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

[Roland Schulz]

Hi,

the OpenMM code is still under review. You can download it using
git fetch https://gerrit.gromacs.org/gromacs refs/changes/83/1283/14 && git
checkout FETCH_HEAD
You can check https://gerrit.gromacs.org/#/c/1283/ for the latest version
of it (as of time of writing the above line gives you the latest).

Roland

On Wed, Aug 29, 2012 at 10:37 AM, jesmin jahan <shraban03 at gmail.com> wrote:

> Thanks David and Szilárd.
>
> I am attaching a log file that I have got from my experiment. Please
> have a look. It says, gromacs version 4.6-dev
> I am using  :-)  VERSION 4.6-dev-20120820-87e5bcf  (-: of Gromacs.
>
> I have used the commands:
>
> git clone git://git.gromacs.org/gromacs.git
> cd gromacs
> git checkout --track -b release-4-6 origin/release-4-6 as written on
> the gromacs website.
>
> to download it and
>
> used cmake .. -DGMX_MPI=ON -DGMX_OPENMP=ON to configure it.
>
> Is it the case that later version of 4.6 has this feature?
>
> Please let me know.
>
> Thanks,
> Jesmin
>
> On Wed, Aug 29, 2012 at 4:27 AM, Szilárd Páll <szilard.pall at cbr.su.se>
> wrote:
> > 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.
> >> --
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> > --
> > gmx-users mailing list    gmx-users at gromacs.org
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>
>
>
> --
> Jesmin Jahan Tithi
> PhD Student, CS
> Stony Brook University, NY-11790.
>



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