2021 10 11 Open NEST Developer Video Conference

previous | list | next

Agenda

1. Welcome
2. Review of NEST User Mailing List
   • new EBRAINS support ticket
3. Project team round
4. In-depth discussion
   • Plasticity models via NESTML
   • NEST-on-wheels (Python packaging)

Mailing list

• https://nest-simulator.org/mailinglist

Project team round

Here we discuss topics that need broader attention, for example questions that came up but are outside a single project's scope, larger planned changes/PRs that affect all teams or pending work that is blocked by external factors.

1. Models / NESTML
   • STDP DOPA synapse now proof-of-concept exists
   • Clopath synapse
     • needs support for delayed values in ODEs, requires extension of NESTML x[t-delay], work in progress
       • comment: native C++ code has a very boiled down ODE that is much simpler, so full-general "delayed value" might not be needed
       • answer: currently only fixed delays are being looked at in NESTML, very much like in the C++ code.
2. PyNEST
   • nothing to report
3. Kernel
   • nothing to report
4. Installation
   • found issue in conda-forge packaging in NEST-3.x packages (not for nest-2.x packages)
     • related to sli-init.sli paths causing exception
   • NEST on wheels (see in-depth)
5. Infrastructure
   • deployment of NESTML now also via pypi, help appreciated with Many-Linux setup of wheels.
6. Documentation
   • nothing to report
7. EBRAINS
   • support request on mailing list (only arrived at Charl) `nest.Create("volume_transmitter")´
8. (Feature) Automated Testing
   • nothing to report
9. (Feature) Extension Module System
   • nothing to report

In-depth discussion

Plasticity models via NESTML

• goal is to move the models for Cerebellum from nest-2.x to nest-3.x
• requires special kernel for update of spikes
• custom volume_transmitter
• currently an extension module that would need to be migrated to the new layout, but possibly implementable in NESTML

ref. https://github.com/dbbs-lab/cereb-nest and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773604/

NEST wheels

• worked on wheels
  • nest has to belinked against static python
  • changing prefix
  • currently using legacy setuptools builder, might need to change
• currently cmake prefix ./install
• need hackathon for 2021-10-22

General wheel-building walk-through

builder to build binary extension

• usually setuptools builder using setup.py
• specify "binary extension" in setup.py, need to override some classes when using cmake (see #2170)
• putting files in the right locations is usually tricky (dir up / dir down / magic names)
• will build binary packages inside the "many-linux image", for each distribution
• wheel is built on the github CI and can be automatically uploaded to PyPI
  • better upload to pypi testing environment first (test.pipy.org), cross-check package, upload to real pypi when package works.

NESTML grammars

• Q: why generate parser and lexer with Python2
• A: Should work with Python3. Please report if it doesn't.