On Mon, Dec 24, 2012, Amparo Garcia Lopez wrote:
> The script and my files run normally in one machhine (4 processors). Speed is 5.21 ns/day. The output file says "running Amber/MPI on 4 nodes"
>
> When I run the script on several machines in parallel the speed doesn't
> increase (or it can get even lower),
This is very common. Unless you have an infiband (or equivalent) connection,
it is likely that you may not be able to scale pmemd beyond a single node.
Gigabit ethernet is not enough, at least for most problems. Basically, you
are being limited by the speed at which coordinates can be communicated
between nodes.
....good luck....dac
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Received on Mon Dec 24 2012 - 22:00:03 PST
