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

[jesmin jahan]

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.

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.