[gmx-users] VSMP cluster performance changes with time

[Mark Abraham]

On 18/08/11, Anupam Nath Jha <anupam at mbu.iisc.ernet.in> wrote:

> 
> 
> Dear all
> 
> I am running a MD (Gromacs - 4.5.3) in VSMP cluster with 24nodes.
> 
> I am writing log files for different ns (1-10) in different files i.e. different
> files for each nano second . The performance goes like following:
> 
> --------------------------
> for 1st ns:
> 
>                (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
> Performance:   1444.719     85.902      3.946      6.082
> Finished mdrun on node 0 Tue Aug 16 21:46:02 2011
> 
> at 2nd ns:
> 
>                 (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
> Performance:    560.393     33.322      1.531     15.679
> Finished mdrun on node 0 Wed Aug 17 13:27:38 2011
> ------------------
> 
> and in case of 3rd ns:
>  it didn't complete the all steps and went in next.
> 
> Is it the problem with the gromacs?
> 

 
Probably not. Assuming you have kept everything else constant, it is likely that other activity on the machine or file system is delaying you somehow. However, in the absence of much basic information (like how many processors you are trying to use) we can't suppose much. Copying and pasting command lines is useful. 
 
Mark
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110818/39daa0e3/attachment.html>