[gmx-users] Strange assignment of atoms to processors with pd

[Erik Marklund]

I should add that this problem only seem to arise when the analyte is 
covered with a thin sheet of water. When simulating a dry analyte I get 
good scaling. In the latter case the charges, and therefore the 
topology, is slightly different.

/Erik

Erik Marklund skrev:
> Hi,
>
> I'm simulating non-periodic systems in vacuo, using constrained 
> h-bonds and particle decomposition. For some of my simulations the 
> cpu-usage seem far from optimal. The first cpu gets no atoms, while 
> the second one gets plenty and the remaining cpus get less than I 
> expected. Is this a bug?
>
>
> An excerpt from the log file:
>
> There are: 2911 Atoms
> There are: 317 VSites
> splitting topology...
> There are 999 charge group borders and 318 shake borders
> There are 318 total borders
> Division over nodes in atoms:
> 0 1960 212 212 212 212 212 208
> Walking down the molecule graph to make constraint-blocks
> CPU= 0, lastcg= -1, targetcg= 499, myshift= 1
> CPU= 1, lastcg= 681, targetcg= 182, myshift= 0
> CPU= 2, lastcg= 734, targetcg= 235, myshift= 7
> CPU= 3, lastcg= 787, targetcg= 288, myshift= 6
> CPU= 4, lastcg= 840, targetcg= 341, myshift= 5
> CPU= 5, lastcg= 893, targetcg= 394, myshift= 4
> CPU= 6, lastcg= 946, targetcg= 447, myshift= 3
> CPU= 7, lastcg= 998, targetcg= 499, myshift= 2
> pd->shift = 7, pd->bshift= 0
> Division of bonded forces over processors
> CPU 0 1 2 3 4 5 6 7
> Workload division
> nnodes: 8
> pd->shift: 7
> pd->bshift: 0
> Nodeid atom0 #atom cg0 #cg
> 0 0 0 0 0
> 1 0 1960 0 682
> 2 1960 212 682 53
> 3 2172 212 735 53
> 4 2384 212 788 53
> 5 2596 212 841 53
> 6 2808 212 894 53
> 7 3020 208 947 52
>
> …
> Total Scaling: 18% of max performance
>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys