Skip to content

Navigation Menu

Sign in
Appearance settings

Search code, repositories, users, issues, pull requests...

Provide feedback

We read every piece of feedback, and take your input very seriously.

Saved searches

Use saved searches to filter your results more quickly

Sign up
Appearance settings
This repository was archived by the owner on Mar 20, 2023. It is now read-only.

Set the initial values of ions properly in direct and file mode transfer #780

Draft
iomaganaris wants to merge 5 commits into master
base: master
Choose a base branch
Loading
from magkanar/fix_global_ions

Conversation

@iomaganaris
Copy link
Contributor

@iomaganaris iomaganaris commented Feb 22, 2022

Description

Fixes issue with ion variables initial values not being in set in file mode transfer of data between NEURON and CoreNEURON.
Even if this seems like an issue it doesn't seem to influence the behavior of some of the simulations I've tried.

Fixes #779

How to test this?
It's pretty difficult to test this so bare with me.
Add the following change to this branch:

diff --git a/coreneuron/mechanism/eion.cpp b/coreneuron/mechanism/eion.cpp
index 25422326..11b2e150 100644
--- a/coreneuron/mechanism/eion.cpp
+++ b/coreneuron/mechanism/eion.cpp
@@ -316,6 +316,7 @@ void nrn_init_ion(NrnThread* nt, Memb_list* ml, int type) {
 int _cntml_padded = ml->_nodecount_padded;
 pd = ml->data;
 ppd = ml->pdata;
+ printf("nrn_init_ion %d %s conci %lf conco %lf charge %lf celsius %lf\n", type, nrn_get_mechname(type), conci0, conco0, charge, celsius);
 // There was no async(...) clause in the initial OpenACC implementation, so
 // no `nowait` clause has been added to the OpenMP implementation. TODO:
 // verify if this can be made asynchronous or if there is a strong reason it
# build NEURON with CoreNEURON using master and this branch and compare the output of the following
git clone -b magkanar/debug_ions git@github.com:neuronsimulator/ringtest.git
<install_dir>/bin/nrnivmodl -coreneuron mod
mpirun -n 2 ./x86_64/special -mpi -python ringtest.py -dumpmodel
mpirun -n 2 ./x86_64/special-core --mpi -d coredat

You can also print the same string in NEURON and compare the results.

Test System

  • OS: Ubuntu 20.04
  • Compiler: GCC 9.3.0
  • Version: master branch
  • Backend:CPU

@iomaganaris iomaganaris changed the title (削除) Magkanar/fix global ions (削除ここまで) (追記) Set the initial values of ions properly in direct and file mode transfer (追記ここまで) Feb 25, 2022
Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

Ion related initial values set in the NEURON parser not passed to CoreNEURON

AltStyle によって変換されたページ (->オリジナル) /