[gmx-users] Error in BlueGene

[Mark Abraham]

On Mon, Feb 4, 2013 at 5:18 PM, Cintia C. Vequi-Suplicy <cintia at if.usp.br>wrote:

>
>
>
> Hello David,
>
> I think it is the pressure.
>

I would think the mentions of pressure are just one of the symptoms. See
http://www.gromacs.org/Documentation/Terminology/Blowing_Up.

You seem to have somewhat more than 100K atoms, which is a bit over 200
atoms/processor for 512 processors. That's down the low end of GROMACS
scaling limits. I asked you earlier to try running with the same number of
processors on the BlueGene as you do locally, and to report the command
lines you were using for the whole transfer and restart process. This will
allow us to see if the problem is in how DD is treating your system, or how
you are managing the transfer between hardware. Until then, nobody can tell
anything.

Mark