[Bioclusters] How can I make blast job running short time on Gridengine

Joseph Landman bioclusters@bioinformatics.org
21 Nov 2002 18:31:33 -0500


  You will need to partition the run into smaller runs, and submit the
smaller runs.  There are a few automated tools to do this in general,
though there are some specific ones for BLAST.  

  You can either code it your self, download something of similar
functionality (not much at this time), or pay for one of the commercial
versions to do this.  I'll post more comments on this in the
not-to-distant future.

  The short answer is that you will need to expend either programming
time, searching time, and/or money to enable better performance on your



On Thu, 2002-11-21 at 14:59, bioinfo Gu wrote:
>                 I have two machines to install SGE. athena is master
>                 and excution host, apollo is only excution host. When
>                 I submit a job from master host with qsub, the job
>                 will be distributed to one of queue(one of host), and
>                 this job will be executed on this machinefor the whole
>                 process. I can not see Gridengine can save execution
>                 time when launch blast job on it.  how can I save
>                 blast running time on Gridengine, do I have to use
>                 Parallel Environment?
>                 Also, how can I setup environmental variable for
>                 specific execution host in batch job script? For
>                 example: 
>                 on one excution host: I need BLASTDB point to path1,
>                 on the second execution host, I want to set BLASTDB to
>                 path2, how can I do that?
>                 Thank you very much in advance.
>                 Grace
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Joseph Landman, Ph.D
Scalable Informatics LLC
email: landman@scalableinformatics.com
  web: http://scalableinformatics.com
phone: +1 734 612 4615