nrn Callbacks for reading mapping information from memory

neurodamus branch https://github.com/BlueBrain/neurodamus/tree/weji/direct_mod to launch coreneuron simulation with in memory mode.

Sep 28 '23 07:09 WeinaJi

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Codecov Report

Attention: Patch coverage is 88.09524% with 10 lines in your changes are missing coverage. Please review.

Project coverage is 67.14%. Comparing base (e3e8625) to head (a3b93c2).

Files	Patch %	Lines
src/coreneuron/io/phase3.cpp	86.11%	5 Missing :warning:
src/coreneuron/io/core2nrn_data_return.cpp	0.00%	2 Missing :warning:
src/nrniv/nrncore_write/io/nrncore_io.cpp	88.23%	2 Missing :warning:
src/coreneuron/io/nrn_filehandler.hpp	75.00%	1 Missing :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2555      +/-   ##
==========================================
+ Coverage   66.92%   67.14%   +0.22%     
==========================================
  Files         560      561       +1     
  Lines      104091   104145      +54     
==========================================
+ Hits        69658    69932     +274     
+ Misses      34433    34213     -220

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Dec 12 '23 15:12 bbpbuildbot

Looks good!! Thanks! Just one extra comment, is it possible to create some unit tests? At least for the nrncore_callbacks (nrnthread_dat3_cell_count, nrnthread_dat3_cellmapping, etc.) I guess for read_phase3() would be a bit more complicated...although i did something similar for LFP populating the cellmapping, mapinfo etc

Dec 14 '23 14:12 jorblancoa

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Jan 14 '24 19:01 bbpbuildbot

Looks good!! Thanks! Just one extra comment, is it possible to create some unit tests? At least for the nrncore_callbacks (nrnthread_dat3_cell_count, nrnthread_dat3_cellmapping, etc.) I guess for read_phase3() would be a bit more complicated...although i did something similar for LFP populating the cellmapping, mapinfo etc

I am trying to add a test but I am not sure where to locate the test. Since we have the callbacks map like

static core2nrn_callback_t cnbs[] = {
    ...
    {"nrn2core_get_dat3_cell_count_", (CNB) nrnthread_dat3_cell_count},
    ...
}

Shall I test function nrn2core_get_dat3_cell_count_ in coreneuron? If so, do I need to call first https://github.com/neuronsimulator/nrn/blob/45cdea7e74b0d695d1597589b47353d728082454/src/nrniv/nrncore_write.cpp#L305 ?

Or shall I test function nrnthread_dat3_cell_count? Is that in the scope of neuron ?

Maybe @pramodk @iomaganaris @jorblancoa have more insights?

Jan 15 '24 15:01 WeinaJi

Copying comments from internal slack discussion:

If your test works for neurodamus tests and if you want a similar test in neuron then I wonder if we should just use ringtest which already in NEURON:

* ringtest has this  setup_nrnbbcore_register_mapping() : https://github.com/neuronsimulator/ringtest/blob/344bd13f8fb94d69e83b6645350f723079b3a21d/ringtest.py#L179

* and that registers section/segment mapping like neurodamus: https://github.com/neuronsimulator/ringtest/blob/344bd13f8fb94d69e83b6645350f723079b3a21d/commonutils.py#L170

We can add a separate CLI flag instead of dumpmodel but I wonder if we can do the following:
 * take one of the existing ringtest for coreneuron
  * in one of the online ringtest, we enable extra CLI flag --report-mapping and that will trigger your part of the code

Jan 27 '24 08:01 pramodk

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