[Bioclusters] Sun bits: solaris optimized blast binaries & a Gridengine-blast integration
note on their website
Chris Dagdigian
bioclusters@bioinformatics.org
Sat, 12 Jul 2003 23:17:29 -0400
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Hi folks,
This forwarded email is from the Sun compbio SIG mailing list. Apologies
in advance if someone already passed this on. I'm still brain dead from
the ISMB/Brisbane meeting...
For people who don't care about the Solaris binaries the link to the
HTML whitepaper on "Integrating BLAST with Grid Engine" is actually very
good.
The paper gives a basic but step-by-step guide to setting up a NCBI
blast aware Grid Engine installation that is not in any way specific to
running on a Sun cluster or even using the commercial version of grid
engine. If you are interested in trying Grid Engine this should be
helpful -- particularly the shell scrips that are given showing how to
submit blast jobs (with embedded SGE directives) into the cluster.
This could be something someone interested in getting an intro to Grid
Engine could use to get things up and running on a Linux laptop or whatever.
The 'missing' info is how to actually configure, tweak and tune the Grid
Engine configuration. The assumption in the whitepaper is that the user
would just use the default queues and config provided by the SGE
installation scripts.
In general this is OK -- the default queues are quite sensible but they
generally come with 1 job slot per CPU which is sometimes good for blast
and sometimes not. There are other parameters that one may want to tweak
as well.
I'd recommend that people following this whitepaper look up the 'Howto'
papers on http://gridengine.sunsource.net and read about how to create
and configure grid engine 'complexes' and 'requestable/consumable
resources'.
As an example of SGE complex usage for bioclusters -- When building
similar systems with dual-CPU compute nodes I like to create a 'hog' or
'greedy' complex that will allow users to request that their job to
have 100% exclusive acccess of a compute node.
With this setup a normal job would look like this:
$ qsub ./myBlastJobScript.sh
If I want my job to take exclusive use of a compute node with no other
jobs running in the remaining job slot I can do this:
$ qsub -l greedy=1 ./myBlastJobScript.sh
Dumb example perhaps but complexes and resources are very very useful in
SGE land and the whitepaper sorta skips over them.
-Chris
--
Chris Dagdigian, <dag@sonsorol.org>
BioTeam Inc. - Independent Bio-IT & Informatics consulting
Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net
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Date: Thu, 10 Jul 2003 15:51:15 -0400
From: Loralyn Mears <loralyn.mears@sun.com>
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Subject: Solaris 32- & 64-bit optimized binaries for NCBI BLAST now posted!
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Sun has some terrific lifesci engineers and I'd like to highlight the recent effort by Bogdan Vasiliu who worked closely with the folks at NCBI (special thanks to Dr. Tom Madden in particular) to bring you the following:
* 1. optimized Solaris 32- & 64-bit binaries for NCBI BLAST
* 2. a method for integrating BLAST with Sun Grid Engine
1. BLAST tuning
NCBI posted new 32 bit and 64 bit Solaris/SPARC
optimized binaries. These new binaries are between 1.3X and 2X faster than the previous ones. They are available from:
ftp://ftp.ncbi.nih.gov/blast/executables/blast-2.2.6-sparc-solaris64.tar.gz
ftp://ftp.ncbi.nih.gov/blast/executables/blast-2.2.6-sparc-solaris32.tar.gz
2. Integrating BLAST with Sun ONE Grid Engine Software (article)
http://developers.sun.com/solaris/articles/integrating_blast.html
This article shows how to integrate BLAST with Sun ONE Grid Engine software. The paper targets system administrators supporting life sciences research teams, however anyone proficient in UNIX system administration should be able to follow these simple instructions.
--
Loralyn Mears, Ph.D.
Market Development - Life Sciences
Sun Microsystems, Inc.
4880 Sadler Road, Suite 210
Glen Allen, VA 23060
TEL: 1-877-483-9575
FAX: 804-290-8112
WITHIN SUN: x.40536
MOBILE: remains the same
loralyn.mears@sun.com
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Sun has some terrific lifesci engineers and I'd like to highlight the recent
effort by Bogdan Vasiliu who worked closely with the folks at NCBI (special
thanks to Dr. Tom Madden in particular) to bring you the following:
<ul>
<li>
1. optimized Solaris 32- & 64-bit binaries for NCBI BLAST</li>
<li>
2. a method for integrating BLAST with Sun Grid Engine</li>
</ul>
<p><br><b>1. BLAST tuning</b>
<p>NCBI posted new 32 bit and 64 bit Solaris/SPARC
<br>optimized binaries. These new binaries are between 1.3X and 2X faster
than the previous ones. They are available from:
<br>
<p><a href="ftp://ftp.ncbi.nih.gov/blast/executables/blast-2.2.6-sparc-solaris64.tar.gz">ftp://ftp.ncbi.nih.gov/blast/executables/blast-2.2.6-sparc-solaris64.tar.gz</a>
<p><a href="ftp://ftp.ncbi.nih.gov/blast/executables/blast-2.2.6-sparc-solaris32.tar.gz">ftp://ftp.ncbi.nih.gov/blast/executables/blast-2.2.6-sparc-solaris32.tar.gz</a>
<br>
<p><b>2. Integrating BLAST with Sun ONE Grid Engine Software (article)</b>
<br> <a href="http://developers.sun.com/solaris/articles/integrating_blast.html">http://developers.sun.com/solaris/articles/integrating_blast.html</a>
<br>
<br>This article shows how to integrate BLAST with Sun ONE Grid Engine
software. The paper targets system administrators supporting life
sciences research teams, however anyone proficient in UNIX system administration
should be able to follow these simple instructions.
<br>
<br>
<p>--
<br>Loralyn Mears, Ph.D.
<br>Market Development - Life Sciences
<br>Sun Microsystems, Inc.
<br>4880 Sadler Road, Suite 210
<br>Glen Allen, VA 23060
<br>TEL: 1-877-483-9575
<br>FAX: 804-290-8112
<br>WITHIN SUN: x.40536
<br>MOBILE: remains the same
<br>loralyn.mears@sun.com
<br> </html>
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