[gmx-developers] domdec initialization
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jun 15 08:25:11 CEST 2013
I have a weird issue using domain decomposition (warning: in a
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
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
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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