[GE users] SunGrid Engine & BLAST

Hrishikesh Deshmukh hdeshmuk at gmail.com
Thu Jan 13 19:29:47 GMT 2005


I was thinking of having 1 machine as master and rest as execution hosts.
Each machine can have their own database,since i work with human db
and its not big for what i want to do.But you are right, if there are
more than on DB then it going to be problem about space!

Hrishi


On Thu, 13 Jan 2005 11:24:11 -0800, David S. <dgs at gs.washington.edu> wrote:
> > 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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