From: Nicolas Sapay (nsapay_at_ucalgary.ca)
Date: Wed Apr 25 2007 - 11:50:59 CDT
I realize that my question lacked of precision... so
1. For the failure of the ld_test I have realized there is pretty useful
README file in each test directory... Problem solved!
2. The compilation of NAMD still failed and I can't identified the
problem for the moment
3. However, it seems that a pre-build version of NAMD (Linus-i686) works
now on our system. I don't now why exactly this was not the case before
since we have not modify or update our PBS server (Torque). It may be
because I have have to my path the path to /opt/mpich/gnu/bin which was
not the case initially (for some reason, only the path to mpiexec was
defined).
Thanks
Nicolas
Nicolas Sapay wrote:
> Hi all NAMDers,
>
> I try to install and run NAMD2.6 on our cluster (Intel Xeon 3.4GHz
> Irwindale) . I'm pretty new on this cluster and more generally on
> cluster management. So, sorry if some questions looks obvious for some
> people.
>
> 1. First of all I have tried to run a pre-build binary (Linus-i686).
> Of course it didn't work : jobs were arbitrarily aborted before the
> end of the computation without error message (command :
> path/to/charmrun ++verbose +p$nproc ++nodelist path/to/nodelist
> /path/to/namd2 path/to/namd.conf > namd.log)
>
> 2. I have try to run namd2 with mpiexec, suspecting a problem with the
> charmrun build (command : mpiexec -p $nproc /path/to/namd2
> path/to/namd.conf > namd.log). mpiexec terminated the job with the
> following error:
> ...
> Info: Found 20 config files.
> Info: Changed directory to
> /home/nsapay/namd/popc_x1/nve_Vtrunc_Etrunc_C100_T0_P1/run03
> Info: Configuration file is part01.conf
> Info: Configuration file is -p4wd
> FATAL ERROR: Simulation config file is not accessible.
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Simulation config file is not accessible.
>
> Charm++ fatal error:
> FATAL ERROR: Simulation config file is not accessible.
>
> Stack Traceback:
> [0] main+0x1bf [0x80df183]
> [1] __libc_start_main+0xd3 [0x2cae23]
> [2] _ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_c+0x59
> [0x80dba71]
> mpiexec: process_obit_event: evt 3 task 0 on compute-10-19.local stat
> 262.
> mpiexec: read_p4_master_port: got port -1.
> mpiexec: Warning: task 0 died with signal 6 (Aborted).
>
> There was clearly a porblem with namd2 which seen some mpi options as
> input files
>
> 3. I have then tried to compile NAMD2.6 from source. Firstly, I have
> built charm++ from the charm-5.9 directory:
> ./build charm++ mpi-linux --basedir=/opt/mpich/gnu --no-build-shared
> -verbose -O -DCMK_OPTIMIZE=1
>
> The build was successful and passed the megatest. However, the lb_test
> during the make command with the error:
> ...
> /usr/bin/ld: cannot find -lmetis
> collect2: ld returned 1 exit status
>
> Then, I have tired to build namd2. I have set TCLDIR, FFTDIR and
> CHARMBASE to the correct locations, configure the installation
> (command: ./config Linux-i686-MPI) and run make. The compilation
> failed with the following error:
> ...
> /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o(.text+0xdd2):
> first defined here
> /usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed
> from 111 in
> /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
> to 154 in /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../libc.a(malloc.o)
> collect2: ld returned 1 exit status
> Fatal Error by charmc in directory
> /home/nsapay/tmp/NAMD_2.6_Source/Linux-i686-MPI
> Command mpiCC -rdynamic -L/opt/mpich/gnu/lib
> -I/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/include
> -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -march=pentiumpro -ffast-math -static
> -L/opt/mpich/gnu/lib -o namd2
> -L/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib
> -I/home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../include
> /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libldb-rand.o
> obj/buildinfo.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/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/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/ComputeNonbondedPProf.o obj/ComputePatch.o obj/ComputePatchPair.o
> obj/ComputePme.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o
> obj/ComputeStir.o obj/ComputeTclBC.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/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 obj/dcdplugin.o moduleinit21980.o
> -lmoduleNeighborLB -lmodulecommlib
> /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libmemory-default.o
> /home/nsapay/tmp/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib/libthreads-default.o
> -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -lmpich -ldl -lm
> -lmoduleNeighborLB -lmodulecommlib -lm returned error code 1
> charmc exiting...
> make: *** [namd2] Error 1
>
> Now, I don't now exactly what I can do. Does anyone have already deal
> with theses kinds of errors? Any advice is welcome!
>
> Thanks
>
> Nicolas
>
> ps: I have enclose to the message the make.o and make.e of the namd2
> building
>
-- [ Nicolas SAPAY, Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University drive NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311
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