[Bioclusters] Web interface (PISE) on top of Sun Grid Engine on Mac Xserve cluster.

[Sergio Ahumada N]

> Applications at this stage include all of the biotools ported to Mac OS=
 X
> by the BioTeam ( http://bioteam.net), such as Altivec optimized BLAST,
> HMMER, FASTA and Clustal and the EMBOSS suite.

Hi Doc !

I have some questions. We had 6 CPUs (3 X Serve running Mac OS X (I think=
 10))
and the performance with optimized BLAST was not good at all. It was so s=
lowly=20
againts a Power Edge DELL  (one to one, and cluster to cluster performace=
).=20
So i want to ask you, what are the options used to BLAST to run ? could y=
ou=20
say it to me ?

> As an example, of performance, I ran a set of 3600 ESTs against Swisspr=
ot
> (BLASTX) using all 8 cpus and the job ran in about 45 minutes.  The sam=
e

This is really fast ! I ran a set of 600 ESTs using BLASTN with "nt" data=
base=20
and the job ran about 10 minutes (10 CPUs Power Edge) .. If I add my 3=20
Xserver to the cluster .. the time increases for the same job (?) .. I do=
n't=20
understand.

> memory machine), but my gut feeling is that the Xserve cluster is runni=
ng
> significantly faster.

We are now running the Xserve without MAC OS X (I don't like windows) .. =
I=20
have installed YellowDog for PPC .. and this works fine .. I compiled the=
=20
ncbi-blast and it's works ! .. but de performance are still bad to me, so=
 ..=20
you can try YellowDog and XFree86 window enviroment :-)

> Dave

Im not contributing to this list, better I shut up myself
--
Sergio Ahumada N
san@inf.utfsm.cl