[Beowulf] [tjrc@sanger.ac.uk: Re: [Bioclusters] topbiocluster.org]

Eugen Leitl eugen at leitl.org
Fri Jun 24 09:18:08 PDT 2005


----- Forwarded message from Tim Cutts <tjrc at sanger.ac.uk> -----

From: Tim Cutts <tjrc at sanger.ac.uk>
Date: Fri, 24 Jun 2005 17:02:50 +0100
To: "Clustering,  compute farming & distributed computing in life science informatics" <bioclusters at bioinformatics.org>
Subject: Re: [Bioclusters] topbiocluster.org
X-Mailer: Apple Mail (2.730)
Reply-To: "Clustering,  compute farming & distributed computing in life science informatics" <bioclusters at bioinformatics.org>


On 24 Jun 2005, at 4:06 pm, Brodie, Kent wrote:

>Taking into account the whole pipeline (including networked I/O,
>formatdb, etc) is both a great idea and will give much more realistic
>results.
>
>I also think that a collection of data would be a catalyst for great
>future discussions and questions, e..g, "how the heck did you get your
>formatdb to run so fast on the 20K data?", the responses would then  
>give
>the rest of us who may be a bit behind in these things great  
>insight and
>ideas.
>
>I'd be VERY interested to see if anyone has results from using cluster
>filesystems, for example.....

Cluster filesystems have *drastically* cut our data distribution  
time.  We can distribute a new multi-GB genome data set to all the  
machines that use cluster filesystems in a few minutes.  The old RLX  
blades, which have to rely on the hierarchy of rsync processes to  
which James referred, trail in a dismal few hours later.

They've also increased performance when running jobs; the machines  
can suck data over the filesystem's GB ethernet faster than the  
individual spindles could supply the data locally.

We've been using cluster filesystems (specifically, GPFS) in  
production since October 2003, for the static datasets; blastables  
and so on.  This is going to continue, and we've been so pleased with  
it as a method, that it's going to be extended.  The number of nodes  
per cluster filesystem (currently 14) will be expanded, hopefully to  
the entire cluster.  Scratch filesystems for the cluster will be  
moved to GPFS or Lustre, rather than NFS, which is where they are  
currently.  We're not wedded to GPFS - Lustre looks good too.

LSF is already running off a GPFS cluster filesystem so that it can  
fail over without the performance sucking because of NFS (yay!  No  
more LSF masters on Tru64! Woohoo!)

The dream of a 1000+ node cluster entirely without NFS takes a step  
closer to reality...

I'd be happy to run one of James' mini pipelines on Sanger's cluster,  
if I could actually persuade Ensembl to give me a couple of hours of  
completely clear air to actually get the benchmark done.  :-)

Tim

-- 
Dr Tim Cutts
Informatics Systems Group, Wellcome Trust Sanger Institute
GPG: 1024D/E3134233 FE3D 6C73 BBD6 726A A3F5  860B 3CDD 3F56 E313 4233

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Bioclusters maillist  -  Bioclusters at bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters

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Eugen* Leitl <a href="http://leitl.org">leitl</a>
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