show me your conv-mach.h from:
charm/mpi-linux/tmp/conv-mach.h
Gengbin
HUSSER Jacky 113956 wrote:
> I am trying to compile NAMD (i.e latest version : 2.5) from source.
>
> My target is a 16 node cluster running with RedHat 7.1 (Kernel
> 2.4.9-34) and MPICH 1.2.2
>
>
>
> It was OK for the net-linux version : No problem at all.
>
> But I encouterd a serious problem with the mpi-linux version :
>
> At the stage where I type 'make' in Linux-i686-MPI I get the following
> message
>
> about an unresolved reference to `cpu_speed_factor' (with an ld exit) :
>
>
>
> Adding file obj/buildinfo.o...
>
> Adding file obj/common.o...
>
> Adding file obj/dcdlib.o...
>
> Adding file obj/erf.o...
>
> Adding file obj/main.o...
>
> Adding file obj/mainfunc.o...
>
> Adding file obj/memusage.o...
>
> Adding file obj/strlib.o...
>
> Adding file obj/AlgSeven.o...
>
> Adding file obj/AlgRecBisection.o...
>
> Adding file obj/AlgNbor.o...
>
> Adding file obj/AtomMap.o...
>
> Adding file obj/BackEnd.o...
>
> Adding file obj/BroadcastMgr.o...
>
> Adding file obj/BroadcastClient.o...
>
> Adding file obj/CollectionMaster.o...
>
> Adding file obj/CollectionMgr.o...
>
> Adding file obj/Communicate.o...
>
> Adding file obj/Compute.o...
>
> Adding file obj/ComputeAngles.o...
>
> Adding file obj/ComputeBonds.o...
>
> Adding file obj/ComputeConsForce.o...
>
> Adding file obj/ComputeConsForceMsgs.o...
>
> Adding file obj/ComputeCylindricalBC.o...
>
> Adding file obj/ComputeDihedrals.o...
>
> Adding file obj/ComputeDPME.o...
>
> Adding file obj/ComputeDPMEMsgs.o...
>
> Adding file obj/ComputeDPMTA.o...
>
> Adding file obj/ComputeEField.o...
>
> Adding file obj/ComputeExt.o...
>
> Adding file obj/ComputeFullDirect.o...
>
> Adding file obj/ComputeHomePatch.o...
>
> Adding file obj/ComputeHomePatches.o...
>
> Adding file obj/ComputeImpropers.o...
>
> Adding file obj/ComputeGlobal.o...
>
> Adding file obj/ComputeGlobalMsgs.o...
>
> Adding file obj/ComputeMap.o...
>
> Adding file obj/ComputeMgr.o...
>
> Adding file obj/ComputeNonbondedSelf.o...
>
> Adding file obj/ComputeNonbondedPair.o...
>
> Adding file obj/ComputeNonbondedUtil.o...
>
> Adding file obj/ComputeNonbondedStd.o...
>
> Adding file obj/ComputeNonbondedFEP.o...
>
> Adding file obj/ComputeNonbondedLES.o...
>
> Adding file obj/ComputePatch.o...
>
> Adding file obj/ComputePatchPair.o...
>
> Adding file obj/ComputePme.o...
>
> Adding file obj/ComputeRestraints.o...
>
> Adding file obj/ComputeSphericalBC.o...
>
> Adding file obj/ComputeStir.o...
>
> Adding file obj/ConfigList.o...
>
> Adding file obj/Controller.o...
>
> Adding file obj/ccsinterface.o...
>
> Adding file obj/DataStream.o...
>
> Adding file obj/DumpBench.o...
>
> Adding file obj/FreeEnergyAssert.o...
>
> Adding file obj/FreeEnergyGroup.o...
>
> Adding file obj/FreeEnergyLambda.o...
>
> Adding file obj/FreeEnergyLambdMgr.o...
>
> Adding file obj/FreeEnergyParse.o...
>
> Adding file obj/FreeEnergyRestrain.o...
>
> Adding file obj/FreeEnergyRMgr.o...
>
> Adding file obj/FreeEnergyVector.o...
>
> Adding file obj/GlobalMaster.o...
>
> Adding file obj/GlobalMasterServer.o...
>
> Adding file obj/GlobalMasterTest.o...
>
> Adding file obj/GlobalMasterIMD.o...
>
> Adding file obj/GlobalMasterTcl.o...
>
> Adding file obj/GlobalMasterSMD.o...
>
> Adding file obj/GlobalMasterFreeEnergy.o...
>
> Adding file obj/GlobalMasterEasy.o...
>
> Adding file obj/GlobalMasterMisc.o...
>
> Adding file obj/GromacsTopFile.o...
>
> Adding file obj/heap.o...
>
> Adding file obj/HomePatch.o...
>
> Adding file obj/IMDOutput.o...
>
> Adding file obj/InfoStream.o...
>
> Adding file obj/LdbCoordinator.o...
>
> Adding file obj/LJTable.o...
>
> Adding file obj/Measure.o...
>
> Adding file obj/MStream.o...
>
> Adding file obj/MigrateAtomsMsg.o...
>
> Adding file obj/Molecule.o...
>
> Adding file obj/NamdCentLB.o...
>
> Adding file obj/NamdNborLB.o...
>
> Adding file obj/NamdState.o...
>
> Adding file obj/NamdOneTools.o...
>
> Adding file obj/Node.o...
>
> Adding file obj/Output.o...
>
> Adding file obj/Parameters.o...
>
> Adding file obj/ParseOptions.o...
>
> Adding file obj/Patch.o...
>
> Adding file obj/PatchMgr.o...
>
> Adding file obj/PatchMap.o...
>
> Adding file obj/PDB.o...
>
> Adding file obj/PDBData.o...
>
> Adding file obj/PmeBase.o...
>
> Adding file obj/PmeKSpace.o...
>
> Adding file obj/PmeRealSpace.o...
>
> Adding file obj/ProcessorPrivate.o...
>
> Adding file obj/ProxyMgr.o...
>
> Adding file obj/ProxyPatch.o...
>
> Adding file obj/Rebalancer.o...
>
> Adding file obj/RecBisection.o...
>
> Adding file obj/ReductionMgr.o...
>
> Adding file obj/RefineOnly.o...
>
> Adding file obj/ScriptTcl.o...
>
> Adding file obj/Sequencer.o...
>
> Adding file obj/Set.o...
>
> Adding file obj/Settle.o...
>
> Adding file obj/SimParameters.o...
>
> Adding file obj/Sync.o...
>
> Adding file obj/TclCommands.o...
>
> Adding file obj/WorkDistrib.o...
>
> Adding file obj/pub3dfft.o...
>
> Adding file obj/vmdsock.o...
>
> Adding file obj/parm.o...
>
> Adding file obj/imd.o...
>
> charmc> ----------- Module dependency search ------------
>
> charmc> ----------- Module dependency search complete ------------
>
> Adding registration for module NeighborLB
>
> Adding registration for module commlib
>
> charmc: Executing /usr/lib/mpich-1.2.2/bin/mpiCC -D__CHARMC__=1
> -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -march=pentiumpro -ffast-math -static
> -c moduleinit.C -o moduleinit.o
>
> charmc: Executing /usr/lib/mpich-1.2.2/bin/mpiCC -rdynamic -O3
> -march=pentiumpro -ffast-math -static
> -L/home/husser/NAMD_Misc/tcl/linux/lib -L/home/husser/tcl-linux/lib
> -L/home/husser/NAMD_Misc/fftw/linux/lib -L/home/husser/fftw-linux/lib
> -L/home/husser/NAMD_Misc/plugins/LINUX
> -L/home/husser/NAMD_Misc/plugins/LINUX/molfile
> -L/home/husser/plugins/LINUX -L/home/husser/plugins/LINUX/molfile
> -I/home/husser/NAMD_Source/charm/mpi-linux/include -o namd2
> -L/home/husser/NAMD_Source/charm/mpi-linux/bin/../lib
> -I/home/husser/NAMD_Source/charm/mpi-linux/bin/../include
> /home/husser/NAMD_Source/charm/mpi-linux/bin/../lib/libldb-rand.o
> obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.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/ComputeCylindricalBC.o
> obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o
> obj/ComputeDPMTA.o obj/ComputeEField.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/ComputePatch.o
> obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o
> obj/ComputeSphericalBC.o obj/ComputeStir.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/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
> moduleinit.o -lmoduleNeighborLB -lmodulecommlib
> /home/husser/NAMD_Source/charm/mpi-linux/bin/../lib/libmemory-default.o
> /home/husser/NAMD_Source/charm/mpi-linux/bin/../lib/libthreads-default.o
> -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -lpmpich -ldl
> -lz -ltcl8.3 -ldl -lsrfftw -lsfftw -lmolfile_plugin -lm
> -lmoduleNeighborLB -lmodulecommlib
>
> /home/husser/NAMD_Misc/tcl/linux/lib/libtcl8.3.a(tclUnixPipe.o): In
> function `TclpCreateTempFile':
>
> tclUnixPipe.o(.text+0xe0): the use of `tmpnam' is dangerous, better
> use `mkstemp'
>
> obj/AlgRecBisection.o: In function `AlgRecBisection::strategy(void)':
>
> obj/AlgRecBisection.o(.text+0xae6): undefined reference to
> `cpu_speed_factor'
>
> obj/AlgRecBisection.o(.text+0xb2f): undefined reference to
> `cpu_speed_factor'
>
> obj/AlgRecBisection.o(.text+0xf62): undefined reference to
> `cpu_speed_factor'
>
> obj/BackEnd.o: In function `BackEnd::init(int, char **)':
>
> obj/BackEnd.o(.text+0x54): undefined reference to `cpu_speed_factor'
>
> obj/BackEnd.o: In function `BackEnd::exit(void)':
>
> obj/BackEnd.o(.text+0x25a): undefined reference to `cpu_speed_factor'
>
> obj/Controller.o(.text+0xd1c): more undefined references to
> `cpu_speed_factor' follow
>
> collect2: ld returned 1 exit status
>
> Fatal Error by charmc in directory /home/husser/NAMD_Source/Linux-i686-MPI
>
> Command /usr/lib/mpich-1.2.2/bin/mpiCC -rdynamic -O3 -march=pentiumpro
> -ffast-math -static -L/home/husser/NAMD_Misc/tcl/linux/lib
> -L/home/husser/tcl-linux/lib -L/home/husser/NAMD_Misc/fftw/linux/lib
> -L/home/husser/fftw-linux/lib -L/home/husser/NAMD_Misc/plugins/LINUX
> -L/home/husser/NAMD_Misc/plugins/LINUX/molfile
> -L/home/husser/plugins/LINUX -L/home/husser/plugins/LINUX/molfile
> -I/home/husser/NAMD_Source/charm/mpi-linux/include -o namd2
> -L/home/husser/NAMD_Source/charm/mpi-linux/bin/../lib
> -I/home/husser/NAMD_Source/charm/mpi-linux/bin/../include
> /home/husser/NAMD_Source/charm/mpi-linux/bin/../lib/libldb-rand.o
> obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.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/ComputeCylindricalBC.o
> obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o
> obj/ComputeDPMTA.o obj/ComputeEField.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/ComputePatch.o
> obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o
> obj/ComputeSphericalBC.o obj/ComputeStir.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/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
> moduleinit.o -lmoduleNeighborLB -lmodulecommlib
> /home/husser/NAMD_Source/charm/mpi-linux/bin/../lib/libmemory-default.o
> /home/husser/NAMD_Source/charm/mpi-linux/bin/../lib/libthreads-default.o
> -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -lpmpich -ldl
> -lz -ltcl8.3 -ldl -lsrfftw -lsfftw -lmolfile_plugin -lm
> -lmoduleNeighborLB -lmodulecommlib returned error code 1
>
> charmc exiting...
>
> make: *** [namd2] Error 1
>
>
>
> I also tested to compile without tcl and plugins : Same behaviour,
> same message
>
>
>
> Any Ideas ?
>
> Thank you very much for your help !
>
> Jack
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:05 CST