Peter Cock wrote:
> On Fri, Jul 29, 2011 at 5:09 PM, Duddy, John <jdu...@illumina.com> wrote:
> > We had similar problems on NFS mounts to Isilon. We traced it to
> > the default timeout for attribute caching on NFS mounts, which
> > does not force a re-read of directory contents (hence file existence
> > or size) for up to 30 seconds.
> >
> > We worked around it by adding no-ac to the mount, but this can
> > drastically increase the network traffic to the isilon, so there are
> > tradeoffs to be made.
> >
> > Even when you solve this, nfsv2 does not have open-close write
> > consistency, so it is possible for a job to complete on a node and
> > Galaxy to try to read the output files while the compute node is
> > still flushing its write cache to the file.
> >
> > All of these scenarios are unlikely on a busy cluster, on which
> > job<->Galaxy interactions will likely occur far enough apart in
> > time for the caches to clear on their own.
> >
> > John Duddy
> 
> Thanks for your comments John, it's good to know others
> have run into similar issues.
> 
> You may be right that on a real test load many of these issues
> would go away - but at least some of the problems I was seeing
> were at start-up or job submission time (and thus prior to the
> cluster actually running the job).
> 
> We may need to re-organise our network topology, right now
> there are probably too many routers/hubs/switches between
> the Galaxy server and the cluster and associated storage,
> making the mapped drive less responsive than it could be.

We do the same as John, disable attribute caching.  I've updated the
wiki with this information:

    http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster

--nate

> 
> Regards,
> 
> Peter
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