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

Smith, Iris smithi4 at ccf.org
Fri Jul 27 22:55:30 CEST 2018


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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