On Tue, Jul 04, 2017, Garima Singh wrote:
>
> I am using fewer nodes this time using
> below pbs script. Job run and and still continue but it only give 7
> ns /day which is very slow.How to get fast result from HPC. Is it slow
> because of Sander module.Can i use PMEMD to get fast calculation using
> HPC.
> mpirun -np 160 sander.MPI ....
I thought I had replied to this earlier, but maybe the answer got lost...
1. 160 is *way* to many threads for sander.MPI. Try something like 8 or 16.
Experiment with your system to find the best number.
2. By all means, run pmemd.MPI: as long as you don't require features unique
to sander, pmemd will almost always be faster, sometimes by a lot (especially
with larger numbers of threads.) Again: run experiments to find the best
number of threads.
....dac
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Received on Tue Jul 04 2017 - 07:00:03 PDT
