NEURON 7.6.7 - Permission denied. Python not available.

AnaLuis
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Joined: Mon May 16, 2022 5:25 am

Re: NEURON 7.6.7 - Permission denied. Python not available.

Post by AnaLuis »

I also didn't realize that when I downloaded the exe file.

Right, I understand. Yes, I think it's possible.

And what about creating a conda virtual environment with python=3.7 and set up NEURON 7.6.7 there? Although I don't exactly know how I would set up/launch NEURON in the environment.

I want to use the PyPNS module. I used it before with NEURON 8.0 and managed to run simulations. But then I discovered the results weren't reliable, based on the PyPNS page https://github.com/chlubba/PyPNS and also in the issues section https://github.com/chlubba/PyPNS/issues/5, justifying why I had to use NEURON 7.6.7.
ted
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Re: NEURON 7.6.7 - Permission denied. Python not available.

Post by ted »

https://github.com/chlubba/PyPNS presents instructions for installation and configuration, including install & config of NEURON 7.6.7. Those instructions don't work?
AnaLuis
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Joined: Mon May 16, 2022 5:25 am

Re: NEURON 7.6.7 - Permission denied. Python not available.

Post by AnaLuis »

In the 'NEURON installation' section, in https://github.com/chlubba/PyPNS, it's mentioned that those instructions are based on another tutorial, which was made for Linux or Mac OS X.

Because I have windows, and when NEURON 8.0 was installed I managed to set up PyPNS, I followed the same logic for version 7.6.7.

But I can try to see how to adapt it.
hines
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Re: NEURON 7.6.7 - Permission denied. Python not available.

Post by hines »

When I use NEURON-8.1.0 with python3.9 on my linux desktop and install PyPNS from github and run

Code: Select all

python -i test.py
I get

Code: Select all

(pypns-39) hines@hines-t7500:~/tmp/pypns$ python -i test.py
	1 
Creating axon 0
Myelinated fiber diameter: [0.97982345]
Number of segments for myelinated axon: 2208

Starting simulation of axon 0
Elapsed time to calculate voltage and membrane current...
352.09 s
Elapsed time to calculate extracellular potential...
21.15 s
Overall processing of axon 0 took 385.83 s.

All axons simulated.
Elapsed time to compute CAP from single axon contributions...
0.00 s
Elapsed time to save CAP data...
0.01 s
bundle saved.
But the Figure 1 generated is not very interesting, Just vertical lines for the three recording mechanisms at time with max at 0.000175 the 10 ms just below 0, then values at 0 from t=10 to 50. Is that what is meant by NEURON 8.1 not working with PyPNS?
see https://github.com/neuronsimulator/nrn/issues/1831
AnaLuis
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Joined: Mon May 16, 2022 5:25 am

Re: NEURON 7.6.7 - Permission denied. Python not available.

Post by AnaLuis »

Yes, the results generated in the simulations were strange.

I saw https://github.com/neuronsimulator/nrn/issues/1831. Thank you for taking a look at the problem and exploring the compatibility between different NEURON versions and PyPNS.
hines
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Re: NEURON 7.6.7 - Permission denied. Python not available.

Post by hines »

https://github.com/chlubba/PyPNS/pull/6 has been merged to master. The expectation is that all versions of NEURON will now produce the same results modulo nondeterministic use of random variables.
AnaLuis
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Joined: Mon May 16, 2022 5:25 am

Re: NEURON 7.6.7 - Permission denied. Python not available.

Post by AnaLuis »

Thank you very much. With the introduced changes I will try to replicate the results of the PyPNS paper with NEURON 8.0 .
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