From: Nicolas Sapay (nsapay_at_ucalgary.ca)
Date: Tue Apr 24 2007 - 17:20:52 CDT
Hi all NAMDers,
I try to install and run NAMD2.6 on our cluster (Intel Xeon 3.4GHz
Irwindale) . I'm pretty new on this cluster and more generally on
cluster management. So, sorry if some questions looks obvious for some
people.
1. First of all I have tried to run a pre-build binary (Linus-i686). Of
course it didn't work : jobs were arbitrarily aborted before the end of
the computation without error message (command : path/to/charmrun
++verbose +p$nproc ++nodelist path/to/nodelist /path/to/namd2
path/to/namd.conf > namd.log)
2. I have try to run namd2 with mpiexec, suspecting a problem with the
charmrun build (command : mpiexec -p $nproc /path/to/namd2
path/to/namd.conf > namd.log). mpiexec terminated the job with the
following error:
...
Info: Found 20 config files.
Info: Changed directory to
/home/nsapay/namd/popc_x1/nve_Vtrunc_Etrunc_C100_T0_P1/run03
Info: Configuration file is part01.conf
Info: Configuration file is -p4wd
FATAL ERROR: Simulation config file is not accessible.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Simulation config file is not accessible.
Charm++ fatal error:
FATAL ERROR: Simulation config file is not accessible.
Stack Traceback:
[0] main+0x1bf [0x80df183]
[1] __libc_start_main+0xd3 [0x2cae23]
[2] _ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_c+0x59
[0x80dba71]
mpiexec: process_obit_event: evt 3 task 0 on compute-10-19.local stat 262.
mpiexec: read_p4_master_port: got port -1.
mpiexec: Warning: task 0 died with signal 6 (Aborted).
There was clearly a porblem with namd2 which seen some mpi options as
input files
3. I have then tried to compile NAMD2.6 from source. Firstly, I have
built charm++ from the charm-5.9 directory:
./build charm++ mpi-linux --basedir=/opt/mpich/gnu --no-build-shared
-verbose -O -DCMK_OPTIMIZE=1
The build was successful and passed the megatest. However, the lb_test
during the make command with the error:
...
/usr/bin/ld: cannot find -lmetis
collect2: ld returned 1 exit status
Then, I have tired to build namd2. I have set TCLDIR, FFTDIR and
CHARMBASE to the correct locations, configure the installation (command:
./config Linux-i686-MPI) and run make. The compilation failed with the
following error:
...
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0xdd2):
first defined here
/usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed from
111 in
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
to 154 in /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)
collect2: ld returned 1 exit status
Fatal Error by charmc in directory
/home/nsapay/tmp/NAMD_2.6_Source/Linux-i686-MPI
Command mpiCC -rdynamic -L/opt/mpich/gnu/lib
-I/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/include
-DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -march=pentiumpro -ffast-math -static
-L/opt/mpich/gnu/lib -o namd2
-L/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib
-I/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../include
/home/nsapay/tmp/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
moduleinit21980.o -lmoduleNeighborLB -lmodulecommlib
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -lmpich -ldl -lm
-lmoduleNeighborLB -lmodulecommlib -lm returned error code 1
charmc exiting...
make: *** [namd2] Error 1
Now, I don't now exactly what I can do. Does anyone have already deal
with theses kinds of errors? Any advice is welcome!
Thanks
Nicolas
ps: I have enclose to the message the make.o and make.e of the namd2
building
rm -f obj/buildinfo.C; echo 'const char *namd_build_date = ' \"`date`\"\; > obj/buildinfo.C; echo 'const char *namd_build_user = ' \"nsapay\"\; >> obj/buildinfo.C; echo 'const char *namd_build_machine = ' \"`hostname`\"\; >> obj/buildinfo.C; cat obj/buildinfo.C; g++ -I/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/include -DCMK_OPTIMIZE=1 -Isrc -Iinc -Iplugins/include -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-i686-MPI\" -O3 -march=pentiumpro -ffast-math -static -o obj/buildinfo.o -c obj/buildinfo.C
const char *namd_build_date = "Tue Apr 24 16:07:59 MDT 2007";
const char *namd_build_user = "nsapay";
const char *namd_build_machine = "tatanka.bio.ucalgary.ca";
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/charmc -verbose -ld++-option \
"-I/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -march=pentiumpro -ffast-math -static" \
-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 \
\
\
\
\
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
rm -f moduleinit21980.C moduleinit21980.o
charmc: Executing mpiCC -D__CHARMC__=1 -I/opt/mpich/gnu/include -c moduleinit21980.C -o moduleinit21980.o
charmc: Executing mpiCC -rdynamic -L/opt/mpich/gnu/lib -I/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -march=pentiumpro -ffast-math -static -L/opt/mpich/gnu/lib -o namd2 -L/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib -I/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../include /home/nsapay/tmp/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 moduleinit21980.o -lmoduleNeighborLB -lmodulecommlib /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -lmpich -ldl -lm -lmoduleNeighborLB -lmodulecommlib -lm
obj/dcdlib.o(.text+0x11db): In function `write_dcdheader(int, char*, int, int, int, int, int, double, int)':
: warning: Using 'getpwuid' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
obj/vmdsock.o(.text+0xa6): In function `vmdsock_connect(void*, char const*, int)':
: warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)(.text+0x14fc): In function `free':
: multiple definition of `free'
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x35bc): first defined here
/usr/bin/ld: Warning: size of symbol `free' changed from 29 in /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o to 175 in /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)(.text+0x3058): In function `malloc':
: multiple definition of `malloc'
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x3583): first defined here
/usr/bin/ld: Warning: size of symbol `malloc' changed from 57 in /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o to 373 in /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)(.text+0x360c): In function `realloc':
: multiple definition of `realloc'
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x3632): first defined here
/usr/bin/ld: Warning: size of symbol `realloc' changed from 40 in /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o to 667 in /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)(.data+0x0): multiple definition of `__libc_malloc_initialized'
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.data+0x10): first defined here
/usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)(.text+0x424): In function `_int_new_arena':
: multiple definition of `_int_new_arena'
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x613): first defined here
/usr/bin/ld: Warning: size of symbol `_int_new_arena' changed from 187 in /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o to 180 in /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)(.text+0xdbc): In function `_int_free':
: multiple definition of `_int_free'
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x2737): first defined here
/usr/bin/ld: Warning: size of symbol `_int_free' changed from 338 in /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o to 1658 in /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)(.text+0x15ac): In function `_int_malloc':
: multiple definition of `_int_malloc'
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x21db): first defined here
/usr/bin/ld: Warning: size of symbol `_int_malloc' changed from 1372 in /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o to 3101 in /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)(.text+0x229c): In function `_int_memalign':
: multiple definition of `_int_memalign'
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x2dd9): first defined here
/usr/bin/ld: Warning: size of symbol `_int_memalign' changed from 397 in /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o to 413 in /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)(.text+0x243c): In function `_int_valloc':
: multiple definition of `_int_valloc'
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x31cb): first defined here
/usr/bin/ld: Warning: size of symbol `_int_valloc' changed from 48 in /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o to 63 in /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)(.text+0x25b0): In function `_int_realloc':
: multiple definition of `_int_realloc'
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x2988): first defined here
/usr/bin/ld: Warning: size of symbol `_int_realloc' changed from 1105 in /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o to 1065 in /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)(.text+0x38a8): In function `__malloc_check_init':
: multiple definition of `__malloc_check_init'
/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0xdd2): first defined here
/usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed from 111 in /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o to 154 in /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)
collect2: ld returned 1 exit status
Fatal Error by charmc in directory /home/nsapay/tmp/NAMD_2.6_Source/Linux-i686-MPI
Command mpiCC -rdynamic -L/opt/mpich/gnu/lib -I/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -march=pentiumpro -ffast-math -static -L/opt/mpich/gnu/lib -o namd2 -L/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib -I/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../include /home/nsapay/tmp/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 moduleinit21980.o -lmoduleNeighborLB -lmodulecommlib /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -lmpich -ldl -lm -lmoduleNeighborLB -lmodulecommlib -lm returned error code 1
charmc exiting...
make: *** [namd2] Error 1
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:36 CST