On Thu, Jun 29, 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.
> mpirun -np 160 sander.MPI ....
160 threads is still *way* to many for sander! Sander will likely max out
at something like 8 to 16 threads. Run a bunch of *short* simulations with
various thread counts to gain some experience with performance.
> Is it slow because of Sander module.Can i use
> PMEMD to get fast calculation using HPC.
pmemd will generally be faster than sander, and will scale better to large
numnber of threads. But don't be afraid to experiment: find out what
pmemd will do on your system, again testing performance vs. number of threads.
...good luck....dac
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Received on Thu Jun 29 2017 - 08:00:02 PDT
