[mvapich-discuss] Can't charm++ with mpicxx
Bjoern Olausson
bjoern.olausson at biochemtech.uni-halle.de
Mon Aug 24 09:04:22 EDT 2009
On Thursday 20 August 2009 19:57:39 Emilio Pasquale Mancini wrote:
> Hi Bjoern,
>
> On 08/20/2009 09:25 AM, Bjoern Olausson wrote:
> > On Tuesday 18 August 2009 01:13:12 Emilio Pasquale Mancini wrote:
> >> Hi Bjoern,
> >> Take a look at:
> >> http://mail.cse.ohio-state.edu/pipermail/mvapich-discuss/2009-March/0021
> >>83. html
> >
> > Mmmh, actually I have OFED 1.3.2 installed (Scientific Linux SL release
> > 5.3 (Boron))
> >
> > But it seems as if removing -DXRC from CFLAGS made it at least compile.
> >
> > Anyway, this does not help compiling charm wit any version of mvapich I
> > compiled on my own.
> >
> >> and
> >> http://mail.cse.ohio-state.edu/pipermail/mvapich-discuss/2006-June/00018
> >>9.h tml
> >
> > #define CMK_MALLOC_USE_GNU_MALLOC 0
> > #define CMK_MALLOC_USE_OS_BUILTIN 1
> >
> > is default in charm 2.1.2
>
> You mean 6.1.2?
>
Yes,sorry for the typo.
> > This problem remains unsolved (with all versions I compiled, including
> > v1.1.
> >
> >> Let me known if this helps
> >
> > No, sorry, didn't help, except that I am now able to compile mvapich
> > v1.1.
>
> I reproduced your error, it seems to be an issue of icc compiler. Using
> gcc it works fine.
> With icc you should disable optimizations, I used the following comman
> line:
>
> ./build charm++ mpi-linux-x86_64-mvapich icc -O -I<path to mpi>/include
> -L<path to mpi>/lib --no-build-shared
>
> Then I resume the charm++ compilation process for the mailinglist:
>
> cd src/arch
> cp -r mpi-linux-x86_64 mpi-linux-x86_64-mvapich
> cd mpi-linux-x86_64-mvapich
>
> Edit conv-mach.h and change (not necessary in Charm++ 6.1.2):
>
> #define CMK_MALLOC_USE_GNU_MALLOC 1
> #define CMK_MALLOC_USE_OS_BUILTIN 0
>
> to:
>
> #define CMK_MALLOC_USE_GNU_MALLOC 0
> #define CMK_MALLOC_USE_OS_BUILTIN 1
>
> Make sure the MVAPICH mpicc and mpiCC are first in your path. Otherwise,
> add the full path to the mpicc and mpiCC commands in conv_mach.sh. If
> the “build” command does not recognize the mpiCC compiler you can to
> edit the conv-mach.sh file changing the line
>
> MPICXX_DEF=mpicxx
>
> to:
>
> #MPICXX_DEF=mpiCC
> MPICXX_DEF=mpicxx
>
>
> cd ../../..
> ./build charm++ mpi-linux-x86_64-mvapich --no-build-shared
>
> or for icc compiler:
>
> ./build charm++ mpi-linux-x86_64-mvapich icc -O -I<path to mpi>/include
> -L<path to mpi>/lib --no-build-shared
>
Okay, now this made charm++ compile, but I can't produce any binary with
charm++. Even the megatest binary fails to build.
The error I get when compiling megatest is the following:
------------------------------------------------------------------------------
Fatal Error by charmc in directory
/home/blub/src/NAMD_2.7b1_Source/charm-6.1.2/mpi-linux-x86_64-mvapich1_1-
icc/tests/charm++/megatest
Command icpc -shared-intel -xO -rdynamic -o pgm -L../../../bin/../lib -
I../../../bin/../include ../../../bin/../lib/libldb-rand.o megatest.o
groupring.o nodering.o varsizetest.o varraystest.o groupcast.o nodecast.o
synctest.o fib.o arrayring.o tempotest.o packtest.o queens.o migration.o
marshall.o priomsg.o priotest.o rotest.o statistics.o templates.o inherit.o
reduction.o bitvector.o immediatering.o callback.o moduleinit5242.o
../../../bin/../lib/libmemory-default.o ../../../bin/../lib/libthreads-
default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl -lm returned
error code 1
charmc exiting...
make: *** [pgm] Error 1
------------------------------------------------------------------------------
For NAMD the error is the following:
------------------------------------------------------------------------------
Fatal Error by charmc in directory /home/blub/src/NAMD_2.7b1_Source/Linux-
x86_64-icc.mpi-linux-x86_64-mvapich1_1-icc
Command icpc -shared-intel -xO -rdynamic -L.rootdir/tcl/lib -
L.rootdir/fftw/lib -I/home/blub/src/NAMD_2.7b1_Source/charm-6.1.2/mpi-linux-
x86_64-mvapich1_1-icc/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -i-static -O2 -ip -
fno-rtti -o namd2 -L/home/blub/src/NAMD_2.7b1_Source/charm-6.1.2/mpi-linux-
x86_64-mvapich1_1-icc/bin/../lib -
I/home/blub/src/NAMD_2.7b1_Source/charm-6.1.2/mpi-linux-x86_64-mvapich1_1-
icc/bin/../include /home/blub/src/NAMD_2.7b1_Source/charm-6.1.2/mpi-linux-
x86_64-mvapich1_1-icc/bin/../lib/libldb-rand.o obj/buildinfo.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/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/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/ComputeNonbondedLES.o
obj/ComputeNonbondedPProf.o obj/ComputeNonbondedCUDA.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/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/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/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/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/RefineTorusLB.o obj/ScriptTcl.o
obj/Sequencer.o obj/Set.o obj/Settle.o obj/SimParameters.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/AtomsDisInfo.o
obj/FileIO.o obj/dcdplugin.o obj/jsplugin.o obj/pdbplugin.o obj/psfplugin.o
moduleinit4100.o -lmoduleNeighborLB -lmodulecommlib
/home/blub/src/NAMD_2.7b1_Source/charm-6.1.2/mpi-linux-x86_64-mvapich1_1-
icc/bin/../lib/libmemory-default.o
/home/blub/src/NAMD_2.7b1_Source/charm-6.1.2/mpi-linux-x86_64-mvapich1_1-
icc/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-
util -lckqt -ldl -ltcl8.3 -ldl -lsrfftw -lsfftw -lm -lmoduleNeighborLB -
lmodulecommlib -lm returned error code 1
charmc exiting...
rm -f moduleinit4100.C moduleinit4100.o
make: *** [namd2] Error 1
------------------------------------------------------------------------------
Please find the complete logs here:
http://daten-transport.de/ansicht.php?id=zEuKTtBxBPf8
Direct Link:
http://daten-transport.de/download.php?id=zEuKTtBxBPf8&dateinummer=4419
Thanks for your help
kind regards
Bjoern
--
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942
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