[gmx-users] OpenMP multithreading mdrun

[Szilárd Páll]

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
>
>
>
>
> ===================================
>
>
>  Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for use
> only by the individual or entity to which it is addressed and may contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the message
> to the intended recipient, you are hereby notified that any dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic or
> hard copy. Thank you.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.