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From: | Ahmad Reza Motezakker |
Subject: | Parallelisation |
Date: | Wed, 12 Jan 2022 10:25:57 +0000 |
Dear All,
Thank you for your recent hints and feedback on parallelization of EspressoMD. Still I have some concern. 1- Since Espresso works with LJ units, what is the definition of a small and large system? All the dimensions are relative but still I am confused. For example, when I talk to other people who works with MD, they talk about million particles but in my system I have at most 40k particles but with very very slow computation speed. 2- In the previous email, on the number of CPUs, you mentioned number of cells must be minimum 2 and maximum 32 in each direction. according to my box size, I set l_skin in a way to have around 30 cells in each direction [ floor(box_l/(LJcut+l_skin)) ]. but no improvement in the calculation time. I should also add that, I have LB fluid in the system, Does the number of LB cells also follow the mentioned rule? I increase the lattice spacing but still no improvement in the timing. 3-During running serial or parallel, my computer ram (64GB+128 swap) will be almost occupied. What is the reason for that? Is there any way to improve that? I just get positions ,velocity and energy.
Thank you very much, Ahmad Reza |
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