NamdCompile Problem

From: HUSSER Jacky 113956 (HUSSER_at_dsvidf.cea.fr)
Date: Thu Dec 16 2004 - 05:17:41 CST

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

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