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~~ nmodl is now installed as a NEURON target so we only need CMAKE_PREFIX_PATH. ~~Additionally, until NOCMODL fails to run from build directory without setting MODLUNIT #3470 is resolved, MODLUNIT must also be set~~ issue fixed!
at build-time, internal 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_WHEEL_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)
for NVHPC, we are hardcoding some of the CLI options for now, which means that one should build NEURON from source, and then use the same installation for building mechanisms (otherwise I cannot guarantee that the mechanism-building will work) looks like it works without too much hardcoding
running special when building from a wheel currently does not work OOTB because of the fact that NEURON hardcodes the path to nrnpyenv.sh. The workaround is to add NEURONHOME=${NEURON_WHEEL_DIR}/.data/share/nrn" to the env added the same workaround as we use for wheels so now it works
I manually tried testing special-core with NVHPC 25.3 and it works without issues. I did not want to add too many new tests since that will be tested anyway once the CMake build itself starts using create_nrnmech instead of calling nrnivmodl (that's planned for part 2)
since this PR introduces a public API, I documented it here

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

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sonarqubecloud · 2025-07-08T15:17:39Z

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

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sonarqubecloud · 2025-09-09T09:54:41Z

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

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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

JCGoran added 3 commits June 19, 2025 13:59

More debugging in create_nrnmech

b87f6c4

Actually update docs to use CMake

64963f9

Forgot to add it to reqs

73f346c

JCGoran added 2 commits June 19, 2025 17:31

Put docs back next to implementation

6b3983f

Add example to create_nrnmech

5f5f413

JCGoran added 2 commits June 20, 2025 12:32

Fix issue with wheels containing wrong paths

9a09835

Fix slashes in installer

66ba781

JCGoran marked this pull request as ready for review June 20, 2025 10:49

JCGoran requested a review from nrnhines June 20, 2025 10:54

JCGoran added 3 commits June 21, 2025 09:35

Add workaround for running special under wheels

e086ace

Update docs for CMake API

a40003f

Fix install dir on Windows

67c2759

JCGoran mentioned this pull request Jun 23, 2025

Proposal: higher-level alternative to nrnivmodl #3460

Open

Merge branch 'master' into jelic/cmake_mechanisms

36887b0

Merge branch 'master' into jelic/cmake_mechanisms

697e1d2

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

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