<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<meta content="text/html;charset=us-ascii" http-equiv="Content-Type">
<body bgcolor="#ffffff" text="#000000">
<tt>Which of these PVFS2 Lustre GPFS have some level of redundancy ?<br>
<pre class="moz-signature" cols="72">===============================================
David Coornaert (<a class="moz-txt-link-abbreviated" href="mailto:firstname.lastname@example.org">email@example.com</a>)
Belgian Embnet Node (<a class="moz-txt-link-freetext" href="http://www.be.embnet.org">http://www.be.embnet.org</a>)
Université Libre de Bruxelles
Laboratoire de Bioinformatique
12, Rue des Professeurs Jeener & Brachet
<pre wrap="">Now that we have all 63 up and running it looks like we are
getting performance issues with NFS much in the same way
that others have reported here. Even moderate job loads
produce trouble - (nfsstats -c show lots of retransmissions),
Are you using NFS over TCP? If not, you probably should. That
introduces some reliability problems, in that NFS/TCP is no
longer stateless. If the file server goes down, clients may
hang. But since your file server is your head node, it's mostly
a moot point. Lose the head node, and you lose the cluster
<pre wrap="">grid engine execds don't report back in so qhost shows nodes not
responding though eventually they will return. On occasion one of
the switches stops and that whole "side" of the cluster disappears.
so we reboot the switch and are back in action. Anyway here are my
questions (thanks for your patience in reading through this)
Has anyone had similar problems with these SMC switches ?
I'm not accustomed to having the switches die like this.
In terms of improving NFS performance I've already
put SGE spool onto the local nodes to try to improve things
but only helps a little. There are various NFS tuning
documents with respect to clusters ( using tcp, atime, rsize,
wsize, etc options to mount). I've experimented with a few of
these (rsize, wsize) though with only very marginal positive impact.
for those with larger clusters and similar issues have you found
a subset of these options to be more key or influential than others ?
If you use NFS/TCP, the "rsize" and "wsize" parameters are
irrelevant. The Linux NFS how-to suggest raising the 'sysctl'
values of "net.core.rmem_max" and "net.core.rmem_default" higher
than their usual values of 64k. You should also pay attention
to the number of 'nfsd' processes running on your server. The
rule of thumb is eight per CPU. In principle, the more clients
you have the more 'nfsd' processes you want. But multiple server
processes contend for resources themselves, so you reach a point
of diminishing returns in starting more.
<pre wrap="">One scenario that has been discussed is bonding two NICs
on the v40z in conjunction with switch trunking. Does anyone
have any opinions or ideas on this ?
If your switch can trunk, go ahead. I trunk together gigabit
ethernet interfaces on a FreeBSD file server. I've some rumours
to the effect that a four-way trunk on Linux can be slower than
a two-way, due to problems in the bonding driver. Regard that
as just hearsay, however, because I don't have any experience
with such things on Linux. You might consider using jumbo
frames, if your switches support that.
<pre wrap="">Lastly is it even worth
it to keep messing with NFS ? And maybe go for GFS.
There are a number of parallel or cluster file systems in
addition to GFS, like PVFS2 (free), Lustre (sort of free),
GPFS (free to universities), TeraFS (commercial), and Ibrix
(commercial). They may not work well for hosting home
directories, because they're not optimized for that sort
of I/O load. They're also, in my experience, rather less
than stable. We built a fifty node cluster with just GPFS,
no NFS and very little local disk. The results were quite
File I/O is one of the major un-solved problems of cluster
computing. Anybody who tells you otherwise is trying to
sell you something.
Bioclusters maillist - <a class="moz-txt-link-abbreviated" href="mailto:Bioclusters@bioinformatics.org">Bioclusters@bioinformatics.org</a>
<a class="moz-txt-link-freetext" href="https://bioinformatics.org/mailman/listinfo/bioclusters">https://bioinformatics.org/mailman/listinfo/bioclusters</a>