Charm++ parallel programming system

[黄须啟 <huangxuqi14 AT mails.ucas.ac.cn>]

Dear Professor:
        When i set up build directory and compile,there is still a error here.
charmc: Executing mpicxx -m64 -fPIC -DCMK_GFORTRAN -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -Iinc -Isrc -fexpensive-optimizations -ffast-math -U_FORTIFY_SOURCE -fno-stack-protector -c moduleinit42411.C -o moduleinit42411.o
charmc> All libraries are: -L.rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../lib -I.rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../include .rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../lib/libldb-rand.o obj/buildinfo.o obj/ComputeMoa.o obj/ComputeMsm.o obj/ComputeMsmMsa.o obj/ComputeMsmSerial.o obj/ComputeFmmSerial.o obj/msm.o obj/msm_longrng.o obj/msm_longrng_sprec.o obj/msm_setup.o obj/msm_shortrng.o obj/msm_shortrng_sprec.o obj/wkfutils.o obj/common.o obj/dcdlib.o obj/erf.o obj/fitrms.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/ComputeAniso.o obj/ComputeBonds.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o obj/ComputeCrossterms.o obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.o obj/ComputeEwald.o obj/ComputeExt.o obj/ComputeGBISser.o obj/ComputeGBIS.o obj/ComputeGromacsPair.o obj/ComputeLCPO.o obj/ComputeFullDirect.o obj/ComputeHomePatch.o obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o obj/ComputeGlobalMsgs.o obj/ComputeGridForce.o obj/ComputeMap.o obj/ComputeMgr.o obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o obj/ComputeNonbondedFEP.o obj/ComputeNonbondedGo.o obj/ComputeNonbondedTI.o obj/ComputeNonbondedLES.o obj/ComputeNonbondedPProf.o obj/ComputeNonbondedTabEnergies.o obj/ComputeNonbondedCUDA.o obj/ComputeNonbondedCUDAExcl.o obj/ComputeNonbondedMIC.o obj/ComputeNonbondedMICKernel.o obj/ComputePatch.o obj/ComputePatchPair.o obj/ComputePme.o obj/OptPme.o obj/OptPmeRealSpace.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o obj/ComputeStir.o obj/ComputeTclBC.o obj/ComputeThole.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/GlobalMasterTMD.o obj/Matrix4Symmetry.o obj/GlobalMasterSymmetry.o obj/GlobalMasterFreeEnergy.o obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o obj/colvar.o obj/colvaratoms.o obj/colvarbias.o obj/colvarbias_abf.o obj/colvarbias_alb.o obj/colvarbias_meta.o obj/colvarbias_restraint.o obj/colvarcomp.o obj/colvarcomp_angles.o obj/colvarcomp_coordnums.o obj/colvarcomp_distances.o obj/colvarcomp_protein.o obj/colvarcomp_rotations.o obj/colvargrid.o obj/colvarmodule.o obj/colvarparse.o obj/colvarproxy_namd.o obj/colvarscript.o obj/colvartypes.o obj/colvarvalue.o obj/GridForceGrid.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/MGridforceParams.o obj/MStream.o obj/MigrateAtomsMsg.o obj/Molecule.o obj/Molecule2.o obj/GoMolecule.o obj/NamdCentLB.o obj/NamdNborLB.o obj/NamdHybridLB.o obj/NamdDummyLB.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/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/RefineTorusLB.o obj/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o obj/SimParameters.o obj/SortAtoms.o obj/Sync.o obj/TclCommands.o obj/TorusLB.o obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o obj/CompressPsf.o obj/PluginIOMgr.o obj/DataExchanger.o obj/ParallelIOMgr.o obj/dcdplugin.o obj/jsplugin.o obj/namdbinplugin.o obj/pdbplugin.o obj/psfplugin.o moduleinit42411.o -lmoduleCkMulticast -lmoduleGreedyLB -lmoduleRefineLB -lmoduleHybridLB -lmoduleNeighborLB .rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../lib/libmemory-default.o .rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../lib/libthreads-default.o -lckmain -lck -lconv-cplus-y -lconv-core -lconv-util -lconv-partition -lckqt -ldl -ltcl8.5 -ldl -lpthread -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB -lmoduleCkMulticast -lm
charmc: Executing mpicxx -m64 -fPIC -DCMK_GFORTRAN -rdynamic -fexpensive-optimizations -ffast-math -L/lustre/researcher/huangxuqi/NAMD_2.10b2_Source/tcl-threaded/lib -L.rootdir/fftw/lib -I.rootdir/charm-6.6.1/mpi-linux-x86_64/include -o namd2 -L.rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../lib -I.rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../include .rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../lib/libldb-rand.o obj/buildinfo.o obj/ComputeMoa.o obj/ComputeMsm.o obj/ComputeMsmMsa.o obj/ComputeMsmSerial.o obj/ComputeFmmSerial.o obj/msm.o obj/msm_longrng.o obj/msm_longrng_sprec.o obj/msm_setup.o obj/msm_shortrng.o obj/msm_shortrng_sprec.o obj/wkfutils.o obj/common.o obj/dcdlib.o obj/erf.o obj/fitrms.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/ComputeAniso.o obj/ComputeBonds.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o obj/ComputeCrossterms.o obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.o obj/ComputeEwald.o obj/ComputeExt.o obj/ComputeGBISser.o obj/ComputeGBIS.o obj/ComputeGromacsPair.o obj/ComputeLCPO.o obj/ComputeFullDirect.o obj/ComputeHomePatch.o obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o obj/ComputeGlobalMsgs.o obj/ComputeGridForce.o obj/ComputeMap.o obj/ComputeMgr.o obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o obj/ComputeNonbondedFEP.o obj/ComputeNonbondedGo.o obj/ComputeNonbondedTI.o obj/ComputeNonbondedLES.o obj/ComputeNonbondedPProf.o obj/ComputeNonbondedTabEnergies.o obj/ComputeNonbondedCUDA.o obj/ComputeNonbondedCUDAExcl.o obj/ComputeNonbondedMIC.o obj/ComputeNonbondedMICKernel.o obj/ComputePatch.o obj/ComputePatchPair.o obj/ComputePme.o obj/OptPme.o obj/OptPmeRealSpace.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o obj/ComputeStir.o obj/ComputeTclBC.o obj/ComputeThole.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/GlobalMasterTMD.o obj/Matrix4Symmetry.o obj/GlobalMasterSymmetry.o obj/GlobalMasterFreeEnergy.o obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o obj/colvar.o obj/colvaratoms.o obj/colvarbias.o obj/colvarbias_abf.o obj/colvarbias_alb.o obj/colvarbias_meta.o obj/colvarbias_restraint.o obj/colvarcomp.o obj/colvarcomp_angles.o obj/colvarcomp_coordnums.o obj/colvarcomp_distances.o obj/colvarcomp_protein.o obj/colvarcomp_rotations.o obj/colvargrid.o obj/colvarmodule.o obj/colvarparse.o obj/colvarproxy_namd.o obj/colvarscript.o obj/colvartypes.o obj/colvarvalue.o obj/GridForceGrid.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/MGridforceParams.o obj/MStream.o obj/MigrateAtomsMsg.o obj/Molecule.o obj/Molecule2.o obj/GoMolecule.o obj/NamdCentLB.o obj/NamdNborLB.o obj/NamdHybridLB.o obj/NamdDummyLB.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/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/RefineTorusLB.o obj/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o obj/SimParameters.o obj/SortAtoms.o obj/Sync.o obj/TclCommands.o obj/TorusLB.o obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o obj/CompressPsf.o obj/PluginIOMgr.o obj/DataExchanger.o obj/ParallelIOMgr.o obj/dcdplugin.o obj/jsplugin.o obj/namdbinplugin.o obj/pdbplugin.o obj/psfplugin.o moduleinit42411.o -lmoduleCkMulticast -lmoduleGreedyLB -lmoduleRefineLB -lmoduleHybridLB -lmoduleNeighborLB .rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../lib/libmemory-default.o .rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../lib/libthreads-default.o -lckmain -lck -lconv-cplus-y -lconv-core -lconv-util -lconv-partition -lckqt -ldl -ltcl8.5 -ldl -lpthread -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB -lmoduleCkMulticast -lm
/lustre/researcher/huangxuqi/NAMD_2.10b2_Source/tcl-threaded/lib/libtcl8.5.a: could not read symbols: No more archived files
collect2: ld returned 1 exit status
Fatal Error by charmc in directory /lustre/researcher/huangxuqi/NAMD_2.10b2_Source/Linux-x86_64-g++
   Command mpicxx -m64 -fPIC -DCMK_GFORTRAN -rdynamic -fexpensive-optimizations -ffast-math -L/lustre/researcher/huangxuqi/NAMD_2.10b2_Source/tcl-threaded/lib -L.rootdir/fftw/lib -I.rootdir/charm-6.6.1/mpi-linux-x86_64/include -o namd2 -L.rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../lib -I.rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../include .rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../lib/libldb-rand.o obj/buildinfo.o obj/ComputeMoa.o obj/ComputeMsm.o obj/ComputeMsmMsa.o obj/ComputeMsmSerial.o obj/ComputeFmmSerial.o obj/msm.o obj/msm_longrng.o obj/msm_longrng_sprec.o obj/msm_setup.o obj/msm_shortrng.o obj/msm_shortrng_sprec.o obj/wkfutils.o obj/common.o obj/dcdlib.o obj/erf.o obj/fitrms.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/ComputeAniso.o obj/ComputeBonds.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o obj/ComputeCrossterms.o obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.o obj/ComputeEwald.o obj/ComputeExt.o obj/ComputeGBISser.o obj/ComputeGBIS.o obj/ComputeGromacsPair.o obj/ComputeLCPO.o obj/ComputeFullDirect.o obj/ComputeHomePatch.o obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o obj/ComputeGlobalMsgs.o obj/ComputeGridForce.o obj/ComputeMap.o obj/ComputeMgr.o obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o obj/ComputeNonbondedFEP.o obj/ComputeNonbondedGo.o obj/ComputeNonbondedTI.o obj/ComputeNonbondedLES.o obj/ComputeNonbondedPProf.o obj/ComputeNonbondedTabEnergies.o obj/ComputeNonbondedCUDA.o obj/ComputeNonbondedCUDAExcl.o obj/ComputeNonbondedMIC.o obj/ComputeNonbondedMICKernel.o obj/ComputePatch.o obj/ComputePatchPair.o obj/ComputePme.o obj/OptPme.o obj/OptPmeRealSpace.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o obj/ComputeStir.o obj/ComputeTclBC.o obj/ComputeThole.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/GlobalMasterTMD.o obj/Matrix4Symmetry.o obj/GlobalMasterSymmetry.o obj/GlobalMasterFreeEnergy.o obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o obj/colvar.o obj/colvaratoms.o obj/colvarbias.o obj/colvarbias_abf.o obj/colvarbias_alb.o obj/colvarbias_meta.o obj/colvarbias_restraint.o obj/colvarcomp.o obj/colvarcomp_angles.o obj/colvarcomp_coordnums.o obj/colvarcomp_distances.o obj/colvarcomp_protein.o obj/colvarcomp_rotations.o obj/colvargrid.o obj/colvarmodule.o obj/colvarparse.o obj/colvarproxy_namd.o obj/colvarscript.o obj/colvartypes.o obj/colvarvalue.o obj/GridForceGrid.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/MGridforceParams.o obj/MStream.o obj/MigrateAtomsMsg.o obj/Molecule.o obj/Molecule2.o obj/GoMolecule.o obj/NamdCentLB.o obj/NamdNborLB.o obj/NamdHybridLB.o obj/NamdDummyLB.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/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/RefineTorusLB.o obj/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o obj/SimParameters.o obj/SortAtoms.o obj/Sync.o obj/TclCommands.o obj/TorusLB.o obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o obj/CompressPsf.o obj/PluginIOMgr.o obj/DataExchanger.o obj/ParallelIOMgr.o obj/dcdplugin.o obj/jsplugin.o obj/namdbinplugin.o obj/pdbplugin.o obj/psfplugin.o moduleinit42411.o -lmoduleCkMulticast -lmoduleGreedyLB -lmoduleRefineLB -lmoduleHybridLB -lmoduleNeighborLB .rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../lib/libmemory-default.o .rootdir/charm-6.6.1/mpi-linux-x86_64/bin/../lib/libthreads-default.o -lckmain -lck -lconv-cplus-y -lconv-core -lconv-util -lconv-partition -lckqt -ldl -ltcl8.5 -ldl -lpthread -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB -lmoduleCkMulticast -lm returned error code 1
charmc exiting...
rm -f moduleinit42411.C moduleinit42411.o
make: *** [namd2] Error 1
    how can i solve this problem, if you can detail procedure i will be appreciate.
    I'm looking forward to your reply!
    sincerely
    huangxuqi

在2015-11-13 13:33:58，黄须啟huangxuqi14 AT mails.ucas.ac.cn写道：

Hi,

Actually, the error message is very clear, SEEK_XXX have already been defined in both

mpi.h and stdio.h.

you need to add

-DMPICH_IGNORE_CXX_SEEK

to your command line.

 

Huiqun Zhou

@Earth Sciences, Nanjing University, China

 

 

------------------ Original ------------------

From:  "黄须啟"<huangxuqi14 AT mails.ucas.ac.cn>;

Date:  Fri, Nov 13, 2015 10:13 AM

To:  "Phil Miller"<mille121 AT illinois.edu>;

Cc:  "Charm Mailing List"<charm AT cs.illinois.edu>;

Subject:  Re: [charm] For problems concerning compiling NAMD

 

Dear Professor:
        The following concrete content is what you need:
       RefineSwapLB.o NeighborLB.o OrbLB.o BlockLB.o GreedyCommLB.o manager.o
ar: creating ../lib/libmoduleCommonLBs.a
/usr/bin/gmake -C libs/ck-libs/completion
gmake[1]: Entering directory `/lustre/researcher/huangxuqi/NAMD_2.10b2_Source/charm-6.6.1/mpi-linux-x86_64/tmp/libs/ck-libs/completion'
../../../../bin/charmc -optimize -production   -c completion.ci
../../../../bin/charmc -optimize -production   -I../../../../tmp -o completion.o completion.C
../../../../bin/charmc -optimize -production   -o ../../../../lib/libmodulecompletion.a completion.o
ar: creating ../../../../lib/libmodulecompletion.a
/bin/cp completion.decl.h ../../../../include
/bin/cp completion.def.h ../../../../include
/bin/cp completion.h ../../../../include
gmake[1]: Leaving directory `/lustre/researcher/huangxuqi/NAMD_2.10b2_Source/charm-6.6.1/mpi-linux-x86_64/tmp/libs/ck-libs/completion'
../bin/charmc -seq  -DCMK_NOT_USE_CONVERSE=1 -o sockRoutines-seq.o sockRoutines.c
../bin/charmc  -optimize -production   -I.   -c -o trace-common.o trace-common.C
../bin/charmc  -optimize -production   -I.   -c -o tracec.o tracec.C
../bin/charmc  -optimize -production   -I.   -c -o tracef.o tracef.C
../bin/charmc  -optimize -production   -I.   -c -o init.o init.C
../bin/charmc  -optimize -production   -I.   -c -o register.o register.C
../bin/charmc  -optimize -production   -I.   -c -o qd.o qd.C
../bin/charmc  -optimize -production   -I.   -c -o ck.o ck.C
../bin/charmc  -optimize -production   -I.   -c -o msgalloc.o msgalloc.C
../bin/charmc  -optimize -production   -I.   -c -o ckfutures.o ckfutures.C
../bin/charmc  -optimize -production   -I.   -c -o ckIgetControl.o ckIgetControl.C
../bin/charmc  -optimize -production   -I.   -c -o debug-message.o debug-message.C
../bin/charmc  -optimize -production   -I.   -c -o debug-charm.o debug-charm.C
../bin/charmc  -optimize -production   -I.   -c -o ckcallback.o ckcallback.C
../bin/charmc  -optimize -production   -I.   -c -o cklocation.o cklocation.C
../bin/charmc  -optimize -production   -I.   -c -o ckarray.o ckarray.C
../bin/charmc  -optimize -production   -I.   -c -o ckreduction.o ckreduction.C
../bin/charmc  -optimize -production   -I.   -c -o ckarrayreductionmgr.o ckarrayreductionmgr.C
../bin/charmc  -optimize -production   -I.   -c -o tempo.o tempo.C
../bin/charmc  -optimize -production   -I.   -c -o waitqd.o waitqd.C
../bin/charmc  -optimize -production   -I.   -c -o LBDatabase.o LBDatabase.C
../bin/charmc  -optimize -production   -I.   -c -o MetaBalancer.o MetaBalancer.C
../bin/charmc  -optimize -production   -I.   -c -o lbdb.o lbdb.C
../bin/charmc  -optimize -production   -I.   -c -o lbdbf.o lbdbf.C
../bin/charmc  -optimize -production   -I.   -c -o ckobjQ.o ckobjQ.C
../bin/charmc  -optimize -production   -I.   -c -o LBAgent.o LBAgent.C
../bin/charmc  -optimize -production   -I.   -c -o LBProfit.o LBProfit.C
../bin/charmc  -optimize -production   -I.   -c -o ckcheckpoint.o ckcheckpoint.C
../bin/charmc  -optimize -production   -I.   -c -o ckmemcheckpoint.o ckmemcheckpoint.C
../bin/charmc  -optimize -production   -I.   -c -o ckevacuation.o ckevacuation.C
../bin/charmc  -optimize -production   -I.   -c -o ckmessagelogging.o ckmessagelogging.C
../bin/charmc  -optimize -production   -I.   -c -o ckcausalmlog.o ckcausalmlog.C
../bin/charmc  -optimize -production   -I.   -c -o ckobjid.o ckobjid.C
../bin/charmc  -optimize -production   -I.   -c -o LBDBManager.o LBDBManager.C
../bin/charmc  -optimize -production   -I.   -c -o LBComm.o LBComm.C
../bin/charmc  -optimize -production   -I.   -c -o LBObj.o LBObj.C
../bin/charmc  -optimize -production   -I.   -c -o LBMachineUtil.o LBMachineUtil.C
../bin/charmc  -optimize -production   -I.   -c -o CentralPredictor.o CentralPredictor.C
../bin/charmc  -optimize -production   -I.   -c -o BaseLB.o BaseLB.C
../bin/charmc  -optimize -production   -I.   -c -o CentralLB.o CentralLB.C
../bin/charmc  -optimize -production   -I.   -c -o HybridBaseLB.o HybridBaseLB.C
../bin/charmc  -optimize -production   -I.   -c -o NborBaseLB.o NborBaseLB.C
../bin/charmc  -optimize -production   -I.   -c -o DistBaseLB.o DistBaseLB.C
../bin/charmc  -optimize -production   -I.   -c -o ckgraphTemp.o ckgraphTemp.C
../bin/charmc  -optimize -production   -I.   -c -o ckgraph.o ckgraph.C
../bin/charmc  -optimize -production   -I.   -c -o LButil.o LButil.C
../bin/charmc  -optimize -production   -I.   -c -o RefinerTemp.o RefinerTemp.C
../bin/charmc  -optimize -production   -I.   -c -o Refiner.o Refiner.C
../bin/charmc  -optimize -production   -I.   -c -o RefinerApprox.o RefinerApprox.C
../bin/charmc  -optimize -production   -I.   -c -o RefinerComm.o RefinerComm.C
../bin/charmc  -optimize -production   -I.   -c -o bitvecset.o bitvecset.c
../bin/charmc  -optimize -production   -I.   -c -o ckset.o ckset.C
../bin/charmc  -optimize -production   -I.   -c -o ckheap.o ckheap.C
../bin/charmc  -optimize -production   -I.   -c -o CommLBHeap.o CommLBHeap.C
../bin/charmc  -optimize -production   -I.   -c -o NullLB.o NullLB.C
../bin/charmc  -optimize -production   -I.   -c -o LBSimulation.o LBSimulation.C
../bin/charmc  -optimize -production   -I.   -c -o ComlibModuleInterface.o ComlibModuleInterface.C
../bin/charmc  -optimize -production   -I.   -c -o modifyScheduler.o modifyScheduler.C
../bin/charmc  -optimize -production   -I.   -c -o charmProjections.o charmProjections.C
../bin/charmc  -optimize -production   -I.   -c -o cktiming.o cktiming.C
../bin/charmc  -optimize -production   -I.   -c -o ckbitvector.o ckbitvector.C
../bin/charmc  -optimize -production   -I.   -c -o pathHistory.o pathHistory.C
../bin/charmc  -optimize -production   -I.   -c -o controlPoints.o controlPoints.C
../bin/charmc  -optimize -production   -I.   -c -o arrayRedistributor.o arrayRedistributor.C
../bin/charmc  -optimize -production   -I.   -c -o cp_effects.o cp_effects.C
../bin/charmc  -optimize -production   -I.   -c -o trace-controlPoints.o trace-controlPoints.C
../bin/charmc  -optimize -production   -I.   -c -o mpi-interoperate.o mpi-interoperate.C
In file included from /opt/intel/impi/4.1.1.036/intel64/include/mpi.h:1279,
                 from mpi-interoperate.h:9,
                 from mpi-interoperate.C:3:
/opt/intel/impi/4.1.1.036/intel64/include/mpicxx.h:95:2: error: #error "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"
/opt/intel/impi/4.1.1.036/intel64/include/mpicxx.h:99:2: error: #error "SEEK_CUR is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"
/opt/intel/impi/4.1.1.036/intel64/include/mpicxx.h:104:2: error: #error "SEEK_END is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"
Fatal Error by charmc in directory /lustre/researcher/huangxuqi/NAMD_2.10b2_Source/charm-6.6.1/mpi-linux-x86_64/tmp
   Command mpicxx -m64 -fPIC -DCMK_GFORTRAN -I../bin/../include -D__CHARMC__=1 -I. -O2 -U_FORTIFY_SOURCE -fno-stack-protector -c mpi-interoperate.C -o mpi-interoperate.o returned error code 1
charmc exiting...
gmake: *** [mpi-interoperate.o] Error 1

   I'm not good at compiling charm ,if you can teel me the detailed procedure, i will be very appreciate of you .
   I'm looking forward to your reply!
   sincerely
   huangxuqi

在2015-11-13 00:21:31,黄须啟<huangxuqi14 AT mails.ucas.ac.cn>写道：
> Hi Huangxuqi,
>
> We'll need to see a few lines of output preceding that message, to see
> the actual compilation error.
>
> Also, it looks like you're compiling an older version of NAMD. 2.10
> was released quite some time ago, and a beta for 2.11 was either just
> posted, or will be shortly. For reasons of performance and
> correctness, users are generally recommended to use the most recent
> release.
>
> Phil
>
> On Thu, Nov 12, 2015 at 7:01 AM, 黄须啟 <huangxuqi14 AT mails.ucas.ac.cn> wrote:
> >
> >
> > Dear Professor:
> >
> >        There is something wrong with my comiling NAMD progress for using the
> > following command :
> >
> >         tar xvf NAMD_2.10b2_Source.tar.gz
> >
> >         cd NAMD_2.10b2_Source
> >
> >         tar xf charm-6.6.1.tar
> >
> >         cd charm-6.6.1
> >
> >       env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production
> >
> >     it shows one fatal error:
> >
> >     Fatal Error by charmc in directory
> > /lustre/researcher/huangxuqi/NAMD_2.10b2_Source/charm-6.6.1/mpi-linux-x86_64/tmp
> >     Command mpicxx -m64 -fPIC -DCMK_GFORTRAN -I../bin/../include
> > -D__CHARMC__=1 -I. -O2 -U_FORTIFY_SOURCE -fno-stack-protector -c
> > mpi-interoperate.C -o mpi-interoperate.o returned error code 1
> > charmc exiting...
> > gmake: *** [mpi-interoperate.o] Error 1
> >
> >     I'm looking forward to your reply!
> >
> >     sincerely
> >
> >     huangxuqi
> >
> >
> >
> >
> >
> >
> >