Initial attempt at implementing VERBATIM. by 1uc · Pull Request #1364 · BlueBrain/nmodl

1uc · 2024-07-22T13:18:57Z

Edit the idea is to temporarily print the NOCMODL macros, e.g. the MOD file:

VERBATIM
_lget_gbl = gbl;
ENDVERBATIM

generates:

        // Setup for VERBATIM
        #define gbl inst.global->gbl
        #define get_gbl get_gbl_globals
        #define _lget_gbl ret_get_gbl
        #define t nt->_t
        // Begin VERBATIM

        _lget_gbl = gbl;
        // End VERBATIM
        #undef gbl
        #undef get_gbl
        #undef _lget_gbl
        #undef t
        // End of cleanup for VERBATIM

One can see the following happening:

       // Translate `gbl` to the correct C++ code:
       #define gbl inst.global->gbl

       // Because the substring `get_gbl` is present we print the
       // full name of the function `get_gbl` (even though it's not
       // needed).
       #define get_gbl get_gbl_globals

       // Same translation logic for the return type.
       #define _lget_gbl ret_get_gbl

There's one more twist relates to threadargs in both NOCMODL and NMODL there's two variations of prototypes: one internalthreadargsproto and threadargsproto. In NOCMODL the number and order of the arguments are the same (their types differ slightly). Therefore, in NOCMODL a single macro is sufficient to call both types, i.e. threadargs works for both types of functions. There is no internalthreadargs. In NMODL the two signatures differ significantly and for this reason we need to massage VERBATIM code to determine which string to substitute for threadargs.

codecov · 2024-07-22T13:46:34Z

Codecov Report

Attention: Patch coverage is 25.00000% with 84 lines in your changes missing coverage. Please review.

Project coverage is 86.23%. Comparing base (c5052b9) to head (63ff7e0).
Report is 2 commits behind head on master.

Files	Patch %	Lines
src/codegen/codegen_neuron_cpp_visitor.cpp	1.23%	80 Missing ⚠️
src/codegen/codegen_coreneuron_cpp_visitor.cpp	87.50%	2 Missing ⚠️
src/codegen/codegen_cpp_visitor.hpp	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1364      +/-   ##
==========================================
- Coverage   86.75%   86.23%   -0.52%     
==========================================
  Files         180      180              
  Lines       13669    13760      +91     
==========================================
+ Hits        11858    11866       +8     
- Misses       1811     1894      +83

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bbpbuildbot · 2024-07-22T13:47:04Z

Logfiles from GitLab pipeline #223048 (:white_check_mark:) have been uploaded here!

Status and direct links:

JCGoran

Overall looks good, though I haven't checked how this is used in NEURON tests or modelDB. Is there a reference somewhere how users can access the variables in VERBATIM (like _lget_gbl)? If not, some docs on how NMODL does it would be great as the main NEURON docs don't really list any rules for the replacement mechanism.

1uc · 2024-10-31T06:51:14Z

Is there a reference somewhere how users can ...

I don't know but I'm not writing one. Users should not use and ideally not know about VERBATIM. It constantly causes severe issues that limit our ability to generate code freely.

nrnhines · 2024-10-31T11:51:49Z

Is there a reference somewhere how users can ...

I don't know but I'm not writing one. Users should not use and ideally not know about VERBATIM. It constantly causes severe issues that limit our ability to generate code freely.

There has never been a promise that use of NEURON internals within mod file VERBATIM blocks would be stable. The assumption is that occasionally VERBATIM can be useful even if intimately tied to a specific version NEURON. An example
is the VERBATIM block in ri.mod of the Traub model which makes use of the details of the internal segment data structure.
https://github.com/ModelDBRepository/82894/blob/master/mod/ri.mod . As in this case, we developers have had some success in supporting published modeldb models. Since NEURON is used in part in the domain of Computational Neuroscience research, it is sometimes necessary for users to extend the program. In practice this sometimes means that the researcher should ask a developer for advice on how to implement the extension needed. Forking and modifying NEURON source is a last resort and in most cases dealing with the issue with a mod file with a VERBATIM block that has knowledge of NEURON internals sufficed.

JCGoran · 2024-10-31T13:01:31Z

There has never been a promise that use of NEURON internals within mod file VERBATIM blocks would be stable.

In that case, I think we need to put a huge warning label in the NEURON docs, currently there is some mention of compatibility issues, but it's not nearly prominent enough.

Regarding the mod file linked: it doesn't work with this NMODL PR as the #defines from the VERBATIM block do not appear anywhere in the cpp file.

1uc · 2024-10-31T14:12:08Z

it doesn't work

Fixed & testing that now. It's related to SUFFIX nothing.

1uc · 2024-10-31T16:09:25Z

Regarding how well it's tested, not very well. It's enough to compile everything we need for the nrn repository. Without it's slowly a bit tedious to make progress towards getting nmodl working for all nrn unit-test.

JCGoran

Seems to work (w/ some non-verbatim-related tweaks) with the built-in NEURON files, great job!

NMODL Repo SHA: BlueBrain/nmodl@af7c882

bbpadministrator pushed a commit to BlueBrain/nmodl-references that referenced this pull request Jul 22, 2024

References for 'BlueBrain/nmodl#1364'.

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1uc force-pushed the 1uc/verbatim branch from 1bd6043 to 63ff7e0 Compare August 12, 2024 08:53

bbpadministrator pushed a commit to BlueBrain/nmodl-references that referenced this pull request Aug 12, 2024

References for 'BlueBrain/nmodl#1364'.

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1uc force-pushed the 1uc/verbatim branch from 63ff7e0 to b22eb33 Compare September 11, 2024 14:35

bbpadministrator pushed a commit to BlueBrain/nmodl-references that referenced this pull request Sep 11, 2024

References for 'BlueBrain/nmodl#1364'.

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bbpadministrator pushed a commit to BlueBrain/nmodl-references that referenced this pull request Sep 12, 2024

References for 'BlueBrain/nmodl#1364'.

e52b6fa

1uc force-pushed the 1uc/verbatim branch 2 times, most recently from b986231 to d30cd25 Compare September 24, 2024 07:08

bbpadministrator pushed a commit to BlueBrain/nmodl-references that referenced this pull request Sep 24, 2024

References for 'BlueBrain/nmodl#1364'.

c83de01

1uc force-pushed the 1uc/verbatim branch from d30cd25 to 2b9ab54 Compare September 25, 2024 08:44

bbpadministrator pushed a commit to BlueBrain/nmodl-references that referenced this pull request Sep 25, 2024

References for 'BlueBrain/nmodl#1364'.

1b84e18

1uc force-pushed the 1uc/verbatim branch from 2b9ab54 to 5476496 Compare October 8, 2024 09:53

bbpadministrator pushed a commit to BlueBrain/nmodl-references that referenced this pull request Oct 8, 2024

References for 'BlueBrain/nmodl#1364'.

e8c05cf

1uc force-pushed the 1uc/verbatim branch 2 times, most recently from b68af04 to 80892d4 Compare October 15, 2024 06:58

1uc force-pushed the 1uc/verbatim branch from 7b25319 to 739ace3 Compare October 30, 2024 08:10

1uc added 12 commits October 30, 2024 14:56

Implement VERBATIM (NEURON version).

fad8972

Fixups.

ba86d6f

Print top-level VERBATIM.

7b7ddc5

Support _threadargs_.

3d1ce91

random verbatim

be30aad

Test RANGE variables used as pointers.

cb06b79

formatting

b12d9c9

Modernize for-loop.

389fda6

Print macros for global and thread variables.

554cdf8

Test VERBATIM globals.

24c5ffe

fixup: test globals

1fa3cb4

pointless changes

c791872

1uc added 5 commits October 30, 2024 14:56

macros for locals.

0c9d986

better macros for locals

81ceeeb

Tests for locals.

5768faa

formatting

d8a9144

essential whitespace.

9f3f497

1uc force-pushed the 1uc/verbatim branch from 155bf96 to 9f3f497 Compare October 30, 2024 14:14

1uc marked this pull request as ready for review October 30, 2024 14:15

JCGoran reviewed Oct 30, 2024

View reviewed changes

1uc added 3 commits October 30, 2024 15:46

Remove: *_overload functions.

6dca96b

Use a constant for a constant.

62bcbb8

Introduce more names.

08e92aa

1uc added 2 commits October 31, 2024 07:52

Use some more naming::.

3b5f00d

Comment get_nonglobal_local_variable_name.

220712e

Check top-level VERBATIM in SUFFIX nothing.

3f272a5

1uc force-pushed the 1uc/verbatim branch from c779d53 to 3f272a5 Compare October 31, 2024 14:10

JCGoran approved these changes Nov 4, 2024

View reviewed changes

1uc merged commit af7c882 into master Nov 4, 2024

1uc deleted the 1uc/verbatim branch November 4, 2024 13:25

JCGoran pushed a commit to neuronsimulator/nrn that referenced this pull request Mar 12, 2025

Initial attempt at implementing VERBATIM. (BlueBrain/nmodl#1364)

04bd752

NMODL Repo SHA: BlueBrain/nmodl@af7c882

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