Charm++ parallel programming system

[Dimar Jaime González Soto <dimar.gonzalez.soto AT gmail.com>]

I builded charm succesfully, but when I tried to make the program I got this error:

collect2: ld returned 1 exit status

Fatal Error by charmc in directory /home/hpcadmin/software/NAMD_2.9_Source/Linux-x86_64-g++

   Command /shared/openmpi-1.6.4/bin/mpicxx -m64 -fPIC -DCMK_GFORTRAN -rdynamic -fexpensive-optimizations -ffast-math -L.rootdir/tcl/lib -L.rootdir/fftw/lib -I.rootdir/charm-6.4.0/mpi-linux-x86_64/include -o namd2 -L.rootdir/charm-6.4.0/mpi-linux-x86_64/bin/../lib -I.rootdir/charm-6.4.0/mpi-linux-x86_64/bin/../include .rootdir/charm-6.4.0/mpi-linux-x86_64/bin/../lib/libldb-rand.o obj/buildinfo.o obj/ComputeMoa.o obj/ComputeMsmMsa.o obj/ComputeMsmSerial.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/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/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/colvarmodule.o obj/colvarparse.o obj/colvar.o obj/colvarvalue.o obj/colvarbias.o obj/colvarbias_abf.o obj/colvarbias_meta.o obj/colvaratoms.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/colvarproxy_namd.o obj/colvargrid.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/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/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/ParallelIOMgr.o obj/dcdplugin.o obj/jsplugin.o obj/namdbinplugin.o obj/pdbplugin.o obj/psfplugin.o moduleinit19974.o -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB .rootdir/charm-6.4.0/mpi-linux-x86_64/bin/../lib/libmemory-default.o .rootdir/charm-6.4.0/mpi-linux-x86_64/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl -ltcl8.5 -ldl -lpthread -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB -lm returned error code 1

charmc exiting...

rm -f moduleinit19974.C moduleinit19974.o

make: *** [namd2] Error 1

Can anyone help me please

2013/3/15 Dimar Jaime González Soto <dimar.gonzalez.soto AT gmail.com>

Hi, I need to build NAMD on a bladecenter IBM HPC. I tried to compile with the follow command:

 env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production

I get this:

 bin         lib_so                  README.ampi      src

build       LICENSE                 README.bigsim    tests

CHANGES     mpi-linux-amd64         README.cygwin    tmp

charm.spec  mpi-linux-x86_64        README.win       VERSION

contrib     mpi-linux-x86_64-ifort  relink.script

include     net-linux-gm            smart-build.log

lib         README                  smart-build.pl

[hpcadmin@head charm-6.4.0]$ env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production

Copying src/scripts/Makefile to mpi-linux-x86_64/tmp

Soft-linking over bin

Soft-linking over lib

Soft-linking over lib_so

Soft-linking over include

Soft-linking over tmp

Generating mpi-linux-x86_64/tmp/conv-mach-pre.sh

Performing '/usr/bin/gmake basics OPTS=-optimize -production QUIET= CONFIG_OPTS=--disable-controlpoint --disable-tracing --disable-tracing-commthread --disable-charmdebug --disable-replay --disable-error-checking --disable-stats ' in mpi-linux-x86_64/tmp

/usr/bin/gmake charmxi

gmake[1]: Entering directory `/home/hpcadmin/software/NAMD_2.9_Source/charm-6.4.0/mpi-linux-x86_64/tmp'

./configure --disable-controlpoint --disable-tracing --disable-tracing-commthread --disable-charmdebug --disable-replay --disable-error-checking --disable-stats

Error checking is disabled

Statistics collection is disabled

Charm tracing is disabled

Charm tracing communication thread is disabled

CharmDebug is disabled

Charm record/replay is disabled

CCS is enabled

Charm control point is disabled

Setting load balancing timer type as 'double'

checking machine name... mpi-linux-x86_64

checking "cp command as"... cp -p

checking "C++ compiler as"... "mpicxx   -DCMK_GFORTRAN     -optimize -production  "

checking "whether C++ compiler works"... "no"

Cannot compile C++ programs with mpicxx   -DCMK_GFORTRAN  

 (check your charm++ version)

*** Please find detailed output in charmconfig.out ***

gmake[1]: *** [conv-autoconfig.h] Error 1

gmake[1]: Leaving directory `/home/hpcadmin/software/NAMD_2.9_Source/charm-6.4.0/mpi-linux-x86_64/tmp'

gmake: *** [headers] Error 2

-------------------------------------------------

Charm++ NOT BUILT. Either cd into mpi-linux-x86_64/tmp and try

Any help is wellcome

--
Atte.

Dimar González Soto

Ingeniero Civil en Informática

Universidad Austral de Chile

F:+056-63-293858
www.australomics.cl

--
Atte.

Dimar González Soto

Ingeniero Civil en Informática

Universidad Austral de Chile

F:+056-63-293858
www.australomics.cl