Re: openMosix (2.4.26) and BLAST

On Wed, Nov 23, 2005 at 11:28:43AM -0500, Joel Hollingsworth wrote:
> 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?

 IIRC, that howto said to put copies of your BLAST databases on each node,
and then to run blast using the database /mnt/mfs/nodenumber/...  oM would
see that blast was doing heavy I/O on files that were actually on
nodenumber, and migrate it there where the I/O actually happens locally.
That was what MFS and DFSA were all about.  Now that they've fallen by the
wayside, there is no way to start a process on one node and have it migrate
and use local files on another node.  You'll have to forget about using
openMosix to distribute BLAST processes.  You could use a batch scheduler to
run blast on other machines which either have their own copy of the BLAST
databases, or which NFS mount them.  (That could turn into the bottleneck,
depending on network bandwidth and the capacity for multiple reads from
different places in the files without having disk seeks be the bottleneck on
the file server.)


-- 
#define X(x,y) x##y
Peter Cordes ;  e-mail: X(peter@cor , des.ca)

"The gods confound the man who first found out how to distinguish the hours!
 Confound him, too, who in this place set up a sundial, to cut and hack
 my day so wretchedly into small pieces!" -- Plautus, 200 BC


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