[gmx-developers] distance restraints and domain decomposition

[Kutzner, Carsten]

> On 7. Jun 2018, at 07:02, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 
> Den 2018-06-06 kl. 15:07, skrev Kutzner, Carsten:
>> Dear developers,
>> we have a ~ 40,000 atom MD system with distance restraints (bond type 6)
>> that does not want to run in parallel, although I assume it should.
>> It runs fine without DD, e.g. -ntmpi 1 -ntomp 20, however with DD the
>> following happens:
>> mdrun -ntmpi 2
>> Fatal error:
>> There is no domain decomposition for 2 ranks that is compatible with the given
>> box and a minimum cell size of 11.4939 nm
>> The maximum distance restraint distance is however at 4.0 nm, so 11.49 nm as
>> reported cannot be true, unless the PBC distance is not taken properly
>> into account. Is this the expected behaviour or worth generating a redmine
>> issue?
>> Thanks,
>>  Carsten
> Which version?
2018

> 
> It should work with OpenMP anyway.
Yes, that works, however we might want to use multiple nodes and/or multiple
GPUs for similar setups in the future.

Carsten

> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> -- 
> Gromacs Developers mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_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-developers or send a mail to gmx-developers-request at gromacs.org.

--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa