Setup for multiple runs of the same model

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theiera
Posts: 8
Joined: Mon Feb 26, 2007 5:37 am

Setup for multiple runs of the same model

Post by theiera » Wed Oct 18, 2017 12:28 pm

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
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Location: Yale University School of Medicine
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Re: Setup for multiple runs of the same model

Post by ted » Thu Oct 19, 2017 12:49 pm

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
Posts: 57
Joined: Tue Aug 18, 2015 3:49 pm

Re: Setup for multiple runs of the same model

Post by salvadord » Fri Oct 20, 2017 12:56 pm

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
Posts: 57
Joined: Tue Aug 18, 2015 3:49 pm

Re: Setup for multiple runs of the same model

Post by salvadord » Sun Oct 22, 2017 10:13 pm

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.

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