Issue running HNN-Netpyne (hnn2) examples

[Moham-Amin]

Hello, my name is Mohamed Amin.

I’ve been working with Dr. Mohamed Sherif, and I’ve had an issue with running the examples on hnn-netpyne.

I use Windows 10, and MS-MPI.

After following instructions in the README, I first got a system error: no such file or directory. I tracked it down to netpyne’s grid.py which had the mpi command assigned as ‘mpirun’, which isn’t recognized as an MS-MPI command. I changed it to ‘mpiexec’.

The error no longer happens now, and instead the terminal stops at ‘Finished submitting jobs...’ and creates the following files in /data/trials: trials_0.err, trials_0.run, trials_0_cfg.json, trials_batch.json, trials_batchSctipt.py, trials_netParamas.py

But it does not create any plots, which is my main issue.

I also tried running the init.py in the hnn_model folder directly, which runs smoothly but still does not produce plots.

I also tried changing the cfg.duration to 10ms to make sure the issue is not very long processor time, but with the same results.

Would appreciate your help on this issue. Thank you.

[Sumayya55]

Hi there, Probably your issue isn't batch-related. I wonder what trials_0.err contains?

Things to try:

• Make sure to set showFig=True in cfg.py cfg.analysis['iplotRaster'] = {'include': pops, 'showFig': True, 'popColors': popColors, 'markerSize': 6, 'orderInverse': True, 'saveFig': True}

• You can also try changing matplotlib's background type if other solutions fail: Check ( init .py) inside netpyne's folder and look for 'Agg', replace it with some other type such as 'TkAgg'; see if that solves your problem.

• Add import pylab; pylab.show() inside your init.py of hnn-netpyne (often unnecessary).

[Moham-Amin]

Hi there, Probably your issue isn't batch-related. I wonder what trials_0.err contains?

Thank you for your help @Sumayya55

Contents of trial_0.err:

In cfg.py for the neocortex model example, I found the code you're referencing between triple quotations like so. I tried removing them.

I also added import pylab; pylab.show() to the same model's init.py file, and changed 'Agg' to 'TkAgg' in netpynes init.py

Now, when running python -i init.py (hnn-netpyne's init.py) directly, I get the plots, which is progress! But when running python -i plot_simulate_alpha.py, I get stuck at the same spot here, with the same trials_0.err file and no plots:

[salvadord]

Based on the .err output the issue seems to come from " file" not defined. However, I am unable to reproduce on my Mac OS, so this might be a Windows-specific error. If you can find any more information about the error, that would be helpful. Otherwise, we will try to reproduce the error on a Windows machine and get back to you.