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.
[email protected] http://folding.bmc.uu.se
--
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