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

[Szilárd Páll]

On Wed, Aug 29, 2012 at 5:32 AM, jesmin jahan <shraban03 at gmail.com> 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.

No it's not. That out put is not from 4.6, you should have an extra
column with the number of threads.

--
Szilárd


> 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.
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists