[gmx-users] OpenMP multithreading mdrun
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
> 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.
> Thank you,
> 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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