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

[jesmin jahan]

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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-- 
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.