NAMD linking problem

From: Valery Miftakhov (valery_at_biozak.com)
Date: Tue Jan 13 2004 - 22:15:59 CST

Hi All,

I am trying to install NAMD from source on my Linux 9.0 and I get to the
stage where I type 'make' in Linux-i686-g++ directory. After that, I get
the following:

---------------
...

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/d/scratch/reports_US/valery/bioinformatics/tcl/linux/lib
-L/home/valeroot/tcl-linux/lib
-L/d/scratch/reports_US/valery/bioinformatics/fftw/linux/lib
-L/home/valeroot/fftw-linux/lib
-L/d/scratch/reports_US/valery/bioinformatics/plugins/LINUX
-L/d/scratch/reports_US/valery/bioinformatics/plugins/LINUX/molfile
-L/home/valeroot/plugins/LINUX -L/home/valeroot/plugins/LINUX/molfile
-I/d/scratch/reports_US/valery/bioinformatics/NAMD_2.5_Source/charm/net-linux/include
-o namd2
-L/d/scratch/reports_US/valery/bioinformatics/NAMD_2.5_Source/charm/net-linux/bin/../lib
-I/d/scratch/reports_US/valery/bioinformatics/NAMD_2.5_Source/charm/net-linux/bin/../include
/d/scratch/reports_US/valery/bioinformatics/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
/d/scratch/reports_US/valery/bioinformatics/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-default.o
/d/scratch/reports_US/valery/bioinformatics/NAMD_2.5_Source/charm/net-linux/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -ldl -lz -ltcl8.3
-ldl -lsrfftw -lsfftw -lmolfile_plugin -lm -lmoduleNeighborLB
-lmodulecommlib
/d/scratch/reports_US/valery/bioinformatics/tcl/linux/lib/libtcl8.3.a(tclUnixPipe.o)(.text+0xe0):
In function `TclpCreateTempFile':
: the use of `tmpnam' is dangerous, better use `mkstemp'
/d/scratch/reports_US/valery/bioinformatics/tcl/linux/lib/libtcl8.3.a(tclBinary.o)(.text+0xbe4):
In function `Tcl_BinaryObjCmd':
: undefined reference to `__ctype_b'
/d/scratch/reports_US/valery/bioinformatics/tcl/linux/lib/libtcl8.3.a(tclBinary.o)(.text+0xc5d):
In function `Tcl_BinaryObjCmd':
: undefined reference to `__ctype_b'
/d/scratch/reports_US/valery/bioinformatics/tcl/linux/lib/libtcl8.3.a(tclBinary.o)(.text+0x1617):
In function `GetFormatSpec':
: undefined reference to `__ctype_b'
/d/scratch/reports_US/valery/bioinformatics/tcl/linux/lib/libtcl8.3.a(tclCmdAH.o)(.text+0x185):
In function `Tcl_CaseObjCmd':
: undefined reference to `__ctype_b'
/d/scratch/reports_US/valery/bioinformatics/tcl/linux/lib/libtcl8.3.a(tclCmdAH.o)(.text+0x22f5):
In function `Tcl_FormatObjCmd':
: undefined reference to `__ctype_b'
/d/scratch/reports_US/valery/bioinformatics/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
/d/scratch/reports_US/valery/bioinformatics/NAMD_2.5_Source/Linux-i686-g++
Command g++ -Wno-deprecated -rdynamic -O3 -march=pentiumpro -ffast-math
-static -L/d/scratch/reports_US/valery/bioinformatics/tcl/linux/lib
-L/home/valeroot/tcl-linux/lib
-L/d/scratch/reports_US/valery/bioinformatics/fftw/linux/lib
-L/home/valeroot/fftw-linux/lib
-L/d/scratch/reports_US/valery/bioinformatics/plugins/LINUX
-L/d/scratch/reports_US/valery/bioinformatics/plugins/LINUX/molfile
-L/home/valeroot/plugins/LINUX -L/home/valeroot/plugins/LINUX/molfile
-I/d/scratch/reports_US/valery/bioinformatics/NAMD_2.5_Source/charm/net-linux/include
-o namd2
-L/d/scratch/reports_US/valery/bioinformatics/NAMD_2.5_Source/charm/net-linux/bin/../lib
-I/d/scratch/reports_US/valery/bioinformatics/NAMD_2.5_Source/charm/net-linux/bin/../include
/d/scratch/reports_US/valery/bioinformatics/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
/d/scratch/reports_US/valery/bioinformatics/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-default.o
/d/scratch/reports_US/valery/bioinformatics/NAMD_2.5_Source/charm/net-linux/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -ldl -lz -ltcl8.3
-ldl -lsrfftw -lsfftw -lmolfile_plugin -lm -lmoduleNeighborLB
-lmodulecommlib returned error code 1
charmc exiting...
make: *** [namd2] Error 1
---------------

Any thoughts? Thank you very much for your help!

-- 
Valery Miftakhov, Ph.D.

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