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

[Berk Hess]

Hi,

Setting -npme 2 is ridicolous.
mdrun estimates the number of PME nodes by itself when you do not specify -npme.
In most cases you need 1/3 or 1/4 of the nodes doing pme.
The default -npme guess of mdrun is usually not bad,
but might need to tuned a bit.
At the end of the md.log file you find the relative PP/PME load
so you can see in which direction you might need to change -npme,
if necessary.

Berk

> Date: Fri, 9 Jan 2009 18:37:37 -0700
> From: nsapay at ucalgary.ca
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Best performace with 0 core for PME calcuation
> 
> 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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