Re: Complie NAMD on Suse Linux

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Feb 07 2005 - 11:56:01 CST

Hello,

It would appear that you need to recompile the tcl distro on your suse
box. The precompiled binaries from the NAMD website are not compatible
with your system configuration.
Download the source from http://sourceforge.net/projects/tcl

regards
Brian

On Thu, 3 Feb 2005, cunning cunning wrote:

> Hello:
>
> I am compiling NAMD on Suse Linux9.2. I followed the guidance of release
> note.
>
> Download TCL, FFTW, and plugins libraries:
> mkdir fftw; cd fftw
> wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux.tar.gz
> tar xzf fftw-linux.tar.gz
> cd ..; mkdir plugins; cd plugins
> wget http://www.ks.uiuc.edu/Research/namd/libraries/plugins-LINUX.tar.gz
> tar xzf plugins-LINUX.tar.gz
> cd ..; mkdir tcl; cd tcl
> wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl-linux.tar.gz
> tar xzf tcl-linux.tar.gz
>
> Unpack NAMD and matching Charm++ source code and enter directory:
> tar xzf NAMD_2.5_Source.tar.gz
> cd NAMD_2.5_Source
> tar xf charm.tar
> cd charm
>
> Build and test the Charm++/Converse library:
> ./build charm++ net-linux -O -DCMK_OPTIMIZE=1
> cd net-linux/pgms/charm++/megatest/
> make pgm
> ./charmrun ++local +p4 ./pgm (also try running on multiple nodes)
> cd ../../../../..
>
> Edit various configuration files:
> vi Make.charm (set CHARMBASE to .rootdir/charm or full path to charm)
> vi arch/Linux-i686.fftw (fix library name and path to files)
> vi arch/All-Unix.plugins (fix path to files)
> vi arch/Linux-i686.tcl (fix library version and path to TCL files)
>
> Set up build directory and compile:
> ./config tcl fftw plugins Linux-i686-g++
> cd Linux-i686-g++
> make
>
> At the last step. I have following error message.
>
> charmc> ----------- Module dependency search ------------
> charmc> ----------- Module dependency search complete ------------
> Adding registration for module NeighborLB
> Adding registration for module commlib
> charmc: Executing g++ -Wno-deprecated -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -Iinc
> -Isrc -O3 -march=pentiumpro -ffast-math -static -c moduleinit.C -o
> moduleinit.o
> charmc: Executing g++ -Wno-deprecated -rdynamic -O3 -march=pentiumpro
> -ffast-math -static -L/home/m0u1971/softwares/namd/tcl/linux/lib
> -L/home/m0u1971/softwares/namd/fftw-linux/linux/lib
> -L/home/m0u1971/softwares/namd/LINUX
> -L/home/m0u1971/softwares/namd/LINUX/molfile -L/home/m0u1971/plugins/LINUX
> -L/home/m0u1971/plugins/LINUX/molfile
> -I/home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/include -o
> namd2
> -L/home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../lib
> -I/home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../include
> /home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-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/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
> /home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-default.o
> /home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../lib/libthreads-default.o
> -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -ldl -ltcl8.3 -ldl
> -lsrfftw -lsfftw -lmolfile_plugin -lm -lmoduleNeighborLB -lmodulecommlib
> /home/m0u1971/softwares/namd/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/m0u1971/softwares/namd/tcl/linux/lib/libtcl8.3.a(tclUnixPipe.o)(.text+0xe0):
> In function `TclpCreateTempFile':
> : warning: the use of `tmpnam' is dangerous, better use `mkstemp'
> /home/m0u1971/softwares/namd/tcl/linux/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xb5b):
> In function `GetGroupAttribute':
> : warning: Using 'getgrgid' in statically linked applications requires at
> runtime the shared libraries from the glibc version used for linking
> /home/m0u1971/softwares/namd/tcl/linux/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xd59):
> In function `SetGroupAttribute':
> : warning: Using 'getgrnam' in statically linked applications requires at
> runtime the shared libraries from the glibc version used for linking
> /home/m0u1971/softwares/namd/tcl/linux/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xba1):
> In function `GetGroupAttribute':
> : warning: Using 'endgrent' in statically linked applications requires at
> runtime the shared libraries from the glibc version used for linking
> /home/m0u1971/softwares/namd/tcl/linux/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xe7d):
> 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+0xb2b): 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/m0u1971/softwares/namd/tcl/linux/lib/libtcl8.3.a(tclUnixFCmd.o)(.text+0xc5e):
> In function `GetOwnerAttribute':
> : warning: Using 'endpwent' in statically linked applications requires at
> runtime the shared libraries from the glibc version used for linking
> /home/m0u1971/softwares/namd/tcl/linux/lib/libtcl8.3.a(tclUnixChan.o)(.text+0xe2e):
> 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+0x2a6): 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/m0u1971/softwares/namd/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-lib/i586-suse-linux/3.3.4/../../../libc.a(malloc.o)(.text+0x1b30):
> In function `__libc_free':
> /usr/src/packages/BUILD/glibc-2.3/malloc/malloc.c:3360: multiple definition
> of `free'
> /home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-default.o(.text+0x2084):
> first defined here
> /usr/lib/gcc-lib/i586-suse-linux/3.3.4/../../../../i586-suse-linux/bin/ld:
> Warning: size of symbol `free' changed from 29 in
> /home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-default.o
> to 165 in /usr/lib/gcc-lib/i586-suse-linux/3.3.4/../../../libc.a(malloc.o)
> /usr/lib/gcc-lib/i586-suse-linux/3.3.4/../../../libc.a(malloc.o)(.text+0x3990):
> In function `__libc_malloc':
> /usr/src/packages/BUILD/glibc-2.3/malloc/malloc.c:3318: multiple definition
> of `malloc'
> /home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-default.o(.text+0x204b):
> first defined here
> /usr/lib/gcc-lib/i586-suse-linux/3.3.4/../../../../i586-suse-linux/bin/ld:
> Warning: size of symbol `malloc' changed from 57 in
> /home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-default.o
> to 412 in /usr/lib/gcc-lib/i586-suse-linux/3.3.4/../../../libc.a(malloc.o)
> /usr/lib/gcc-lib/i586-suse-linux/3.3.4/../../../libc.a(malloc.o)(.text+0x3ed0):
> In function `__libc_realloc':
> /usr/src/packages/BUILD/glibc-2.3/malloc/malloc.c:3403: multiple definition
> of `realloc'
> /home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-default.o(.text+0x20fa):
> first defined here
> /usr/lib/gcc-lib/i586-suse-linux/3.3.4/../../../../i586-suse-linux/bin/ld:
> Warning: size of symbol `realloc' changed from 40 in
> /home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-default.o
> to 472 in /usr/lib/gcc-lib/i586-suse-linux/3.3.4/../../../libc.a(malloc.o)
> /home/m0u1971/softwares/namd/tcl/linux/lib/libtcl8.3.a(tclBinary.o)(.text+0xbe4):
> In function `Tcl_BinaryObjCmd':
> : undefined reference to `__ctype_b'
> /home/m0u1971/softwares/namd/tcl/linux/lib/libtcl8.3.a(tclBinary.o)(.text+0xc5d):
> In function `Tcl_BinaryObjCmd':
> : undefined reference to `__ctype_b'
> /home/m0u1971/softwares/namd/tcl/linux/lib/libtcl8.3.a(tclBinary.o)(.text+0x1617):
> In function `GetFormatSpec':
> : undefined reference to `__ctype_b'
> /home/m0u1971/softwares/namd/tcl/linux/lib/libtcl8.3.a(tclCmdAH.o)(.text+0x185):
> In function `Tcl_CaseObjCmd':
> : undefined reference to `__ctype_b'
> /home/m0u1971/softwares/namd/tcl/linux/lib/libtcl8.3.a(tclCmdAH.o)(.text+0x22f5):
> In function `Tcl_FormatObjCmd':
> : undefined reference to `__ctype_b'
> /home/m0u1971/softwares/namd/tcl/linux/lib/libtcl8.3.a(tclCmdAH.o)(.text+0x23f8):
> more undefined references to `__ctype_b' follow
> collect2: ld returned 1 exit status
> Fatal Error by charmc in directory
> /home/m0u1971/softwares/namd/NAMD_2.5_Source/Linux-i686-g++
> Command g++ -Wno-deprecated -rdynamic -O3 -march=pentiumpro -ffast-math
> -static -L/home/m0u1971/softwares/namd/tcl/linux/lib
> -L/home/m0u1971/softwares/namd/fftw-linux/linux/lib
> -L/home/m0u1971/softwares/namd/LINUX
> -L/home/m0u1971/softwares/namd/LINUX/molfile -L/home/m0u1971/plugins/LINUX
> -L/home/m0u1971/plugins/LINUX/molfile
> -I/home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/include -o
> namd2
> -L/home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../lib
> -I/home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../include
> /home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-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/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.oobj/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
> /home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-default.o
> /home/m0u1971/softwares/namd/NAMD_2.5_Source/charm/net-linux/bin/../lib/libthreads-default.o
> -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -ldl -ltcl8.3 -ldl
> -lsrfftw -lsfftw -lmolfile_plugin -lm -lmoduleNeighborLB -lmodulecommlib
> returned error code 1
> charmc exiting...
> make: *** [namd2] Error 1
>
>
> Anybody know how to solve this?
> Thanks a lot.
>
> _________________________________________________________________
> MSN Explorer: http://explorer.msn.com/lccn/
>

************************************************
  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
  P.O. Box 808, L-448 bennion1_at_llnl.gov
  7000 East Avenue phone: (925) 422-5722
  Livermore, CA 94550 fax: (925) 424-6605
************************************************

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