cmake: export targets, allow building mechanisms via CMake, part 1 #3468

JCGoran · 2025-06-04T12:36:42Z

Split off from #2746 since that PR was getting a bit too large.

Context

Currently we build mechanisms (mod files) using a hand-written Makefile. As a result, we need to ship a bunch of Make-specific tools with NEURON. This also does not work (or at least, not without a lot of workarounds) in a cross-platform manner.

This PR allows one to build NEURON mechanisms with CMake, using any generator we want. The way it achieves this is by exposing the create_nrnmech CMake function, which works as follows:

cmake_minimum_required(VERSION 3.15)
project(modfile_test)

find_package(neuron REQUIRED)

create_nrnmech(NEURON CORENEURON SPECIAL MOD_FILES
  modfile1.mod
  path/to/modfile2.mod)

Note that the NEURON, CORENEURON, and SPECIAL toggle whether one builds libnrnmech, libcorenrnmech, and the special executable (enabling CORENEURON and SPECIAL together enables the special-core executable as well).

One can then build the targets via:

cmake -B build
cmake --build build

which can then be loaded into NEURON as usual:

nrniv -dll build/libnrnmech.so

Additional notes

the NEURON config file must be visible to CMake, i.e. it must be added to CMAKE_PREFIX_PATH, and the nmodl executable must be in PATH. Additionally, until NOCMODL fails to run from build directory without setting MODLUNIT #3470 is resolved, MODLUNIT must also be set
at build-time, mechanisms are still built with make, but this can be fixed later (nrnivmodl touches a lot of the internal code as well, so the changeset would be much larger)
when shipping wheels, the CMAKE_PREFIX_PATH should include {NEURON_INSTALL_DIR}/.data/lib/cmake, though I am not sure how to obtain it without running any external utilities
CMake and any of the generators should be available on the user machine. We could update the Python requirements to include cmake and ninja, but since this feature is a bit experimental, I'm not sure how useful it is
I've not tested anything on Windows, so I'm not sure how cross-platform it really is (i.e. we ship NEURON with msys2 or whatever else is there, but CMake would probably try to use MSVC if it's installed)

This PR aims to allow dependent projects to build their models via CMake rather than a combination of shell scripts and Makefiles. In the long term, this may help facilitate building natively on Windows. To try: ``` git clone -b imported-main https://github.com/BlueBrain/neurodamus-models.git cd neurodamus-models ``` Create a `CMakeLists.txt` with contents like: ```cmake cmake_minimum_required(VERSION 3.28) project(newrodamus) find_package(neuron REQUIRED) create_libnrnmech(MOD_FILES neocortex/mod/v6/CaDynamics_DC0.mod neocortex/mod/v6/Ca_HVA2.mod neocortex/mod/v6/Ca_LVAst.mod neocortex/mod/v6/DetAMPANMDA.mod neocortex/mod/v6/DetGABAAB.mod neocortex/mod/v6/GluSynapse.mod neocortex/mod/v6/Ih.mod neocortex/mod/v6/K_Pst.mod neocortex/mod/v6/K_Tst.mod neocortex/mod/v6/KdShu2007.mod neocortex/mod/v6/NaTg.mod neocortex/mod/v6/Nap_Et2.mod neocortex/mod/v6/ProbAMPANMDA_EMS.mod neocortex/mod/v6/ProbGABAAB_EMS.mod neocortex/mod/v6/SK_E2.mod neocortex/mod/v6/SKv3_1.mod neocortex/mod/v6/StochKv3.mod neocortex/mod/v6/TTXDynamicsSwitch.mod neocortex/mod/v6/VecStim.mod neocortex/mod/v6/gap.mod neocortex/mod/v6/netstim_inhpoisson.mod ) ``` Then build and install: ``` cmake -B build -S . -GNinja -DCMAKE_INSTALL_PREFIX=x86_64 cmake --build build cmake --install build ``` To be continued‥

Always use resolved absolute paths in CMake since nocmodl has some trouble with symlinks.

* add docs and various args

Also finally add (hacky) test

github-actions · 2025-06-04T13:23:37Z

✔️ 535bb1c -> artifacts URL

azure-pipelines · 2025-06-04T13:37:11Z

✔️ 535bb1c -> Azure artifacts URL

azure-pipelines · 2025-06-04T14:31:35Z

✔️ 3a7bb98 -> Azure artifacts URL

github-actions · 2025-06-04T14:49:16Z

✔️ 3a7bb98 -> artifacts URL

github-actions · 2025-06-04T16:21:42Z

✔️ 908dc4e -> artifacts URL

azure-pipelines · 2025-06-04T16:34:06Z

✔️ 908dc4e -> Azure artifacts URL

github-actions · 2025-06-05T10:30:24Z

✔️ 1462039 -> artifacts URL

azure-pipelines · 2025-06-05T10:34:45Z

✔️ 1462039 -> Azure artifacts URL

azure-pipelines · 2025-06-05T11:37:50Z

✔️ 446fb48 -> Azure artifacts URL

JCGoran · 2025-06-04T13:06:13Z

cmake/neuronMechMaker.cmake

+# - create a `special-core` executable in the `CMAKE_HOST_SYSTEM_PROCESSOR` subdirectory from the `coreneuron.cpp` file
+# - link the above executable to the `corenrnmech` library
+# Note that any other files created are basically noise.
+# create_nrnmech(


See below for the full API of create_nrnmech.

github-actions · 2025-06-05T13:21:53Z

✔️ ebbe6f5 -> artifacts URL

azure-pipelines · 2025-06-05T13:22:29Z

✔️ ebbe6f5 -> Azure artifacts URL

sonarqubecloud · 2025-06-05T14:16:28Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

azure-pipelines · 2025-06-05T14:40:50Z

✔️ 81c1d1f -> Azure artifacts URL

JCGoran · 2025-06-05T14:42:36Z

launch-nvhpc-ci

github-actions · 2025-06-05T14:47:07Z

✔️ 81c1d1f -> artifacts URL

codecov · 2025-06-05T14:48:13Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 68.42%. Comparing base (e560105) to head (81c1d1f).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #3468      +/-   ##
==========================================
+ Coverage   68.40%   68.42%   +0.02%     
==========================================
  Files         682      682              
  Lines      116565   116565              
==========================================
+ Hits        79731    79760      +29     
+ Misses      36834    36805      -29

☔ View full report in Codecov by Sentry.
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JCGoran · 2025-06-05T14:55:54Z

NVHPC CI failed for commit 81c1d1f, see logs at https://gist.github.com/JCGoran/45276e21690eda095f22ed47ca02b052
Possibly missing build files: install_manifest.txt
Possibly missing log files: test.log

matz-e and others added 21 commits August 14, 2024 16:03

Bump stuff.

2df2103

Fix formatting

87cc65b

Merge branch 'master' into export-cmake

fd75527

Add fmt to linked libs for testing

489c390

Also link fmt in Python build

65fc1ee

Put back the original hh.mod

047732d

Fix issue with corenrn target

86895cb

Merge branch 'master' into export-cmake

5947fa8

Fix issues with paths

6a8c83b

Always use resolved absolute paths in CMake since nocmodl has some trouble with symlinks.

Merge branch 'master' into jelic/cmake_mechanisms

3b8d0fb

Update create_nrnmech

58a380f

* add docs and various args

Remove comments

f0eaccc

Add tentative test

c0f168a

Neuron config

758142c

Fix include paths

32c2cc1

Also finally add (hacky) test

Add NEURON and special

6a8ed75

Formatting

6988505

Better config

b00f3dc

Merge branch 'master' into jelic/cmake_mechanisms

2caa145

Formatting

535bb1c

Appease MODLUNIT

3a7bb98

Workaround for NOCMODL

908dc4e

Merge branch 'master' into jelic/cmake_mechanisms

a121ef7

Use same compiler as used by system

1462039

Disable CMake mechanism test if using sanitizers

446fb48

Use -nopython when launching special

ebbe6f5

JCGoran commented Jun 5, 2025

View reviewed changes

Disable test on coverage as well

81c1d1f

cmake: export targets, allow building mechanisms via CMake, part 1 #3468

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