Hi Ted, Does the "default mpirun command" implementation match the build environment for quest_ompi.x ? ie., what mpi implementation (mpich, LAM/MPI, OPENMPI, or other) was quest_ompi.x compiled/linked with? and does that match the result of "which mpirun"? You might try running a job using your PBS system that simply executes the which mpirun command and see what you get. HTH, Mac McCalla Houston
________________________________ From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On Behalf Of Ted Yu Sent: 06 February 2009 10:02 To: Open MPI Users; Ralph Castain Subject: Re: [OMPI users] Global Communicator Just to make sure, because I have to use open mpi for this program: I'm using the default mpirun command. When I type "man mpirun", these are the first few lines: MPIRUN(1) OPEN MPI COMMANDS MPIRUN(1) NAME orterun, mpirun, mpiexec - Execute serial and parallel jobs in Open MPI. Note: mpirun, mpiexec, and orterun are all exact synonyms for each other. Using any of the names will result in exactly identical behav- ior. Ted --- On Fri, 2/6/09, Ralph Castain <r...@lanl.gov> wrote: From: Ralph Castain <r...@lanl.gov> Subject: Re: [OMPI users] Global Communicator To: ted...@wag.caltech.edu, "Open MPI Users" <us...@open-mpi.org> Date: Friday, February 6, 2009, 7:55 AM Hi Ted From what I can tell, you are not using Open MPI, but mpich's mpirun. You might want to ask for help on their mailing list. Ralph On Feb 6, 2009, at 8:49 AM, Ted Yu wrote: Thanx for the reply. I guess I should go back a step: I had used the openmpi version on my system which is simply: "mpirun -machinefile $PBS_NODEFILE -np $NPROCS ${CODE} >/ul/tedhyu/fuelcell/HOH/test/HH.out" This did not work because I was just getting a blank output. I tried this older version because at least i was getting an output. "/opt/mpich-1.2.5.10-ch_p4-gcc/bin/mpirun -machinefile $PBS_NODEFILE -np $NPROCS ${CODE} >/ul/tedhyu/fuelcell/HOH/test/HH.out" I think this older version is failing me for whatever reason. Do you have any clue? I read somewhere that new versions of mpirun adds extra commandline arguments to the end of the line. Therefore the newer version of mpirun may be not be giving an output because it sees all extra commandline arguments after my output file >/ul/tedhyu/fuelcell/HOH/test/HH.out This is where I'm reading that there are extra commandline arguments for a version of mpirun: https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/2008-February/02 9333.html Again, I'm new at this, and I'm just guessing. Any ideas of where to turn would be helpful! Ted --- On Thu, 2/5/09, doriankrause <doriankra...@web.de> wrote: From: doriankrause <doriankra...@web.de> Subject: Re: [OMPI users] Global Communicator To: ted...@wag.caltech.edu, "Open MPI Users" <us...@open-mpi.org> Date: Thursday, February 5, 2009, 11:14 PM Ted Yu wrote: > I'm trying to run a job based on openmpi. For some reason, the program and the global communicator are not in sync and it reads that there is only one processors, whereas, there should be 2 or more. Any advice on where to look? Here is my PBS script. Thanx! > > PBS SCRIPT: > #!/bin/sh > ### Set the job name > #PBS -N HH > ### Declare myprogram non-rerunable > #PBS -r n > ### Combine standard error and standard out to one file. > #PBS -j oe > ### Have PBS mail you results > #PBS -m ae > #PBS -M ted...@wag.caltech.edu > ### Set the queue name, given to you when you get a reservation. > #PBS -q workq > ### Specify the number of cpus for your job. This example will run on 32 cpus > ### using 8 nodes with 4 processes per node. > #PBS -l nodes=1:ppn=2,walltime=70:00:00 > # Switch to the working directory; by default PBS launches processes from your home directory. > # Jobs should only be run from /home, /project, or /work; PBS returns results via NFS. > PBS_O_WORKDIR=/temp1/tedhyu/HH > export CODE=/project/source/seqquest/seqquest_source_v261j/hive_CentOS4.5_paral lel/build_261j/quest_ompi.x > > echo Working directory is $PBS_O_WORKDIR > mkdir -p $PBS_O_WORKDIR > cd $PBS_O_WORKDIR > rm -rf * > cp /ul/tedhyu/fuelcell/HOH/test/HH.in ./lcao.in > cp /ul/tedhyu/atom_pbe/* . > echo Running on host `hostname` > echo Time is `date` > echo Directory is `pwd` > echo This jobs runs on the following processors: > echo `cat $PBS_NODEFILE` > Number=`wc -l $PBS_NODEFILE | awk '{print $1}'` > > export Number > echo ${Number} > # Define number of processors > NPROCS=`wc -l < $PBS_NODEFILE` > # And the number or hosts > NHOSTS=`cat $PBS_NODEFILE|uniq|wc -l` > echo This job has allocated $NPROCS cpus > echo NHOSTS > #mpirun -machinefile $PBS_NODEFILE ${CODE} >/ul/tedhyu/fuelcell/HOH/test/HH.out > #mpiexec -np 2 ${CODE} >/ul/tedhyu/fuelcell/HOH/test/HH.out > /opt/mpich-1.2.5.10-ch_p4-gcc/bin/mpirun -machinefile $PBS_NODEFILE -np $NPROCS ${CODE} >/ul/tedhyu/fuelcell/HOH/test/HH.out > cd .. > rm -rf HH > > > Please note, that you are mixing Open MPI (API/Library) with MPICH (mpirun). This is a mistake I like to make, too. If you use the ompi mpiexec program, it probably works. Dorian > > > > ------------------------------------------------------------------------ > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users _______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users
