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Re: Parallelization

From: Rudolf Weeber
Subject: Re: Parallelization
Date: Wed, 29 Dec 2021 19:23:20 +0100

Hi Ahmad,
On Wed, Dec 29, 2021 at 05:08:18PM +0000, Ahmad Reza Motezakker wrote:
> Is there any tutorial or any document on EspressoMD parallelization? I really 
> appreciate your help. Any suggestion or experience will be really helpful for 
> me.
Do you just want to run a simulation in parallel, or do you want to extend 
Espresso andneed to write parallel code for that.
If it is about running, you use
mpirun -np <n> ./pypresso <> <arguments>
where <n> is the number of processor cores you want to run on.
More is not necessarily better, as parallelizaiton requires communicaiton, 
whicht akes time of its own.
For pure Lennard-Jones-systems parallelizaiton tends not to be worth it belwo 
10k particles. If you use electrostatics or other computaiton-intensive 
algorithms, the number is lower.
In practice, just time some 100 integration steps using the Python `time` or 
`timeit`modules and pick the number of cpu cores which serves you best.

Hope that helps!
Regareds, Rudolf

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