[gmx-users] OpenMP multithreading mdrun

Szilárd Páll pall.szilard at gmail.com
Wed Jul 25 16:43:48 CEST 2018


On Wed, Jul 25, 2018 at 4:27 PM Smith, Iris <smithi4 at ccf.org> wrote:

> Good Morning Gromacs Users,
>
> Gromacs 2018.2 was recently installed on our intel-based HPC cluster using
> OpenMP (without MPI).
>
> Can I still utilize multiple threads within one node when utilizing mdrun?
> If so, do I need to call openmp and export OMP_NUM_THREADS in my script?
>

OpenMP enables multi-threading within mdrun, so yes, you can. Unless it's
been disabled, you can also use the built-in therads-based MPI (called
thread-MPI); see:
http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html#running-mdrun-within-a-single-node


> For example when using 20 threads:
>
> module load openmpi/gcc/64/3.1.1
> module load gromacs/2018.2
> export OMP_NUM_THREADS=2
>
> gmx mdrun -ntomp 20 -s wt.tpr -deffnm wt -v
>

-ntomp and OMP_NUM_THREADS are synonymous; it's enough if you set either,
but if you set both you have to set them to identical values, the above
will not work.

--
Szilárd


>
> Thank you,
> Iris
>
>
> [/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1326358176]
>
> Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
> Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195  |
> (216) 445-7885
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