[gmx-users] why it is so slow in Blue gene?

[Hannes Loeffler]

On Tue, 24 Apr 2012 15:42:15 +0200
Albert <mailmd2011 at gmail.com> wrote:

> hello:
> 
>    I am running a 60,000 atom system with 128 core in a blue gene 
> cluster. and it is only 1ns/day.... here is the script I used for 

You don't give any information what exact system that is (L/P/Q?), if
you run single or double precision and what force field you are using.
But for a similar sized system using a united atom force field in
single precision we find about 4 ns/day on a BlueGene/P (see our
benchmarking reports on
http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx).  I would
expect a run with the CHARMM 27 force field in double precision to be
roughly 3 times slower.  We found scaling to 128 cores to be
reasonably good. Also, check our report for problems when compiling
with higher optimisation.

Hannes.
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