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

David S. dgs at gs.washington.edu
Fri Jun 24 12:10:41 PDT 2005


On Fri, Jun 24, 2005 at 06:18:08PM +0200, Eugen Leitl wrote:
> ----- Forwarded message from Tim Cutts <tjrc at sanger.ac.uk> -----
> 
> On 24 Jun 2005, at 4:06 pm, Brodie, Kent wrote:
> 
> >
> >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.

I guess that we've had the opposite experience with GPFS.  We have
that file system on Linux x86 in an NSD configuration, with two 
servers attached to a SAN distributing the the file system to about 
fifty execution nodes over gigabit ethernet.  This cluster run 
bioinformatics applications - lots of BLAST.  Concurrent BLAST jobs 
can run quite slowly reading the databases from GPFS.  Just yesterday 
someone ran BLAST accross twenty-five nodes in that fashion, and the 
individual processes shambled along, barely using more than 15% of 
the CPU.  Meanwhile the NSD servers were showing loads of around 
twenty, and the GPFS file was annoyingly unresponsive in interactive 
use.  MEGABLAST is even worse.  The folks around here have given up 
on running concurrent MEGABLASTs in GPFS, and instead first stage the 
databases they need to local disk on the execution hosts.

A large part of the problem could be the SATA disks in the SAN, but
that's what we have to work with.  We're vaguely casting about for
alternatives to GPFS.  One study I've found comparing cluster or
parallel file systems

	http://www.linuxclustersinstitute.org/Linux-HPC-Revolution/Archive/PDF05/17-Oberg_M.pdf

indicates that alternative aren't very much better.

David S.

> 



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