[gmx-users] offloading PME to GPUs

[Szilárd Páll]

Please see the user guide:
http://manual.gromacs.org/documentation/2018.5/user-guide/mdrun-performance.html#gpu-accelerated-calculation-of-pme
--
Szilárd

On Thu, Feb 7, 2019 at 3:18 PM jing liang <jingliang2015 at gmail.com> wrote:
>
> Hi,
>
> thanks for this information. I wonder if PME offload has been implemented
> for more than one
> node simulations? I tried the following command for running on two nodes
> (with 4 ranks each
> and 4 OpenMP threads)
>
> mpirun -np 8 gmx_mpi mdrun -nb gpu -pme gpu -npme 1 -ntomp 4 -dlb yes
>
> the log files when the simulation finishes says:
>
>
> On 7 MPI ranks doing PP, each using 4 OpenMP threads, and
> on 1 MPI rank doing PME, using 4 OpenMP threads
>
> Thus, it seems that only 1 PME rank (on a single node was offloaded)?
>
>
>
>
> El mié., 6 feb. 2019 a las 15:42, Kevin Boyd (<kevin.boyd at uconn.edu>)
> escribió:
>
> > Hi,
> >
> > 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
> > PME on GPUs
> > http://manual.gromacs.org/current/user-guide/mdrun-performance.html
> > 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).
> >
> > Kevin
> >
> >
> > 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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