[Bioclusters] Cluster ideas/suggestions

Micha Bayer michab at dcs.gla.ac.uk
Thu Jan 13 10:43:31 EST 2005


if you have dedicated machines then Condor and BLAST can work reasonably
well together because you can keep target databases preinstalled on all
your machines. This gets you around the i/o issues.

We run BLAST on Condor that way and it seems pretty reasonable. There is
also a very large Condor Pool at Wisconsin Uni which is used for BLAST
and it does a hell of a lot of useful work. 


On Thu, 2005-01-13 at 15:34, Nick D'Angelo wrote:
> All great ideas, thank you for them so far.
> I should have mentioned, that the cluster is required to run Blast, CLusta1W
> and RNAfold.
> Currently I have three Fedora machines, kind of all doing independent work
> in isolation of each other and we manually setup the jobs to run until
> completed.
> Nick 
> -----Original Message-----
> From: Micha Bayer [mailto:michab at dcs.gla.ac.uk]
> Sent: Thursday, January 13, 2005 10:01 AM
> To: Clustering, compute " farming & distributed computing in life
> science informatics
> Subject: Re: [Bioclusters] Cluster ideas/suggestions
> Hi,
> this sounds like you might want to look at Condor. Condor is an
> excellent tool for doing just that sort of thing (desktop cycle
> harvesting). 
> It can be installed on Linux or Windows machines, and it is highly
> configurable. One can set machines up so that jobs never run when the
> user is working, so that users don't even know a job is lurking in the
> background on their machine.  
> This would save you the trouble of having to reboot the machines, and
> you would get extra cycles during the day when users are in their coffee
> break etc. 
> Very nice package, free , very mature and great documentation. We run a
> Condor pool here and we think it is excellent. There is also a large
> user community already with mailing lists etc and good support
> otherwise.
> http://www.cs.wisc.edu/condor/
> If you have a pool of users who trust you to run jobs on their machines
> then this is just the ticket.
> cheers
> Micha
> On Thu, 2005-01-13 at 14:34, Nick D'Angelo wrote:
> > In speaking to our R and D managers, they posed a good question.
> > 
> > What about their desktop machines (relatively New Dell PCs), have them
> > automatically shutdown and reboot, say at 8:00 pm and then join the
> cluster
> > until 05:00 am.
> > 
> > Then at 5:00 am, initiate another reboot that will present the Windows
> Login
> > for the 'normal business day'.
> > 
> > This would make great use of the hundreds of computers that are mostly
> > sitting idle during the off hours 'normal business day'.
> > 
> > Thoughts, suggestions always appreciated, thanks.
> > 
> > Nick
> > 
> > In case you need to know,  I am likely going to install the BioBrew v3.x
> > which has just been pre-leased in Beta I believe.
> > _______________________________________________
> > Bioclusters maillist  -  Bioclusters at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bioclusters
Dr Micha M Bayer
Grid Developer, BRIDGES Project
National e-Science Centre, Glasgow Hub
246c Kelvin Building
University of Glasgow
Glasgow G12 8QQ
Scotland, UK
Email: michab at dcs.gla.ac.uk
Project home page: http://www.brc.dcs.gla.ac.uk/projects/bridges/
Personal Homepage: http://www.brc.dcs.gla.ac.uk/~michab/
Tel.: +44 (0)141 330 2958

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