Re: Compilation of NAMD from Source (Cray XC40)

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue Oct 13 2015 - 15:04:02 CDT

Hi Stefan,

Here is a thread that may help you. It describes how I managed to solve the issue. Although this was sometime ago and did not compile NAMD since then.

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/2354.html

Cheers
Vlad

On October 13, 2015 8:10:44 PM GMT+02:00, "Richter, Stefan" <stefan.richter_at_h-its.org> 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
>>

-- 
Sent from my Android device with K-9 Mail. Please excuse my brevity.

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:22:06 CST