Setting LSF Grid Plug-in Options

You can control options such as the queue, host, and resources. It is recommended that you review the LSF grid plug-in limitations before using the LSF grid plug-in.

Before you begin:

Before you begin working with the LSF grid plug-in, there are some general requirements that are helpful to know.

  • Direct and unrestricted access to run the LSF commands is required.
  • Only command-line codes are supported.
  • If it is necessary to transfer input/output files to/from the grid, this must be done through the “-f” advanced option (see the bsub man page), if available. If it is not available, you must use another mechanism.
  • Jobs can be submitted only under the security credentials of the job submitter in Isight.
  • The job status will be 0 for LSF’s “DONE” status or 1 for any other LSF job status.

  1. Double-click the OS Command component icon .
    The OS Command Component Editor appears.
  2. From the OS Command Component Editor, click the Grid tab.
  3. From the Grid system list, select LSF.
  4. If desired, click Command is Script File.

    If you select this option, Isight assumes that the script defined on the Basic tab is a compatible LSF script that will be spooled to the batch system and executed by LSF as a sequence of commands. The script type must be compatible with the target system. In addition, on Linux systems, the "#!…" syntax must be used within the script to specify the script’s execution shell. The script type selected on the Basic tab is ignored in this situation.

  5. Enter the following information, as desired.

    You can edit one or all of the values. You can also accept the default values.

    OptionDescription
    Queue Specifies the queue where the job will run. You can obtain the available queue names from the LSF bqueues command. Refer to the bsub -q option on the man page for more information.
    Hosts Lists the candidate hosts (space-separated) where the job will run. Refer to the bsub -m option for more information.
    Resources Specifies the resource requirements for the LSF job. Refer to the bsub -R option for more information.
    Number of Parallel Job Processors Enter the number of processors that LSF will reserve for the job. This is important for scheduling MPI-parallel codes with LSF so that the correct resources are reserved. The processors selected by LSF are passed to the MPI code internally by LSF. If you decide to end an LSF job that is running an MPI code, LSF must know what CPUs are being used by the job so that it can handle all of the processes.
  6. Click Automatically transfer input/output files (bsub -f) to automatically transfer files to the grid.

    This process uses only the bsub -f mechanism. In addition, this process requires that rcp does not require passwords and that no firewall is enabled in your LSF setup. This functionality is required only if there is no shared file system in the LSF cluster or with a heterogeneous cluster (mixture of Windows and Linux systems, which cannot have a shared filesystem). The most common use of this option is when Isight runs on a Windows computer and the LSF plug-in is used to run codes on a remote Linux computer. Consult with your local LSF administrator to determine whether this option is enabled.

  7. To use any bsub arguments that are not provided in the component editor, click Advanced to access the Additional Grid Options dialog box.
    1. Type the commands in the large text area using standard bsub command-line option syntax (see the bsub man page). Line breaks are ignored, so the commands can be space-separated and/or on separate lines.

      Typically, these options are those that are used less frequently. However, there may be a need for them in specific scenarios. For example, you could use -G for fairshare scheduling or -M to change the per-process memory limit.

    2. Click OK to return to the OS Command Component Editor.
  8. Click OK to save your changes and to close the OS Command Component Editor.