[gmx-users] MD PME in parallel

[e.akhmatskaya at fle.fujitsu.com]

Hi David,

>I have run it using LAM and SCALI networks, in both cases it crashes at
>the end when writing the coordinates (confout.gro). It writes roughly
>6000 lines out of 23000.
Sounds familiar to me! I had this scenario on the Linux cluster too.

>You implied somehow that the problem only occurs when you have no water
on node 0. 
This is what I thought. Now I think it is more complicated. It depends on
distribution of water molecules but in more sophisticated way.

>There is a workaround for that, the -load option of grompp
>allows you to modify the division over nodes, e.g.:
>grompp -load "1.1 1.0 1.0 1.0 1.0"
Thanks for the idea! Yes, playing with this option I can make those
benchmarks running on all machines. However, performance becomes very
upsetting. This is not surprising as I change the load blindly. Perhaps, I
can play further and change the load on a few more processors to improve
load balance but I still believe that there should be some nice fix for the
code. I didn't find any so far ... 

Cheers,

Elena.
_____________________________________________
Elena Akhmatskaya
Research Scientist
Physical & Life Sciences
Fujitsu Laboratories of Europe Ltd (FLE)
Hayes Park Central
Hayes End Road
Hayes, Middlesex
UB4 8FE
UK
tel: +44 (0) 2086064859
e-mail: e.akhmatskaya at fle.fujitsu.com
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