Python3 update for "Brownian dynamics simulation"

[alex4200]

Expected behavior

Should work for python3

Actual Behavior (please include screenshot if possible)

Several incompatibility issues.

Steps to reproduce the problem

1. Clone notebook
2. Change kernel
3. Run all cells

Optional infrastructural data (user, platform, browser, environment, ...)

Guidelines

When updating the notebook you might consider some of the Guidelines to provide an improved look & feel.

[StefanGIT]

It looks like this is due to problems in python3 compatibility of the underlying SDA bootstrap script that is installed in /opt/minimal-sda_flex-7.2.2 Would it be possible to upgrade this to sda_flex-7.2.3? I have attached this here as a zip file. sda_flex-7.2.3-minimal.zip

[StefanGIT]

In addition to installing this new SDA version, also the environment variable SDAHOME needs to be set. The notebook gets the SDA directory by the call sdaDir = os.environ['SDAHOME']

[alex4200]

I need to check with the admins of the Collab on how this can be implemented. But adding a cell like the following

!wget https://github.com/cnr-ibf-pa/hbp-bsp-issues/files/4148695/sda_flex-7.2.3-minimal.zip
!unzip sda_flex-7.2.3-minimal.zip
!cd minimal-sda_flex-7.2.3/src && make clean && make
os.environ['SDAHOME'] = "/home/jovyan/minimal-sda_flex-7.2.3"

will install the new version, and make the notebook work with python3.

[StefanGIT]

I have copied the change to the private MolecularUseCases area. It was working now using python3. How to get this to the public area?

[StefanGIT]

@alex4200 The sda notebook is now working in the public area: https://collab.humanbrainproject.eu/#/collab/50197/nav/344097 with changes to download sda from github pages. Once SDA can be used from /opt/, let me know.

[antonelepfl]

@alex4200 Could you re-check if this is working properly? Is this on the BSP Prod?

[alex4200]

Usecase has been checked on STAGE. Will be merged soon to PROD