[Bioclusters] How can I make blast job running short time on Gridengine
bioinfo Gu
bioclusters@bioinformatics.org
Fri, 22 Nov 2002 07:26:54 -0800 (PST)
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Hi Joseph,
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.
Thank you very much, could you simply tell me what tools are available now?
Joe
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
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<P>Hi Joseph,
<P>You will need to partition the run into smaller runs, and submit the<BR>smaller runs. There are a few automated tools to do this in general,<BR>though there are some specific ones for BLAST. <BR></P>
<P>Thank you very much, could you simply tell me what tools are available now? </P>
<P><BR>Joe<BR><BR><BR><BR>On Thu, 2002-11-21 at 14:59, bioinfo Gu wrote:<BR>> I have two machines to install SGE. athena is master<BR>> and excution host, apollo is only excution host. When<BR>> I submit a job from master host with qsub, the job<BR>> will be distributed to one of queue(one of host), and<BR>> this job will be executed on this machinefor the whole<BR>> process. I can not see Gridengine can save execution<BR>> time when launch blast job on it. how can I save<BR>> blast running time on Gridengine, do I have to use<BR>> Parallel Environment?<BR>> <BR>> Also, how can I setup environmental variable for<BR>> specific execution host in batch job script? For<BR>> example: <BR>> <BR>> on one excution host: I need BLASTDB point to path1,<BR>> on the second execution host, I want to set BLASTDB to<BR>> path2, how can I do that?<BR>> <BR>> Thank you very much in advance.<BR>> <BR>> Grace<BR>> <BR>> <BR>&g
t; <BR>> ______________________________________________________<BR>> Do you Yahoo!?<BR>> Yahoo! Mail Plus - Powerful. Affordable. Sign up now<BR>> <BR>> <BR>> ______________________________________________________________________<BR>> Do you Yahoo!?<BR>> Yahoo! Mail Plus - Powerful. Affordable. Sign up now<BR>-- <BR>Joseph Landman, Ph.D<BR>Scalable Informatics LLC<BR>email: landman@scalableinformatics.com<BR>web: http://scalableinformatics.com<BR>phone: +1 734 612 4615<BR><BR>_______________________________________________<BR>Bioclusters maillist - Bioclusters@bioinformatics.org<BR>https://bioinformatics.org/mailman/listinfo/bioclusters</P><p><br><hr size=1>Do you Yahoo!?<br>
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