Re: Compiling NAMD on Linux cluster

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Fri May 28 2004 - 15:48:41 CDT

Is your Linux redhat9?
You need to download the precompiled tcl and fftw for RH9 from the
namd download page.

Gengbin

On Fri, 28 May 2004, Xin Chen wrote:

> 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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