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mguidon opened this issue Jan 23, 2018 · 0 comments
Closed
2 of 6 tasks

Nerve electrophysiology model (NEURON) #2

mguidon opened this issue Jan 23, 2018 · 0 comments

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@mguidon
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mguidon commented Jan 23, 2018 •
edited by drniiken
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User story

As a user I want to be able to run neuron simulations. For this purpose I need to be able to import hoc files or create splines representing neurons. Also I want to couple them to an external potential from a EM solver.

Definition of done

  • Yale neuron in a container
  • s4l_neuron in a container
  • users must be able to assign trajectories and specify parameters (similar to s4l simulation settings)
  • link to exposing potential from EM solver
  • at the current time, we only need to support the MRG model (motor or sensory)
  • tbd: what do we store? (point sensor? line sensor?)

Background

  • User story for this and the EM case is to be able to reproduce the two verfication models provided by Warren Grill
  • (also consider Eilif's input and format ... start with S4L side possibly)
odeimaiz added a commit that referenced this issue Apr 27, 2018
@odeimaiz
Merge pull request #2 from sanderegg/odeimaiz-feature/integrate-jupyter
02f3f4e 
wait until services are up and running before returning
@drniiken drniiken mentioned this issue Aug 13, 2018
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@pcrespov pcrespov mentioned this issue Aug 24, 2018
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@drniiken drniiken closed this as completed Jan 9, 2019
@ghost ghost removed the review label Jan 9, 2019
@pcrespov pcrespov mentioned this issue Jun 6, 2019
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GitHK added a commit that referenced this issue Jan 21, 2021
@GitHK @sanderegg @pcrespov
bugfix: addressed issues when acquiring mpi_lock in sidecar (#2093)
9e0d6df 
* mpi locking got refacted to use multiprocessing

* it should no longer be possible to start multiple MPI nodes in case of errors

* minor refactor

* added more comments and written in a more clear logic

* Update mpi_lock.py

updating comment

* added tests for mpi_lock module

* refactored fucntion names

* migrated function to private

* semplified mpi_lock acquisition

* updated docstring and comment

* final refactor to the mpi_locking using a proper

* Update services/sidecar/src/simcore_service_sidecar/mpi_lock.py

Co-authored-by: Sylvain <[email protected]>

* inverted test oder

* before trying to acquire lock, make sure redis is working

* adding more debug

* Git hk fix mpi sidecar locking (#2)

* Minor cleanup in pytest_simcore/docker_swarm and redis_service

* Minor

* tests improvmentsd
- adde dmore cases
- patched redis config properly

* improved mpi_lock for high concurrency

* Update test_mpi_lock.py

we do not have such high concurrency

Co-authored-by: Andrei Neagu <[email protected]>
Co-authored-by: Sylvain <[email protected]>
Co-authored-by: Pedro Crespo-Valero <[email protected]>
@odeimaiz odeimaiz mentioned this issue Feb 4, 2022
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@bisgaard-itis bisgaard-itis mentioned this issue Nov 7, 2024
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@pcrespov @drniiken @mguidon @sanderegg