[gmx-users] Best performace with 0 core for PME calcuation

[Nicolas]

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


-------------- next part --------------
A non-text attachment was scrubbed...
Name: nsapay.vcf
Type: text/x-vcard
Size: 310 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090109/7bda5453/attachment.vcf>