[gmx-users] offloading PME to GPUs

Kevin Boyd kevin.boyd at uconn.edu
Wed Feb 6 15:41:45 CET 2019


Your log file will definitely tell you whether PME was offloaded.

The performance gains depend on your hardware, particularly the CPU/GPU
balance. There have been a number of threads on this forum discussing this
topic, if you search back through the gmx_user archives. The gist of it is
that with you can balance a good GPU with ~4 CPU cores, though that's
dependent on the CPU quality as well.

The docs in Gromacs 2019 have been updated to include examples on running
Search for "-pme gpu". The examples should mostly apply if you're using
Gromacs 2018 as well (although you won't have the -bonded options).


On Wed, Feb 6, 2019 at 9:29 AM jing liang <jingliang2015 at gmail.com> wrote:

> Hello,
> I understood from the documentation:
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmanual.gromacs.org%2Fdocumentation%2F2018-current%2Fuser-guide%2Fmdrun-performance.html&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7Caec25493f30d483d29e008d68c3f8aad%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636850601922827903&amp;sdata=QvfmUT6Ua70zXuDezkO%2Bzunj8WX72qyGBpQvcIRm%2BgA%3D&amp;reserved=0
> that PME can be now offloaded to GPUs in v2018. I'm using SLURM in a
> machine with 24
> cores, I wonder if the following script would be able to offload PME to
> GPUs
> #SBATCH -n 2
> #SBATCH -c 12
> #SBATCH --gpu:2
> slurun gmx_mpi mdrun -ntomp 12 -npme 0 -dlb yes  -v -deffnm step1
> Is there some information in the log files which can allow me to see if PME
> has been
> offloaded and what was the performance gain upon using GPUs?
> Thanks.
> --
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