icc compilation problem

From: Sean Michael Whipkey (smw4s_at_unix.mail.virginia.edu)
Date: Thu Jul 01 2004 - 16:19:55 CDT

I'm trying to install namd using the Intel compilers on the head node of our
Linux cluster.

I run the make.

At the end, I get this error (apologizing in advance for line wrap):

charmc> ----------- Module dependency search ------------
charmc> ----------- Module dependency search complete ------------
Adding registration for module NeighborLB
Adding registration for module commlib
charmc: Executing icpc -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -Iinc -Isrc -O2 -march=pentiumpro -mcpu=pentium4 -ip -fno-rtti -c moduleinit.C -o moduleinit.o
charmc: Executing icpc -i_dynamic -O2 -march=pentiumpro -mcpu=pentium4 -ip -fno-rtti -L/usr/local/tcl/linux/lib -L/root/tcl-linux/lib -L/usr/local/fftw/linux/lib -L/root/fftw-linux/lib
-L/usr/local/plugins/LINUX -L/usr/local/plugins/LINUX/molfile -L/root/plugins/LINUX -L/root/plugins/LINUX/molfile -I/usr/local/namd/charm/net-linux-icc/include -o namd2
-L/usr/local/namd/charm/net-linux-icc/bin/../lib -I/usr/local/namd/charm/net-linux-icc/bin/../include /usr/local/namd/charm/net-linux-icc/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 /usr/local/namd/charm/net-linux-icc/bin/../lib/libmemory-default.o /usr/local/namd/charm/net-linux-icc/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
/usr/local/tcl/linux/lib/libtcl8.3.a(tclUnixPipe.o)(.text+0xe0): In function `TclpCreateTempFile':
: the use of `tmpnam' is dangerous, better use `mkstemp'
/usr/local/tcl/linux/lib/libtcl8.3.a(tclBinary.o)(.text+0xbe4): In function `Tcl_BinaryObjCmd':
: undefined reference to `__ctype_b'
/usr/local/tcl/linux/lib/libtcl8.3.a(tclBinary.o)(.text+0xc5d): In function `Tcl_BinaryObjCmd':
: undefined reference to `__ctype_b'
/usr/local/tcl/linux/lib/libtcl8.3.a(tclBinary.o)(.text+0x1617): In function `GetFormatSpec':
: undefined reference to `__ctype_b'
/usr/local/tcl/linux/lib/libtcl8.3.a(tclCmdAH.o)(.text+0x185): In function `Tcl_CaseObjCmd':
: undefined reference to `__ctype_b'
/usr/local/tcl/linux/lib/libtcl8.3.a(tclCmdAH.o)(.text+0x22f5): In function `Tcl_FormatObjCmd':
: undefined reference to `__ctype_b'
/usr/local/tcl/linux/lib/libtcl8.3.a(tclCmdAH.o)(.text+0x23f8): more undefined references to `__ctype_b' follow
Fatal Error by charmc in directory /usr/local/namd/Linux-i686-icc
Command icpc -i_dynamic -O2 -march=pentiumpro -mcpu=pentium4 -ip -fno-rtti -L/usr/local/tcl/linux/lib -L/root/tcl-linux/lib -L/usr/local/fftw/linux/lib -L/root/fftw-linux/lib -L/usr/local/plugins/LINUX
-L/usr/local/plugins/LINUX/molfile -L/root/plugins/LINUX -L/root/plugins/LINUX/molfile -I/usr/local/namd/charm/net-linux-icc/include -o namd2 -L/usr/local/namd/charm/net-linux-icc/bin/../lib
-I/usr/local/namd/charm/net-linux-icc/bin/../include /usr/local/namd/charm/net-linux-icc/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 /usr/local/namd/charm/net-linux-icc/bin/../lib/libmemory-default.o /usr/local/namd/charm/net-linux-icc/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

I've been fighting this all day. We're not working on clustering
it right now; it just has to work on the head node.

Any help?

Thanks!

Sean 

-- 
Sean Michael Whipkey, Systems Engineer - UVA SEAS Information
Technology Office 111 Small Hall - 434.982.4561 - smw4s_at_virginia.edu

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