[gmx-users] decomposition error: -rdd and -dds do not influence the number of ranks

[Mark Abraham]

Hi,

On Sat, 23 Jul 2016 05:07 Chang Woon Jang <changwoonjang at gmail.com> wrote:

> Dear MarK Abraham and Grimaces Users,
>
>    Due to the limitation of Message body. I would like to open another
> ticket.
>
>    I have tried DD control options such as -rdd and -dds but still the same
> error comes out. The key is to change the number of ranks.


Yes, i already suggested some numbers you want to try.

These DD control
> options do not influence the number of ranks. I also changed the number of
> processes in parallel machine. This does not influence the number of ranks.
>

I don't know what you mean by that.

Therefore, the ranks appeared in the error message is different with the
> number of processes.
>
> Would you guide me how to change the number of ranks specified in the error
> message?
>

As you'll have read on the link I gave, a domain is mapped to a rank, and
needs at least one thread per rank. So choose the number of threads to be
the number of ranks you want, eg gmx mdrun -nt 12 for 2x2x3 DD grid. You're
using the group cutoff scheme, so openmp isn't available, so that will
start 12 thread-MPI ranks. That also won't fill your node's cores, so mdrun
needs to be told that you're doing that deliberately and for it to take
ownership of its cores, by using the -pin on option also. Experiment until
you find maximum performance (but based on the limited information I have,
my suggestion seems best).

Mark


> Best regards,
> Changwoon Jang,
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>