[gmx-users] Problem with OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi

[David van der Spoel]

On 2012-08-29 05:32, jesmin jahan wrote:
> Dear All,
>
> I have installed gromacs VERSION 4.6-dev-20120820-87e5bcf with
> -DGMX_MPI=ON . I am assuming as OPENMP is default, it will be
> automatically installed.
>
> My Compiler is
> /opt/apps/intel11_1/mvapich2/1.6/bin/mpicc Intel icc (ICC) 11.1 20101201
>
> And I am using OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi -s imd.tpr
>
> I was hopping this will run 16 processes each with 12 threads.
> However, in the log file I saw something like this:
>
>   R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>
>   Computing:         Nodes     Number     G-Cycles    Seconds     %
> -----------------------------------------------------------------------
>   Domain decomp.        16          1        0.027        0.0     1.8
>   Comm. coord.          16          1        0.002        0.0     0.1
>   Neighbor search       16          1        0.113        0.1     7.7
>   Force                 16          1        1.236        0.8    83.4
>   Wait + Comm. F        16          1        0.015        0.0     1.0
>   Update                16          1        0.005        0.0     0.4
>   Comm. energies        16          1        0.008        0.0     0.5
>   Rest                  16                   0.076        0.0     5.1
> -----------------------------------------------------------------------
>   Total                 16                   1.481        0.9   100.0
> -----------------------------------------------------------------------
>
>
> Its not clear whether each of the 16 nodes runs 12 threads internally or not.
>
Check your mpirun syntax. It may only give 16 cores to mdrun.

> If anyone knows about this, please let me know.
>
> Thanks for help.
>
> Best Regards,
> Jesmin
>
>
>
> --
> Jesmin Jahan Tithi
> PhD Student, CS
> Stony Brook University, NY-11790.
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se