Hello,
I'm trying to do a benchmark with Gromacs 4 on our cluster, but I don't
completely understand the results I obtain. The system I used is a 128
DOPC bilayer hydrated by ~18800 SPC for a total of ~70200 atoms. The
size of the system is 9.6x9.6x10.1 nm^3. I'm using the following parameters:
* nstlist = 10
* rlist = 1
* Coulombtype = PME
* rcoulomb = 1
* fourier spacing = 0.12
* vdwtype = Cutoff
* rvdw = 1
The cluster itself has got 2 procs/node connected by Ethernet 100 MB/s.
I'm using mpiexec to run Gromacs. When I use -npme 2 -ddorder
interleave, I get:
ncore Perf (ns/day) PME (%)
1 0,00 0
2 0,00 0
3 0,00 0
4 1,35 28
5 1,84 31
6 2,08 27
8 2,09 21
10 2,25 17
12 2,02 15
14 2,20 13
16 2,04 11
18 2,18 10
20 2,29 9
So, above 6-8 cores, the PP nodes are spending too much time waiting for
the PME nodes and the perf forms a plateau. When I use -npme 0, I get:
ncore Perf (ns/day) PME (%)
1 0,43 33
2 0,92 34
3 1,34 35
4 1,69 36
5 2,17 33
6 2,56 32
8 3,24 33
10 3,84 34
12 4,34 35
14 5,05 32
16 5,47 34
18 5,54 37
20 6,13 36
I obtain much better performances when there is no PME nodes, while I
was expecting the opposite. Does someone have an explanation for that?
Does that means domain decomposition is useless below a certain real
space cutoff? I'm quite confused.
Thanks,
Nicolas
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fn:Nicolas Sapay
n:Sapay;Nicolas
org:University of Calgary;Biological department
adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada
email;internet:nsa...@ucalgary.ca
title:Post-doctoral fellow
tel;work:403-220-6869
x-mozilla-html:TRUE
url:http://moose.bio.ucalgary.ca/
version:2.1
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