[gmx-users] Stampede multiple gpu nodes simulation

[Mark Abraham]

Hi,

This sounds like a good question for the Stampede user documentation,
and/or sysadmins. :-)

Mark

On Sat, Sep 12, 2015 at 9:36 PM <devapriyachem at gmail.com> wrote:

> Hello,
>
> I have been trying to run a MD simulation on Stampede cluster using the gpu
> queue. Using only 1 node, I get roughly 42 ns/day performance. I have
> around
> 42,000 atoms in my system.
>
> However, I am unable to get this system to run using 2 or more gpu nodes. I
> have encountered errors from GPU devices not found to oversubscribing
> logical
> cores on the first node.
>
> #SBATCH -p gpu               # Queue name
> #SBATCH -N 2                   # Total number of nodes requested (16
> cores/node)
>
> One of my attempts was as follows:
>
> ibrun -n 2 -N 1 mdrun_mpi_gpu -s md-01.tpr -x md-01.xtc -e md-01.edr -g
> md-01.log
>
> If anyone has experience setting up multi-node runs on gpu queue on
> Stampede
> and could share their insight, I would be very grateful.
>
> Thanks,
> Deva
>
>
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