[gmx-users] Stampede multiple gpu nodes simulation
jzg579 at gmail.com
Tue Sep 15 00:58:59 CEST 2015
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
2015-09-12 14:36 GMT-05:00 <devapriyachem at gmail.com>:
> 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
> 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
> cores on the first node.
> #SBATCH -p gpu # Queue name
> #SBATCH -N 2 # Total number of nodes requested (16
> 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
> If anyone has experience setting up multi-node runs on gpu queue on
> and could share their insight, I would be very grateful.
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