From: Kevin Jander (waverunnergp_at_gmail.com)
Date: Mon Jul 09 2007 - 16:07:16 CDT
Hello,
I am getting an error when trying to compile NAMD with MPI. I am able
to compile charmrun successfully and run the megatest. Here is what I
have tried so far:
Compiled charm with the following commands (charmrun has been run
successfully with megatest for each scenario):
./build charm++ mpi-linux
./build charm++ mpi-linux --no-shared -O -DCMK_OPTIMIZE=1
Changed -lmpich to -lmpi in src/arch/mpi-linux/conv-mach.sh.
Set CMK_MALLOC_USE_GNU_MALLOC to 0 and CMK_MALLOC_USE_OS_BUILTIN to 1
in src/arch/mpi-linux/conf-mach.h.
It will error out after the Module dependency search is complete.
Here is the end of the output when the error starts.
/usr/lib/gcc/i386-redhat-linux/3.4.6/../../../libc.a(malloc.o)(.text+0x38a8):
In function `__malloc_check_init':
: multiple definition of `__malloc_check_init'
/opt/lam/gnu/lib/libmpi.a(malloc.o)(.text+0x49c): first defined here
/usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed
from 151 in /opt/lam/gnu/lib/libmpi.a(malloc.o) to 154 in
/usr/lib/gcc/i386-redhat-linux/3.4.6/../../../libc.a(malloc.o)
collect2: ld returned 1 exit status
mpiCC: No such file or directory
Fatal Error by charmc in directory /home/kevin/NAMD_2.6_Source/Linux-i686-MPI
Command mpiCC -rdynamic -L/home/kevin/tcl/linux/lib
-L/home/kevin/tcl/lib -L/home/kevin/fftw/linux/lib
-L/home/kevin/fftw/lib
-I/home/kevin/NAMD_2.6_Source/charm-5.9/mpi-linux/include
-DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -march=pentiumpro -ffast-math -static
-o namd2 -L/home/kevin/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib
-I/home/kevin/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../include
/home/kevin/NAMD_2.6_Source/charm-5.9/mpi-linux/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 moduleinit17492.o
-lmoduleNeighborLB -lmodulecommlib
/home/kevin/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
/home/kevin/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -lmpi -ldl -lz
-ltcl8.3 -ldl -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib
returned error code 1
charmc exiting...
rm -f moduleinit17492.C moduleinit17492.o
make: *** [namd2] Error 1
Don't know if it makes a difference or not, but I am running Rocks
4.2.1. Anyone help ya'll could give would be greatly appreciated.
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