May 2020

 Time: 15.5.2020, 16:00 CEST; 10:00 EST Place: Zoom

NOTE: Please contact one of the NEURON developers for the link if you are interested to join.

Agenda

• NEURON News / Announcements (2 min)
• Introduction from "new" members (5 min)
• New neuron_nightly wheels with Azure CI : what is it? (4 min)
• A new versioning scheme for NEURON (8 min)
• Change 6.3 to 37? : What else remains to make NEURON a modern major general neural simulator? (Celsius default)
• Software Engineering of NEURON codebase (7-10 mins)
  • Practicalities & Goals
  • How / When
  • Which parts to start with : HOC/NMODL/Solver/legacy libraries
• Technical discussion on issues:
  • Sundials v 5. Very different NVector for threads and mpi. NEURON currently uses homemade implementations for these. See branch cvode3. A subbranch, idainit, is much more robust for IDA initialization but comes at a cost of an extra algebraic variable for each extracellular layer, i.e. vm = vi - ve .
  • Error handling.
• Next Release 8.0 Milestone on GitHub
• Next Meeting : Call for suggestions / presentations!

Meeting Minutes

Supporting slides here

Attendees

• Michael Hines (MH)
• Robert McDougal (RM)
• Salvador Dura-Bernal (SD)
• Bill Lyton (BL)
• James King (JK)
• Pramod Kumbhar (PK)
• Omar Awile (OA)
• Fernando Pereira (FP)
• Ioannis Magkanaris (IM)
• Alessandro Cattabiani (AC)
• Wouter Klijn (WK)
• Blake Caldwell (BC)
• Nicolas Cornu (NC)
• Joe Graham (JG)
• Kaeld

Discussion

Introduction of New Members

• WK :
  • Role at FZJ and HBP : leading coupling of simulators, with easy to use framework for multi-scale simulations.
    • Different scales and different simulators are doing good job but how to connect them?
    • HBP has dedicated task to develop framework
  • At least 3 use cases/ users interested with NEURON and coupling with NEST
  • New interface being developed, alternative to MUSIC. Core developer of MUSIC involved
  • Not actively contributing in NEURON but would like to get use cases supported. Can provide plugins to do heavy lifting.
• RM : What was not supported by supported by MUSIC?
  • Some of the limitations mentioned by Felix (as part of BBP's ISC work)
  • Limited developer bandwidth
• NC :
  • Working at BBP and working on CoreNEURON since last 2-3 months
  • Improving CoreNEURON codebase with OOP

This new interface should be look at for NEURON/CoreNEURON integration (from BBP side for HBP use cases)

New neuron_nightly wheels with Azure CI

• Wheel has more improvements :support MPI and Interviews added 🎉
• https://test.pypi.org/simple is now deprecated, just use pip install neuron-nightly !
• neuron-nightly : development snapshot is built every night on Azure -CI
• make sure to not have neuron and neuron-nightly installed together
• Azure CI workflow is merged to master
• Every night new wheel is built pushed to Pypi if all tests pass

Thanks JG for testing OS X wheel with Anaconda MPI : one needs to set

export MPI_LIB_NRN_PATH=/Applications/anaconda3/lib/libmpi.dylib

• One caveat : don't install neuron vs. neuron-nightly

QA:

• Does pip3 update neuron-nightly work and automatically bump the version to the next nightly build? => Yes
• Right now, xquartz opens on a mac when you do “from neuron import h”. Is it possible to not do that unless someone does a “from neuron import gui”? It takes a while to start up xquartz. => PK will open an issue

Versioning scheme for NEURON

WIP : Meeting notes are incomplete and being updated

Next meeting June 19, 2020, 16:00 CEST; 10:00 EDT