Re: AW: Compilation of NAMD from Source (Cray XC40)

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Oct 13 2015 - 17:00:08 CDT

This is the actual error:

/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libhugetlbfs.a(hugeutils.o):
In function `gethugepagesize':
/usr/src/packages/BUILD/cray-libhugetlbfs-2.16/hugeutils.c:871: multiple definition of `gethugepagesize'
.rootdir/charm-6.6.1/gni-crayxc/bin/../lib/cray_tlbhack.o:cray_tlbhack.c:(.text+0x0): first defined here

We've just encountered this recently ourselves, see
https://charm.cs.illinois.edu/redmine/issues/841

The fix is to remove the following lines from src/scripts/charmc:

if [ -z "$NATIVE" -a -n "$UGNI_CFLAGS" ]
then
     linkopt=`env | grep "HUGETLB[0-9]*[MKG]_POST_LINK_OPTS" 2> /dev/null`
     test -z "$linkopt" && POST_LIBRARIES=`AddList $POST_LIBRARIES $CHARMLIB/cray_tlbhack.o`
fi

or you can define an environment variable that trips the test:

export HUGETLB0M_POST_LINK_OPTS=DUMMY

Jim

On Tue, 13 Oct 2015, Richter, Stefan wrote:

> Thanks, i still get an error, see attached log file.

Stefan

________________________________________
Von: Jim Phillips <jim_at_ks.uiuc.edu>
Gesendet: Dienstag, 13. Oktober 2015 17:03
An: namd-l_at_ks.uiuc.edu; Richter, Stefan
Betreff: Re: namd-l: Compilation of NAMD from Source (Cray XC40)

Hi,

The fix is when building Charm++ to also build the CkLoop library, so
instead of:

./build charm++ ...

use:

./build 'charm++ ckloop' ...

The quotes are important.

For an existing Charm++ build you can run "make ckloop" in the builds tmp
directory, e.g., "cd multicore-linux64/tmp; make ckloop".

Sorry for the inconvenience. I'm going to be switching the nightly builds
to a newer Charm++ that builds the CkLoop library be default soon.

Jim

On Tue, 13 Oct 2015, Richter, Stefan wrote:

> I try to compile NAMD on a Cray XC40. I've loaded the craype-hugepages8M and swapped the PrgEnv-cray to PrgEnv-intel. Also downloaded fftw and tcl and tcl-threaded. After building charm++ with ./build charm++ gni-crayxc --with-production i tried to build NAMD with: ./config CRAY-XC-intel --charm-arch gni-crayxc && cd CRAY-XC-intel && make
>
>
> It starts of for a while, but then i get the following error:
>
> .
>
> Adding registration for module RefineLB
> Adding registration for module GreedyLB
> Adding registration for module CkMulticast
> Adding registration for module CkLoop
> charmc: Executing CC -I/opt/cray/rca/1.0.0-2.0502.57212.2.56.ari/include -I/opt/cray/alps/5.2.3-2.0502.9295.14.14.ari/include -I/opt/cray/gni-headers/4.0-1.0502.10317.9.2.ari/include -I/opt/cray/pmi/5.0.9-1.0000.10911.0.0.ari/include -I/opt/cray/ugni/6.0-1.0502.10245.9.9.ari/include -I/opt/cray/wlm_detect/1.0-1.0502.57063.1.1.ari/include -I/opt/cray/krca/1.0.0-2.0502.57202.2.45.ari/include -I/opt/cray-hss-devel/7.2.0/include -I/opt/cray/gni-headers/4.0-1.0502.10317.9.2.ari/include -I/opt/cray/ugni/6.0-1.0502.10245.9.9.ari/include -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -Iinc -Isrc -O2 -ip -no-vec -U_FORTIFY_SOURCE -c moduleinit19697.C -o moduleinit19697.o
> charmc> All libraries are: -L.rootdir/charm-6.6.1/gni-crayxc/bin/../lib -I.rootdir/charm-6.6.1/gni-crayxc/bin/../include .rootdir/charm-6.6.1/gni-crayxc/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/CudaUtils.o obj/ccsinterface.o obj/DataStream.o obj/DeviceCUDA.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/fstream_namd.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_histogram.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 obj/tcl_psfgen.o obj/charmm_file.o obj/charmm_parse_topo_defs.o obj/extract_alias.o obj/hash.o obj/hasharray.o obj/memarena.o obj/pdb_file.o obj/pdb_file_extract.o obj/psf_file.o obj/psf_file_extract.o obj/topo_defs.o obj/topo_mol.o obj/topo_mol_output.o obj/topo_mol_pluginio.o obj/stringhash.o moduleinit19697.o -lmoduleCkLoop -lmoduleCkMulticast -lmoduleGreedyLB -lmoduleRefineLB -lmoduleHybridLB -lmoduleNeighborLB .rootdir/charm-6.6.1/gni-crayxc/bin/../lib/libmemory-default.o .rootdir/charm-6.6.1/gni-crayxc/bin/../lib/libthreads-default.o -lckmain -lck -lconv-cplus-y -lconv-core -lconv-util -lconv-partition -lckqt -ldl -lrt -ltcl8.5 -ldl -lsrfftw -lsfftw -lm .rootdir/charm-6.6.1/gni-crayxc/bin/../lib/cray_tlbhack.o -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB -lmoduleCkMulticast -lmoduleCkLoop -lm
> charmc: Executing CC -I/opt/cray/rca/1.0.0-2.0502.57212.2.56.ari/include -I/opt/cray/alps/5.2.3-2.0502.9295.14.14.ari/include -I/opt/cray/gni-headers/4.0-1.0502.10317.9.2.ari/include -I/opt/cray/pmi/5.0.9-1.0000.10911.0.0.ari/include -I/opt/cray/ugni/6.0-1.0502.10245.9.9.ari/include -I/opt/cray/wlm_detect/1.0-1.0502.57063.1.1.ari/include -I/opt/cray/krca/1.0.0-2.0502.57202.2.45.ari/include -I/opt/cray-hss-devel/7.2.0/include -I/opt/cray/gni-headers/4.0-1.0502.10317.9.2.ari/include -I/opt/cray/ugni/6.0-1.0502.10245.9.9.ari/include -O2 -ip -no-vec -L.rootdir/tcl/lib -L.rootdir/fftw/lib -I.rootdir/charm-6.6.1/gni-crayxc/include -o namd2 -L.rootdir/charm-6.6.1/gni-crayxc/bin/../lib -I.rootdir/charm-6.6.1/gni-crayxc/bin/../include .rootdir/charm-6.6.1/gni-crayxc/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/CudaUtils.o obj/ccsinterface.o obj/DataStream.o obj/DeviceCUDA.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/fstream_namd.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_histogram.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 obj/tcl_psfgen.o obj/charmm_file.o obj/charmm_parse_topo_defs.o obj/extract_alias.o obj/hash.o obj/hasharray.o obj/memarena.o obj/pdb_file.o obj/pdb_file_extract.o obj/psf_file.o obj/psf_file_extract.o obj/topo_defs.o obj/topo_mol.o obj/topo_mol_output.o obj/topo_mol_pluginio.o obj/stringhash.o moduleinit19697.o -lmoduleCkLoop -lmoduleCkMulticast -lmoduleGreedyLB -lmoduleRefineLB -lmoduleHybridLB -lmoduleNeighborLB .rootdir/charm-6.6.1/gni-crayxc/bin/../lib/libmemory-default.o .rootdir/charm-6.6.1/gni-crayxc/bin/../lib/libthreads-default.o -lckmain -lck -lconv-cplus-y -lconv-core -lconv-util -lconv-partition -lckqt -ldl -lrt -ltcl8.5 -ldl -lsrfftw -lsfftw -lm .rootdir/charm-6.6.1/gni-crayxc/bin/../lib/cray_tlbhack.o -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB -lmoduleCkMulticast -lmoduleCkLoop -lm
> ld: cannot find -lmoduleCkLoop
> .rootdir/tcl/lib/libtcl8.5.a(tclLoadDl.o): In function `TclpDlopen':
> tclLoadDl.c:(.text+0x42): warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
> ld: cannot find -lmoduleCkLoop
> /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libhugetlbfs.a(hugeutils.o): In function `gethugepagesize':
> /usr/src/packages/BUILD/cray-libhugetlbfs-2.16/hugeutils.c:871: multiple definition of `gethugepagesize'
> .rootdir/charm-6.6.1/gni-crayxc/bin/../lib/cray_tlbhack.o:cray_tlbhack.c:(.text+0x0): first defined here
> .rootdir/tcl/lib/libtcl8.5.a(tclUnixCompat.o): In function `TclpGetGrGid':
> tclUnixCompat.c:(.text+0x81): warning: Using 'getgrgid' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
> .rootdir/tcl/lib/libtcl8.5.a(tclUnixCompat.o): In function `TclpGetGrNam':
> tclUnixCompat.c:(.text+0x71): warning: Using 'getgrnam' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
> .rootdir/tcl/lib/libtcl8.5.a(tclUnixCompat.o): In function `TclpGetPwNam':
> tclUnixCompat.c:(.text+0x51): warning: Using 'getpwnam' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
> .rootdir/tcl/lib/libtcl8.5.a(tclUnixCompat.o): In function `TclpGetPwUid':
> tclUnixCompat.c:(.text+0x61): warning: Using 'getpwuid' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
> .rootdir/tcl/lib/libtcl8.5.a(tclUnixChan.o): In function `CreateSocketAddress':
> tclUnixChan.c:(.text+0x1aca): warning: Using 'getaddrinfo' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
> /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
> /usr/src/packages/BUILD/glibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp'
> .rootdir/tcl/lib/libtcl8.5.a(tclUnixCompat.o): In function `TclpGetHostByAddr':
> tclUnixCompat.c:(.text+0xa1): warning: Using 'gethostbyaddr' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
> obj/vmdsock.o: In function `vmdsock_connect(void*, char const*, int)':
> vmdsock.C:(.text+0x75): warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
> .rootdir/tcl/lib/libtcl8.5.a(tclIOSock.o): In function `TclSockGetPort':
> tclIOSock.c:(.text+0x53): warning: Using 'getservbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
> Fatal Error by charmc in directory /zhome/academic/HLRS/xhi/xhiricht/software/NAMD_CVS-2015-10-13_Source/CRAY-XC-intel
> Command CC -I/opt/cray/rca/1.0.0-2.0502.57212.2.56.ari/include -I/opt/cray/alps/5.2.3-2.0502.9295.14.14.ari/include -I/opt/cray/gni-headers/4.0-1.0502.10317.9.2.ari/include -I/opt/cray/pmi/5.0.9-1.0000.10911.0.0.ari/include -I/opt/cray/ugni/6.0-1.0502.10245.9.9.ari/include -I/opt/cray/wlm_detect/1.0-1.0502.57063.1.1.ari/include -I/opt/cray/krca/1.0.0-2.0502.57202.2.45.ari/include -I/opt/cray-hss-devel/7.2.0/include -I/opt/cray/gni-headers/4.0-1.0502.10317.9.2.ari/include -I/opt/cray/ugni/6.0-1.0502.10245.9.9.ari/include -O2 -ip -no-vec -L.rootdir/tcl/lib -L.rootdir/fftw/lib -I.rootdir/charm-6.6.1/gni-crayxc/include -o namd2 -L.rootdir/charm-6.6.1/gni-crayxc/bin/../lib -I.rootdir/charm-6.6.1/gni-crayxc/bin/../include .rootdir/charm-6.6.1/gni-crayxc/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/CudaUtils.o obj/ccsinterface.o obj/DataStream.o obj/DeviceCUDA.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/fstream_namd.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_histogram.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 obj/tcl_psfgen.o obj/charmm_file.o obj/charmm_parse_topo_defs.o obj/extract_alias.o obj/hash.o obj/hasharray.o obj/memarena.o obj/pdb_file.o obj/pdb_file_extract.o obj/psf_file.o obj/psf_file_extract.o obj/topo_defs.o obj/topo_mol.o obj/topo_mol_output.o obj/topo_mol_pluginio.o obj/stringhash.o moduleinit19697.o -lmoduleCkLoop -lmoduleCkMulticast -lmoduleGreedyLB -lmoduleRefineLB -lmoduleHybridLB -lmoduleNeighborLB .rootdir/charm-6.6.1/gni-crayxc/bin/../lib/libmemory-default.o .rootdir/charm-6.6.1/gni-crayxc/bin/../lib/libthreads-default.o -lckmain -lck -lconv-cplus-y -lconv-core -lconv-util -lconv-partition -lckqt -ldl -lrt -ltcl8.5 -ldl -lsrfftw -lsfftw -lm .rootdir/charm-6.6.1/gni-crayxc/bin/../lib/cray_tlbhack.o -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB -lmoduleCkMulticast -lmoduleCkLoop -lm returned error code 1
> charmc exiting...
> rm -f moduleinit19697.C moduleinit19697.o
> make: *** [namd2] Error 1
>
> ?
>
>
>
>
> Dr. Stefan Richter
> Software and IT Specialist
> Molecular and Cellular Modeling Group (MCM)
> HITS gGmbH
> Schloss-Wolfsbrunnenweg 35
> 69118 Heidelberg
> Germany
>
> phone: +49 - 6221 - 533 279
> fax: +49 6221 533298
> email: Stefan.Richter_at_h-its.org
> http://www.h-its.org
> _________________________________________________
> Amtsgericht Mannheim / HRB 337446
> Managing Directors:
> Dr. h. c. Dr.-Ing. E. h. Klaus Tschira
> Prof. Dr.-Ing. Andreas Reuter
>

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:23 CST