From: Devang Jane (devangjane_at_gmail.com)
Date: Thu Aug 08 2013 - 13:15:38 CDT
hi all,
I am compiling NAMD2.9 on Xeon Phi from source code, I first compile the
Charmv6.5.0 with -mmic successfully, however, when I compile NAMD2.9 using
the following command, I got no luck, could anyone help me with this?
./config Linux-x86_64-icc --charm-arch multicore-linux64 icc
cd Linux-x86_64-icc
then I got the error:
icpc: command line warning #10121: overriding '-shared-intel' with
'-i-static'
icpc: warning #10237: -lcilkrts linked in dynamically, static library not
available
ipo: warning #11010: file format not recognized for
.rootdir/charm-6.5.0//bin/../lib/libldb-rand.o
ipo: warning #11010: file format not recognized for obj/buildinfo.o
ipo: warning #11010: file format not recognized for obj/ComputeMoa.o
ipo: warning #11010: file format not recognized for obj/ComputeMsmMsa.o
ipo: warning #11010: file format not recognized for obj/ComputeMsmSerial.o
ipo: warning #11010: file format not recognized for obj/msm.o
ipo: warning #11010: file format not recognized for obj/msm_longrng.o
ipo: warning #11010: file format not recognized for obj/msm_longrng_sprec.o
ipo: warning #11010: file format not recognized for obj/msm_setup.o
ipo: warning #11010: file format not recognized for obj/msm_shortrng.o
ipo: warning #11010: file format not recognized for obj/msm_shortrng_sprec.o
ipo: warning #11010: file format not recognized for obj/wkfutils.o
ipo: warning #11010: file format not recognized for obj/common.o
ipo: warning #11010: file format not recognized for obj/dcdlib.o
ipo: warning #11010: file format not recognized for obj/erf.o
ipo: warning #11010: file format not recognized for obj/fitrms.o
ipo: warning #11010: file format not recognized for obj/main.o
ipo: warning #11010: file format not recognized for obj/mainfunc.o
ipo: warning #11010: file format not recognized for obj/memusage.o
ipo: warning #11010: file format not recognized for obj/strlib.o
ipo: warning #11010: file format not recognized for obj/AlgSeven.o
ipo: warning #11010: file format not recognized for obj/AlgRecBisection.o
ipo: warning #11010: file format not recognized for obj/AlgNbor.o
ipo: warning #11010: file format not recognized for obj/AtomMap.o
ipo: warning #11010: file format not recognized for obj/BackEnd.o
ipo: warning #11010: file format not recognized for obj/BroadcastMgr.o
ipo: warning #11010: file format not recognized for obj/BroadcastClient.o
ipo: warning #11010: file format not recognized for obj/CollectionMaster.o
ipo: warning #11010: file format not recognized for obj/CollectionMgr.o
ipo: warning #11010: file format not recognized for obj/Communicate.o
ipo: warning #11010: file format not recognized for obj/Compute.o
ipo: warning #11010: file format not recognized for obj/ComputeAngles.o
ipo: warning #11010: file format not recognized for obj/ComputeAniso.o
ipo: warning #11010: file format not recognized for obj/ComputeBonds.o
ipo: warning #11010: file format not recognized for obj/ComputeConsForce.o
ipo: warning #11010: file format not recognized for
obj/ComputeConsForceMsgs.o
ipo: warning #11010: file format not recognized for obj/ComputeCrossterms.o
ipo: warning #11010: file format not recognized for
obj/ComputeCylindricalBC.o
ipo: warning #11010: file format not recognized for obj/ComputeDihedrals.o
ipo: warning #11010: file format not recognized for obj/ComputeDPME.o
ipo: warning #11010: file format not recognized for obj/ComputeDPMEMsgs.o
ipo: warning #11010: file format not recognized for obj/ComputeDPMTA.o
ipo: warning #11010: file format not recognized for obj/ComputeEField.o
ipo: warning #11010: file format not recognized for obj/ComputeEwald.o
ipo: warning #11010: file format not recognized for obj/ComputeExt.o
ipo: warning #11010: file format not recognized for obj/ComputeGBISser.o
ipo: warning #11010: file format not recognized for obj/ComputeGBIS.o
ipo: warning #11010: file format not recognized for obj/ComputeLCPO.o
ipo: warning #11010: file format not recognized for obj/ComputeFullDirect.o
ipo: warning #11010: file format not recognized for obj/ComputeHomePatch.o
ipo: warning #11010: file format not recognized for obj/ComputeHomePatches.o
ipo: warning #11010: file format not recognized for obj/ComputeImpropers.o
ipo: warning #11010: file format not recognized for obj/ComputeGlobal.o
ipo: warning #11010: file format not recognized for obj/ComputeGlobalMsgs.o
ipo: warning #11010: file format not recognized for obj/ComputeGridForce.o
ipo: warning #11010: file format not recognized for obj/ComputeMap.o
ipo: warning #11010: file format not recognized for obj/ComputeMgr.o
ipo: warning #11010: file format not recognized for
obj/ComputeNonbondedSelf.o
ipo: warning #11010: file format not recognized for
obj/ComputeNonbondedPair.o
ipo: warning #11010: file format not recognized for
obj/ComputeNonbondedUtil.o
ipo: warning #11010: file format not recognized for
obj/ComputeNonbondedStd.o
ipo: warning #11010: file format not recognized for
obj/ComputeNonbondedFEP.o
ipo: warning #11010: file format not recognized for obj/ComputeNonbondedGo.o
ipo: warning #11010: file format not recognized for obj/ComputeNonbondedTI.o
ipo: warning #11010: file format not recognized for
obj/ComputeNonbondedLES.o
ipo: warning #11010: file format not recognized for
obj/ComputeNonbondedPProf.o
ipo: warning #11010: file format not recognized for
obj/ComputeNonbondedTabEnergies.o
ipo: warning #11010: file format not recognized for
obj/ComputeNonbondedCUDA.o
ipo: warning #11010: file format not recognized for
obj/ComputeNonbondedCUDAExcl.o
ipo: warning #11010: file format not recognized for obj/ComputePatch.o
ipo: warning #11010: file format not recognized for obj/ComputePatchPair.o
ipo: warning #11010: file format not recognized for obj/ComputePme.o
ipo: warning #11010: file format not recognized for obj/OptPme.o
ipo: warning #11010: file format not recognized for obj/OptPmeRealSpace.o
ipo: warning #11010: file format not recognized for obj/ComputeRestraints.o
ipo: warning #11010: file format not recognized for obj/ComputeSphericalBC.o
ipo: warning #11010: file format not recognized for obj/ComputeStir.o
ipo: warning #11010: file format not recognized for obj/ComputeTclBC.o
ipo: warning #11010: file format not recognized for obj/ComputeThole.o
ipo: warning #11010: file format not recognized for obj/ConfigList.o
ipo: warning #11010: file format not recognized for obj/Controller.o
ipo: warning #11010: file format not recognized for obj/ccsinterface.o
ipo: warning #11010: file format not recognized for obj/DataStream.o
ipo: warning #11010: file format not recognized for obj/DumpBench.o
ipo: warning #11010: file format not recognized for obj/FreeEnergyAssert.o
ipo: warning #11010: file format not recognized for obj/FreeEnergyGroup.o
ipo: warning #11010: file format not recognized for obj/FreeEnergyLambda.o
ipo: warning #11010: file format not recognized for obj/FreeEnergyLambdMgr.o
ipo: warning #11010: file format not recognized for obj/FreeEnergyParse.o
ipo: warning #11010: file format not recognized for obj/FreeEnergyRestrain.o
ipo: warning #11010: file format not recognized for obj/FreeEnergyRMgr.o
ipo: warning #11010: file format not recognized for obj/FreeEnergyVector.o
ipo: warning #11010: file format not recognized for obj/GlobalMaster.o
ipo: warning #11010: file format not recognized for obj/GlobalMasterServer.o
ipo: warning #11010: file format not recognized for obj/GlobalMasterTest.o
ipo: warning #11010: file format not recognized for obj/GlobalMasterIMD.o
ipo: warning #11010: file format not recognized for obj/GlobalMasterTcl.o
ipo: warning #11010: file format not recognized for obj/GlobalMasterSMD.o
ipo: warning #11010: file format not recognized for obj/GlobalMasterTMD.o
ipo: warning #11010: file format not recognized for obj/Matrix4Symmetry.o
ipo: warning #11010: file format not recognized for
obj/GlobalMasterSymmetry.o
ipo: warning #11010: file format not recognized for
obj/GlobalMasterFreeEnergy.o
ipo: warning #11010: file format not recognized for obj/GlobalMasterEasy.o
ipo: warning #11010: file format not recognized for obj/GlobalMasterMisc.o
ipo: warning #11010: file format not recognized for obj/colvarmodule.o
ipo: warning #11010: file format not recognized for obj/colvarparse.o
ipo: warning #11010: file format not recognized for obj/colvar.o
ipo: warning #11010: file format not recognized for obj/colvarvalue.o
ipo: warning #11010: file format not recognized for obj/colvarbias.o
ipo: warning #11010: file format not recognized for obj/colvarbias_abf.o
ipo: warning #11010: file format not recognized for obj/colvarbias_meta.o
ipo: warning #11010: file format not recognized for obj/colvaratoms.o
ipo: warning #11010: file format not recognized for obj/colvarcomp.o
ipo: warning #11010: file format not recognized for obj/colvarcomp_angles.o
ipo: warning #11010: file format not recognized for
obj/colvarcomp_coordnums.o
ipo: warning #11010: file format not recognized for
obj/colvarcomp_distances.o
ipo: warning #11010: file format not recognized for obj/colvarcomp_protein.o
ipo: warning #11010: file format not recognized for
obj/colvarcomp_rotations.o
ipo: warning #11010: file format not recognized for obj/colvarproxy_namd.o
ipo: warning #11010: file format not recognized for obj/colvargrid.o
ipo: warning #11010: file format not recognized for obj/GridForceGrid.o
ipo: warning #11010: file format not recognized for obj/GromacsTopFile.o
ipo: warning #11010: file format not recognized for obj/heap.o
ipo: warning #11010: file format not recognized for obj/HomePatch.o
ipo: warning #11010: file format not recognized for obj/IMDOutput.o
ipo: warning #11010: file format not recognized for obj/InfoStream.o
ipo: warning #11010: file format not recognized for obj/LdbCoordinator.o
ipo: warning #11010: file format not recognized for obj/LJTable.o
ipo: warning #11010: file format not recognized for obj/Measure.o
ipo: warning #11010: file format not recognized for obj/MGridforceParams.o
ipo: warning #11010: file format not recognized for obj/MStream.o
ipo: warning #11010: file format not recognized for obj/MigrateAtomsMsg.o
ipo: warning #11010: file format not recognized for obj/Molecule.o
ipo: warning #11010: file format not recognized for obj/Molecule2.o
ipo: warning #11010: file format not recognized for obj/GoMolecule.o
ipo: warning #11010: file format not recognized for obj/NamdCentLB.o
ipo: warning #11010: file format not recognized for obj/NamdNborLB.o
ipo: warning #11010: file format not recognized for obj/NamdHybridLB.o
ipo: warning #11010: file format not recognized for obj/NamdDummyLB.o
ipo: warning #11010: file format not recognized for obj/NamdState.o
ipo: warning #11010: file format not recognized for obj/NamdOneTools.o
ipo: warning #11010: file format not recognized for obj/Node.o
ipo: warning #11010: file format not recognized for obj/Output.o
ipo: warning #11010: file format not recognized for obj/Parameters.o
ipo: warning #11010: file format not recognized for obj/ParseOptions.o
ipo: warning #11010: file format not recognized for obj/Patch.o
ipo: warning #11010: file format not recognized for obj/PatchMgr.o
ipo: warning #11010: file format not recognized for obj/PatchMap.o
ipo: warning #11010: file format not recognized for obj/PDB.o
ipo: warning #11010: file format not recognized for obj/PDBData.o
ipo: warning #11010: file format not recognized for obj/PmeBase.o
ipo: warning #11010: file format not recognized for obj/PmeKSpace.o
ipo: warning #11010: file format not recognized for obj/PmeRealSpace.o
ipo: warning #11010: file format not recognized for obj/ProcessorPrivate.o
ipo: warning #11010: file format not recognized for obj/ProxyMgr.o
ipo: warning #11010: file format not recognized for obj/ProxyPatch.o
ipo: warning #11010: file format not recognized for obj/Rebalancer.o
ipo: warning #11010: file format not recognized for obj/RecBisection.o
ipo: warning #11010: file format not recognized for obj/ReductionMgr.o
ipo: warning #11010: file format not recognized for obj/RefineOnly.o
ipo: warning #11010: file format not recognized for obj/RefineTorusLB.o
ipo: warning #11010: file format not recognized for obj/ScriptTcl.o
ipo: warning #11010: file format not recognized for obj/Sequencer.o
ipo: warning #11010: file format not recognized for obj/Set.o
ipo: warning #11010: file format not recognized for obj/Settle.o
ipo: warning #11010: file format not recognized for obj/SimParameters.o
ipo: warning #11010: file format not recognized for obj/SortAtoms.o
ipo: warning #11010: file format not recognized for obj/Sync.o
ipo: warning #11010: file format not recognized for obj/TclCommands.o
ipo: warning #11010: file format not recognized for obj/TorusLB.o
ipo: warning #11010: file format not recognized for obj/WorkDistrib.o
ipo: warning #11010: file format not recognized for obj/pub3dfft.o
ipo: warning #11010: file format not recognized for obj/vmdsock.o
ipo: warning #11010: file format not recognized for obj/parm.o
ipo: warning #11010: file format not recognized for obj/imd.o
ipo: warning #11010: file format not recognized for obj/CompressPsf.o
ipo: warning #11010: file format not recognized for obj/PluginIOMgr.o
ipo: warning #11010: file format not recognized for obj/ParallelIOMgr.o
ipo: warning #11010: file format not recognized for obj/dcdplugin.o
ipo: warning #11010: file format not recognized for obj/jsplugin.o
ipo: warning #11010: file format not recognized for obj/namdbinplugin.o
ipo: warning #11010: file format not recognized for obj/pdbplugin.o
ipo: warning #11010: file format not recognized for obj/psfplugin.o
ipo: warning #11010: file format not recognized for
.rootdir/charm-6.5.0//bin/../lib/libmemory-default.o
ipo: warning #11010: file format not recognized for
.rootdir/charm-6.5.0//bin/../lib/libthreads-default.o
ld: .rootdir/charm-6.5.0//bin/../lib/libldb-rand.o: Relocations in generic
ELF (EM: 181)
ld: .rootdir/charm-6.5.0//bin/../lib/libldb-rand.o: Relocations in generic
ELF (EM: 181)
.rootdir/charm-6.5.0//bin/../lib/libldb-rand.o: could not read symbols:
File in wrong format
Fatal Error by charmc in directory
/home-2/yiyu/M20900-test/NAMD/NAMD_2.9_Source/Linux-x86_64-icc
Command icpc -shared-intel -rdynamic -i-static -O2 -ip -fno-rtti -no-vec
-L.rootdir/tcl-threaded/lib -L.rootdir/fftw/lib -fPIC
-I.rootdir/charm-6.5.0//include -o namd2 -L.rootdir/charm-6.5.0//bin/../lib
-I.rootdir/charm-6.5.0//bin/../include
.rootdir/charm-6.5.0//bin/../lib/libldb-rand.o obj/buildinfo.o
obj/ComputeMoa.o obj/ComputeMsmMsa.o obj/ComputeMsmSerial.o obj/msm.o
obj/msm_longrng.o obj/msm_longrng_sprec.o obj/msm_setup.o
obj/msm_shortrng.o obj/msm_shortrng_sprec.o obj/wkfutils.o obj/common.o
obj/dcdlib.o obj/erf.o obj/fitrms.o obj/main.o obj/mainfunc.o
obj/memusage.o obj/strlib.o obj/AlgSeven.o obj/AlgRecBisection.o
obj/AlgNbor.o obj/AtomMap.o obj/BackEnd.o obj/BroadcastMgr.o
obj/BroadcastClient.o obj/CollectionMaster.o obj/CollectionMgr.o
obj/Communicate.o obj/Compute.o obj/ComputeAngles.o obj/ComputeAniso.o
obj/ComputeBonds.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o
obj/ComputeCrossterms.o obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o
obj/ComputeDPME.o obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o
obj/ComputeEField.o obj/ComputeEwald.o obj/ComputeExt.o
obj/ComputeGBISser.o obj/ComputeGBIS.o obj/ComputeLCPO.o
obj/ComputeFullDirect.o obj/ComputeHomePatch.o obj/ComputeHomePatches.o
obj/ComputeImpropers.o obj/ComputeGlobal.o obj/ComputeGlobalMsgs.o
obj/ComputeGridForce.o obj/ComputeMap.o obj/ComputeMgr.o
obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o
obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o
obj/ComputeNonbondedFEP.o obj/ComputeNonbondedGo.o obj/ComputeNonbondedTI.o
obj/ComputeNonbondedLES.o obj/ComputeNonbondedPProf.o
obj/ComputeNonbondedTabEnergies.o obj/ComputeNonbondedCUDA.o
obj/ComputeNonbondedCUDAExcl.o obj/ComputePatch.o obj/ComputePatchPair.o
obj/ComputePme.o obj/OptPme.o obj/OptPmeRealSpace.o obj/ComputeRestraints.o
obj/ComputeSphericalBC.o obj/ComputeStir.o obj/ComputeTclBC.o
obj/ComputeThole.o obj/ConfigList.o obj/Controller.o obj/ccsinterface.o
obj/DataStream.o obj/DumpBench.o obj/FreeEnergyAssert.o
obj/FreeEnergyGroup.o obj/FreeEnergyLambda.o obj/FreeEnergyLambdMgr.o
obj/FreeEnergyParse.o obj/FreeEnergyRestrain.o obj/FreeEnergyRMgr.o
obj/FreeEnergyVector.o obj/GlobalMaster.o obj/GlobalMasterServer.o
obj/GlobalMasterTest.o obj/GlobalMasterIMD.o obj/GlobalMasterTcl.o
obj/GlobalMasterSMD.o obj/GlobalMasterTMD.o obj/Matrix4Symmetry.o
obj/GlobalMasterSymmetry.o obj/GlobalMasterFreeEnergy.o
obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o obj/colvarmodule.o
obj/colvarparse.o obj/colvar.o obj/colvarvalue.o obj/colvarbias.o
obj/colvarbias_abf.o obj/colvarbias_meta.o obj/colvaratoms.o
obj/colvarcomp.o obj/colvarcomp_angles.o obj/colvarcomp_coordnums.o
obj/colvarcomp_distances.o obj/colvarcomp_protein.o
obj/colvarcomp_rotations.o obj/colvarproxy_namd.o obj/colvargrid.o
obj/GridForceGrid.o obj/GromacsTopFile.o obj/heap.o obj/HomePatch.o
obj/IMDOutput.o obj/InfoStream.o obj/LdbCoordinator.o obj/LJTable.o
obj/Measure.o obj/MGridforceParams.o obj/MStream.o obj/MigrateAtomsMsg.o
obj/Molecule.o obj/Molecule2.o obj/GoMolecule.o obj/NamdCentLB.o
obj/NamdNborLB.o obj/NamdHybridLB.o obj/NamdDummyLB.o obj/NamdState.o
obj/NamdOneTools.o obj/Node.o obj/Output.o obj/Parameters.o
obj/ParseOptions.o obj/Patch.o obj/PatchMgr.o obj/PatchMap.o obj/PDB.o
obj/PDBData.o obj/PmeBase.o obj/PmeKSpace.o obj/PmeRealSpace.o
obj/ProcessorPrivate.o obj/ProxyMgr.o obj/ProxyPatch.o obj/Rebalancer.o
obj/RecBisection.o obj/ReductionMgr.o obj/RefineOnly.o obj/RefineTorusLB.o
obj/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o obj/SimParameters.o
obj/SortAtoms.o obj/Sync.o obj/TclCommands.o obj/TorusLB.o
obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o
obj/CompressPsf.o obj/PluginIOMgr.o obj/ParallelIOMgr.o obj/dcdplugin.o
obj/jsplugin.o obj/namdbinplugin.o obj/pdbplugin.o obj/psfplugin.o
moduleinit26161.o -lmoduleGreedyLB -lmoduleRefineLB -lmoduleHybridLB
-lmoduleNeighborLB .rootdir/charm-6.5.0//bin/../lib/libmemory-default.o
.rootdir/charm-6.5.0//bin/../lib/libthreads-default.o -lck -lconv-cplus-y
-lconv-core -lconv-util -lpthread -lckqt -ldl -ltcl8.5 -ldl -lpthread
-lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB
-lmoduleGreedyLB -lm returned error code 1
charmc exiting...
rm -f moduleinit26161.C moduleinit26161.o
make: *** [namd2] Error 1
Does anyone build on Xeon Phi successfully? I think it must be the issue
caused by the charm++ which is built with -mmic, but I don;t know how to
fix here.
Thanks,
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