From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Tue Jun 15 2004 - 11:39:49 CDT
It is still like you linked with an incompatible version of
pre-compiled fftw lib. Make sure you download the right one and have the
correct library path.
Alternatively, you can also compile from source code. Checkout the NAMD
wiki for compilation instructions.
Gengbin
On Tue, 15 Jun 2004 ghg_at_xalt.am wrote:
> 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/Compu
teHomePatch.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/Gro
macsTopFile.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
>
>
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:44 CST