[gmx-users] [EXT] Re: OpenMP multithreading mdrun

[Smith, Iris]

Thank you Szilárd!

 

Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195  | (216) 445-7885
 
 

On 7/25/18, 10:44 AM, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Szilárd Páll" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of pall.szilard at gmail.com> wrote:

    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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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.