[Beowulf] MPI and Redhat9 NFS slow down

Kumaran Rajaram kums at mpi.mpi-softtech.com
Tue Aug 24 10:30:41 EDT 2004


Jack,

   If your application does not use MPI-IO to read/write from/to NFS, you
may disable the 'noac' mount option. The 'noac' mount option prevents the
client from caching file attributes. This means that every file operation
on the client that requires file attribute information results in a
GETATTR operation to retrieve a file's attribute information for the
server. You can also try different values for rsize, wsize mount options
and try enabling Jumbo frames in the GigE switch + set MTU of eth0
appropriately. Probably you can try diagnosing the NFS performance using
'nfsstat' utility.

  You can as well approach 'nfs at lists.sourceforge.net' and they might give
you some valuable suggestions.

-Kums
__
Kumaran Rajaram
Verari Systems, Inc.
Phone: 205-314-3471 x208

On Mon, 23 Aug 2004, Jack Chen wrote:

> Hi all,
>
> I'm not sure if this is the right place to post this question.  If it
> is not, please tell me where's the best place to get help on this,
> thanks..
>
> 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.  I have installed the latest MPICH 1.2.6
> with Portland Group Compiler (5.2-1) using ssh.  Everything worked
> fine with the mpi example programs (cpi, pi3p etc)and 'make testing'.
> 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.
>
> For example:
> If I start the job on master node using 4 processors (mpirun -np 4)
> and write to the master node (master2 0),
> PIxxx file:
> master2 0 /master2/home/chenj/CMAQ_v4.3/Run/cctm/CCTM_e2a
> node103 1 /master2/home/chenj/CMAQ_v4.3/Run/cctm/CCTM_e2a
> node103 1 /master2/home/chenj/CMAQ_v4.3/Run/cctm/CCTM_e2a
> node104 1 /master2/home/chenj/CMAQ_v4.3/Run/cctm/CCTM_e2a
>
> 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.
>
> I have tried to mount the drive using different parameters (rw,soft
> and rw,hard,bg,intr,noac) and increased the nfsd daemon from 8 to 16
> on the NSF server, but nothing change.
>
> If you have any idea on what is going on, please help!
>
> Any help/suggestion are greatly appreciated.
>
> Jack
>
>  Jack Chen
>  Laboratory for Atmospheric Research
>  Dept.of Civil & Environmental Engineering
>  Washington State University
>  Pullman, WA 99164-2910
>  509.335.5738
>  509.335.7632 (FAX)
>
>
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