[Bioclusters] MPIBLAST web submission to SGE queue?

Lance Davidow bioclusters@bioinformatics.org
Thu, 15 Jan 2004 11:39:15 -0500

Hello Joe,

Thanks for the rapid reply. It seems like all of our cluster and 
Bioinformatics questions lead to you ;-)
Thanks for helping us newbies in the past.

We have run practice command-line NCBI blast jobs and MPIBLAST jobs 
controlled by SGE scheduling. We would like to have a web front end 
before opening up the cluster to regular users. My initial plan is 
that the computer-savvy heavy users who want to blast one genome 
against another will use command lines and will be given shell 
accounts on the frontend as long as they promise to submit all 
serious jobs via SGE and not directly thru the shell. I suppose 
eventually we should have a separate login node that is an SGE 
submission node only and not allow any users to login to the frontend 
so that no users could put any jobs on the worker nodes except via 
SGE. We need a webBLAST interface with a rapid turnaround for the 
"regular users"  (There are 3000 researchers at MGH and each one is 
the world's greatest and most important scientist ;-) who are 
frustrated with the NCBI 25 minute turnaround times for single 
web-blast jobs at mid-day. We thought hooking the web interface to 
MPIBLAST would provide the fastest turnaround. Again, we would like 
to try first running the webserver on the frontend, but it may prove 
more secure and efficient to have a separate webserver computer which 
is an SGE submission node later on.

I would eventually like to have the skill to be able to quickly 
migrate the qsub section of  WWWBlastWrap.pl for SGE. But for now, if 
I could get help, we could make maximal use of our cluster sooner if 
we use someone else's work.


>Hi Lance:
>   I might be able to help here :)  Please send an email offline, and we
>can talk.
>On Wed, 2004-01-14 at 15:13, Lance Davidow wrote:
>>  We would like to compare regular NCBI Web Blast on a 22-node Dell
>>  1750 ROCKS cluster with a web-enabled MPIBLAST. The potential utility
>>  is that MPIBLAST will have a faster turnaround time for interactive
>>  web users under low cluster load.
>  > The 1.20 version of MPIBLAST comes with the script WWWBlastWrap.pl to
>>  modify the NCBI wwwBlast and submit an MPIBLAST request from the web
>>  page to an openPBS queue. Our cluster is using Grid Engine as its
>>  scheduler. Has anyone modified this script to allow the submission
>>  via web page of MPIBLAST jobs to the Parallel Environment of SGE? We
>>  are currently using MPIBLAST via command line only, with Joe
>>  Landman's sge_mpiblast script.
>>  Thanks,
>>  Lance
>Bioclusters maillist  -  Bioclusters@bioinformatics.org

Lance Davidow, PhD
Director of Bioinformatics
Dept of Molecular Biology
Mass General Hospital
Boston MA 02114
Fax: 617.726-6893