On Tue, Oct 1, 2013 at 12:00 PM, Biao Ma <jackyma1981.gmail.com> wrote:
> Hi, all.
>
> I plan to run my CpHMD job on 208 processors at 26 nodes, but it's stopped
> with Error "Must have more residues than processors!"
> Now I redo the job on 80 processors and no problem.
>
> Could anyone explain the reason of the error?
> Weather the number of processors cannot more than the numbers of system's
> residues?
>
This is only sander -- pmemd does not have this limitation. [1] Sander
splits up the workload for different processors on a per-residue basis. If
you have more processors than residues, some processors would be assigned 0
residues. It is an implementation detail, but I would not expect sander to
scale to that many processors even with GB.
Also, I suggest that you run some short benchmarking calculations with
Amber before deciding on the number of processors that you are going to
use. More is not always better, and these short simulations can help you
decide how to make the best use of your resources.
HTH,
Jason
[1] pmemd requires that the number of atoms be at least 10x the number of
processors (so each processor is responsible for at least 10 atoms).
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 01 2013 - 09:30:10 PDT
