[gmx-users] Scaling on dual athlon

Stefano Piana piana at inorg.chem.ethz.ch
Sat Oct 19 13:41:07 CEST 2002

Hallo, I am a brand new user :-)
I am very happy of Gromacs, still I have problems with the parallel 
I compiled with the lam-mpi standard options and I made some tests to see the 
scaling between one and two processors on a dual athlon. I report the results 
to provide some statistics and to ask for suggestions on how to improve the 
parallel performance.
I tried different systems in water (8071 and 39941 atoms) with PME. These are 
the timings in seconds:
              nsteps   1cpu      2cpu     1/2 cpu ratio
Sh3 protein   1000     87        64        1.36
(8071 Atoms)  5000     462       332       1.39
(39941 Atoms)  100     63        43        1.46
               1000     628      427        1.47

Is this the maximum performance I should expect or can I improve a bit?
Somewhere I read that the parallel implementation of the PME is not very 
efficient; however PME takes only 3-4% of my cpu. 10 to 20% is taken by the 
FFT that should be parallelized (?). Most of the rest (40-60%) is burnt by the 
wat-wat interaction.


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