[gmx-users] Multithread run issues

[Mark Abraham]

Hi,

On Sun, Oct 9, 2016 at 2:06 PM Mahmood Naderan <mahmood.nt at gmail.com> wrote:

> Hi,
>
> Users issue the command "mdrun -v" and that will automatically read input
>
> files in the working directory. There are two issue with that which I am
>
> not aware of the solution.
>
>
>
> 1- How the number of cores can be changed?
>

http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html


>
> 2- Viewing the output of "top" command, it is saying that mdrun uses 400%
>
> cpu. That mean 4 cores are occupied. Problem is that we prefer to see four
>
> processes each consumes 100% cpu. Why? Because in the first situation, PBS
>
> wrongly sees that one cores is used (while 4 cores are used), but in the
>
> later, it will correctly sees 4 cores.
>

This is not a problem to solve by running applications differently. You
will have users running jobs with single ranks/processes that use threading
of various kinds to fill the cores. That's a feature, not a bug. Either
configure PBS to cope with decades-old technology, or don't worry about it.
:-)

As I read the documentation, I think the replacement of "mdrun -v" should be
>
>
>
> mpirun -np N mdrun -v
>
>
>
> Am I correct?
>

No, because that mdrun isn't configured with MPI support (else it would be
called mdrun_mpi). If it was, then mpirun -np N mdrun_mpi is plausible, but
less efficient than the alternatives. Your mdrun is using the built in
thread-MPI that you can read about at that link.

Mark


>
>
>
> Regards,
>
> Mahmood
>
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