[gmx-users] Running GROMACS in parallel

Mark Abraham mark.abraham at anu.edu.au
Fri Nov 10 01:28:08 CET 2006

> Hi folks,
> I'd need an help to run GROMACS in parallel on a cluster with x86_64
> architecture, with BioBrew 4.1.2-1 roll (GROMACS is one of the programs
> included in the package). After launching lamboot (with no problems) on 5
> nodes of this machine (with names lilligridgiga,lilligridgiga2/3/4/5),
> with
> 2 CPUs each, I'm trying to do the speptide tutorial running the final full
> MD in parallel. Therefore, I used the grompp -np 10 program (all other
> settings left as in the tutorial), and after that I made several attempts
> to
> launch mdrun. Here a brief resume of all my trials and of error messages
> received:

I'd suggest walking before running. Get gromacs working on one machine
with two cpus, and then maybe two machines with one cpu each before you go
and throw all this extra complexity around.


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