From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Mar 09 2005 - 13:33:35 CST
Hi again,
Things with compilation worked good, but now I have this message:
ld: cannot find -lpmpich
Fatal Error by charmc in directory
/home/bscl2/espinoza/namd/NAMD_2.5_Source/Linux-ia64-MPT-icc
Command icpc -i_dynamic -rdynamic
-L/home/bscl2/espinoza/namd/linuxia64/lib -L/home/bscl2/espinoza/tcl/lib
-L/home/bscl2/espinoza/namd/linuxia64/lib
-L/home/bscl2/espinoza/fftw-linux/lib
-I/home/bscl2/espinoza/namd/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux
-ia64-icc/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O2 -ftz -IPF_fma
-IPF_fltacc -IPF_flt_eval_method0 -IPF_fp_speculationfast -o namd2
-L/home/bscl2/espinoza/namd/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux
-ia64-icc/bin/../lib
-I/home/bscl2/espinoza/namd/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux
-ia64-icc/bin/../include
/home/bscl2/espinoza/namd/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-i
a64-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 moduleinit2917.o
-lmoduleNeighborLB -lmodulecommlib
/home/bscl2/espinoza/namd/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-i
a64-icc/bin/../lib/libmemory-default.o
/home/bscl2/espinoza/namd/charm-mpi-linux-ia64-ifort-mpt-icc/mpi-linux-i
a64-icc/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core
-lconv-util -lm -lckqt -lpmpich -lmpich -ldl -lz -ltcl8.3 -ldl -lsrfftw
-lsfftw -lm -lmoduleNeighborLB -lmodulecommlib returned error code 1
charmc exiting...
rm -f moduleinit2917.C moduleinit2917.o
make: *** [namd2] Error 1
I think this is more 'technical' question, but I don't know what to do
in this case, do you have a suggestion? Sorry for the inconveniences!
Michel
-----Original Message-----
From: Gengbin Zheng [mailto:gzheng_at_ks.uiuc.edu]
Sent: Tuesday, March 08, 2005 6:44 PM
To: Michel Espinoza-Fonseca
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: namd on Altix
yes, you need to recompile Charm in that case.
cd ~/namd/charm-mpi-linux-ia64-ifort-mpt-icc/
remove the directory mpi-linux-ia64-ifort-mpt-icc
and run:
./build charm++ mpi-linux-ia64 ifort mpt icc -O -DCMK_OPTIMIZE
Gengbin
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