[Bioclusters] Sequest Cluster problems

Jeremy Maris jeremym at biols.susx.ac.uk
Thu Mar 2 10:14:04 EST 2006

Hi Guy,

We're shortly to get a 16 node linux license  + server node for SEQUEST
and I'm hoping to get it working on our Suse 9.3 cluster (preferably using
EMT64 nodes though maybe plain 32 bit Xeon) configuring it as a priority SGE job
that displaces other long running jobs.

I'd be grateful for your config info; when we get the software and if I
fail to get it going do you mind if I give you a ring to discuss

Lucas Bowler (who runs our proteomics facility) might also be in touch re
any guidance you might have.

Thanks for your time!

> >
> > The first problem we have is when we start the PVM (by clicking "Start
> > PVM" in the Cluster Manager), we always get the following error for Node
> > 2, even if "Cleanup Nodes" has been clicked prior to starting PVM:
> I've wasted rather too much time on bioworks over the past few weeks.  I
> managed to get it working, (master on win2003 and slaves on debian), but
> it wasn't a pleasant experience.
> A few "top tips":
> Before you start pvm on the master, make sure there a no stray pvm
> processes hanging around on the slave nodes. (the master tends not to
> clean up after itself particularly well.)
> Check that the slave nodes are configured *exactly* as detailed in the
> instructions. There are a lot of hard coded paths in the bioworks code, so
> if pvmd or the ini files are somewhere other than where the docs say they
> should be (even if they are on your path) it won't work.
> > Does anyone have encountered the same problems and have any solution for
> > that?  Considering the fact that we invested close to 40 000$ into this
> > cluster (hardware and software costs), we really wish to make it works
> > without having to restart our computers every few hours!!
> > And does anyone know if it's more stable to run the nodes under Windows
> > rather than Linux?
> AFAIK the master can only run on windows, so you're stuck with that.
> If you want details on our config, let me know.
> Cheers,
> Guy
> -- 
> Dr. Guy Coates,  Informatics System Group
> The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
> Tel: +44 (0)1223 834244 x 6925
> Fax: +44 (0)1223 494919
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
Jeremy Maris, Computing Manager, School of Life Sciences,
John Maynard Smith Building, University of Sussex, Falmer, Brighton BN1 9QG
j.maris at sussex.ac.uk Tel: +44 (0) 1273 678060 Fax: +44 (0) 1273 678433

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