Re: namd on Altix

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Wed Mar 09 2005 - 13:36:21 CST

again, like I said, you need to compile charm like

./build charm++ mpi-linux-ia64 ifort mpt icc -O -DCMK_OPTIMIZE

and you did mpi-linux-ia64 with icc only.

Gengbin

Michel Espinoza-Fonseca wrote:

>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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