Namd RedHat9 compilation problem

From: ghg_at_xalt.am
Date: Tue Jun 15 2004 - 05:56:36 CDT

I compiled charm, megatest passed OK.
downloaded tcl fftw and plugins for RH9.
in namd2.5/arch changed tcl fftw and plugins path to full paths
changed path to full path to charm in make.charm
after some errors in compilation of namd tryed ./config fftw
Linux-i686 , without tcl and plugins, all ok. After it, make in Linux-i686, generated error:

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/ghg/NAMD/Temp/NAMD_2.5_Source/fftw/linux/lib -L/home/ghg/fftw-linux/lib -I/home/ghg/NAMD/Temp/NAMD_2.5_Source/charm/net-linux/include -o namd2 -L/home/ghg/NAMD/Temp/NAMD_2.5_Source/charm/net-linux/bin/../lib -I/home/ghg/NAMD/Temp/NAMD_2.5_Source/charm/net-linux/bin/../include /home/ghg/NAMD/Temp/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/Compute
HomePatch.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/ghg/NAMD/Temp/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-default.o /home/ghg/NAMD/Temp/NAMD_2.5_Source/charm/net-linux/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -ldl -lz -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib
/home/ghg/NAMD/Temp/NAMD_2.5_Source/fftw/linux/lib/libsfftw.a(wisdom.o)(.text+0x366): In function `read_int':
: undefined reference to `__ctype_b'
/home/ghg/NAMD/Temp/NAMD_2.5_Source/fftw/linux/lib/libsfftw.a(wisdom.o)(.text+0x399): In function `read_int':
: undefined reference to `__ctype_b'
/home/ghg/NAMD/Temp/NAMD_2.5_Source/fftw/linux/lib/libsfftw.a(wisdom.o)(.text+0x3fd): In function `read_int':
: undefined reference to `__ctype_b'
/home/ghg/NAMD/Temp/NAMD_2.5_Source/fftw/linux/lib/libsfftw.a(wisdom.o)(.text+0x456): In function `read_int':
: undefined reference to `__ctype_b'
/home/ghg/NAMD/Temp/NAMD_2.5_Source/fftw/linux/lib/libsfftw.a(wisdom.o)(.text+0x4b6): In function `fftw_import_wisdom':
: undefined reference to `__ctype_b'
/home/ghg/NAMD/Temp/NAMD_2.5_Source/fftw/linux/lib/libsfftw.a(wisdom.o)(.text+0x506): more undefined references to `__ctype_b' follow
collect2: ld returned 1 exit status
Fatal Error by charmc in directory /home/ghg/NAMD/Temp/NAMD_2.5_Source/Linux-i686-g++
Command g++ -Wno-deprecated -rdynamic -O3 -march=pentiumpro -ffast-math -static -L/home/ghg/NAMD/Temp/NAMD_2.5_Source/fftw/linux/lib -L/home/ghg/fftw-linux/lib -I/home/ghg/NAMD/Temp/NAMD_2.5_Source/charm/net-linux/include -o namd2 -L/home/ghg/NAMD/Temp/NAMD_2.5_Source/charm/net-linux/bin/../lib -I/home/ghg/NAMD/Temp/NAMD_2.5_Source/charm/net-linux/bin/../include /home/ghg/NAMD/Temp/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/Groma
csTopFile.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/ghg/NAMD/Temp/NAMD_2.5_Source/charm/net-linux/bin/../lib/libmemory-default.o /home/ghg/NAMD/Temp/NAMD_2.5_Source/charm/net-linux/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -ldl -lz -lsrfftw -lsfftw -lm -!
 lmoduleN
eighborLB -lmodulecommlib returned error code 1
charmc exiting...
make: *** [namd2] Error 1

Thank's for help

Hrant

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