parallel processing - shared memory and population dynamics on a landscape

Question

I would like to parallelize population dynamics for individuals moving on a 2D landscape. The landscape will be divided into cells with each processing core operating on individuals that exist in a specific cell.

The problem is that because the individuals move they travel between cells. Meanwhile the positions of individuals in a given cell (and its neighboring cells) must be known at any point in time in order to determine when pairs of individuals can mate.

In openMPI, it would be necessary to pass the structures of individuals (in this case, a list of mutations, and their locations in a genome) as messages whenever they move to a different cell, which would be very slow.

However, it seems that in OpenMP there is a way for the processing cores to share the memory for the entire list of genomes / individuals (i.e., for all cells). In this case, there would be no need for message passing, and the code could be very efficient.

Is my understanding of openMP correct? The nodes on my cluster each contain 32 processing cores. Does this mean I am limited to sharing memory among these 32 cores?

Thank you

question from:https://stackoverflow.com/questions/65932565/shared-memory-and-population-dynamics-on-a-landscape

Answer 1

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