RxD with ParallelContext

Extending NEURON to handle reaction-diffusion problems.

Moderators: hines, wwlytton, ramcdougal

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itaru
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Joined: Wed Jan 29, 2020 10:15 pm
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RxD with ParallelContext

Post by itaru »

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?
ramcdougal
Posts: 267
Joined: Fri Nov 28, 2008 3:38 pm
Location: Yale School of Public Health

Re: RxD with ParallelContext

Post by ramcdougal »

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).
itaru
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Joined: Wed Jan 29, 2020 10:15 pm
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Re: RxD with ParallelContext

Post by itaru »

More examples are appreciated, should I look for them in the upstream RxD folder?
itaru
Posts: 27
Joined: Wed Jan 29, 2020 10:15 pm
Contact:

Re: RxD with ParallelContext

Post by itaru »

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.
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