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

[Erik Marklund]

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