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Integrating Sun N1 Grid Engine Software With Globus Toolkit

Currently, there is no utility software provided by Globus that provides integration between the Globus Toolkit and Sun N1 Grid Engine software (as there is for other cluster job managers such as PBS or LSF), but there are a few open source packages that enable Globus Toolkit to submit jobs to Sun N1 Grid Engine software job managers.

For this article, we used the integration software provided by the London e-Science Centre. For more information, refer to http://www.lesc.ic.ac.uk/projects/epic-gt-sge.html.

To Integrate Sun N1 Grid Engine Software With Globus Toolkit

  1. Download the following three packages:

    • globus_gram_job_manager_setup_sge-0.11.tar.gz, which contains Perl code to generate SGE scripts from RSL specification

    • mmjfs_sge_setup-0.0.tar.gz, which configures the MasterSGEManagedJobFactoryService as a Globus Toolkit 3.x service

    • mjs_sge_setup-0.0.tar.gz, which provides the job execution service used by MMJFS

  2. Copy the packages to your $<GLOBUS_SOURCE_INSTALLER> directory, then install them.

  3. $ gpt-build globus_gram_job_manager_setup_sge-0.11.tar.gz
    $ gpt-build mmjfs_sge_setup-0.0.tar.gz
    $ gpt-build mjs_sge_setup-0.0.tar.gz
    $ gpt-postinstall

    It is possible for your MPI distribution not to be properly detected during the installation.

  4. If the MPI distribution is not detected, edit the <GLOBUS_LOCATION>/lib/perl/Globus/GRAM/JobManager/sge.pm file, checking the line defining the mpirun variable.

  5. This line should point to your mpirun executable.

    1. If this line does not point to your mpirun executable, modify the value of the variable to do so.

    2. Check the pe_mpi variable to ensure that it has the value mpi or mpich corresponding to the MPI parallel environment configured for Sun N1 Grid Engine software.

    There is one minor bug in the integration code, specifically in the section that translates RSL requests to Sun N1 Grid Engine software job scripts, that causes MPI jobs to fail.

  6. To fix the minor bug in the integration code, edit the sge.pm script at the section containing the lines "Where to write output and error?" by modifying the lines on the else branch:

  7.  $sge_job_script->print("#\$ -o " . $description->stdout() . ".real\n");
      $sge_job_script->print("#\$ -e " . $description->stderr() . ".real\n");

    to read as follows:

    $sge_job_script->print("#\$ -o " . $description->stdout() . "\n");
      $sge_job_script->print("#\$ -e " . $description->stderr() . "\n");

    The problem is that for some job runs, when the script tries to create the /dev/null.real files and fails, the job terminates in error. This fix solves the problem.

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