Re: FW: NAMD 2.6, AMD64, MVAPICH2 compile error

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Thu Mar 19 2009 - 16:31:27 CDT

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Greetings namder's

 I am having trouble compiling NAMD2.6
this is an AMD64 system with inifiniband and MVAPICH2

 My build output is below:
 
 admin-02-01:/usr/local/src/NAMD_2.6_Source/Linux-amd64-MPI # make
 rm -f obj/buildinfo.C; echo 'const char *namd_build_date = ' \"`date`\"\; >
obj/buildinfo.C; echo 'const char *namd_build_user = ' \"root\"\; >>
obj/buildinfo.C; echo 'const char *namd_build_machine = ' \"`hostname`\"\; >>
obj/buildinfo.C; cat obj/buildinfo.C;
g++ -I/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/include -DCMK_OPTIMIZE=1 -Isrc -Iinc   -Iplugins/include -I/usr/local/src/NAMD_2.6_Source/tcl/linux-amd64/include -I/root/tcl/include -DNAMD_TCL -I/usr/local/src/NAMD_2.6_Source/fftw/linux-amd64/include -I/root/fftw/include -DNAMD_FFTW  -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\"  -O3 -m64 -fexpensive-optimizations -ffast-math  -o
obj/buildinfo.o -c obj/buildinfo.C
 const char *namd_build_date =  "Wed Mar 18 14:37:42 CDT 2009";
 const char *namd_build_user =  "root";
 const char *namd_build_machine =  "admin-02-01";
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/charmc -verbose -ld++-option
\
 "-I/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -m64 -fexpensive-optimizations -ffast-math "
\
 -module NeighborLB -module commlib -language charm++ \
 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 \
  \
  \
 -L/usr/local/src/NAMD_2.6_Source/tcl/linux-amd64/lib -L/root/tcl/lib -ltcl8.3 -ldl
\
 -L/usr/local/src/NAMD_2.6_Source/fftw/linux-amd64/lib -L/root/fftw/lib -lsrfftw -lsfftw
\
 obj/dcdplugin.o \
  \
 -lm -o namd2
 Verbose mode set
 Adding file obj/buildinfo.o...
 Adding file obj/common.o...
 Adding file obj/dcdlib.o...
 Adding file obj/erf.o...
 Adding file obj/fitrms.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/ComputeCrossterms.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/ComputeEwald.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/ComputeNonbondedPProf.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/ComputeTclBC.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/GlobalMasterTMD.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...
 Adding file obj/dcdplugin.o...
 charmc> ----------- Module dependency search ------------
 charmc> ----------- Module dependency search complete ------------
 Adding registration for module NeighborLB
 Adding registration for module commlib
 charmc: Executing mpicxx -D__CHARMC__=1 -c moduleinit1529.C -o
moduleinit1529.o
 charmc: Executing
mpicxx -rdynamic -L/usr/local/src/NAMD_2.6_Source/tcl/linux-amd64/lib -L/root/tcl/lib -L/usr/local/src/NAMD_2.6_Source/fftw/linux-amd64/lib -L/root/fftw/lib -I/usr/local/src/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/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib -I/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../include /usr/local/src/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
moduleinit1529.o -lmoduleNeighborLB -lmodulecommlib /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o /usr/local/src/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/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`malloc_usable_size':
 mvapich_malloc.c:(.text+0x280): multiple definition of `malloc_usable_size'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x1e9): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `malloc_usable_size' changed from 48
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 51 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`_int_free':
 mvapich_malloc.c:(.text+0x5e0): multiple definition of `_int_free'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x87a): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `_int_free' changed from 771
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 573 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`__malloc_check_init':
 mvapich_malloc.c:(.text+0x850): multiple definition of `__malloc_check_init'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x30b0): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `__malloc_check_init' changed from 120
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 113 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.data+0x0):
multiple definition of `__malloc_hook'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
(.data+0x0): first defined here
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.bss+0x8):
multiple definition of `__free_hook'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
(.bss+0x8): first defined here
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.data+0x8):
multiple definition of `__realloc_hook'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
(.data+0x8): first defined here
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.data+0x10):
multiple definition of `__memalign_hook'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
(.data+0x10): first defined here
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.bss+0x10):
multiple definition of `__after_morecore_hook'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
(.bss+0x10): first defined here
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`_int_malloc':
 mvapich_malloc.c:(.text+0xb70): multiple definition of `_int_malloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0xdc1): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `_int_malloc' changed from 2863
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 3045 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`_int_memalign':
 mvapich_malloc.c:(.text+0x1760): multiple definition of `_int_memalign'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x1ba7): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `_int_memalign' changed from 525
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 583 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`_int_valloc':
 mvapich_malloc.c:(.text+0x19b0): multiple definition of `_int_valloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x1db4): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `_int_valloc' changed from 63
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 62 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`_int_realloc':
 mvapich_malloc.c:(.text+0x1a30): multiple definition of `_int_realloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x1df3): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `_int_realloc' changed from 1365
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 858 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`_int_new_arena':
 mvapich_malloc.c:(.text+0x1e40): multiple definition of `_int_new_arena'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x2348): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `_int_new_arena' changed from 214
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 158 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`independent_comalloc':
 mvapich_malloc.c:(.text+0x2460): multiple definition of
`independent_comalloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x24cf): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `independent_comalloc' changed from 137
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 142 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`independent_calloc':
 mvapich_malloc.c:(.text+0x24f0): multiple definition of `independent_calloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x2558): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `independent_calloc' changed from 146
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 167 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`mallopt':
 mvapich_malloc.c:(.text+0x2800): multiple definition of `mallopt'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x33bd): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `mallopt' changed from 14
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 5 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.bss+0x0):
multiple definition of `__malloc_initialize_hook'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
(.bss+0x0): first defined here
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`pvalloc':
 mvapich_malloc.c:(.text+0x2a20): multiple definition of `pvalloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x33cb): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `pvalloc' changed from 129
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 170 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`valloc':
 mvapich_malloc.c:(.text+0x2ad0): multiple definition of `valloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x3e91): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `valloc' changed from 78
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 135 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`mallinfo':
 mvapich_malloc.c:(.text+0x2cc0): multiple definition of `mallinfo'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x31b): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `mallinfo' changed from 39
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 139 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`malloc_trim':
 mvapich_malloc.c:(.text+0x2d50): multiple definition of `malloc_trim'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x788): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `malloc_trim' changed from 49
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 110 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`calloc':
 mvapich_malloc.c:(.text+0x2dc0): multiple definition of `calloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x3f41): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `calloc' changed from 84
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 800 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`free':
 mvapich_malloc.c:(.text+0x30e0): multiple definition of `free'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0xc22): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `free' changed from 34
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 236 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`cfree':
 mvapich_malloc.c:(.text+0x31d0): multiple definition of `cfree'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0xc60): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `cfree' changed from 34
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 5 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`malloc':
 mvapich_malloc.c:(.text+0x31e0): multiple definition of `malloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x3f95): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `malloc' changed from 78
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 364 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`memalign':
 mvapich_malloc.c:(.text+0x3350): multiple definition of `memalign'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x3edf): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `memalign' changed from 98
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 407 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`realloc':
 mvapich_malloc.c:(.text+0x35a0): multiple definition of `realloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x2d8f): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `realloc' changed from 72
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 488 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`malloc_set_state':
 mvapich_malloc.c:(.text+0x38d0): multiple definition of `malloc_set_state'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x34b4): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `malloc_set_state' changed from 887
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 1013 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`malloc_get_state':
 mvapich_malloc.c:(.text+0x3cd0): multiple definition of `malloc_get_state'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x2dd7): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `malloc_get_state' changed from 376
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 476 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/src/NAMD_2.6_Source/tcl/linux-amd64/lib/libtcl8.3.a(tclUnixPipe.o):
In function `TclpCreateTempFile':
 tclUnixPipe.c:(.text+0xe0): warning: the use of `tmpnam' is dangerous, better
use `mkstemp'
 collect2: ld returned 1 exit status
 Fatal Error by charmc in
directory /usr/local/src/NAMD_2.6_Source/Linux-amd64-MPI
    Command
mpicxx -rdynamic -L/usr/local/src/NAMD_2.6_Source/tcl/linux-amd64/lib -L/root/tcl/lib -L/usr/local/src/NAMD_2.6_Source/fftw/linux-amd64/lib -L/root/fftw/lib -I/usr/local/src/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/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib -I/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../include /usr/local/src/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
moduleinit1529.o -lmoduleNeighborLB -lmodulecommlib /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o /usr/local/src/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 moduleinit1529.C moduleinit1529.o
 make: *** [namd2] Error 1
 
 
 Thank you,
 
 -Will
 
 --
 Will Curry
  Sr. HPC Systems Analyst
  Center for Computational Science
  Tulane University
  voice: (504) 862-8393
 --
 
 --
 Will Curry
  Sr. HPC Systems Analyst
  Center for Computational Science
  Tulane University
  voice: (504) 862-8393
 --
 
 ------ Forwarded Message
 From: Will Curry <wcurry_at_tulane.edu>
 Date: Wed, 18 Mar 2009 14:39:06 -0500
 To: <namd_at_ks.uiuc.edu>
 Conversation: NAMD 2.6, AMD64, MVAPICH2 compile error
 Subject: NAMD 2.6, AMD64, MVAPICH2 compile error
 
 I am having trouble compiling NAMD.  My build error is below:
 
 admin-02-01:/usr/local/src/NAMD_2.6_Source/Linux-amd64-MPI # make
 rm -f obj/buildinfo.C; echo 'const char *namd_build_date = ' \"`date`\"\; >
obj/buildinfo.C; echo 'const char *namd_build_user = ' \"root\"\; >>
obj/buildinfo.C; echo 'const char *namd_build_machine = ' \"`hostname`\"\; >>
obj/buildinfo.C; cat obj/buildinfo.C;
g++ -I/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/include -DCMK_OPTIMIZE=1 -Isrc -Iinc   -Iplugins/include -I/usr/local/src/NAMD_2.6_Source/tcl/linux-amd64/include -I/root/tcl/include -DNAMD_TCL -I/usr/local/src/NAMD_2.6_Source/fftw/linux-amd64/include -I/root/fftw/include -DNAMD_FFTW  -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\"  -O3 -m64 -fexpensive-optimizations -ffast-math  -o
obj/buildinfo.o -c obj/buildinfo.C
 const char *namd_build_date =  "Wed Mar 18 14:37:42 CDT 2009";
 const char *namd_build_user =  "root";
 const char *namd_build_machine =  "admin-02-01";
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/charmc -verbose -ld++-option
\
 "-I/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -m64 -fexpensive-optimizations -ffast-math "
\
 -module NeighborLB -module commlib -language charm++ \
 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 \
  \
  \
 -L/usr/local/src/NAMD_2.6_Source/tcl/linux-amd64/lib -L/root/tcl/lib -ltcl8.3 -ldl
\
 -L/usr/local/src/NAMD_2.6_Source/fftw/linux-amd64/lib -L/root/fftw/lib -lsrfftw -lsfftw
\
 obj/dcdplugin.o \
  \
 -lm -o namd2
 Verbose mode set
 Adding file obj/buildinfo.o...
 Adding file obj/common.o...
 Adding file obj/dcdlib.o...
 Adding file obj/erf.o...
 Adding file obj/fitrms.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/ComputeCrossterms.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/ComputeEwald.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/ComputeNonbondedPProf.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/ComputeTclBC.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/GlobalMasterTMD.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...
 Adding file obj/dcdplugin.o...
 charmc> ----------- Module dependency search ------------
 charmc> ----------- Module dependency search complete ------------
 Adding registration for module NeighborLB
 Adding registration for module commlib
 charmc: Executing mpicxx -D__CHARMC__=1 -c moduleinit1529.C -o
moduleinit1529.o
 charmc: Executing
mpicxx -rdynamic -L/usr/local/src/NAMD_2.6_Source/tcl/linux-amd64/lib -L/root/tcl/lib -L/usr/local/src/NAMD_2.6_Source/fftw/linux-amd64/lib -L/root/fftw/lib -I/usr/local/src/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/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib -I/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../include /usr/local/src/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
moduleinit1529.o -lmoduleNeighborLB -lmodulecommlib /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o /usr/local/src/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/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`malloc_usable_size':
 mvapich_malloc.c:(.text+0x280): multiple definition of `malloc_usable_size'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x1e9): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `malloc_usable_size' changed from 48
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 51 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`_int_free':
 mvapich_malloc.c:(.text+0x5e0): multiple definition of `_int_free'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x87a): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `_int_free' changed from 771
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 573 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`__malloc_check_init':
 mvapich_malloc.c:(.text+0x850): multiple definition of `__malloc_check_init'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x30b0): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `__malloc_check_init' changed from 120
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 113 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.data+0x0):
multiple definition of `__malloc_hook'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
(.data+0x0): first defined here
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.bss+0x8):
multiple definition of `__free_hook'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
(.bss+0x8): first defined here
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.data+0x8):
multiple definition of `__realloc_hook'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
(.data+0x8): first defined here
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.data+0x10):
multiple definition of `__memalign_hook'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
(.data+0x10): first defined here
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.bss+0x10):
multiple definition of `__after_morecore_hook'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
(.bss+0x10): first defined here
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`_int_malloc':
 mvapich_malloc.c:(.text+0xb70): multiple definition of `_int_malloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0xdc1): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `_int_malloc' changed from 2863
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 3045 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`_int_memalign':
 mvapich_malloc.c:(.text+0x1760): multiple definition of `_int_memalign'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x1ba7): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `_int_memalign' changed from 525
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 583 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`_int_valloc':
 mvapich_malloc.c:(.text+0x19b0): multiple definition of `_int_valloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x1db4): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `_int_valloc' changed from 63
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 62 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`_int_realloc':
 mvapich_malloc.c:(.text+0x1a30): multiple definition of `_int_realloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x1df3): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `_int_realloc' changed from 1365
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 858 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`_int_new_arena':
 mvapich_malloc.c:(.text+0x1e40): multiple definition of `_int_new_arena'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x2348): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `_int_new_arena' changed from 214
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 158 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`independent_comalloc':
 mvapich_malloc.c:(.text+0x2460): multiple definition of
`independent_comalloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x24cf): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `independent_comalloc' changed from 137
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 142 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`independent_calloc':
 mvapich_malloc.c:(.text+0x24f0): multiple definition of `independent_calloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x2558): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `independent_calloc' changed from 146
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 167 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`mallopt':
 mvapich_malloc.c:(.text+0x2800): multiple definition of `mallopt'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x33bd): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `mallopt' changed from 14
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 5 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o):(.bss+0x0):
multiple definition of `__malloc_initialize_hook'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:
(.bss+0x0): first defined here
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`pvalloc':
 mvapich_malloc.c:(.text+0x2a20): multiple definition of `pvalloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x33cb): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `pvalloc' changed from 129
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 170 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`valloc':
 mvapich_malloc.c:(.text+0x2ad0): multiple definition of `valloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x3e91): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `valloc' changed from 78
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 135 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`mallinfo':
 mvapich_malloc.c:(.text+0x2cc0): multiple definition of `mallinfo'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x31b): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `mallinfo' changed from 39
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 139 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`malloc_trim':
 mvapich_malloc.c:(.text+0x2d50): multiple definition of `malloc_trim'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x788): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `malloc_trim' changed from 49
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 110 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`calloc':
 mvapich_malloc.c:(.text+0x2dc0): multiple definition of `calloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x3f41): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `calloc' changed from 84
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 800 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`free':
 mvapich_malloc.c:(.text+0x30e0): multiple definition of `free'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0xc22): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `free' changed from 34
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 236 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`cfree':
 mvapich_malloc.c:(.text+0x31d0): multiple definition of `cfree'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0xc60): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `cfree' changed from 34
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 5 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`malloc':
 mvapich_malloc.c:(.text+0x31e0): multiple definition of `malloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x3f95): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `malloc' changed from 78
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 364 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`memalign':
 mvapich_malloc.c:(.text+0x3350): multiple definition of `memalign'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x3edf): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `memalign' changed from 98
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 407 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`realloc':
 mvapich_malloc.c:(.text+0x35a0): multiple definition of `realloc'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x2d8f): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `realloc' changed from 72
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 488 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`malloc_set_state':
 mvapich_malloc.c:(.text+0x38d0): multiple definition of `malloc_set_state'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x34b4): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `malloc_set_state' changed from 887
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 1013 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o): In function
`malloc_get_state':
 mvapich_malloc.c:(.text+0x3cd0): multiple definition of `malloc_get_state'
 /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o:memory.c:
(.text+0x2dd7): first defined here
 /usr/lib64/gcc/x86_64-suse-linux/4.1.0/../../../../x86_64-suse-linux/bin/ld:
Warning: size of symbol `malloc_get_state' changed from 376
in /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
to 476 in /usr/local/opt/mvapich2-intel/lib/libmpich.a(mvapich_malloc.o)
 /usr/local/src/NAMD_2.6_Source/tcl/linux-amd64/lib/libtcl8.3.a(tclUnixPipe.o):
In function `TclpCreateTempFile':
 tclUnixPipe.c:(.text+0xe0): warning: the use of `tmpnam' is dangerous, better
use `mkstemp'
 collect2: ld returned 1 exit status
 Fatal Error by charmc in
directory /usr/local/src/NAMD_2.6_Source/Linux-amd64-MPI
    Command
mpicxx -rdynamic -L/usr/local/src/NAMD_2.6_Source/tcl/linux-amd64/lib -L/root/tcl/lib -L/usr/local/src/NAMD_2.6_Source/fftw/linux-amd64/lib -L/root/fftw/lib -I/usr/local/src/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/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib -I/usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../include /usr/local/src/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
moduleinit1529.o -lmoduleNeighborLB -lmodulecommlib /usr/local/src/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o /usr/local/src/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 moduleinit1529.C moduleinit1529.o
 make: *** [namd2] Error 1
 
 
 Thank you,
 
 -Will
 
 --
 Will Curry
  Sr. HPC Systems Analyst
  Center for Computational Science
  Tulane University
  voice: (504) 862-8393
 --
 
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