NAMD-MPI compilation on P4 cluster

From: Amit Paliwal (paliwal_at_jhu.edu)
Date: Sat Sep 04 2004 - 18:37:55 CDT

Hi,
I am facing some problems which I believe have been previously discussed
in this forum. I am trying to compile NAMD with MPI on this intel
pentium 4 cluster that is running on redhat Linux ES and has intel c++
compilers. Not getting anywhere with icc I decided to go with gcc.

1) I was able to compile charm++ by the following command:

  ./build charm++ mpi-linux gcc --no-shared -I/usr/local/mpich/include
-l/usr/local/mpich/lib -lpthread -lpmpich

( i found the above command in mailing list but what does --no-shared do
? And does it matter if you link .so or .a mpich libraries ? while
compiling it does print that it cant find fortran 90 compiler but doesnt
complain further ... )

I then moved mpi-linux-gcc to mpi-linux directory and updated all the
soft links in charm directory.

2) I then ran into issues with fftw and had to download redhat 9 version
of compiled fftw library. ( Compiling separately with g++ was giving
some problems but redhat 9.0 seems to be working )

3) I ran the following command:
./config fftw Linux-i686-MPI

cd Linux-i686-MPI

make

Below is the final fragment of output and I cant seem to figure out what
seems to be going wrong. Any comments are welcome.

thanks ,
Amit.

-----------------------------------------------------------------------

-L/home/osu3704/NAMD_2.5_Source/fftw-linux/lib
-L/home/osu3704/fftw-linux/lib -lsrfftw -lsfftw \
  \
-lm -o namd2
Verbose mode set
passing unrecognized option -march=pentiumpro to all compilers and linkers
passing unrecognized option -ffast-math to all compilers and linkers
passing unrecognized option -static to all compilers and linkers
Adding file obj/buildinfo.o...
Adding file obj/common.o...
Adding file obj/dcdlib.o...
Adding file obj/erf.o...
Adding file obj/main.o...
Adding file obj/mainfunc.o...
Adding file obj/memusage.o...
Adding file obj/strlib.o...
Adding file obj/AlgSeven.o...
Adding file obj/AlgRecBisection.o...
Adding file obj/AlgNbor.o...
Adding file obj/AtomMap.o...
Adding file obj/BackEnd.o...
Adding file obj/BroadcastMgr.o...
Adding file obj/BroadcastClient.o...
Adding file obj/CollectionMaster.o...
Adding file obj/CollectionMgr.o...
Adding file obj/Communicate.o...
Adding file obj/Compute.o...
Adding file obj/ComputeAngles.o...
Adding file obj/ComputeBonds.o...
Adding file obj/ComputeConsForce.o...
Adding file obj/ComputeConsForceMsgs.o...
Adding file obj/ComputeCylindricalBC.o...
Adding file obj/ComputeDihedrals.o...
Adding file obj/ComputeDPME.o...
Adding file obj/ComputeDPMEMsgs.o...
Adding file obj/ComputeDPMTA.o...
Adding file obj/ComputeEField.o...
Adding file obj/ComputeExt.o...
Adding file obj/ComputeFullDirect.o...
Adding file obj/ComputeHomePatch.o...
Adding file obj/ComputeHomePatches.o...
Adding file obj/ComputeImpropers.o...
Adding file obj/ComputeGlobal.o...
Adding file obj/ComputeGlobalMsgs.o...
Adding file obj/ComputeMap.o...
Adding file obj/ComputeMgr.o...
Adding file obj/ComputeNonbondedSelf.o...
Adding file obj/ComputeNonbondedPair.o...
Adding file obj/ComputeNonbondedUtil.o...
Adding file obj/ComputeNonbondedStd.o...
Adding file obj/ComputeNonbondedFEP.o...
Adding file obj/ComputeNonbondedLES.o...
Adding file obj/ComputePatch.o...
Adding file obj/ComputePatchPair.o...
Adding file obj/ComputePme.o...
Adding file obj/ComputeRestraints.o...
Adding file obj/ComputeSphericalBC.o...
Adding file obj/ComputeStir.o...
Adding file obj/ConfigList.o...
Adding file obj/Controller.o...
Adding file obj/ccsinterface.o...
Adding file obj/DataStream.o...
Adding file obj/DumpBench.o...
Adding file obj/FreeEnergyAssert.o...
Adding file obj/FreeEnergyGroup.o...
Adding file obj/FreeEnergyLambda.o...
Adding file obj/FreeEnergyLambdMgr.o...
Adding file obj/FreeEnergyParse.o...
Adding file obj/FreeEnergyRestrain.o...
Adding file obj/FreeEnergyRMgr.o...
Adding file obj/FreeEnergyVector.o...
Adding file obj/GlobalMaster.o...
Adding file obj/GlobalMasterServer.o...
Adding file obj/GlobalMasterTest.o...
Adding file obj/GlobalMasterIMD.o...
Adding file obj/GlobalMasterTcl.o...
Adding file obj/GlobalMasterSMD.o...
Adding file obj/GlobalMasterFreeEnergy.o...
Adding file obj/GlobalMasterEasy.o...
Adding file obj/GlobalMasterMisc.o...
Adding file obj/GromacsTopFile.o...
Adding file obj/heap.o...
Adding file obj/HomePatch.o...
Adding file obj/IMDOutput.o...
Adding file obj/InfoStream.o...
Adding file obj/LdbCoordinator.o...
Adding file obj/LJTable.o...
Adding file obj/Measure.o...
Adding file obj/MStream.o...
Adding file obj/MigrateAtomsMsg.o...
Adding file obj/Molecule.o...
Adding file obj/NamdCentLB.o...
Adding file obj/NamdNborLB.o...
Adding file obj/NamdState.o...
Adding file obj/NamdOneTools.o...
Adding file obj/Node.o...
Adding file obj/Output.o...
Adding file obj/Parameters.o...
Adding file obj/ParseOptions.o...
Adding file obj/Patch.o...
Adding file obj/PatchMgr.o...
Adding file obj/PatchMap.o...
Adding file obj/PDB.o...
Adding file obj/PDBData.o...
Adding file obj/PmeBase.o...
Adding file obj/PmeKSpace.o...
Adding file obj/PmeRealSpace.o...
Adding file obj/ProcessorPrivate.o...
Adding file obj/ProxyMgr.o...
Adding file obj/ProxyPatch.o...
Adding file obj/Rebalancer.o...
Adding file obj/RecBisection.o...
Adding file obj/ReductionMgr.o...
Adding file obj/RefineOnly.o...
Adding file obj/ScriptTcl.o...
Adding file obj/Sequencer.o...
Adding file obj/Set.o...
Adding file obj/Settle.o...
Adding file obj/SimParameters.o...
Adding file obj/Sync.o...
Adding file obj/TclCommands.o...
Adding file obj/WorkDistrib.o...
Adding file obj/pub3dfft.o...
Adding file obj/vmdsock.o...
Adding file obj/parm.o...
Adding file obj/imd.o...

charmc> ----------- Module dependency search ------------
charmc> ----------- Module dependency search complete ------------
Adding registration for module NeighborLB
Adding registration for module commlib
charmc: Executing g++ -Wno-deprecated -D__CHARMC__=1
-I/usr/local/mpich/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3
-march=pentiumpro -ffast-math -static -c moduleinit.C -o moduleinit.o
charmc: Executing g++ -rdynamic -O3 -march=pentiumpro -ffast-math
-static -L/usr/local/mpich/lib
-L/home/osu3704/NAMD_2.5_Source/fftw-linux/lib
-L/home/osu3704/fftw-linux/lib
-I/home/osu3704/NAMD_2.5_Source/charm/mpi-linux/include -o namd2
-L/home/osu3704/NAMD_2.5_Source/charm/mpi-linux/bin/../lib
-I/home/osu3704/NAMD_2.5_Source/charm/mpi-linux/bin/../include
/home/osu3704/NAMD_2.5_Source/charm/mpi-linux/bin/../lib/libldb-rand.o
obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.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/ComputeBonds.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o
obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o
obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.o
obj/ComputeExt.o obj/ComputeFullDirect.o obj/ComputeHomePatch.o
obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o
obj/ComputeGlobalMsgs.o obj/ComputeMap.o obj/ComputeMgr.o
obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o
obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o
obj/ComputeNonbondedFEP.o obj/ComputeNonbondedLES.o obj/ComputePatch.o
obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o
obj/ComputeSphericalBC.o obj/ComputeStir.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/GlobalMasterFreeEnergy.o
obj/GlobalMasterEasy.o obj/GlobalMasterMisc.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/MStream.o
obj/MigrateAtomsMsg.o obj/Molecule.o obj/NamdCentLB.o obj/NamdNborLB.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/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o
obj/SimParameters.o obj/Sync.o obj/TclCommands.o obj/WorkDistrib.o
obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o moduleinit.o -lpmpich
-lpthread -lmoduleNeighborLB -lmodulecommlib
/home/osu3704/NAMD_2.5_Source/charm/mpi-linux/bin/../lib/libmemory-default.o
/home/osu3704/NAMD_2.5_Source/charm/mpi-linux/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -lpmpich -ldl -lz
-lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib
obj/dcdlib.o(.text+0x1066): In function `write_dcdheader(int, char*,
int, int, int, int, int, double, int)':
: Using 'getpwuid' in statically linked applications requires at runtime
the shared libraries from the glibc version used for linking
obj/vmdsock.o(.text+0x96): In function `vmdsock_connect(void*, char
const*, int)':
: Using 'gethostbyname' in statically linked applications requires at
runtime the shared libraries from the glibc version used for linking
/usr/local/mpich/lib/libpmpich.a(intra_fns_new.o)(.text+0x2e28): In
function `intra_Reduce':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(intra_fns_new.o)(.text+0x2f2e): In
function `intra_Reduce':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x52): In function
`async_event_handler':
: undefined reference to `VAPI_event_record_sym'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x5c): In function
`async_event_handler':
: undefined reference to `VAPI_event_syndrome_sym'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x301): In function
`MPID_VIA_Init':
: undefined reference to `VAPI_open_hca'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x318): In function
`MPID_VIA_Init':
: undefined reference to `EVAPI_get_hca_hndl'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x355): In function
`MPID_VIA_Init':
: undefined reference to `VAPI_query_hca_port_prop'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x398): In function
`MPID_VIA_Init':
: undefined reference to `EVAPI_set_async_event_handler'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x6b7): In function
`MPID_VIA_Finalize':
: undefined reference to `EVAPI_clear_async_event_handler'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x788): In function
`ib_vapi_init':
: undefined reference to `VAPI_alloc_pd'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x7b8): In function
`ib_vapi_init':
: undefined reference to `VAPI_create_cq'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x8d3): In function
`ib_vapi_init':
: undefined reference to `VAPI_create_qp'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x919): In function
`ib_vapi_init':
: undefined reference to `VAPI_query_qp'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x966): In function
`ib_vapi_init':
: undefined reference to `VAPI_strerror'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0xb4e): In function
`ib_vapi_qp_enable':
: undefined reference to `VAPI_modify_qp'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0xc6f): In function
`ib_vapi_qp_enable':
: undefined reference to `VAPI_modify_qp'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0xd9a): In function
`ib_vapi_qp_enable':
: undefined reference to `VAPI_modify_qp'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0xe43): In function
`ib_vapi_qp_enable':
: undefined reference to `VAPI_query_qp'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x1212): In function
`ib_vapi_qp_enable':
: undefined reference to `VAPI_register_mr'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x1245): In function
`ib_vapi_qp_enable':
: undefined reference to `VAPI_strerror'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x134d): In function
`ib_vapi_qp_enable':
: undefined reference to `VAPI_register_mr'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x1380): In function
`ib_vapi_qp_enable':
: undefined reference to `VAPI_strerror'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x16fc): In function
`ib_vapi_finalize':
: undefined reference to `VAPI_deregister_mr'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x171a): In function
`ib_vapi_finalize':
: undefined reference to `VAPI_deregister_mr'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x1780): In function
`ib_vapi_finalize':
: undefined reference to `VAPI_destroy_qp'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x17d4): In function
`ib_vapi_finalize':
: undefined reference to `VAPI_destroy_cq'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x181e): In function
`ib_vapi_finalize':
: undefined reference to `VAPI_dealloc_pd'
/usr/local/mpich/lib/libpmpich.a(viainit.o)(.text+0x1845): In function
`ib_vapi_finalize':
: undefined reference to `EVAPI_release_hca_hndl'
/usr/local/mpich/lib/libpmpich.a(viacheck.o)(.text+0x170): In function
`poll_error':
: undefined reference to `VAPI_wc_status_sym'
/usr/local/mpich/lib/libpmpich.a(viacheck.o)(.text+0x17a): In function
`poll_error':
: undefined reference to `VAPI_cqe_opcode_sym'
/usr/local/mpich/lib/libpmpich.a(viacheck.o)(.text+0x58a): In function
`MPID_DeviceCheck':
: undefined reference to `VAPI_poll_cq'
/usr/local/mpich/lib/libpmpich.a(viacheck.o)(.text+0x1492): In function
`viadev_incoming_eager_start':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(viacheck.o)(.text+0x169e): In function
`viadev_incoming_eager_next':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(viacheck.o)(.text+0x1bbb): In function
`viadev_rendezvous_push':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(viacheck.o)(.text+0x1e8a): In function
`viadev_incoming_r3_data':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(viacheck.o)(.text+0x22a2): In function
`viutil_spinandwaitcq':
: undefined reference to `VAPI_poll_cq'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x139): In function
`viadev_backlog_send':
: undefined reference to `VAPI_post_sr'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x158): In function
`viadev_backlog_send':
: undefined reference to `EVAPI_post_inline_sr'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x18b): In function
`viadev_backlog_send':
: undefined reference to `VAPI_strerror'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x2fc): In function
`viadev_post_send':
: undefined reference to `VAPI_post_sr'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x31b): In function
`viadev_post_send':
: undefined reference to `EVAPI_post_inline_sr'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x34e): In function
`viadev_post_send':
: undefined reference to `VAPI_strerror'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x556): In function
`post_fast_rdma':
: undefined reference to `VAPI_post_sr'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x57a): In function
`post_fast_rdma':
: undefined reference to `EVAPI_post_inline_sr'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x5ad): In function
`post_fast_rdma':
: undefined reference to `VAPI_strerror'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x6f9): In function
`post_fast_rdma_with_completion':
: undefined reference to `VAPI_post_sr'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x71d): In function
`post_fast_rdma_with_completion':
: undefined reference to `EVAPI_post_inline_sr'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x750): In function
`post_fast_rdma_with_completion':
: undefined reference to `VAPI_strerror'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x959): In function
`viadev_post_rdmawrite':
: undefined reference to `VAPI_post_sr'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x978): In function
`viadev_post_rdmawrite':
: undefined reference to `EVAPI_post_inline_sr'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0x9ab): In function
`viadev_post_rdmawrite':
: undefined reference to `VAPI_strerror'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0xa90): In function
`viadev_post_recv':
: undefined reference to `VAPI_post_rr'
/usr/local/mpich/lib/libpmpich.a(viapriv.o)(.text+0xac3): In function
`viadev_post_recv':
: undefined reference to `VAPI_strerror'
/usr/local/mpich/lib/libpmpich.a(vbuf.o)(.text+0x76): In function
`deallocate_vbufs':
: undefined reference to `VAPI_deregister_mr'
/usr/local/mpich/lib/libpmpich.a(vbuf.o)(.text+0x2b4): In function
`allocate_vbuf_region':
: undefined reference to `_intel_fast_memset'
/usr/local/mpich/lib/libpmpich.a(vbuf.o)(.text+0x399): In function
`allocate_vbuf_region':
: undefined reference to `VAPI_register_mr'
/usr/local/mpich/lib/libpmpich.a(vbuf.o)(.text+0x3cc): In function
`allocate_vbuf_region':
: undefined reference to `VAPI_strerror'
/usr/local/mpich/lib/libpmpich.a(dreg.o)(.text+0x838): In function
`dreg_evict':
: undefined reference to `VAPI_deregister_mr'
/usr/local/mpich/lib/libpmpich.a(dreg.o)(.text+0x86b): In function
`dreg_evict':
: undefined reference to `VAPI_strerror'
/usr/local/mpich/lib/libpmpich.a(dreg.o)(.text+0xb2c): In function
`dreg_new_entry':
: undefined reference to `VAPI_register_mr'
/usr/local/mpich/lib/libpmpich.a(dreg.o)(.text+0xbd5): In function
`dreg_new_entry':
: undefined reference to `VAPI_strerror'
/usr/local/mpich/lib/libpmpich.a(mpid_smpi.o)(.text+0x889): In function
`smpi_finish':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(mpid_smpi.o)(.text+0xd08): In function
`smpi_finish':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(mpid_smpi.o)(.text+0xf08): In function
`smpi_finish':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(mpid_smpi.o)(.gnu.linkonce.t.MPID_SMP_Eagerb_save_short+0x87):
In function `MPID_SMP_Eagerb_save_short':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(mpid_smpi.o)(.gnu.linkonce.t.MPID_SMP_Eagerb_unxrecv_start_short+0x2c):
In function `MPID_SMP_Eagerb_unxrecv_start_short':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(mpid_smpi.o)(.gnu.linkonce.t.MPID_SMP_Eagerb_isend_short+0x103):
more undefined references to `_intel_fast_memcpy' follow
/usr/local/mpich/lib/libpmpich.a(irecv.o)(.text+0x136): In function
`MPI_Irecv':
: undefined reference to `_intel_fast_memset'
/usr/local/mpich/lib/libpmpich.a(pkutil.o)(.text+0x296): In function
`MPIR_Pack2':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(pkutil.o)(.text+0x744): In function
`MPIR_Unpack2':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(viasend.o)(.text+0x287): In function
`MPID_VIA_self_start':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(viasend.o)(.text+0x339): In function
`MPID_VIA_self_start':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(viasend.o)(.text+0x4fd): In function
`MPID_VIA_self_finish':
: undefined reference to `_intel_fast_memcpy'
/usr/local/mpich/lib/libpmpich.a(viasend.o)(.text+0x77f): more undefined
references to `_intel_fast_memcpy' follow
collect2: ld returned 1 exit status
Fatal Error by charmc in directory
/home/osu3704/NAMD_2.5_Source/Linux-i686-MPI
Command g++ -rdynamic -O3 -march=pentiumpro -ffast-math -static
-L/usr/local/mpich/lib -L/home/osu3704/NAMD_2.5_Source/fftw-linux/lib
-L/home/osu3704/fftw-linux/lib
-I/home/osu3704/NAMD_2.5_Source/charm/mpi-linux/include -o namd2
-L/home/osu3704/NAMD_2.5_Source/charm/mpi-linux/bin/../lib
-I/home/osu3704/NAMD_2.5_Source/charm/mpi-linux/bin/../include
/home/osu3704/NAMD_2.5_Source/charm/mpi-linux/bin/../lib/libldb-rand.o
obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.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/ComputeBonds.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o
obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o
obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.o
obj/ComputeExt.o obj/ComputeFullDirect.o obj/ComputeHomePatch.o
obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o
obj/ComputeGlobalMsgs.o obj/ComputeMap.o obj/ComputeMgr.o
obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o
obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o
obj/ComputeNonbondedFEP.o obj/ComputeNonbondedLES.o obj/ComputePatch.o
obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o
obj/ComputeSphericalBC.o obj/ComputeStir.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/GlobalMasterFreeEnergy.o
obj/GlobalMasterEasy.o obj/GlobalMasterMisc.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/MStream.o
obj/MigrateAtomsMsg.o obj/Molecule.o obj/NamdCentLB.o obj/NamdNborLB.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/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o
obj/SimParameters.o obj/Sync.o obj/TclCommands.o obj/WorkDistrib.o
obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o moduleinit.o -lpmpich
-lpthread -lmoduleNeighborLB -lmodulecommlib
/home/osu3704/NAMD_2.5_Source/charm/mpi-linux/bin/../lib/libmemory-default.o
/home/osu3704/NAMD_2.5_Source/charm/mpi-linux/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt -lpmpich -ldl -lz
-lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib returned error
code 1
charmc exiting...

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