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

[Justin A. Lemkul]

vivek sharma wrote:
> HI MArtin,
> I am using here the infiniband having speed more than 10 gbps..Can you 
> suggest some option to scale better in this case.
> 

What % imbalance is being reported in the log file?  What fraction of the load 
is being assigned to PME, from grompp?  How many processors are you assigning to 
the PME calculation?  Are you using dynamic load balancing?

All of these factors affect performance.

-Justin

> With Thanks,
> Vivek
> 
> 2008/11/11 Martin Höfling <martin.hoefling at gmx.de 
> <mailto:martin.hoefling at gmx.de>>
> 
>     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
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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