On Wed, Nov 28, 2012, Fabian Glaser wrote:
>
> I am successfully but very slowly running MD on 84 processors, about a
> rate of 1/2 ns a day, with sander using the following command:
>
> mpirun -np 84 sander -O -i prod.in -p protein.prmtop -c
> protein_equil.rst -o protein_prod.out -x protein_prod.mdcrd -r
> protein_prod.rst
This is way wrong: you are running 84 copies of the same (single-cpu) sander
program. All the outputs are writing over each other.
>
> When I try the same with sander.MPI, nothing seems to happen, I mean the
> job runs, but no output files are ever written, I guess I am doing some
> trivial mistake....
Do the parallel test cases run? Have you tried a small example with your
inputs (e.g. -np 2, set nstlim to 10 and ntpr=1)?
Even when you get everything running, sander.MPI is unlikely to scale well to
84 threads. You need to run pmemd.MPI to get good parallel scaling (unless
this is a GB calculation; then sander.MPI in principle can scale well).
...dac
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Received on Wed Nov 28 2012 - 08:00:03 PST
