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Re: Parallelization

From: Ahmad Reza Motezakker
Subject: Re: Parallelization
Date: Thu, 30 Dec 2021 08:06:35 +0000

Dear Rudolf/Dear Jean-Noel,

Thank you very much for your help. I just need parallelization to run a simulation. 

I really appreciate if you provide a general document on parallelization (also in Jupyter) with details. For example, how to divide the box, collecting results and etc.

Thank you for your efforts,

Ahmad Reza

From: Rudolf Weeber <>
Sent: Wednesday, December 29, 2021 7:23:20 PM
To: Ahmad Reza Motezakker
Subject: Re: Parallelization
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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