[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 
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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