Re: Complie NAMD on Suse Linux

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Mon Feb 07 2005 - 13:02:32 CST

One thing I suspect Suse 9.2 does not like is that -rdynamic and -static
appears at same time:

g++ -Wno-deprecated -rdynamic -O3 -march=pentiumpro -ffast-math -static

You can get rid of -static in namd2/arch Makefile, this probably can get
rid of those complaints about multiple definitions of malloc.
We compiled on Suse9.1 without problem though.

Gengbin

Jason Lee 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/

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