Using LSF with Lion Bioscience SRS

SRS is Lion Bioscience's Data Integration Platform, in which data is extracted by all other Lion Bioscience applications or third-party products. LSF works with the batch queue feature of SRS to provide load sharing and allow users to manage their running and completed jobs.

Configuring LSF for SRS

To configure LSF for SRS:

  • LSF HPC features must be enabled.

  • SRS 6.1 and higher, available from Lion Bioscience, must be installed.

During installation, lsfinstall adds the Boolean resource lion to the Resource section of lsf.shared.

If only some of your hosts can accept SRS jobs, configure the Host section of lsf.cluster.cluster_name to identify those hosts.

Edit LSF_ENVDIR/conf/lsf.cluster.cluster_name file and add the srs resource to the hosts that can run Lion jobs:

Begin Host
HOSTNAME    model   type  server  r1m   mem   swp  RESOURCES
hostA       !       !       1     3.5   ()    ()   ()
hostB       !       !       1     3.5   ()    ()   (lion)
hostC       !       !       1     3.5   ()    ()   ()
End Host

You must also configure SRS for batch queues. When SRS batch queueing is enabled, users select from the available batch queues displayed next to the application Launch button in the Application Launch page.

Submitting and monitoring SRS jobs

Use bsub to submit the job, including parameters required for SRS.

As soon as the application is submitted, you can monitor the progress of the job. When applications are launched and batch queues are in use, an icon appears. The icon looks like a "new mail" icon in an email program when jobs are running, and looks like a "read mail" icon when all launched jobs are complete. You can click this icon at any time to:

  • Check the status of running jobs

  • See which jobs have completed

  • Delete jobs

  • Kill running jobs

You can also view the application results or launch another application against those results, using the results of the initial job as input for the next job.