Parallelisation

[Ahmad Reza Motezakker]

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