[Bioclusters] Sequest on Linux

Twigger Simon simont at mcw.edu
Tue Aug 16 11:23:48 EDT 2005

Hi Chris,

My group is running Sequest on an IBM JS20 cluster (Suse linux). My  
knowledge of the gory details is not sufficient to really answer your  
questions, however, I can share my quick thoughts and I believe our  
SysAdmin (Kent Brodie) is also on the list and will get back to you  
with more of the real details.

Our current configuration has a Windows headnode running 8 dual  
processor JS20 nodes. Sequest uses PVM for job distribution and once  
you have it set up it seems to do a decent job with only a few  
hiccups here and there. We did not look at trying to integrate with  
LSF or SGE. We prototyped the port of Sequest to the PowerPC  
architecture in collaboration with IBM and Thermo and so stayed with  
a vanilla PVM-Sequest system and we currently dont run anything else  
on the cluster. I see no reason why we cant run other things on there  
(and that is the plan ultimately), but I dont know enough to  
speculate about how well PVM and LSF/SGE would play together.

We haven't been generating vast quantities of data that we've want to  
store as we've been mainly developing experimental techniques.  
However, we're gearing up to start creating more results that we will  
be keeping over the long term so we would be very interested in  
chatting more about what we have and what you are thinking.

You can find a little more info on our website (proteomics.mcw.edu)  
but the bioinformatics section is rather out of date and something I  
now notice I have to fix. There is also an overview of what we are  
trying to do in the area of proteomics and bioinformatics on the  
NHLBI Proteomics website, this was an overview presentation I gave a  
little while back so it doesnt have much detail.


Kent will be able to answer your real questions but lets chat more  
about how you are working on this as we'd love to share experiences  
and learn from what you are trying.



On Aug 15, 2005, at 11:46 PM, Botka, Christopher wrote:

> Is anyone out there running Sequest on Linux for MS analysis?  We  
> are in the process of setting up a modest sized cluster to run  
> Sequest and would be interested in sharing info and experiences  
> with anyone out there who might be doing the same.
> Some issues:
>    1. I/O requirements – what’s the minimum thruput needed to run  
> Sequest.  We are gong to test both SATA and FC drives with multiple  
> types of interconnects, as well as local SCSI drives.
>    2. Integration of the Thermo queuing system with other job  
> management systems (LSF/SGE etc) – Can Sequest be integrated into a  
> general purpose cluster?
>    3. Middle to long term storage requirements and back up strategies.
> Thanks,
> Chris
> botka at joslin.harvard.edu
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters


Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6595
AIM/iChat: simontatmcw

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