From: roberte_at_organ.su.se
Date: Sat May 07 2005 - 05:54:18 CDT
--
I'm a Ph D student at the University of Stockholm, department of Organic
chemistry. We are trying to build a linux cluster using the clustermatic 5
approach (on a Mandrake 10X base-OP), to run MD simulations with the NAMD
program. However when compiling the the source code we are running into
problems. Our initial problems with the charm++ scripts have been solved by
using the new charm5.8 downloaded from the charm++ website.
As seen from other websites and (NAMD Wiki) we put this into the NAMD source
library and compiled it accordingly. Also downloading the tcl8.3.5 libs and
the FFTws from www.fftw.org (version 2.1.5) and compiling it with our gcc
compilier (CFLAG = -static, on both the fftw and tcl), however the following
problem still occurs (below), when making the NAMD executable :
------------------------------------
(Files needed:
(from -------->http://homepage.mac.com/choonpeng/NAMD_Installation_Notes.html)
NAMD_2.5_Source.tar.gz
tcl8.3.5.tar.gz (from TCL/TK website)
plugins.tar.gz (from NAMD website)
charm_src.tar.gz (latest source from Charm++ website at UIUC; to replace charm
source inside NAMD distribution).These were downloaded and used)
---------------------------------
export CFLAGS="-O -static"
cd /space/tmp/extra_libs/Source/tcl8.3.5/unix
./configure --disable-shared --prefix=/usr/local/test
make
make install
cd /space/tmp/extra_libs/Source/fftw-2.1.5
./configure --enable-float --enable-type-prefix --enable-static
--prefix=/usr/local/test
make
make install
cd /space/tmp/NAMD_2.5_Source
rm -fr Linux-i686-Clustermatic
nano arch/All-Unix.plugins
PLUGINDIR=/space/tmp/extra_libs
nano arch/Linux-i686.fftw
< FFTDIR=/space/tmp/extra_libs/linux
> FFTDIR=/usr/local/test
nano arch/Linux-i686.tcl
< TCLDIR=/space/tmp/extra_libs/linux
> TCLDIR=/usr/local/test
./config tcl fftw plugins Linux-i686-Clustermatic <--this goes smoothly
cd Linux-i686-Clustermatic
make
Everything works and runs ok so far.....but then ...
charmc> ----------- Module dependency search ------------
charmc> ----------- Module dependency search complete ------------
Adding registration for module NeighborLB
Adding registration for module commlib
charmc: Executing g++ -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3
-march=pentiumpro -ffast-math -static -c moduleinit.C -o moduleinit.o
charmc: Executing g++ -rdynamic -O3 -march=pentiumpro -ffast-math
-static -L/usr/local/test/lib -L/root/tcl-linux/lib
-L/usr/local/test/lib -L/root/fftw-linux/lib
-L/space/tmp/extra_libs/LINUX -L/space/tmp/extra_libs/LINUX/molfile
-L/root/plugins/LINUX -L/root/plugins/LINUX/molfile
-I/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/include -o
namd2
-L/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib
-I/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../include
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libldb-rand.o
obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.o obj/main.o
obj/mainfunc.o obj/memusage.o obj/strlib.o obj/AlgSeven.o
obj/AlgRecBisection.o obj/AlgNbor.o obj/AtomMap.o obj/BackEnd.o
obj/BroadcastMgr.o obj/BroadcastClient.o obj/CollectionMaster.o
obj/CollectionMgr.o obj/Communicate.o obj/Compute.o obj/ComputeAngles.o
obj/ComputeBonds.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o
obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o
obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.o
obj/ComputeExt.o obj/ComputeFullDirect.o obj/ComputeHomePatch.o
obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o
obj/ComputeGlobalMsgs.o obj/ComputeMap.o obj/ComputeMgr.o
obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o
obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o
obj/ComputeNonbondedFEP.o obj/ComputeNonbondedLES.o obj/ComputePatch.o
obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o
obj/ComputeSphericalBC.o obj/ComputeStir.o obj/ConfigList.o
obj/Controller.o obj/ccsinterface.o obj/DataStream.o obj/DumpBench.o
obj/FreeEnergyAssert.o obj/FreeEnergyGroup.o obj/FreeEnergyLambda.o
obj/FreeEnergyLambdMgr.o obj/FreeEnergyParse.o obj/FreeEnergyRestrain.o
obj/FreeEnergyRMgr.o obj/FreeEnergyVector.o obj/GlobalMaster.o
obj/GlobalMasterServer.o obj/GlobalMasterTest.o obj/GlobalMasterIMD.o
obj/GlobalMasterTcl.o obj/GlobalMasterSMD.o obj/GlobalMasterFreeEnergy.o
obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o obj/GromacsTopFile.o
obj/heap.o obj/HomePatch.o obj/IMDOutput.o obj/InfoStream.o
obj/LdbCoordinator.o obj/LJTable.o obj/Measure.o obj/MStream.o
obj/MigrateAtomsMsg.o obj/Molecule.o obj/NamdCentLB.o obj/NamdNborLB.o
obj/NamdState.o obj/NamdOneTools.o obj/Node.o obj/Output.o
obj/Parameters.o obj/ParseOptions.o obj/Patch.o obj/PatchMgr.o
obj/PatchMap.o obj/PDB.o obj/PDBData.o obj/PmeBase.o obj/PmeKSpace.o
obj/PmeRealSpace.o obj/ProcessorPrivate.o obj/ProxyMgr.o
obj/ProxyPatch.o obj/Rebalancer.o obj/RecBisection.o obj/ReductionMgr.o
obj/RefineOnly.o obj/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o
obj/SimParameters.o obj/Sync.o obj/TclCommands.o obj/WorkDistrib.o
obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o moduleinit.o
-lmoduleNeighborLB -lmodulecommlib
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -lbproc -ltcl8.3
-ldl -lsrfftw -lsfftw -lmolfile_plugin -lm -lmoduleNeighborLB
-lmodulecommlib
/usr/local/test/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
/usr/local/test/lib/libtcl8.3.a(tclUnixPipe.o)(.text+0xdd): In function
`TclpCreateTempFile':
: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/usr/local/test/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xc3b): In function
`GetGroupAttribute':
: warning: Using 'getgrgid' in statically linked applications requires
at runtime the shared libraries from the glibc version used for linking
/usr/local/test/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xe4d): In function
`SetGroupAttribute':
: warning: Using 'getgrnam' in statically linked applications requires
at runtime the shared libraries from the glibc version used for linking
/usr/local/test/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xc86): In function
`GetGroupAttribute':
: warning: Using 'endgrent' in statically linked applications requires
at runtime the shared libraries from the glibc version used for linking
/usr/local/test/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xf60): 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+0x121b): 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
/usr/local/test/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xd46): In function
`GetOwnerAttribute':
: warning: Using 'endpwent' in statically linked applications requires
at runtime the shared libraries from the glibc version used for linking
/usr/local/test/lib/libtcl8.3.a(tclUnixChan.o)(.text+0xf64): 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+0xc6): 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/local/test/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-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)(.data+0x10):
multiple definition of `__libc_malloc_initialized'
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o(.data+0x10):
first defined here
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)(.text+0x3140):
In function `_int_malloc':
: multiple definition of `_int_malloc'
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o(.text+0x316f):
first defined here
/usr/bin/ld: Warning: size of symbol `_int_malloc' changed from 2223 in
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o
to 1546 in
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)(.text+0xd00):
In function `__malloc_check_init':
: multiple definition of `__malloc_check_init'
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o(.text+0x9d7):
first defined here
/usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed from
113 in
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o
to 144 in
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)(.text+0x3750):
In function `_int_free':
: multiple definition of `_int_free'
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o(.text+0x3a1e):
first defined here
/usr/bin/ld: Warning: size of symbol `_int_free' changed from 608 in
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o
to 629 in
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)(.text+0xbb0):
In function `_int_new_arena':
: multiple definition of `_int_new_arena'
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o(.text+0x83c):
first defined here
/usr/bin/ld: Warning: size of symbol `_int_new_arena' changed from 284
in
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o
to 190 in
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)(.text+0x3b20):
In function `_int_realloc':
: multiple definition of `_int_realloc'
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o(.text+0x3e4b):
first defined here
/usr/bin/ld: Warning: size of symbol `_int_realloc' changed from 1929 in
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o
to 964 in
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)(.text+0x3ef0):
In function `_int_memalign':
: multiple definition of `_int_memalign'
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o(.text+0x45d4):
first defined here
/usr/bin/ld: Warning: size of symbol `_int_memalign' changed from 647 in
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o
to 433 in
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)(.text+0x4320):
In function `_int_valloc':
: multiple definition of `_int_valloc'
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o(.text+0x4c3a):
first defined here
/usr/bin/ld: Warning: size of symbol `_int_valloc' changed from 58 in
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o
to 62 in
/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.4/../../../libc.a(malloc.o)
collect2: ld returned 1 exit status
Fatal Error by charmc in directory
/space/tmp/NAMD_2.5_Source/Linux-i686-Clustermatic
Command g++ -rdynamic -O3 -march=pentiumpro -ffast-math -static
-L/usr/local/test/lib -L/root/tcl-linux/lib -L/usr/local/test/lib
-L/root/fftw-linux/lib -L/space/tmp/extra_libs/LINUX
-L/space/tmp/extra_libs/LINUX/molfile -L/root/plugins/LINUX
-L/root/plugins/LINUX/molfile
-I/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/include -o
namd2
-L/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib
-I/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../include
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libldb-rand.o
obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.o obj/main.o
obj/mainfunc.o obj/memusage.o obj/strlib.o obj/AlgSeven.o
obj/AlgRecBisection.o obj/AlgNbor.o obj/AtomMap.o obj/BackEnd.o
obj/BroadcastMgr.o obj/BroadcastClient.o obj/CollectionMaster.o
obj/CollectionMgr.o obj/Communicate.o obj/Compute.o obj/ComputeAngles.o
obj/ComputeBonds.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o
obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o
obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.o
obj/ComputeExt.o obj/ComputeFullDirect.o obj/ComputeHomePatch.o
obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o
obj/ComputeGlobalMsgs.o obj/ComputeMap.o obj/ComputeMgr.o
obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o
obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o
obj/ComputeNonbondedFEP.o obj/ComputeNonbondedLES.o obj/ComputePatch.o
obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o
obj/ComputeSphericalBC.o obj/ComputeStir.o obj/ConfigList.o
obj/Controller.o obj/ccsinterface.o obj/DataStream.o obj/DumpBench.o
obj/FreeEnergyAssert.o obj/FreeEnergyGroup.o obj/FreeEnergyLambda.o
obj/FreeEnergyLambdMgr.o obj/FreeEnergyParse.o obj/FreeEnergyRestrain.o
obj/FreeEnergyRMgr.o obj/FreeEnergyVector.o obj/GlobalMaster.o
obj/GlobalMasterServer.o obj/GlobalMasterTest.o obj/GlobalMasterIMD.o
obj/GlobalMasterTcl.o obj/GlobalMasterSMD.o obj/GlobalMasterFreeEnergy.o
obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o obj/GromacsTopFile.o
obj/heap.o obj/HomePatch.o obj/IMDOutput.o obj/InfoStream.o
obj/LdbCoordinator.o obj/LJTable.o obj/Measure.o obj/MStream.o
obj/MigrateAtomsMsg.o obj/Molecule.o obj/NamdCentLB.o obj/NamdNborLB.o
obj/NamdState.o obj/NamdOneTools.o obj/Node.o obj/Output.o
obj/Parameters.o obj/ParseOptions.o obj/Patch.o obj/PatchMgr.o
obj/PatchMap.o obj/PDB.o obj/PDBData.o obj/PmeBase.o obj/PmeKSpace.o
obj/PmeRealSpace.o obj/ProcessorPrivate.o obj/ProxyMgr.o
obj/ProxyPatch.o obj/Rebalancer.o obj/RecBisection.o obj/ReductionMgr.o
obj/RefineOnly.o obj/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o
obj/SimParameters.o obj/Sync.o obj/TclCommands.o obj/WorkDistrib.o
obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o moduleinit.o
-lmoduleNeighborLB -lmodulecommlib
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libmemory-default.o
/space/tmp/NAMD_2.5_Source/charm/net-linux-clustermatic/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -lbproc -ltcl8.3
-ldl -lsrfftw -lsfftw -lmolfile_plugin -lm -lmoduleNeighborLB
-lmodulecommlib returned error code 1
charmc exiting...
make: *** [namd2] Error 1
---------------------------------------
Any help or insight into the problem is appreciated
/Robert Eklund.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:25 CST