[gmx-developers] Reference coordinates in mdrun - Availability at all nodes

[Tsjerk Wassenaar]

Hi Mark,

Thanks. It makes sense not to store the full array at each node, which
would require more memory than strictly necessary. The drawback is
doing DD every time on something that doesn't change, but I see that
that's required to maintain consistency of indices. Using the
t_forcerec seems a bit of hack, but might indeed be the best way.

Cheers,

Tsjerk

On Tue, Jan 5, 2010 at 11:00 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Tsjerk Wassenaar wrote:
>>
>> Hi,
>>
>> For some reason, I'm reading in a set of reference coordinates in
>> mdrun (do_md). These should be available during the entire run, but
>> obviously, I have to ensure that they are available at each node in
>> order not to compromise efficiency. Could any of you give a pointer
>> (no pun intended, but please, not a void pointer :p) on how to achieve
>> that?
>
> It won't be straightforward. The DD algorithm doesn't replicate full
> position arrays across processors, so there's a bunch of messy indexing that
> goes on. Presumably you'll need to subject your reference coordinates to the
> same decomposition so that indices match on the nodes. If so, you can just
> add another rvec * to t_forcerec, load it earlier, and use the global vs
> local machinery that's already used for the positions. I suggest stepping
> through the (start of the) DD in the do_md loop.
>
> Mark
> --
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-developers-request at gromacs.org.
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist