Setup for multiple runs of the same model

[theiera]

Hello Salvador,
Hello NetPyners,

I'm finally stating to use netpyne for my simulations, wonderful project you made!

At the Janelia Farm you told me that it is possible to have in one simulation multiple runs of the same model automatically managing the output data and their analysis.
I feel quite "stupid" right now but from the Tutorial I cannot understand how this could be done.
I expected to find this info in the "Simulation cofinguration" of the documentation and I had no success.

Best regards,
Sergio Solinas

[ted]

It's not as simple as a loop that implements something like this pseudocode?

Code: Select all

for condition in list_of_conditions
  run a simulation assuming condition
  process results of simulation

[salvadord]

Hi Sergio, thanks for using the tool and asking this useful question!

If you just want to explore parameters manually, you can modify them in simConfig and netParams and then just change 'simLabel' (in simConfig) so the output is saved to different output files.

However, NetPyNE has a built-in Batch class that allows you to set the parameters and range of values you want to explore and takes care of running all the sims using mpi and NEURON's Bulletin Board (or SLURM/PBS for HPCs), saving output, etc

I'm writing a short tutorial on this which I hope to have ready tonite, but in the mean time you can have a look at this example: https://github.com/Neurosim-lab/netpyne ... /batchCell

salva

[salvadord]

I added a short tutorial on running batch simulations: http://www.neurosimlab.org/netpyne/tuto ... tutorial-8

Hope it helps... and please let me know if you have any more questions.