From: fu guoxing (fuguoxing_at_gmail.com)
Date: Tue Nov 08 2005 - 06:23:10 CST
Helo, everyone,
I was just compiling NAMD_2.6b1 on a Suse9.3 computer (dual Xeon
processores). I downloaded the NAMD_2.6b1_Source and followed the
guidence to install it. The former steps were all OK, but there was a
problem with the last one.
> Set up build directory and compile:
> ./config tcl fftw plugins Linux-i686-g++
> cd Linux-i686-g++
> make
The following is part of the error message.
charmc> ----------- Module dependency search ------------
charmc> ----------- Module dependency search complete ------------
Adding registration for module NeighborLB
Adding registration for module commlib
charmc: Executing g++ -D__CHARMC__=1 -c moduleinit8860.C -o moduleinit8860.o
charmc: Executing g++ -Wl,--allow-multiple-definition -rdynamic
-L/home/dong/programs/tclnamd/lib -L/home/fu/
tcl/lib -L/home/dong/programs/fftwnamd/lib -L/home/fu/fftw/lib
-I/home/fu/programs/NAMD_2.6b1_Source/charm-5.
9/net-linux/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -march=pentiumpro
-ffast-math
-static -o namd2 -L/home/f
u/programs/NAMD_2.6b1_Source/charm-5.9/net-linux/bin/../lib
-I/home/fu/programs/NAMD_2.6b1_Source/charm-5.9/n
et-linux/bin/../include
/home/fu/programs/NAMD_2.6b1_Source/charm-5.9/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/Alg
Seven.o obj/AlgRecBisection.o obj/AlgNbor.o obj/AtomMap.o obj/BackEnd.o
obj/BroadcastMgr.o obj/BroadcastClien
t.o obj/CollectionMaster.o obj/CollectionMgr.o obj/Communicate.o obj/Compute.o
obj/ComputeAngles.o obj/Comput
eBonds.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/ComputeFu
llDirect.o obj/ComputeHomePatch.o obj/ComputeHomePatches.o
obj/ComputeImpropers.o
obj/ComputeGlobal.o obj/Com
puteGlobalMsgs.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/Comp
utePatch.o obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o
obj/ComputeSphericalBC.o obj/Compu
teStir.o obj/ComputeTclBC.o obj/ConfigList.o obj/Controller.o obj/ccsinterface.o
obj/DataStream.o obj/DumpBen
ch.o obj/FreeEnergyAssert.o obj/FreeEnergyGroup.o obj/FreeEnergyLambda.o
obj/FreeEnergyLambdMgr.o obj/FreeEne
rgyParse.o obj/FreeEnergyRestrain.o obj/FreeEnergyRMgr.o obj/FreeEnergyVector.o
obj/GlobalMaster.o obj/Global
MasterServer.o obj/GlobalMasterTest.o obj/GlobalMasterIMD.o
obj/GlobalMasterTcl.o
obj/GlobalMasterSMD.o obj/G
lobalMasterFreeEnergy.o obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o
obj/GromacsTopFile.o obj/heap.o obj/Hom
ePatch.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/Nod
e.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/ProxyPat
ch.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 obj/dcdplugin.o moduleinit8860.o
-lmoduleNeighborLB
-lmodulecommlib /home/fu/p
rograms/NAMD_2.6b1_Source/charm-5.9/net-linux/bin/../lib/libmemory-default.o
/home/fu/programs/NAMD_2.6b1_Sou
rce/charm-5.9/net-linux/bin/../lib/libthreads-default.o -lck -lconv-cplus-y
-lconv-core -lconv-util -lm -lckq
t -ldl -lz -ltcl8.3 -ldl -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib
/usr/lib/gcc-lib/i586-suse-linux/3.3.4/../../../../i586-suse-linux/bin/ld:
cannot
find -ltcl8.3
collect2: ld returned 1 exit status
Fatal Error by charmc in directory
/home/fu/programs/NAMD_2.6b1_Source/Linux-i686-g++
Command g++ -Wl,--allow-multiple-definition -rdynamic
-L/home/dong/programs/tclnamd/lib -L/home/fu/tcl/lib
-L/home/dong/programs/fftwnamd/lib -L/home/fu/fftw/lib
-I/home/fu/programs/NAMD_2.6b1_Source/charm-5.9/net-l
inux/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -march=pentiumpro -ffast-math
-static -o namd2 -L/home/fu/progr
ams/NAMD_2.6b1_Source/charm-5.9/net-linux/bin/../lib
-I/home/fu/programs/NAMD_2.6b1_Source/charm-5.9/net-linu
x/bin/../include
/home/fu/programs/NAMD_2.6b1_Source/charm-5.9/net-linux/bin/../lib/libldb-rand.o
obj/buildin
fo.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/ComputeTclBC.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 obj/dcdplugin.o moduleinit8860.o -lmoduleNeighborLB
-lmodulecommlib
/home/fu/programs/NAMD_2.6b1_Source/charm-5.9/net-linux/bin/../lib/libmemory-defau
lt.o
/home/fu/programs/NAMD_2.6b1_Source/charm-5.9/net-linux/bin/../lib/libthreads-defa
ult.o -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -ldl-lz
-ltcl8.3 -ldl
-lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib returned error code 1
charmc exiting...
rm -f moduleinit8860.C moduleinit8860.o
make: *** [namd2] Error 1
Some people told me that NAMD was not compatible with Linux 2.6
kernel. Is this true? Are there any methods to solve this problem?
Thank you very much for your help.
Guoxing Fu
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