[Bioclusters] namd Linux-i686-MPI compilation problem..
genie lfs
lfs.use at gmail.com
Tue Apr 11 06:45:37 EDT 2006
hello all...
i am trying to build Linux-i686-MPI on my OSCAR cluster.. the cluster
configuration is a 6 node one, with master and clients on Fedora Core
3,parallel implementation being Mpich-1.2.7..
the charm++ build was proper with the sample tests also running perfectly..
when i try to compile the namd using the command..
./config Linux-i686-MPI and make in the Linux-i686-MPI directory..i
run into problems.. sample output is provided below..
i have compiled tcl-8.4 with option --disable-shared ..
and fftw-2.1.5 with the option --enable-float --enable-type-prefix
--enable-static
the small fragment of the error pasted below...
can somebody please point out the error and the necessary correction...
please reply
thanks
santhu
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 mpiCC -D__CHARMC__=1 -c moduleinit19007.C -o moduleinit19007.o
charmc: Executing mpiCC -rdynamic
-L/home/admin/namd/NAMD_SOURCE/tcl/linux/lib -L/root/tcl/lib
-L/home/admin/namd/NAMD_SOURCE/fftw/linux/lib -L/root/fftw/lib
-I/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/include
-DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -march=pentiumpro -ffast-math -static
-o namd2 -L/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib
-I/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../include
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libldb-rand.o
obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.o obj/main.o
obj/mainfunc.o obj/memusage.o obj/strlib.o obj/AlgSeven.o
obj/AlgRecBisection.o obj/AlgNbor.o obj/AtomMap.o obj/BackEnd.o
obj/BroadcastMgr.o obj/BroadcastClient.o obj/CollectionMaster.o
obj/CollectionMgr.o obj/Communicate.o obj/Compute.o
obj/ComputeAngles.o obj/ComputeBonds.o obj/ComputeConsForce.o
obj/ComputeConsForceMsgs.o obj/ComputeCylindricalBC.o
obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o
obj/ComputeDPMTA.o obj/ComputeEField.o obj/ComputeExt.o
obj/ComputeFullDirect.o obj/ComputeHomePatch.o
obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o
obj/ComputeGlobalMsgs.o obj/ComputeMap.o obj/ComputeMgr.o
obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o
obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o
obj/ComputeNonbondedFEP.o obj/ComputeNonbondedLES.o obj/ComputePatch.o
obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o
obj/ComputeSphericalBC.o obj/ComputeStir.o obj/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/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 moduleinit19007.o -lmoduleNeighborLB -lmodulecommlib
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -lmpich -ldl
-lz -ltcl8.3 -ldl -lsrfftw -lsfftw -lm -lmoduleNeighborLB
-lmodulecommlib
/home/admin/namd/NAMD_SOURCE/tcl/linux/lib/libtcl8.3.a(tclLoadDl.o)(.text+0x35):
In function `TclpLoadFile':
: warning: Using 'dlopen' in statically linked applications requires
at runtime the shared libraries from the glibc version used for
linking
/home/admin/namd/NAMD_SOURCE/tcl/linux/lib/libtcl8.3.a(tclUnixPipe.o)(.text+0xe2):
In function `TclpCreateTempFile':
: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/home/admin/namd/NAMD_SOURCE/tcl/linux/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xc26):
In function `GetGroupAttribute':
: warning: Using 'getgrgid' in statically linked applications requires
at runtime the shared libraries from the glibc version used for
linking
/home/admin/namd/NAMD_SOURCE/tcl/linux/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xe38):
In function `SetGroupAttribute':
: warning: Using 'getgrnam' in statically linked applications requires
at runtime the shared libraries from the glibc version used for
linking
/home/admin/namd/NAMD_SOURCE/tcl/linux/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xc71):
In function `GetGroupAttribute':
: warning: Using 'endgrent' in statically linked applications requires
at runtime the shared libraries from the glibc version used for
linking
/home/admin/namd/NAMD_SOURCE/tcl/linux/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xf4d):
In function `SetOwnerAttribute':
: warning: Using 'getpwnam' in statically linked applications requires
at runtime the shared libraries from the glibc version used for
linking
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
/home/admin/namd/NAMD_SOURCE/tcl/linux/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xd31):
In function `GetOwnerAttribute':
: warning: Using 'endpwent' in statically linked applications requires
at runtime the shared libraries from the glibc version used for
linking
/home/admin/namd/NAMD_SOURCE/tcl/linux/lib/libtcl8.3.a(tclUnixChan.o)(.text+0xf01):
In function `TcpGetOptionProc':
: warning: Using 'gethostbyaddr' 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
/home/admin/namd/NAMD_SOURCE/tcl/linux/lib/libtcl8.3.a(tclIOSock.o)(.text+0x47):
In function `TclSockGetPort':
: warning: Using 'getservbyname' in statically linked applications
requires at runtime the shared libraries from the glibc version used
for linking
/usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)(.text+0x1380):
In function `free':
: multiple definition of `free'
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x35bd):
first defined here
/usr/bin/ld: Warning: size of symbol `free' changed from 29 in
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
to 175 in /usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)(.text+0x2c70):
In function `malloc':
: multiple definition of `malloc'
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x3584):
first defined here
/usr/bin/ld: Warning: size of symbol `malloc' changed from 57 in
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
to 373 in /usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)(.text+0x30a0):
In function `realloc':
: multiple definition of `realloc'
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x3633):
first defined here
/usr/bin/ld: Warning: size of symbol `realloc' changed from 40 in
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
to 531 in /usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)(.data+0x0):
multiple definition of
`__libc_malloc_initialized'/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.data+0x10):
first defined here
/usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)(.text+0x424):
In function `_int_new_arena':
: multiple definition of `_int_new_arena'
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x619):
first defined here
/usr/bin/ld: Warning: size of symbol `_int_new_arena' changed from 187
in /home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
to 180 in /usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)(.text+0xe30):
In function `_int_free':
: multiple definition of `_int_free'
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x273e):
first defined here
/usr/bin/ld: Warning: size of symbol `_int_free' changed from 338 in
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
to 1162 in /usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)(.text+0x1430):
In function `_int_malloc':
: multiple definition of `_int_malloc'
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x21e2):
first defined here
/usr/bin/ld: Warning: size of symbol `_int_malloc' changed from 1372
in /home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
to 2643 in /usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)(.text+0x1f54):
In function `_int_memalign':
: multiple definition of `_int_memalign'
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x2de0):
first defined here
/usr/bin/ld: Warning: size of symbol `_int_memalign' changed from 397
in /home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
to 413 in /usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)(.text+0x20f4):
In function `_int_valloc':
: multiple definition of `_int_valloc'
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x31d2):
first defined here
/usr/bin/ld: Warning: size of symbol `_int_valloc' changed from 48 in
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
to 63 in /usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)(.text+0x2268):
In function `_int_realloc':
: multiple definition of `_int_realloc'
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x298f):
first defined here
/usr/bin/ld: Warning: size of symbol `_int_realloc' changed from 1105
in /home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
to 898 in /usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)
/usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)(.text+0x3438):
In function `__malloc_check_init':
: multiple definition of `__malloc_check_init'
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0x74a):
first defined here
/usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed
from 111 in /home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
to 103 in /usr/lib/gcc/i386-redhat-linux/3.4.2/../../../libc.a(malloc.o)
collect2: ld returned 1 exit status
Fatal Error by charmc in directory
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/Linux-i686-MPI
Command mpiCC -rdynamic
-L/home/admin/namd/NAMD_SOURCE/tcl/linux/lib -L/root/tcl/lib
-L/home/admin/namd/NAMD_SOURCE/fftw/linux/lib -L/root/fftw/lib
-I/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/include
-DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -march=pentiumpro -ffast-math -static
-o namd2 -L/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib
-I/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../include
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libldb-rand.o
obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.o obj/main.o
obj/mainfunc.o obj/memusage.o obj/strlib.o obj/AlgSeven.o
obj/AlgRecBisection.o obj/AlgNbor.o obj/AtomMap.o obj/BackEnd.o
obj/BroadcastMgr.o obj/BroadcastClient.o obj/CollectionMaster.o
obj/CollectionMgr.o obj/Communicate.o obj/Compute.o
obj/ComputeAngles.o obj/ComputeBonds.o obj/ComputeConsForce.o
obj/ComputeConsForceMsgs.o obj/ComputeCylindricalBC.o
obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o
obj/ComputeDPMTA.o obj/ComputeEField.o obj/ComputeExt.o
obj/ComputeFullDirect.o obj/ComputeHomePatch.o
obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o
obj/ComputeGlobalMsgs.o obj/ComputeMap.o obj/ComputeMgr.o
obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o
obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o
obj/ComputeNonbondedFEP.o obj/ComputeNonbondedLES.o obj/ComputePatch.o
obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o
obj/ComputeSphericalBC.o obj/ComputeStir.o obj/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/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 moduleinit19007.o -lmoduleNeighborLB -lmodulecommlib
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
/home/admin/namd/NAMD_SOURCE/NAMD_2.6b1_Source/charm-5.9/mpi-linux/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -lmpich -ldl
-lz -ltcl8.3 -ldl -lsrfftw -lsfftw -lm -lmoduleNeighborLB
-lmodulecommlib returned error code 1
charmc exiting...
rm -f moduleinit19007.C moduleinit19007.o
make: *** [namd2] Error 1
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