[gmx-developers] domdec initialization
mark.j.abraham at gmail.com
Sat Jun 15 20:39:49 CEST 2013
If your branch is fairly up to date, then I would suspect this might be
another/known issue with affinities and Sander's update to threadMPI in
972ab1f9a0. There's supposed to be a partial fix
https://gerrit.gromacs.org/2433 that still seems to have some issues. NFI
what is relevant.
On Sat, Jun 15, 2013 at 8:25 AM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:
> I have a weird issue using domain decomposition (warning: in a
> non-standard branch).
> On one machine it stops after:
> Initializing Domain Decomposition on 8 nodes
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
> two-body bonded interactions: 67.844 nm, WAXS Debye, atoms 7183 7652
> multi-body bonded interactions: 0.425 nm, Proper Dih., atoms 2633 2641
> Minimum cell size due to bonded interactions: 74.628 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm
> Estimated maximum distance required for P-LINCS: 0.819 nm
> ERROR: The initial cell size (8.951949) is smaller than the cell size
> limit (74.628166)
> Program mdrun, VERSION 5.0-dev-20130613-766db7a-**unknown
> Source code file: /home/spoel/GG/waxs/gromacs/**src/gromacs/mdlib/domdec.c,
> line: 6641
> on the other machine running the same binary it does not stop. There is a
> difference between the machines though, since one of them is old it gives
> this warning:
> Using 8 MPI threads
> WARNING: Oversubscribing the available 0 logical CPU cores with 8
> thread-MPI threads.
> This will cause considerable performance loss!
> Since the check al the way above is dependent on a clause
> if (nc[XX] > 0)
> it could be that the information on the number of threads is only
> effectuated in the domain decomposition AFTER the check for cell sizes.
> In other words I suspect that the handling of number of threads (I pass
> -nt 8) does not work completely as expected (which probably would hold in
> the master branch too then).
> I could try to make a test case against the master branch...
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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