Send Bioclusters mailing list submissions to bioclusters at bioinformatics.org To subscribe or unsubscribe via the World Wide Web, visit https://bioinformatics.org/mailman/listinfo/bioclusters or, via email, send a message with subject or body 'help' to bioclusters-request at bioinformatics.org You can reach the person managing the list at bioclusters-owner at bioinformatics.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Bioclusters digest..." Today's Topics: 1. RE: Sequest on Linux (Brodie, Kent) ---------------------------------------------------------------------- Message: 1 Date: Tue, 16 Aug 2005 10:43:36 -0500 From: "Brodie, Kent" <brodie at mcw.edu> Subject: RE: [Bioclusters] Sequest on Linux To: "Clustering, compute farming & distributed computing in life science informatics" <bioclusters at bioinformatics.org> Message-ID: <8F78639AC56F4143B267FE5F5A1B92C8C5E0 at guyton.phys.mcw.edu> Content-Type: text/plain; charset="us-ascii" Hi. As Simon introduced, we're running Sequest on Linux. The installation happens to be Suse 8; that's what was chosen because that provided the best powerpc support at that time. Ultimately, we'll likely switch the nodes to RedHat later this year to match up with out other Linux servers. For Sequest, the particular flavor does not matter too much. The head node of our Sequest environment is a Windows 2000 Server. That was a requirement from what I know. (The JS20/Sequest install here pre-dated my arrival...). >From what I have seen, there's not really all that much I/O required to make the Sequest animal work. Most of the bandwidth needs are really going to be on the network side, I believe. That's where our JS20 bladecenter excels, because of the common network backplane. The chunks of data being analyzed are really nothing more than bits of text.. The Sequest head node basically blasts stuff to the remote worker nodes via RSH/etc. The raw files (FASTA and so on) used for comparative analysis are all copied to the worker nodes "ahead of time", and the data file chunks being analyzed just really aren't that large. In out environment, the JS20's have two little 40-GB 2.5" internal SCSI drives on the blades. The primary drive only has 3G used (operating system, apps, sequest), and the secondary drive only has 1.6G used (raw data files). I do not suspect you're going to notice huge Sequest time differences based on the drives..... (I could be wrong?). For backups, we really don't care much, since each worker node is more or less a clone of the other. A dead node is easily replicated. We do keep weekly backups of the first node "just in case". For integration, my understanding is that A Sequest-installed series of systems can co-exist with other job scheduler environments on the same cluster. As I mentioned earlier, RSH playes a huge part in keeping Sequest talking. The technical communication between the nodes just really isn't that complicated, and my assumption is something like LSF/SGE/PBS/etc could peacefully co-exist. If you have further scientific-like queries, Simon will tackle those, and I'll be happy to address any other sysadmin-like questions you may have. --Kent C. Brodie, MS Department of Physiology Human & Molecular Genetics Center Medical College of Wisconsin > -----Original Message----- > From: bioclusters-bounces+brodie=mcw.edu at bioinformatics.org > [mailto:bioclusters-bounces+brodie=mcw.edu at bioinformatics.org] On Behalf > Of Botka, Christopher > Sent: Monday, August 15, 2005 11:46 PM > To: bioclusters at bioinformatics.org > Subject: [Bioclusters] Sequest on Linux > > > 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 ------------------------------ _______________________________________________ Bioclusters maillist - Bioclusters at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bioclusters End of Bioclusters Digest, Vol 10, Issue 9 ******************************************