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

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

Open iomaganaris opened this issue 2 years ago • 1 comments

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 [email protected]: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

Feb 22 '22 15:02 iomaganaris

Logfiles from GitLab pipeline #40210 (:white_check_mark:) have been uploaded here!

Status and direct links:

Feb 25 '22 12:02 bbpbuildbot

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

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