[gmx-users] Scaling/performance on Gromacs 4

[Carsten Kutzner]

Hi Sara,

my guess is that 1500 steps are not at all sufficient for a benchmark on 64 cores. 
The dynamic load balancing will need more time to adapt the domain sizes
for optimal balance. 
It is also important that you reset the timers when the load is balanced (to get
clean performance numbers); you might want to use the -resethway switch for that. 
g_tune_pme will help you find the performance optimum on any number of nodes, 
from 4.5 on it is included in Gromacs.

Carsten


Am Feb 20, 2012 um 5:12 PM schrieb Sara Campos:

> Dear GROMACS users
> 
> My group has had access to a quad processor, 64 core machine (4 x Opteron 6274 @ 2.2 GHz with 16 cores)
> and I made some performance tests, using the following specifications:
> 
> System size: 299787 atoms
> Number of MD steps: 1500
> Electrostatics treatment: PME
> Gromacs version: 4.0.4
> MPI: LAM
> Command ran: mpirun -ssi rpi tcp C mdrun_mpi ...
> 
> #CPUS          Time (s)   Steps/s
> 64             195.000     7.69
> 32             192.000     7.81
> 16             275.000     5.45
> 8              381.000     3.94
> 4              751.000     2.00
> 2             1001.000     1.50
> 1             2352.000     0.64
> 
> The scaling is not good. But the weirdest is the 64 processors performing
> the same as 32. I see the plots from Dr. Hess on the GROMACS 4 paper on JCTC
> and I do not understand why this is happening. Can anyone help?
> 
> Thanks in advance,
> Sara
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