NAMD build problems on PowerPC under Red Hat Enterprise

From: Lane, William (William.Lane_at_cshs.org)
Date: Wed Oct 16 2013 - 11:37:12 CDT

OS is Red Hat Enterprise Linux Server release 5.9 (Tikanga).

Hardware is a Power5 system with 16 cores (96 GiB of RAM)

I'm using IBM's xlC compiler (the evaluation version).

I've built and tested the charm++ installation and it passed all the tests run
as a result of make test.

I ran the following to create the make file:
./config Linux-POWER-xlC --charm-base /home/winnt/CSMC/lanew/NAMD/charm-6.5.1 --charm-arch multicore-linux-ppc-xlc64 --without-tcl --without-fftw

I then ran make and eventually get the following errors (why is the xlC compiler using the
GNU linker in usr/bin?):

charmc: Executing xlC_r -q64 -O -qnohot -qstrict -qaggrcopy=nooverlap -qalias=ansi -qarch=auto -qtune=auto -qfloat=rsqrt:fltint -I/home/winnt/CSMC/lanew/NAMD/charm-6.5.1/multicore-linux-ppc-xlc64/include -o namd2 -L/home/winnt/CSMC/lanew/NAMD/charm-6.5.1/multicore-linux-ppc-xlc64/bin/../lib -I/home/winnt/CSMC/lanew/NAMD/charm-6.5.1/multicore-linux-ppc-xlc64/bin/../include /home/winnt/CSMC/lanew/NAMD/charm-6.5.1/multicore-linux-ppc-xlc64/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/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/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/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 moduleinit27854.o -lmoduleCkMulticast -lmoduleGreedyLB -lmoduleRefineLB -lmoduleHybridLB -lmoduleNeighborLB /home/winnt/CSMC/lanew/NAMD/charm-6.5.1/multicore-linux-ppc-xlc64/bin/../lib/libmemory-default.o /home/winnt/CSMC/lanew/NAMD/charm-6.5.1/multicore-linux-ppc-xlc64/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -lpthread -ldl -lm -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB -lmoduleCkMulticast -lm
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strIjEESsRKT_RKjS5_' changed from 268 in obj/colvarmodule.o to 272 in obj/colvarparse.o
/usr/bin/ld: Warning: size of symbol `_ZNSt6vectorIiSaIiEE20_M_allocate_and_copyIN9__gnu_cxx17__normal_iteratorIPKiS1_EEEEPijT_S9_' changed from 256 in obj/GlobalMasterTMD.o to 252 in obj/colvarparse.o
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strIN11colvarvalue4TypeEEESsRKT_RKjS7_' changed from 272 in obj/colvarmodule.o to 268 in obj/colvarvalue.o
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strI11colvarvalueEESsRKT_RKjS6_' changed from 272 in obj/colvarparse.o to 268 in obj/colvarbias.o
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strIN11colvarvalue4TypeEEESsRKT_RKjS7_' changed from 268 in obj/colvarmodule.o to 272 in obj/colvarbias.o
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strIdEESsRKT_RKjS5_' changed from 268 in obj/colvarmodule.o to 272 in obj/colvarbias_meta.o
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strIjEESsRKT_RKjS5_' changed from 272 in obj/colvarmodule.o to 268 in obj/colvarbias_meta.o
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strI11colvarvalueEESsRKT_RKjS6_' changed from 268 in obj/colvarparse.o to 272 in obj/colvarbias_meta.o
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strISt4fposI11__mbstate_tEEESsRKT_RKjS8_' changed from 280 in obj/colvarbias.o to 276 in obj/colvarbias_meta.o
/usr/bin/ld: Warning: size of symbol `_ZNSt6vectorI11colvarvalueSaIS0_EE20_M_allocate_and_copyIN9__gnu_cxx17__normal_iteratorIPKS0_S2_EEEEPS0_jT_SA_' changed from 264 in obj/colvarparse.o to 268 in obj/colvarbias_meta.o
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strIjEESsRKT_RKjS5_' changed from 268 in obj/colvarmodule.o to 272 in obj/colvaratoms.o
/usr/bin/ld: Warning: size of symbol `_ZNSt6vectorIiSaIiEE20_M_allocate_and_copyIN9__gnu_cxx17__normal_iteratorIPKiS1_EEEEPijT_S9_' changed from 252 in obj/GlobalMasterTMD.o to 256 in obj/colvaratoms.o
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strIdEESsRKT_RKjS5_' changed from 272 in obj/colvarmodule.o to 268 in obj/colvarcomp.o
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strIdEESsRKT_RKjS5_' changed from 268 in obj/colvarmodule.o to 272 in obj/colvarcomp_distances.o
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strIdEESsRKT_RKjS5_' changed from 272 in obj/colvarmodule.o to 268 in obj/colvarcomp_protein.o
/usr/bin/ld: Warning: size of symbol `_ZStplIcSt11char_traitsIcESaIcEESbIT_T0_T1_EPKS3_RKS6_' changed from 172 in obj/colvarmodule.o to 184 in obj/colvarproxy_namd.o
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strINS_7rvectorEEESsRKT_RKjS6_' changed from 272 in obj/colvarparse.o to 268 in obj/colvarproxy_namd.o
/usr/bin/ld: Warning: size of symbol `_ZNSt6vectorIN12colvarmodule4atomESaIS1_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS1_S3_EERKS1_' changed from 1288 in obj/colvaratoms.o to 1304 in obj/colvarproxy_namd.o
/usr/bin/ld: Warning: size of symbol `_ZSt24__uninitialized_copy_auxIN9__gnu_cxx17__normal_iteratorIPN12colvarmodule4atomESt6vectorIS3_SaIS3_EEEES8_ET0_T_SA_S9_12__false_type' changed from 340 in obj/colvaratoms.o to 324 in obj/colvarproxy_namd.o
/usr/bin/ld: Warning: size of symbol `_ZN11colvar_gridIjE8read_rawERSi' changed from 940 in obj/colvarbias_abf.o to 956 in obj/colvargrid.o
/usr/bin/ld: Warning: size of symbol `_ZN12colvarmodule6to_strIjEESsRKT_RKjS5_' changed from 272 in obj/colvarmodule.o to 268 in obj/colvargrid.o
/usr/bin/ld: Warning: size of symbol `_ZStplIcSt11char_traitsIcESaIcEESbIT_T0_T1_EPKS3_RKS6_' changed from 184 in obj/colvarmodule.o to 172 in obj/colvargrid.o
/usr/bin/ld: Warning: size of symbol `_ZNSt6vectorIiSaIiEE20_M_allocate_and_copyIN9__gnu_cxx17__normal_iteratorIPKiS1_EEEEPijT_S9_' changed from 256 in obj/GlobalMasterTMD.o to 252 in obj/colvargrid.o
/usr/bin/ld: Warning: size of symbol `_ZN13PDBAtomRecordD1Ev' changed from 60 in obj/PDB.o to 52 in obj/PDBData.o
/usr/bin/ld: Warning: size of symbol `_ZN22ProxyCombinedResultMsgC1Ev' changed from 132 in obj/ProxyMgr.o to 140 in obj/ProxyPatch.o
/usr/bin/ld: Warning: size of symbol `_ZSt16__insertion_sortIPiEvT_S1_' changed from 248 in obj/ComputePme.o to 220 in obj/ParallelIOMgr.o
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/buildinfo.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeMoa.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeMsm.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeMsmMsa.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeMsmSerial.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeFmmSerial.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/msm.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/msm_longrng.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/msm_longrng_sprec.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/msm_setup.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/msm_shortrng.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/msm_shortrng_sprec.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/wkfutils.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/common.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/dcdlib.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/erf.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/fitrms.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/main.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/mainfunc.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/memusage.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/strlib.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/AlgSeven.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/AlgRecBisection.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/AlgNbor.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/AtomMap.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/BackEnd.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/BroadcastMgr.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/BroadcastClient.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/CollectionMaster.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/CollectionMgr.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Communicate.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Compute.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeAngles.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeAniso.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeBonds.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeConsForce.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeConsForceMsgs.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeCrossterms.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeCylindricalBC.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeDihedrals.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeDPME.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeDPMEMsgs.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeDPMTA.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeEField.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeEwald.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeExt.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeGBISser.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeGBIS.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeLCPO.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeFullDirect.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeHomePatch.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeHomePatches.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeImpropers.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeGlobal.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeGlobalMsgs.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeGridForce.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeMap.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeMgr.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedSelf.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedPair.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedUtil.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedStd.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedFEP.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedGo.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedTI.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedLES.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedPProf.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedTabEnergies.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedCUDA.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedCUDAExcl.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedMIC.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeNonbondedMICKernel.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputePatch.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputePatchPair.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputePme.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/OptPme.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/OptPmeRealSpace.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeRestraints.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeSphericalBC.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeStir.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeTclBC.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ComputeThole.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ConfigList.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Controller.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ccsinterface.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/DataStream.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/DumpBench.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/FreeEnergyAssert.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/FreeEnergyGroup.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/FreeEnergyLambda.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/FreeEnergyLambdMgr.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/FreeEnergyParse.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/FreeEnergyRestrain.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/FreeEnergyRMgr.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/FreeEnergyVector.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GlobalMaster.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GlobalMasterServer.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GlobalMasterTest.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GlobalMasterIMD.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GlobalMasterTcl.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GlobalMasterSMD.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GlobalMasterTMD.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Matrix4Symmetry.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GlobalMasterSymmetry.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GlobalMasterFreeEnergy.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GlobalMasterEasy.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GlobalMasterMisc.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvarmodule.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvarparse.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvar.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvarvalue.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvarbias.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvarbias_abf.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvarbias_meta.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvaratoms.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvarcomp.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvarcomp_angles.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvarcomp_coordnums.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvarcomp_distances.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvarcomp_protein.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvarcomp_rotations.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvarproxy_namd.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/colvargrid.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GridForceGrid.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GromacsTopFile.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/heap.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/HomePatch.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/IMDOutput.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/InfoStream.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/LdbCoordinator.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/LJTable.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Measure.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/MGridforceParams.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/MStream.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/MigrateAtomsMsg.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Molecule.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Molecule2.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/GoMolecule.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/NamdCentLB.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/NamdNborLB.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/NamdHybridLB.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/NamdDummyLB.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/NamdState.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/NamdOneTools.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Node.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Output.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Parameters.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ParseOptions.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Patch.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/PatchMgr.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/PatchMap.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/PDB.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/PDBData.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/PmeKSpace.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/PmeRealSpace.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ProcessorPrivate.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ProxyMgr.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ProxyPatch.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Rebalancer.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/RecBisection.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ReductionMgr.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/RefineOnly.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/RefineTorusLB.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ScriptTcl.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Sequencer.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Set.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Settle.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/SimParameters.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/SortAtoms.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/Sync.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/TclCommands.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/TorusLB.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/WorkDistrib.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/pub3dfft.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/vmdsock.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/parm.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/imd.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/CompressPsf.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/PluginIOMgr.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/DataExchanger.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/ParallelIOMgr.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/dcdplugin.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/jsplugin.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/namdbinplugin.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/pdbplugin.o' is incompatible with powerpc:common64 output
/usr/bin/ld: warning: powerpc:common architecture of input file `obj/psfplugin.o' is incompatible with powerpc:common64 output
obj/ComputeMoa.o: In function `__sinit65535()':
src/ComputeMoa.C:(.text+0x14): relocation truncated to fit: R_PPC_REL24 against `std::ios_base::Init::Init()'
src/ComputeMoa.C:(.text+0x2c): relocation truncated to fit: R_PPC_REL24 against `__cxa_atexit'
obj/ComputeMoa.o: In function `__srterm__0()':
src/ComputeMoa.C:(.text+0x54): relocation truncated to fit: R_PPC_REL24 against `std::ios_base::Init::~Init()'
obj/ComputeMoa.o: In function `std::vector<int, std::allocator<int> >::__dftbdt(std::_Vector_base<int, std::allocator<int> >*)':
src/ComputeMoa.C:(.text+0x88): relocation truncated to fit: R_PPC_REL24 against `operator delete(void*)'
obj/ComputeMsm.o: In function `__sinit65535()':
src/ComputeMsm.C:(.text+0x14): relocation truncated to fit: R_PPC_REL24 against `std::ios_base::Init::Init()'
src/ComputeMsm.C:(.text+0x2c): relocation truncated to fit: R_PPC_REL24 against `__cxa_atexit'
obj/ComputeMsm.o: In function `__srterm__0()':
src/ComputeMsm.C:(.text+0x54): relocation truncated to fit: R_PPC_REL24 against `std::ios_base::Init::~Init()'
obj/ComputeMsm.o: In function `MsmC1HermiteGridCutoff::compute_specialized(GridMsg*)':
src/ComputeMsm.C:(.text+0x108): relocation truncated to fit: R_PPC_REL24 against `memcpy'
/opt/ibmcmp/vacpp/12.1/bin/.orig/xlC_r: 1501-224 (S) fatal error in /usr/bin/ld: signal 11 received
Fatal Error by charmc in directory /home/winnt/CSMC/lanew/NAMD/Linux-POWER-xlC
   Command xlC_r -q64 -O -qnohot -qstrict -qaggrcopy=nooverlap -qalias=ansi -qarch=auto -qtune=auto -qfloat=rsqrt:fltint -I/home/winnt/CSMC/lanew/NAMD/charm-6.5.1/multicore-linux-ppc-xlc64/include -o namd2 -L/home/winnt/CSMC/lanew/NAMD/charm-6.5.1/multicore-linux-ppc-xlc64/bin/../lib -I/home/winnt/CSMC/lanew/NAMD/charm-6.5.1/multicore-linux-ppc-xlc64/bin/../include /home/winnt/CSMC/lanew/NAMD/charm-6.5.1/multicore-linux-ppc-xlc64/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/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/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/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 moduleinit27854.o -lmoduleCkMulticast -lmoduleGreedyLB -lmoduleRefineLB -lmoduleHybridLB -lmoduleNeighborLB /home/winnt/CSMC/lanew/NAMD/charm-6.5.1/multicore-linux-ppc-xlc64/bin/../lib/libmemory-default.o /home/winnt/CSMC/lanew/NAMD/charm-6.5.1/multicore-linux-ppc-xlc64/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -lpthread -ldl -lm -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB -lmoduleCkMulticast -lm returned error code 251
charmc exiting...
rm -f moduleinit27854.C moduleinit27854.o
make: *** [namd2] Error 1
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This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:46 CST