RE: openMosix (2.4.26) and BLAST

I've ran BLAST before but not in an OM environment.  It should work with
NFS, but might be slow as compared to luster or ibrix, or any of the
major parallel file systems.  (depending on your hardware of the file
servers naturally)  Just place your database on your shared disk,
whichever that may be and you are in business.

The files I was using for BLAST were about 500GB uncompressed, so it was
very IO intense.


BLAST can be a hard compile.  Let me know if you have any problems and I
could possibly dig up a Makefile that I used if I still have it around.


-evan T.

-----Original Message-----
From: openmosix-general-admin-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
[mailto:openmosix-general-admin-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org] On Behalf Of Joel
Hollingsworth
Sent: Wednesday, November 23, 2005 10:29 AM
To: openmosix-general-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
Subject: [openMosix-general] openMosix (2.4.26) and BLAST

Hi all.

I'm currently setting following the instructions from the David  
States Research Laboratory page on running BLAST on openmosix (http:// 
stateslab.bioinformatics.med.umich.edu/software/OM_BLAST_patch/ 
openmosixpatch.html).  The instructions use oMFS to place the  
databases on all of the machines. oMFS is no longer supported in  
2.4.26-openmosix.

Has anyone run BLAST under the 2.4.26-openmosix kernel? Can we now  
use NFS instead of oMFS and have it work in a similar fashion (i.e.  
just migrate the process not the database)? Suggestions?

Thanks in advance,

-joel


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