[gmx-users] Scaling on IBM/SP2 vs. Linux/AMD

[K.A. Feenstra]

Alan Wilter Sousa da Silva wrote:
> Weird! Is your ps/hour rate right?

I'd say so, they correspond to the web-site numbers and also
to yours: 48 ps/day = 2.3 ps/h. So I' missing about 10% of the
raw single CPU performance. This could be due to anything:
kernel or libc versions, nfs load on CPU, whatever...

> 	Here is my incomplete benchmark for the same dppc.
> 
> GMX 3.1.3 default single precision, LAM-MPI, -sort -shuffle
>
[...]
 >
> The first cluster run better when using cpus from different computers.
> So, e.g., using 2 cpus on the same node scales worse (124.488 ps/day) than
> above (first table).
> 
> I could use MPI-CH, but LAM-MPI is much better (faster, more friendly).

I've used MPI-CH, since that was the default on our cluster. IIRC, LAM
is also installed, so I'll try and make a comparison. Also, as I mentioned,
the 'short-message-length' parameter to MPI (compile time) has not been
optimized, which should decrease latency and hence increase scaling.

Still my network performance seems very bad indeed. Could it be due to
having two cards per node? One is dedicated to the MPI communication,
the other for 'normal' networking (login, nfs etc.)?

I'm impressed by the Gbit network performance: apparently the Gb card
is capable of saturating the bus to your CPU, making it faster than
two CPU's sharing the same bus to memory?


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "If You See Me Getting High, Knock Me Down"               |
|        | (Red Hot Chili Peppers)                                   |
|________|___________________________________________________________|