Compiling NAMD on Linux cluster

From: Xin Chen (xinchen_at_ic.sunysb.edu)
Date: Fri May 28 2004 - 15:14:12 CDT

Hi,

I am trying to compile NAMD on Linux following the procedure:

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

But in the last step, I met a error, the error messeng is attached. Anyone
has any idea about that? Thanks.

Sincerely yours,

Xin Chen

----------------------------error massage --------------

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=p
entiumpro -ffast-math -static -c moduleinit.C -o moduleinit.o
charmc: Executing
g++ -Wno-deprecated -rdynamic -O3 -march=pentiumpro -ffast-math -static -L/n
fs/s1r1p2/xinchen/tcl/linux/lib -L/nfs/s1r1p2/xinchen/tcl-linux/lib -L/nfs/s
1r1p2/xinchen/fftw/linux/lib -L/nfs/s1r1p2/xinchen/fftw-linux/lib -L/nfs/s1r
1p2/xinchen/plugins/LINUX -L/nfs/s1r1p2/xinchen/plugins/LINUX/molfile -L/nfs
/s1r1p2/xinchen/plugins/LINUX -L/nfs/s1r1p2/xinchen/plugins/LINUX/molfile -I
/nfs/s1r1p2/xinchen/NAMD_2.5_Source/charm/net-linux/include -o
namd2 -L/nfs/s1r1p2/xinchen/NAMD_2.5_Source/charm/net-linux/bin/../lib -I/nf
s/s1r1p2/xinchen/NAMD_2.5_Source/charm/net-linux/bin/../include
/nfs/s1r1p2/xinchen/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
/nfs/s1r1p2/xinchen/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-def
ault.o
/nfs/s1r1p2/xinchen/NAMD_2.5_Source/charm/net-linux/bin/../lib/libthreads-de
fault.o -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -ldl -lz -ltc
l8.3 -ldl -lsrfftw -lsfftw -lmolfile_plugin -lm -lmoduleNeighborLB -lmodulec
ommlib
/nfs/s1r1p2/xinchen/tcl/linux/lib/libtcl8.3.a(tclUnixPipe.o)(.text+0xe0): In
function `TclpCreateTempFile':
: the use of `tmpnam' is dangerous, better use `mkstemp'
/nfs/s1r1p2/xinchen/tcl/linux/lib/libtcl8.3.a(tclBinary.o)(.text+0xbe4): In
function `Tcl_BinaryObjCmd':
: undefined reference to `__ctype_b'
/nfs/s1r1p2/xinchen/tcl/linux/lib/libtcl8.3.a(tclBinary.o)(.text+0xc5d): In
function `Tcl_BinaryObjCmd':
: undefined reference to `__ctype_b'
/nfs/s1r1p2/xinchen/tcl/linux/lib/libtcl8.3.a(tclBinary.o)(.text+0x1617): In
function `GetFormatSpec':
: undefined reference to `__ctype_b'
/nfs/s1r1p2/xinchen/tcl/linux/lib/libtcl8.3.a(tclCmdAH.o)(.text+0x185): In
function `Tcl_CaseObjCmd':
: undefined reference to `__ctype_b'
/nfs/s1r1p2/xinchen/tcl/linux/lib/libtcl8.3.a(tclCmdAH.o)(.text+0x22f5): In
function `Tcl_FormatObjCmd':
: undefined reference to `__ctype_b'
/nfs/s1r1p2/xinchen/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
/nfs/s1r1p2/xinchen/NAMD_2.5_Source/Linux-i686-g++
Command
g++ -Wno-deprecated -rdynamic -O3 -march=pentiumpro -ffast-math -static -L/n
fs/s1r1p2/xinchen/tcl/linux/lib -L/nfs/s1r1p2/xinchen/tcl-linux/lib -L/nfs/s
1r1p2/xinchen/fftw/linux/lib -L/nfs/s1r1p2/xinchen/fftw-linux/lib -L/nfs/s1r
1p2/xinchen/plugins/LINUX -L/nfs/s1r1p2/xinchen/plugins/LINUX/molfile -L/nfs
/s1r1p2/xinchen/plugins/LINUX -L/nfs/s1r1p2/xinchen/plugins/LINUX/molfile -I
/nfs/s1r1p2/xinchen/NAMD_2.5_Source/charm/net-linux/include -o
namd2 -L/nfs/s1r1p2/xinchen/NAMD_2.5_Source/charm/net-linux/bin/../lib -I/nf
s/s1r1p2/xinchen/NAMD_2.5_Source/charm/net-linux/bin/../include
/nfs/s1r1p2/xinchen/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
/nfs/s1r1p2/xinchen/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-def
ault.o
/nfs/s1r1p2/xinchen/NAMD_2.5_Source/charm/net-linux/bin/../lib/libthreads-de
fault.o -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -ldl -lz -ltc
l8.3 -ldl -lsrfftw -lsfftw -lmolfile_plugin -lm -lmoduleNeighborLB -lmodulec
ommlib returned error code 1
charmc exiting...
make: *** [namd2] Error 1

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