[gmx-users] mdrun load sharing between dual processor machine

[Erik Lindahl]

Hi Lynne,

>
>
> I''ve just noticed that when I run the normal version of gromacs 
> (mdrun) on my new dual athlon linux machines, that it doesn't fully 
> load both processors. According to top, although I'm getting 99.9% cpu 
> usage for mdrun, it also says that cpu0 is working at about 80% and 
> cpu1 is working at only about 20%. This adds up to 100% of one cpu. 
> Does this mean I need to use the mpi version to fully utilise both 
> processors? 

The released version of Gromacs only supports MPI-based parallel runs, 
i.e. for 3 dual nodes you should prepare an input file for 6 processors, 
and then use LAM or MPICH to tell the system to run two processes on 
each node. LAM handles this quite nicely.

We're working on a split-level parallelization setup that will utilize 
all CPUs on a node automatically, and load-balance between them.

Cheers,

Erik