podman run -v “$(pwd):/workdir” brian1 python behaviors.py
and of course got this msg
python: can’t open file ‘behaviors.py’: [Errno 13] Permission denied
so tried this instead
podman run -u (id -u):(id -g) -v “$(pwd):/workdir” brian1 python behaviors.py
(sorry, haven’t figured out how the “preformatted text” markup is supposed to work, so a couple of dollar signs aren’t showing in that line) and got the same msg. This under Rocky linux 9.3 (RHEL semiclone) with latest updates. What next?
Hi @xnm. I’m afraid I cannot reproduce this on my machine, i.e.:
podman pull docker.io/briansimulator/brian1.4.3
podman tag briansimulator/brian1.4.3 brian1
podman run -v "$(pwd):/workdir" brian1 python behaviors.py
runs without a permission error. It raises an exception about the access optimize, but this is fixed by adding from scipy import optimize to the script. The permission issue we mention in the documentation is with respect to files written by the script – this does not apply here. I don’t have experience with RHEL/Rocky Linux, but this problem does not seem to be related to the Brian 1 container itself but rather to your local environment (how/where you downloaded the files, the podman version you are using, etc.).
All that said, if you are interested in the results of Toubul & Brette 2008, you can also use the Brian 2 version of their code, included as an example in the Brian dicumentation: Example: Touboul_Brette_2008 — Brian 2 2.5.4 documentation
Hope that helps!
Marcel
PS:
sorry, haven’t figured out how the “preformatted text” markup is supposed to work
Pre-formatted text uses markdown syntax, i.e. either enclose text in `single backticks` for in-inline formatting, or in
Thanks for the prompt and very helpful reply, Marcel!
Touboul & Brette 2008 is a very nice nonlinear dynamical system analysis. But I was looking for something much simpler–in particular, something that corresponds to Naud et al. 2008. And sure enough, there it is in the Brian documentation!