www.neuron.yale.edu

Hi all,
I am looking at the Calcium Wave Tutorial at: https://neuron.yale.edu/neuron/docs/rea ... lcium-wave , this works on my MacBook Pro perfectly with the latest official release of NEURON. Now I am wondering if RxD is designed to work well with ParallelContexts?

Yes.

Intracellular reaction-diffusion (both 1D and 3D) parallelizes trivially as all cell-to-cell communication is through the regular spike exchange or gap junction mechanisms. (You still need ParallelContext for those, but you get the full speedup from splitting the cells onto different processors without having to add a single additional ParallelContext call to support rxd.)

Extracellular reaction-diffusion (e.g. think of neurons and astrocytes interacting via extracellular potassium concentrations) works with ParallelContext; see the model from Newton et al. 2018. ParallelContext speeds up the network parts of the simulation, but does not itself speed up the actual extracellular reaction-diffusion simulation. You can, however, speed up extracellular and 3D intracellular using threads, e.g. rxd.nthread(4).

More examples are appreciated, should I look for them in the upstream RxD folder?

I looked in the "test/rxd" directory, but could not find usage examples of RxD + the ParallelContext class. As I am having a problem incorporating
RxD statements into my Python script, examples would be appreciated.