Running NEURON code on a supercomputer

Once you have gotten access to a supercomputer, you will want to run your model code on it as soon as possible! Below, I’ve listed a few steps/issues I’ve run into when setting up my NEURON code on a new supercomputer. The first two (installing NEURON, writing a job submission script) can be avoided by using the Neuroscience Gateway portal, aka the NSG. The NSG is a great option for getting started with large scale, parallel NEURON modeling – you can get a free account with some computing time right away, and it is well supported.

If you decide not to use the NSG, or if you like it but decide you want to scale up your project even more, then you will have additional considerations for using NEURON on another supercomputer. Here are some solutions that may be useful for you: Continue reading

Access a supercomputer for your NEURON modeling

NEURON code can easily be run in parallel (on many processors at once), saving you a large amount of time. This applies to both large-scale network simulations and very small simulations that you need to run hundreds of times to explore a parameterspace. To run NEURON in parallel, you need access to a computer with multiple processors or cores. Here are some ideas of how to find one. Continue reading