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

Hannes Loeffler Hannes.Loeffler at stfc.ac.uk
Tue Apr 24 18:01:12 CEST 2012

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.

Scanned by iCritical.

More information about the gromacs.org_gmx-users mailing list