[Bioclusters] inconsistent output from simple BLAST job

Kumaran Rajaram kums at mpi.mpi-softtech.com
Wed Nov 24 14:46:27 EST 2004


  This is good to hear. Moving the data to compute nodes may improve the
I/O performance, but it increases the complexity of managing the data
(moving the data in/out from/to server), if there are large number of
nodes in cluster. You may use parallel file systems if you want to improve
I/O performance, however, you many have to dedicate and configure some
nodes as I/O nodes.

  Using NFS, I'd recommend the following to improve the I/O performance.

Improve NFS performance
i) Go for atleast NFS version 3 (mount option use nfsvers=3).
ii) Use read and write size of 32K. (r/wsize = 32K)
iii) Have the NFS clients to use TCP against default UDP. (mount option
specify tcp)

Improve Network performance
iv) On the compute nodes and server nodes, enable Jumbo frames (MTU=9000)
in the NIC.
v) Do Ethernet Channel Bonding (2 or more GigE pipes to a single bond0
interface) on the server to improve the network bandwidth of the I/O
server. Make sure the GigE switch supports this technology.


On Wed, 24 Nov 2004 peter_webb at agilent.com wrote:

> Hi Joe, Kums,
> Per the suggestions given, and another received privately, we've set the NFS options to
> rw,noac,rsize=8192,wsize=8192,timeo=14,intr
> In 16 hours of testing, I've seen no errors (good!!!), but have noticed that things are running slower (bad, but preferable to the previous state of affairs).  The amount of data being moved in the tests is quite small, and processor utilization is low, so I don't have a smoking gun; I'm looking at moving files over to temporary storage on the compute nodes rather than continuously accessing them over the network.
> Thanks for the help to date, if you have any comments on the options, please let me know.
> Thanks,
> Peter
> > From: Joe Landman <landman at scalableinformatics.com>
> > Subject: Re: [Bioclusters] inconsistent output from simple BLAST job
> > To: bioclusters at bioinformatics.org
> > Message-ID: <41A25DCD.1080500 at scalableinformatics.com>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Hi Peter:
> >
> >   Could you tell us what your NFS mount options are for the
> > node?  Could
> > be a case of async writes and bad flushing of output.
> >
> > Joe
> >
> > Message: 3
> > Date: Mon, 22 Nov 2004 16:21:11 -0600 (CST)
> > From: Kumaran Rajaram <kums at mpi.mpi-softtech.com>
> > Subject: Re: [Bioclusters] inconsistent output from simple BLAST job
> > To: "Clustering,	compute farming & distributed computing in life
> > 	science informatics"	<bioclusters at bioinformatics.org>
> > Message-ID: <Pine.GSO.4.58.0411221616180.27252 at mpi.mpi-softtech.com>
> > Content-Type: TEXT/PLAIN; charset=US-ASCII
> >
> >
> > Peter,
> >
> >    Use NFSv3 and mount NFS with "noac" option. "noac" disables file
> > attribute caching and should by default flush write operation to the
> > disks (on the server). It checks for changes in file
> > attributes for read
> > operation. The disadvantage with this option is that it
> > degrades the file
> > write performance.
> >
> > HTH,
> > -Kums
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