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

[Erik Marklund]

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.
>>
>> /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