[gmx-users] Stampede multiple gpu nodes simulation

[jia jia]

Dear Deva:
I'm also trying working out how run gromacs on stampede with parallel. I
just got some tests on 4.6 version and got similar speed as your single
test. At least for 4.6 version, the parallel can be run by
#SBATCH -N 1
#SBATCH -n 2
ibrun mdrun_mpi_gpu .........
I'm still making benchmark on 4.6.  And I could not repeat this use the 5.0
version.
Cheers
Guang



2015-09-12 14:36 GMT-05:00 <devapriyachem at gmail.com>:

> 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
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>