Need help to build NAMD on Xeon Phi

[Vivian_Lin]

I am trying to run NAMD on Xeon Phi, I have compiled charm++ with -mmic flag in advance, however, when I try to compile NAMD. I keep on get this error after link to Charm:

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 moduleinit31002.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 moduleinit31002.C moduleinit31002.o
make: *** [namd2] Error 1

I didn't get a  lot of answers from the other people's experience, could anyone help me with it?

Thanks,

[Sumedh_N_Intel]

The NAMD port for the Intel Xeon Phi coprocessor hasn't been released yet and currently is not completely stable. Hence, there are no concrete set of directions for porting the code. I will let you know as soon as the initial version is released. 

[Vivian_Lin]

Thanks Sumedh

[CH_Cheng]

 If the version of NAMD for Xeon Phi is released (beta version is OK), please let me know it too. Thanks a lot!
 

[TaylorIoTKidd]

I am working on finding the status of the port. This is a holiday weekend so I may not get you a response until later next week.

--
Taylor
 

[TaylorIoTKidd]

Intel's NAMD optimizations have been passed to the NAMD team. It's up to them to verify and make them available to the NAMD community. Intel continues to work on additional optimizations and will pass those to the NAMD team when they are mature enough.

--
Taylor