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March 2020

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Omar Awile edited this page Apr 17, 2020 · 2 revisions

Opening

The NEURON developers organized a meeting via zoom to discuss matters related to NEURON and give updates on the related projects on March 20th 2020 at 15.00 CET.

Present

  • Michael Hines
  • Robert McDougal
  • Adam Newton
  • Salvador Dura-Bernal
  • Bill Lyton
  • Joe Graham
  • James King
  • Pramod Kumbhar
  • Omar Awile
  • Fernando Pereira
  • Ioannis Magkanaris
  • Alexandru Savulescu
  • Nicolas Cornu
  • Alessandro Cattabiani

Supporting slides

NEURON build system

  • CMake now stable in master along with Autotools
  • Michael Hines: Autotools will be deprecated in near future.

Morphology loading

  • Interest by Robert McDougal / Bill Lyton to rework the morphology loading API and possibly create a python interface that is understandable by more people (like students)
  • Question about .H5 morphology reading performance (probably better but not tested)

CoreNeuron refactoring

  • Refactoring of the folders structure to make it easier for new developers to get more familiar with the code
  • Omar Awile suggested to do something similar in NEURON in future

CoreNeuron integration

  • Better integration of NEURON with CoreNEURON
  • Enabled building of NEURON with CoreNEURON and NMODL as submodules through the CMake build system
  • Use of normal compiler (gcc/clang) for better performance with the NMODL ISPC backend instead of Intel compiler which has good performance but is commercial product and not available in google cloud/AWS

GPU Integration

  • There is acceleration in the simulation time in the ringtest but we have to test if the same applies in the production circuits which are more complex and include more mechanisms
  • Work in fixing issues that are described in the slides

Python distribution

  • Work towards making NEURON pip installable
  • Question about manylinux by Michael Hines

Pyiter

GUI-redirect

  • HTML style GUI that can automatically sync variables with NEURON
  • A bit of python to create the window and connect it with NEURON.
  • Some issues with Parallel Compute Tool and calling private functions from templates
  • Question from Bill Lyton about what language is used and if there is anything more high level
    • Answer from Robert: HTML is used, which is used universally
  • GUI (buttons, etc) differentiates based on the OS (Mac/Linux)

NetPyNE

  • Salvador Dura-Bernal was able to run CoreNeuron with Michael Hines’ fix in randomiser
  • There was an issue with some mod files in M1 circuit (also reported in https://github.com/BlueBrain/CoreNeuron/issues/220)
  • New postdoc in NetPyNE to import a new circuit model in NetPyNE
  • Collaboration with google to make calls from NetPyNE into the HPC system they have allocated and runs in kubernetes
  • Comment on that by Salvador:
  • If coreneuron is working well NetPyNE can also use CoreNeuron for that
  • Also use Coreneuron with Neuron and NetPyNE in the coming Neuron+NetPyNE courses (one in July)
  • Meeting with Michele Migliore in Italy (probably not happening because of the coronavirus situation in Italy)

Neuron meeting frequency

  • The NEURON development team agreed to start with a monthly call, every 3rd Friday of the month at 15:00 CET 16:00 CEST)

Neuron versions

  • Michael Hines wants to have pyiter in next release
  • There was a discussion and people suggested to switch to 8.0.0 since we have some important additions (the new cmake-based build system in particular) because people will know that this is a major new release and they would expect that improvements will come in next minor versions
  • Also Omar, Michael, Fernando and others discussed and suggested to
    • Use master branch only for developing
    • Create a tag from a commit there with the name of the new version (ex.7.8) and then branch with the same name (7.8)
  • Fixes of the version 7.8 will go to the branch and the tag will point to the first commit
  • Master will cherry-pick (or merge) commits from the branches (fixes)
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