[gmx-users] Gromacs 4 Scaling Benchmarks...

[Mark Abraham]

vivek sharma wrote:
> 
> 
> 2008/11/11 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     vivek sharma wrote:
> 
>         HI MArtin,
>         I am using here the infiniband having speed more than 10
>         gbps..Can you suggest some option to scale better in this case.
> 
> 
>     What % imbalance is being reported in the log file?  What fraction
>     of the load is being assigned to PME, from grompp?  How many
>     processors are you assigning to the PME calculation?  Are you using
>     dynamic load balancing?
> 
> 
> Everybody thanks for your usefull suggestions..
> What do you mean by % imbalance reported in log file. I don't know how 
> to assign the specific load to PME, but I can see that around 37% of the 
> computation is being used by PME.
> I am not assigning PME nodes separately. I have no idea of dynamic load 
> balancing and how to use it  ?

For the moment, you just need to look for information in your grompp 
output and your log file, like Justin asked.

To find out how to use things, check out mdrun -h and the version 4 
manual. There's some relevant discussion in this thread 
http://www.gromacs.org/pipermail/gmx-users/2008-October/036856.html

Mark