[gmx-users] Scaling Problems

[Mehmet Suezen]

Hello,
Which configure options have you used during compilation?
Optimized loops greatly enchanced performance.

Cheeers, Mehmet 

On Tue, 17 Sep 2002, Dallas Warren wrote:

> Having some problems with scaling of GROMACS onto multiple boxes.  Just 
> want to see if the system I am simulating is may be too small to scale 
> well, or if there are some settings with may be LAM or even default GROMACS 
> that I need to be adjusting.
> 
> System:
>          Intel P733 Dual Processor
>          Linux Redhat 7.3
>          LAM 6.5.4
>          100 base Ethernet
> 
> MD Simulation:
>          7.5 nm cube
>          16 molecules, 16 Na, + water
>          42,000 atoms
>          500 steps
>          0.002 ps step
>          PME
> 
> grompp switches:
>          -sort
>          -shuffle
>          -np #
> 
> Initiation of mdrun:
>          mpirun C mdrun -s .....
> 
> Results (time to perform the mdrun calculation):
>          1 CPU / 1 box - 480 seconds
>          2 CPU / 1 box - 340 seconds
>          2 CPU / 2 box - 400 seconds
>          4 CPU / 2 box - 420 seconds
> 
> Some suggestions and guidance would be greatly appreciated :-)
> 
> Catch ya,
> 
> Dr. Dallas Warren
> Research Fellow
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy
> Monash University
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9076
>