nrnbbcore_write code re-organisation

[alexsavulescu]

This PR targets nrnbbcore_write code re-organisation (and a few minor updates).
It represents a first step for its refactoring.

[nrnhines]

I think that this refactoring is a good time to replace nrnbbcore_write with nrncore_write (and any other nrnbbcore prefixes with nrncore).

[alexsavulescu]

I think that this refactoring is a good time to replace nrnbbcore_write with nrncore_write (and any other nrnbbcore prefixes with nrncore).

Noted.

@alkino thank you for the review, this PR is however just about re-organising the code. Will tackle those when refactoring is of interest. Just made a few changes, will tag those so you can have a look.

[alexsavulescu]

Used this to have a sort of integration test, outputs are the same wrt master:

• https://github.com/BlueBrain/CoreNeuron/tree/master/tests/integration

[pramodk]

This PR is almost good for merge.

I didn't comment on the code style aspects as we want to limit this PR for code re-organisation and not changing the implementation.

[nrnhines]

This is too much to pore over in detail. I trust things are just being copied to other places and enough include stuff is added to make everything consistent. It is a transition pull request to be extensively modified later. I wish #717 had made it in before this. When @pramodk approves, in it goes, unless we prefer to keep in different branch that receives pull requests til it is mature or nicely polished.

[alexsavulescu]

@nrnhines I propose to review #717 and wait for it to get merged before, so that I can move your modifications accordingly.
In the meantime I will do a bit of polishing.

[pramodk]

as most of the changes are just re-organisation of code without any change is logic, I am also OK to merge this PR sooner. (after Alex give green signal)

[pramodk]

I am triggering CI at BBP server as a sanity check. Will report is here once those tests passes.
Simulation CI job on BBP server is here.

[pramodk]

I am seeing below error:

Reports Buffering Info : flushBufferScalar: 1, nextReportFlush: 25, steps_to_buffer: 300 
19 special: NEURON model internal structures are out of date
19  in /jenkins/05/workspace/hpc.SimulationStack/INSTALL_HOME/install/linux-rhel7-x86_64/intel-19.0.4/neurodamus-neocortex-develop-6735d5/lib/hoc/init.hoc near line 262
19  {cvode.cache_efficient(1)}
25 special: NEURON model internal structures are out of date
25  in /jenkins/05/workspace/hpc.SimulationStack/INSTALL_HOME/install/linux-rhel7-x86_64/intel-19.0.4/neurodamus-neocortex-develop-6735d5/lib/hoc/init.hoc near line 262
25  {cvode.cache_efficient(1)}
                           ^
1 special: NEURON model internal structures are out of date
1  in /jenkins/05/workspace/hpc.SimulationStack/INSTALL_HOME/install/linux-rhel7-x86_64/intel-19.0.4/neurodamus-neocortex-develop-6735d5/lib/hoc/init.hoc near line 262
1  {cvode.cache_efficient(1)}

I wonder if this behaviour was introduced in master branch itself. I started new CI job for master branch of NEURON.

[pramodk]

The issue I described in previous comment comes from the older commit in the master branch and we will handle that separately.

Discussed with Robert on slack and we will go ahead with the merge.