[gmx-users] gromacs parallel problem

[Mark Abraham]

mario ciappy wrote:
> Dear All,
> I configured gromacs 3.3.3 for parallel runs, using the precompiled 
> packeges on ubuntu server 8.04, with LAM program 7.1.2 ( alreay present 
> in server verison). I tried with d.villin benchmark but I detected an 
> decrease of performance increasing the node's number.
> The obtained results for 1 node are:
>                        (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
> Performance:      6.686      1.437      8.471      2.833
> The obtained results for 7 nodes are:
>                     (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
> Performance:      5.169      1.112      6.545      3.667
> 
> I have a cluster of 7 nodes (pentium 4 3.2 Ghz with RAM 2Gb) connected 
> on 10/100 Mbps dual speed up hub.
> I don't know if it is a configuration problem (because with precompiled 
> packages I couldn't use the configuration parameters described on web) 
> or an hardware problem due to hub.

One can get what one pays for with network hardware. Search in the 
archives for posts by Carsten Kutzner with lots of comments here.

Mark