[gmx-users] Simulation on multi nodes performance

[Mark Abraham]

Hi,

There's some useful background at
http://manual.gromacs.org/documentation/2016.4/user-guide/mdrun-performance.html

Whether you want mpirun -np X mdrun_mpi or mpirun -np X gmx_mpi mdrun
depends whether GROMACS was configured to build only mdrun.

Otherwise, the logfile is indeed your friend - so that you can see whether
mdrun agreed with what you thought the hardware was, and in the performance
report at the end to see what took lots of time.

Mark

On Mon, Nov 27, 2017 at 7:21 AM Ali Ahmed <aa5635737 at gmail.com> wrote:

> Hello GMX users
>
> I'm trying to do simulations on multi nodes so I used  8 nodes (128
> processors). AS I see there is no difference between 1 node and 8 nodes.
>
> I used these commands:
>
> -------
>
> load apps/gromacs-2016
>
> load apps/openmpi-2.1.1
>
> gmx grompp -f EMZ.mdp -c BOX.gro -p TOP.top -o EMZ.tpr
>
> mpirun -np 128 mdrun_mpi -v -deffnm EMZ
>
> --------
>
> I'm kind of confused about the right commands
>
> Any comment will be helpful
>
> Thanks in advance
>
> Ali
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