[GE users] SunGrid Engine & BLAST

David S. dgs at gs.washington.edu
Thu Jan 13 19:24:11 GMT 2005

> I'm interested in how well this works out for you.  As much of a
> writeup as you care to do wrt getting SGE to work on OS X would be
> appreciated.
> I am purchasing a Mac cluster for BLASTing also.
> I anticipate using iNquiry for my job management, although SGE is an
> option also (as is Apple's Xgrid, as a last resort.)
> I haven't pursued SGE very far, other than to lurk this list, but I
> understand that NFS serving on 10.3 isn't so hot;  expected to greatly
> improve on 10.4.  What exactly the limitations of NFS on 10.3 isn't
> clear, but if you're using straight up Apple nodes I think you'd do
> better with (unencrypted) AFP;  is that an option with SGE?

You don't *need* NFS for SGE.  I run it out of GPFS on one cluster,
and some on this list use AFS, if I recall correctly.  You can also
keep SGE without a shared file system, installing it strictly on the
local disk of each host.  The Grid Engine web page has instructions
for doing that.

You also don't *need* NFS for BLAST, and indeed you may not want it,
depending on how many hosts will read you BLAST databases concurrently,
and how many NFS servers you have accomodating them.  Lots of folks 
keep the BLAST databases on local disk, for performance reasons.  Those 
databases these days take up around 150 GB, in total, so you'd want to 
have some large disks your hosts.  If your system supports it, you 
may rather keep the databases in one of those fancy parallel file
systems, like PVFS, GFS, Lustre, GPFS, etc.

David S.


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