#118 bsub runCA

Assembly_pipeline
open
Jason Miller
Feature (48)
5
2010-01-25
2010-01-21
Anonymous
No

I'm trying to want to do some distributed computation with runCA using bsub on a LSF.
Has anyone tried it, or documented bsub commands corresponding to qsub commands?

Best,
Magdalena Zarowiecki
Wellcome Trust Sanger Institute

Discussion

  • Jason Miller
    Jason Miller
    2010-01-25

    • assigned_to: nobody --> jasonmiller9704
     
  • Jason Miller
    Jason Miller
    2010-01-25

    We don't run the LSF grid job control engine. Do you know SGE and LSF? If so, then we would be much obliged if you could help us enhance our grid support by porting our SGE commands to LSF. Maybe you could explore the issue and report back. For starters, you could identify yourself by logging in to Source Forge and submitting a new feature request. (This request is attributed to Nobody because the submitter wasn't logged in.) Then, consider that we use three SGE features. (1) submit a job (2) submit a series of jobs (3) submit a job but don't run until after this other job finishes. What are the equivalent LSF commands? To get more specifics, you can issue runCA with "useGrid=1 scriptOnGrid=0". The runCA exec will print out 'qsub' commands to submit the parallel pieces. Perhaps you can convert those to LSF commands. In the end, if indeed there are one-for-one counterparts in LSF for all our SGE comands, we'll be happy to offer a 'runCA -LSF' option. -- Jason Miller