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

[David van der Spoel]

Erik Marklund wrote:
> David van der Spoel skrev:
>> 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?
> Turned off in all cases. The VSites mentioned in the log file is the 
> 4:th particle on the tip4p-water molecules.
OK. Did you try a one step run with -debug?
It may give more info on the partitioning.

>>>
>>> /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