From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Fri Jan 16 2004 - 15:46:09 CST
Hi,
Did you use the precompiled tcl library downloaded from namd website?
They are compiled on rh7, and is not compatiable with rh9.
You have to compile tcl yourself into static form (.a instead of .so) and
same thing to fftw.
I have created a new NAMD wiki webpage called "NamdCompile" with some
instructions of how to compile namd accessories. Hope it helps.
Gengbin
On Tue, 13 Jan 2004, Valery Miftakhov wrote:
> 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.
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:18 CST