[gmx-users] parallel simulation

[pratibha kapoor]

I would like to run one simulation in parallel so that it utilises all the
available nodes and cores. For that,
I have compiled gromacs with mpi enabled and also installed openmpi on my
machine.
I am using the following command:
mpirun -np 4 mdrun_mpi -v -s *.tpr

When i use top command, I get:

PID  USER   PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND

22449 root      20   0  107m  59m 3152 R    25           2.9   0:05.42
mdrun_mpi
22450 root      20   0  107m  59m 3152 R    25           2.9   0:05.41
mdrun_mpi
22451 root      20   0  107m  59m 3152 R    25           2.9   0:05.41
mdrun_mpi
22452 root      20   0  107m  59m 3152 R    25           2.9   0:05.40
mdrun_mpi

Similarly when i use mpirun -np 2 mdrun_mpi -v -s *.tpr, I get

PID  USER   PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
22461 root      20   0  108m  59m 3248 R   50          3.0   5:58.64
mdrun_mpi
22462 root      20   0  108m  59m 3248 R   50           3.0   5:58.56
mdrun_mpi

If I look at %CPU column, it is actually 100/(no. of processes)
Why is all the cpu not 100% utilised?
Also if I compare my performance, it is significantly hampered.
Please suggest me the way so that I can run one simulation on all available
nodes, cores and threads.
Thanks in advance.