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How to Submit a MPI Job, using OpenMPI, over TCP/IP

  • This primer describes how to submit parallel MPI jobs, using the OpenMPI implementation (GNU compiler, ORTE), over TCP/IP
  • The executable(s) MUST be compiled and linked using OpenMPI
  • The primer on compilers describe how to compile and link using OpenMPI.
  • An executable compiled w/ an other compiler (Intel, PGI, etc) should not be submitted this way. It may run, but is likely to give you grief.

  • There is a different primer that explains how to submit OpenMPI jobs to access the IB fabric.

To Submit a Job

  • The basics on how to submit a job are described in the primer's introduction on job submission, so read that one first.
  • The job file include the command to launch your OpenMPI program, using the mpirun command.
  • The number of processors and the machinefile (list of hosts to use) is not explicitly specified (hardwired) with the mpirun command.
  • You must invoke the corresponding mpirun (OpenMPI implementation, aka ORTE), see example below.
  • The qsub file (or command)
    • will request a number of processors (CPUs, cores)
    • and specify the corresponding PE (parallel environment), via the qsub command
  • The job scheduler will grant the request and determine the hosts list for that specific job (i.e., the machinefile)
  • The jobs file can specify the PE and the number of processors via an embedded directive (i.e., #$ -pe orte 8)

Example

A Minimal Job File

  • Let's assume that you want to run the OpenMPI executable mycode
    [t]csh syntax [ba]sh syntax
    hydra% cat mycode-csh.job hydra% cat mycode-sh.job
    setenv  OMPI_MCA_plm_rsh_disable_qrsh 1 export OMPI_MCA_plm_rsh_disable_qrsh=1
    /opt/openmpi/bin/mpirun -np $NSLOTS mycode /opt/openmpi/bin/mpirun -np $NSLOTS mycode
  • Note that the env var $NSLOTS is not defined in the job file,
  • The variable NSLOTS will be set by the Grid Engine at execution time and holds the number of granted slots.

A Minimal qsub File

  • The corresponding qsub file is
    [t]csh syntax [ba]sh syntax
    hydra% cat mycode-csh.qsub hydra% cat mycode-sh.qsub
    qsub -pe orte 8 \ qsub -pe orte 8 \
    -cwd -j y \ -cwd -j y \
    -N mycode \ -N mycode \
    -o mycode.log \ -o mycode.log \
    mycode-csh.job -S /bin/sh \
      mycode-sh.job

NOTE

  • The above example requests 8 processors (CPUs, cores); adjust that number to your needs.
  • The flag -pe orte 8 is the flag that tells SGE to use the parallel environment (PE) orte and requests 8 processors.
    • ORTE is the PE to use with and only with OpenMPI executables.
    • the -pe orte 8 flag can be embedded (using #$) in the job file, like any other one
  • An other page describes in more detail the available queues.
  • For OpenMPI over TPC/IP use the queues, sTN.q, mTN.q or lTN.q.
    These correspond to the short, medium and long execution time respectively, (the queue is specified with the -q flag).
  • Options passed to qsub override embedded directives in the job file (including -pe or -q)

Details for Experienced Users

  • At run-time, the scheduler defines the following OpenMPI specific variables:
    NSLOTS The granted number of slots, or number of processors for this MPI run
    PE_HOSTFILE The file name that lists the distribution of processors over the compute nodes

  • Hence you can use, in the jobs file, the commands
    echo number of slots is $NSLOTS to print out the granted value of NSLOTS
    echo pe host file is $PE_HOSTFILE  
    cat $PE_HOSTFILE to print out the name and content of the PE_HOSTFILE

More Examples

Look, on hydra, in ~hpc/tests/mpi/gnu for some examples.

  • To execute them, create a test directory and extract the compressed tar-ball:
hydra% mkdir -p ~/tests/mpi/gnu/orte
hydra% cd ~/tests/mpi/gnu/orte
hydra% tar xvzf ~hpc/tests/mpi/gnu/orte/tests.tgz

  • Build the executable
hydra% make

  • Run (some) of the tests
hydra% source hello-csh.qsub
hydra% source hello-sh.qsub
hydra% qsub hello-csh-opts.job
hydra% qsub -pe orte 4 hello-csh-opts.job
hydra% qsub -pe orte 4 hello-sh-opts.job

Run only one job at a time, use qstat to monitor the job, then look at the hello.log file.

-- SylvainKorzennikHPCAnalyst - 20 Jan 2012

Topic revision: r7 - 2012-07-12 - SylvainKorzennikHPCAnalyst
 
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