[gmx-users] Gromacs 4 Scaling Benchmarks...

[Martin Höfling]

Am Dienstag 11 November 2008 12:06:06 schrieb vivek sharma:


> I have also tried scaling gromacs for a number of nodes ....but was not
> able to optimize it beyond 20 processor..on 20 nodes i.e. 1 processor per

As mentioned before, performance strongly depends on the type of interconnect 
you're using between your processes. Shared Memory, Ethernet, Infiniband, 
NumaLink, whatever...

I assume you're using ethernet (100/1000 MBit?), you can tune here to some 
extend as described in:

Kutzner, C.; Spoel, D. V. D.; Fechner, M.; Lindahl, E.; Schmitt, U. W.; Groot, 
B. L. D. & Grubmüller, H. Speeding up parallel GROMACS on high-latency 
networks Journal of Computational Chemistry, 2007 

...but be aware that principal limitations of ethernet remain. To come around 
this, you might consider to invest in the interconnect. If you can come out 
with <16 cores, shared memory nodes will give you the "biggest bang for the 
buck".

Best
          Martin