The log file for the job should tell you whether it was running peer-to-peer or not.
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`'
On Feb 27, 2015, at 09:15, Stefano Motta <s.motta17.campus.unimib.it<mailto:s.motta17.campus.unimib.it>> wrote:
2015-02-27 14:06 GMT+01:00 Jason Swails <jason.swails.gmail.com<mailto:jason.swails.gmail.com>>:
Why are you using 'nohup'? I would definitely recommend *against* doing
that in a PBS script. The only time that's really useful is if you want
to run a job interactively and don't want it to die if either your
terminal closes or your ssh session dies.
you are right, I copied the command from a previous calculation I've done
on a remote machine.
Do you know if the two GPUs are connected via Peer-to-Peer? Check the
"Multi GPU" section of
http://ambermd.org/gpus/ for more information.
I have not found information about the connection between 2 GPUs of the
same node, the only information I've found is that: *"All the nodes are
interconnected through a custom Infiniband network, allowing for a low
latency/high bandwidth interconnection." *This is the machine I'm using:
http://www.hpc.cineca.it/content/eurora-user-guide#systemarchitecture
It may be that there is nothing you can do to improve scaling, and that
you're better off just running 2 separate jobs (or using replica
exchange, for instance).
I'm already using advanced molecular dynamics such as aMD, so I preferred
not to use replica exchange with that, but it is a possibility. It's a
shame to have access to a machine with such a great number of GPUs, and can
use only one GPU at a time.
Thanks anyway for your support,
Sincerely
Stefano Motta
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Received on Fri Feb 27 2015 - 07:30:03 PST
