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.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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