Re: NAMD for Stampede2

From: Vermaas, Joshua (
Date: Wed Aug 09 2017 - 17:45:00 CDT

Hi Maria,

Jim Phillips has a set of NAMD submission scripts that you can try out.
See /home1/00288/tg455591/NAMD_scripts, which you can then edit for your
own purposes. Do some experimentation in terms of the processes per node
and hyperthreading. Depending on the system size and the number of
nodes, different configurations can have radically different performance.


On 08/09/2017 09:33 AM, Maria Bykhovskaia wrote:
> Hi,
> Did anybody optimized NAMD scripts for Stampede2? I have a system of
> about 200,000 atoms. If anybody has an idea of what would be the
> optimal -n (total tasks) and -N (nodes), or tasks-per-node on
> Stampede2, I'll greatly appreciate if you share that.
> Thanks,
> Maria

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:30 CST