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

[David van der Spoel]

Erik Marklund wrote:
> 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.
How about vsites? Did you happen to turn them off as well in the vacuum 
case?
> 
> /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
>>
> 
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se