Complie NAMD on Suse Linux

From: Jason Lee (hellocunning_at_hotmail.com)
Date: Mon Feb 07 2005 - 09:32:02 CST

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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.

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• Next message: Wen Li: "question on running NAMD2 using Amber files (fwd)"
• Previous message: Wen Li: "question on running NAMD2 using Amber files"
• Next in thread: Gengbin Zheng: "Re: Complie NAMD on Suse Linux"
• Reply: Gengbin Zheng: "Re: Complie NAMD on Suse Linux"
• Maybe reply: Jason Lee: "Re: Complie NAMD on Suse Linux"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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