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

[Nicolas]

Nicolas a écrit :
> 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:
Little mistake: I used the wrong cluster specifications. There is 4 
cores per nodes and they communicate with Infiniband.
> 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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