[Beowulf] MPI and Redhat9 NFS slow down

Tod Hagan tod at gust.sr.unh.edu
Thu Aug 26 14:32:09 EDT 2004


On Mon, 2004-08-23 at 18:52, Jack Chen wrote:
> We recently built a 8-node PC Linux cluster running RedHat 9 (kernel:
> 2.4.20-8smp #1 SMP).  We use this system to run EPA's CMAQ
> photochemical grid model...However when I tried to run any program that write output to other nfs
> mounted drives I get very long delay.  I'm not sure where the problem
> is.  I know the NFS automount is working fine because if I start the
> job with just one processor (mpirun -np 1), I don't experience the
> slow down.
> 
> If I start the job on master node using 4 processors (mpirun -np 4)
> and write to the master node (master2 0)...the run takes 168 sec
> 
> If I start the same job but write the output to any other nfs mounted
> drives besides the master node, the job will be extremely slow.  In
> this case the same job took 10962 sec.

Jack,

We've started running CCTM parallel here too.

It's my impression that CCTM is very I/O intensive, and for that reason
you should do all node zero I/O locally instead of to an NFS-mounted
partition. Note that while all nodes pass data via MPI to node 0 which
does the netCDF writes, the compute nodes read data via NFS/netCDF/ioapi
throughout the run. It's possible that some of the read-only files
holding input data could be located on an NFS-mount somewhere other than
node 0 with little penalty, but I haven't tried this.

If you really need to use an NFS mount for data, Kumaran Rajaram's
suggestion to disable the 'noac' mount option is worth trying since
MPI-IO isn't being used. And the other NFS optimizations suggested as
well.

I've been working under the assumption that all data should be local to
node 0, so I'll be interested to see how you fare with NFS.

By the way, I queried the CMAQ help desk for information regarding CCTM
parallel I/O, here's the URL:

http://bugz.unc.edu/show_bug.cgi?id=1120

The CMAQ help desk (which is really just a product entry in the CMAS
bugzilla database) is likely the best place to ask your question. I've
had good response on a couple of issues.


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