Beniamino Sciacca wrote:
> Hi community!
> this is my question:
> I've two pc (centrino duo and AMD 64 X2), and i use molecular mechanics
> software (gromacs).
> I need to use both my two pc to simulate faster. The kernel in the pc is
> the same (2.6....).
> The pc are connected by an hub (10Mbps).
> How can i run simulation in parallel with both the pc?
> LAM is installed in both the pc, and during the compilation of gromacs i
> enabled LAM; so before starting "mdrun" i type "lamboot", and then
> mdrun.......
> What must I do to tell mdrun to use both the machines?
> thanks very much for your help
>
> Beniamino Sciacca
It's been a while since I used gromacs, but a quick glance at their
documentation turned up the '-np' parameter to both grompp and mdrun. I
remember using this and having things work. Check out the documentation
for both grompp and mdrun, as they need the exact same -np argument:
http://www.gromacs.org/external/online_reference_manual.html
As Brian mentioned, you probably need a hostfile to have lamboot set up
both of your nodes. Check out section 4.4 of the LAM user's guide.
IIRC, gromacs is very communications-intensive. I wouldn't be surprised
if gromacs ran slower on your two nodes over a 10mbps hub than it did on
just one of the machines. As Brian suggested, you should really get
something better. If the two machines are all you need connected, a
crossover cable might be sufficient as well.
Andrew
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