[gmx-users] Re: parallel simulation

[pratibha kapoor]

To add : I am running simulations on institute cluster with 8 nodes (2
cores each).
Please suggest me the way so that I can run one simulation on all available
nodes, cores and threads.
Thanks in advance.



On Mon, Oct 7, 2013 at 1:55 PM, pratibha kapoor
<kapoorpratibha7 at gmail.com>wrote:

> 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.
>