Big list of NEURON dependencies

[JCGoran]

This is an attempt at listing all of the various dependencies of NEURON (and its components), in as much detail as possible (as an aside, this information is usually referred to as the software bill of materials (SBOM)). The goal of this exercise is to gain an overview of what it takes to run NEURON on various platforms, as well as see if any of the dependencies can be removed in the future. As such, this list is expected to evolve over time.
Note that transitive Python dependencies will not be included here because there are too many to count (see ci/requirements.txt to check what are the exact versions of the Python dependencies used in the CI).

NOTE: I will start with a disclaimer: This list is incomplete; you can help by expanding it.

Last updated: 2025-12-04

Some of the software properties that will be listed:

• type (executable, script, library, etc.)
• version, either exact or supported/tested range
• component(s) of NEURON that use it, if any
• vendoring: vendored (i.e. shipped as a git submodule or somehow part the NEURON repo), or external (downloaded from somewhere else on the Internet)
• used at stage(s) (pre-build, build, test, install, runtime, other)
• which CMake build configuration options enable its use (usually in the form <CMAKE_KEY>=<CMAKE_VALUE>)
• supported platforms (all, Linux-only, MacOS-only, Windows-only, Unix-like/POSIX only)
• other NEURON dependencies it depends on, if any
• external resources, if any (for example, links to project websites)

The version of NEURON used for creating this list is 823fb26.

NOTE: "other dependencies" will not include the following, i.e. they are assumed to be present on a given system (or a given dependency statically links to it):

• the C++ standard library, notably:
  • libstdc++ (on Linux)
  • libc++ (on Linux or MacOS)
• the C standard library, notably:
  • glibc (on Linux)
  • system library (on MacOS)

NEURON components

For the purposes of this list, NEURON is considered to be composed of the following components:

• the NEURON simulator (including the nrniv library, NOCMODL translator, and nrnivmodl wrapper script)
• the coreNEURON simulator
• the HOC interpreter
• the Python bindings
• the NMODL transpiler
• the RX3D extension
• the MUSIC extension
• the Interviews GUI
• the various tests (written in Python or C++)
• NEURON documentation, both source (RST, Markdown, source code comments) and build artifacts (HTML)

The list

Homebrew

• type: executable (CLI)
• version(s): 4.5.11-4-g3bec117
• NEURON components: none
• vendoring: external
• stage(s): pre-build
• build configuration: none
• supported platforms: MacOS, Linux
• other dependencies:
  • bash
• external resources:
  • homepage: https://brew.sh

GNU Compiler Collection (GCC)

• type: executable (CLI)
• version(s): 9-15
• NEURON components: nrnivmodl (?)
• vendoring: external
• stage(s): build, runtime (nrnivmodl)
• build configuration: any
• supported platforms: POSIX only
• other dependencies:

Clang

NOTE: alternative to GCC.

• type: executable (CLI)
• version(s): >= 5
• NEURON components: nrnivmodl (?)
• vendoring: external
• stage(s): build, runtime (nrnivmodl)
• build configuration:
• supported platforms: POSIX only
• other dependencies:

NVIDIA HPC SDK (NVHPC)

• type: executable (CLI)
• version(s): 25.03 (current CI)
• NEURON components: nrnivmodl (?)
• vendoring: external
• stage(s): build, runtime (nrnivmodl)
• build configuration: CORENRN_ENABLE_GPU=ON NRN_ENABLE_CORENEURON=ON
• supported platforms: Linux
• other dependencies:
  • GCC

GNU Make

• type: executable
• version(s):
• NEURON components: nrnivmodl
• vendoring: external
• stage(s): build, runtime
• build configuration: -G 'Unix makefiles' (default on POSIX)
• supported platforms: all (I think)
• other dependencies:

Ninja

• type: executable (CLI)
• version(s):
• NEURON components: none
• vendoring: external
• stage(s): build
• build configuration: with -G Ninja
• supported platforms: all
• other dependencies:

Bash

• type: executable (CLI)
• version(s):
• NEURON components: various
• vendoring: external
• stage(s): pre-build, runtime, test
• build configuration: any
• supported platforms: all
• other dependencies:

grep

• type: executable (CLI)
• version(s):
• NEURON components:
• vendoring: external
• stage(s): build, runtime (mkthreadsafe, nrnpyenv.sh)
• build configuration:
• supported platforms:
• other dependencies:

git

• type: executable (CLI)
• version(s): any
• NEURON components: none
• vendoring: external
• stage(s): pre-build
• build configuration: any
• supported platforms: all
• other dependencies:

lcov

• type: executable (CLI)
• version(s): 1.14
• NEURON components: tests
• vendoring: external
• stage(s): test
• build configuration: NRN_ENABLE_COVERAGE=ON
• supported platforms:
• other dependencies:
• external resources:
  • PR with update to lcov 2, which exhibits strange behavior: Add support for parallel lcov #3451

sed

• type: executable (CLI)
• version(s):
• NEURON components: various runtime scripts
• vendoring: external
• stage(s): pre-build (?), build, runtime
• build configuration: any
• supported platforms: all (?)
• other dependencies:
  • bash (only on Windows)

X11

• type: library
• version(s): any
• NEURON components: GUI
• vendoring: external
• stage(s): build, runtime
• build configuration:
• supported platforms:
• other dependencies:

Interviews

• type: library
• version(s):
• NEURON components: GUI
• vendoring: internal
• stage(s): build
• build configuration: NRN_ENABLE_INTERVIEWS=ON
• supported platforms: MacOS, Linux, Windows (?)
• other dependencies:
  • X11

caliper

• type: library
• version(s):
• NEURON components:
• vendoring: external
• stage(s): build
• build configuration: NRN_ENABLE_PROFILING=ON NRN_PROFILER=caliper
• supported platforms: Linux
• other dependencies: none
• external resources:
  • homepage: https://github.com/LLNL/Caliper

Intel VTune Profiler

• type: executable (CLI)
• version(s):
• NEURON components: none
• vendoring: external
• stage(s): build
• build configuration: NRN_ENABLE_PROFILING=ON NRN_PROFILER=caliper
• supported platforms: Linux
• other dependencies: none
• external resources:
  • homepage: https://www.intel.com/content/www/us/en/developer/tools/oneapi/vtune-profiler.html

doxygen

• type: executable (CLI)
• version(s):
• NEURON components: docs
• vendoring: external
• stage(s): build
• build configuration: NRN_ENABLE_DOCS=ON
• supported platforms:
• other dependencies:

ffmpeg

• type: executable (CLI)
• version(s):
• NEURON components: docs
• vendoring: external
• stage(s): build
• build configuration: NRN_ENABLE_DOCS=ON
• supported platforms:
• other dependencies:

jupyter

• type: executable
• version(s):
• NEURON components: docs
• vendoring: external
• stage(s): build
• build configuration: NRN_ENABLE_DOCS=ON
• supported platforms: all
• other dependencies:
  • Python

pandoc

• type: executable
• version(s):
• NEURON components: docs
• vendoring: external
• stage(s): build
• build configuration: NRN_ENABLE_DOCS=ON
• supported platforms:
• other dependencies:

sphinx

• type: executable
• version(s):
• NEURON components: docs
• vendoring: external
• stage(s): build
• build configuration: NRN_ENABLE_DOCS=ON
• supported platforms:
• other dependencies:
  • Python

MUSIC

• type: library
• version(s):
• NEURON components:
• vendoring: external
• stage(s): build, runtime (?)
• build configuration: NRN_ENABLE_MUSIC=ON
• supported platforms:
• other dependencies:
  • Python
  • mpi4py

Threads

• type: library
• version(s):
• NEURON components:
• vendoring:
• stage(s):
• build configuration:
• supported platforms:
• other dependencies:

likwid

• type:
• version(s):
• NEURON components:
• vendoring:
• stage(s):
• build configuration:
• supported platforms:
• other dependencies:

CUDA

• type: library
• version(s):
• NEURON components:
• vendoring: external
• stage(s): build, runtime (nrnivmodl)
• build configuration: CORENRN_ENABLE_GPU=ON
• supported platforms: Linux
• other dependencies:
  • NVHPC

sonata

• type:
• version(s):
• NEURON components:
• vendoring:
• stage(s):
• build configuration:
• supported platforms:
• other dependencies:

boost

• type:
• version(s):
• NEURON components:
• vendoring:
• stage(s): build
• build configuration: NRN_ENABLE_CORENEURON=ON
• supported platforms: Linux
• other dependencies:

OpenSSL

• type: library
• version(s):
• NEURON components:
• vendoring: external
• stage(s): build
• build configuration: NRN_ENABLE_TESTS=ON, NRN_ENABLE_DIGEST=ON
• supported platforms: MacOS, Linux
• other dependencies:

CMake

• type: executable (CLI)
• version(s): 3.18-3.31.8
• NEURON components: all
• vendoring: external
• stage(s): pre-build, test (ctest), install (optional)
• build configuration: any
• supported platforms: all
• other dependencies: none
• external resources:
  • download link: https://cmake.org/download/
  • Ubuntu package: https://launchpad.net/cmake
  • Debian package: https://packages.debian.org/stable/cmake

Python

• type: executable (CLI), library
• version(s): 3.9-3.14
• NEURON components: nrniv, NMODL
• vendoring: external
• stage(s): build, runtime
• build configuration: NRN_ENABLE_PYTHON=ON, NRN_ENABLE_CORENEURON=ON
• supported platforms: all
• other dependencies:

Flex

• type: CLI, library
• version(s): >= 2.6
• NEURON components: nocmodl, nrniv, NMODL
• vendoring: external
• stage(s): build
• build configuration:
• supported platforms:
• other dependencies:

Bison

• type: executable (CLI)
• version(s): >= 3.7
• NEURON components: nocmodl, NMODL
• vendoring: external
• stage(s): build
• build configuration: any
• supported platforms:
• other dependencies:

Readline

• type: library
• version(s):
• NEURON components: HOC interpreter, Python bindings
• vendoring: external
• stage(s): build
• build configuration:
• supported platforms: Linux, MacOS
• other dependencies:

Curses

• type:
• version(s):
• NEURON components:
• vendoring:
• stage(s):
• build configuration:
• supported platforms:
• other dependencies:

Termcap

• type:
• version(s):
• NEURON components:
• vendoring:
• stage(s):
• build configuration:
• supported platforms:
• other dependencies:

Cython

• type: executable (CLI)
• version(s): see ci/requirements.txt
• NEURON components: RX3D, MUSIC
• vendoring: external
• stage(s): build
• build configuration: NRN_ENABLE_RX3D=ON, NRN_ENABLE_MUSIC=ON
• supported platforms: all
• other dependencies:
  • Python

MPI

NOTE: MPI is not technically an implementation, but a specification, of which there a several implementations. We currently use OpenMPI and MPICH on POSIX platforms, and Microsoft MPI on Windows.

• type:
• version(s):
• NEURON components:
• vendoring: external
• stage(s): build, runtime
• build configuration: NRN_ENABLE_MPI=ON, NRN_ENABLE_MPI_DYNAMIC=ON
• supported platforms: depends on implementation
• other dependencies:

Powershell

• type: CLI
• version(s): ???
• NEURON components: none
• vendoring: external
• stage(s): pre-build
• build configuration: any
• supported platforms: Windows
• other dependencies: none

NSIS

• type: CLI
• version(s): 3.05
• NEURON components: ???
• vendoring: external
• stage(s): build
• build configuration: any
• supported platforms: Windows
• other dependencies: none
• external resources:
  • download link: http://prdownloads.sourceforge.net/nsis/nsis-3.05-setup.exe
  • plugin: https://nsis.sourceforge.io/mediawiki/images/7/7f/EnVar_plugin.zip

backward

• type: library
• version(s):
• NEURON components: nrniv, nmodl
• vendoring: vendored
• stage(s): build
• build configuration: NRN_ENABLE_BACKTRACE=ON
• supported platforms: Linux (maybe MacOS)
• other dependencies:
  • unwind or libunwind
  • libbfd, libdw, libdwarf, libelf
• external resources:
  • homepage: https://github.com/bombela/backward-cpp

dlfcn

• type: library
• version(s):
• NEURON components: nrniv (?), MUSIC, NMODL (?)
• vendoring: external
• stage(s): build
• build configuration:
• supported platforms: POSIX-only
• other dependencies: none
• external resources:

dlfcn-win32

• type: library
• version(s):
• NEURON components: nrniv (?), MUSIC, NMODL (?)
• vendoring: vendored
• stage(s): build
• build configuration:
• supported platforms: Windows
• other dependencies: none
• external resources:
  • issue for moving to submodule: Move dlfcn to its own submodule #3443

Jinja

• type: executable (CLI)
• version(s): see ci/requirements.txt
• NEURON components: NMODL
• vendoring: external
• stage(s): build
• build configuration: NRN_ENABLE_CORENEURON=ON, NRN_ENABLE_NMODL=ON
• supported platforms: MacOS, Linux
• other dependencies:
  • Python
• external resources:
  • homepage: https://github.com/pallets/jinja

NumPy

• type: library
• version(s): see ci/requirements.txt
• NEURON components: RX3D, others (?)
• vendoring: external
• stage(s): build (RX3D only), test, runtime
• build configuration: NRN_ENABLE_RX3D=ON
• supported platforms: MacOS, Linux
• other dependencies:
  • Python
• external resources:
  • homepage: https://github.com/numpy/numpy/

PyYAML

• type: library
• version(s): see ci/requirements.txt
• NEURON components: NMODL
• vendoring: external
• stage(s): build
• build configuration: NRN_ENABLE_CORENEURON=ON, NRN_ENABLE_NMODL=ON
• supported platforms: MacOS, Linux
• other dependencies:
  • Python
• external resources:
  • homepage: https://github.com/yaml/pyyaml

Scikit-build-core

• type: library
• version(s): see ci/requirements.txt
• NEURON components: none
• vendoring: external
• stage(s): pre-build (wheel)
• build configuration: none (tool invokes CMake itself)
• supported platforms: MacOS, Linux
• other dependencies:
  • Python
• external resources:
  • homepage: https://github.com/scikit-build/scikit-build-core

setuptools-scm

• type: library
• version(s): see ci/requirements.txt
• NEURON components: none
• vendoring: external
• stage(s): build
• build configuration: none
• supported platforms: MacOS, Linux
• other dependencies:
  • Python
• external resources:
  • homepage: https://github.com/pypa/setuptools-scm

CLI11

• type: library
• version(s): 2.4.2
• NEURON components: coreNEURON, NMODL
• vendoring: vendored
• stage(s): build
• build configuration: NRN_ENABLE_CORENEURON=ON, NRN_ENABLE_NMODL=ON
• supported platforms: MacOS, Linux
• other dependencies: none
• external resources:
  • homepage: https://github.com/CLIUtils/CLI11

Pybind11

• type: library
• version(s):
• NEURON components: NMODL
• vendoring: vendored
• stage(s): build
• build configuration:
• supported platforms:
• other dependencies:

Nanobind

• type: library
• version(s):
• NEURON components: Python bindings
• vendoring: vendored
• stage(s): build
• build configuration: NRN_ENABLE_PYTHON=ON
• supported platforms:
• other dependencies:

Eigen

• type: library
• version(s):
• NEURON components: nrniv, NMODL
• vendoring: vendored
• stage(s):
• build configuration:
• supported platforms:
• other dependencies:

Catch2

• type: library
• version(s):
• NEURON components:
• vendoring: vendored
• stage(s): build
• build configuration: NRN_ENABLE_TESTS=ON
• supported platforms:
• other dependencies:

Spdlog

• type: library
• version(s):
• NEURON components: NMODL
• vendoring: vendored
• stage(s): build
• build configuration:
• supported platforms:
• other dependencies:

fmt

• type: library
• version(s):
• NEURON components: nrniv, NMODL
• vendoring: vendored
• stage(s): build
• build configuration:
• supported platforms:
• other dependencies:

Random123

• type: library
• version(s):
• NEURON components:
• vendoring: vendored
• stage(s): build
• build configuration:
• supported platforms:
• other dependencies:

SymPy

• type: library
• version(s): >= 1.3 (runtime), see ci/requirements.txt (CI only)
• NEURON components: NMODL
• vendoring: external
• stage(s): build, runtime (nmodl)
• build configuration: NRN_ENABLE_CORENEURON=ON, NRN_ENABLE_NMODL=ON
• supported platforms: MacOS, Linux
• other dependencies:
  • Python
• external resources:
  • homepage: https://github.com/sympy/sympy

find-libpython

• type: library
• version(s): see ci/requirements.txt (CI only), any (runtime)
• NEURON components: NMODL
• vendoring: external
• stage(s): runtime
• build configuration: NRN_ENABLE_CORENEURON=ON, NRN_ENABLE_NMODL=ON
• supported platforms: MacOS, Linux
• other dependencies:
  • Python
• external resources:
  • homepage: https://github.com/ktbarrett/find_libpython

Packaging

• type: library
• version(s): >= 22.0
• NEURON components:
• vendoring: external
• stage(s): runtime
• build configuration:
• supported platforms: all
• other dependencies:
  • Python

cibuildwheel

• type: executable (CLI)
• version(s): >= 3.2.1
• NEURON components: none
• vendoring: external
• stage(s): pre-build
• build configuration: none
• supported platforms: MacOS, Linux
• other dependencies:
  • Python
  • Docker/Podman (Linux-only)
• external resources:
  • homepage: https://github.com/pypa/cibuildwheel

Setuptools

• type: library
• version(s): see ci/requirements.txt (CI only), any (runtime)
• NEURON components:
• vendoring: external
• stage(s): runtime
• build configuration:
• supported platforms: all
• other dependencies:
  • Python
• external resources:
  • homepage: https://github.com/pypa/setuptools

OpenMP

• type: library
• version(s): any (?)
• NEURON components: coreNEURON
• vendoring: external
• stage(s): build
• build configuration: NRN_ENABLE_CORENEURON=ON, CORENRN_ENABLE_GPU=ON
• supported platforms: Linux
• other dependencies:

OpenACC

• type: library
• version(s): any (?)
• NEURON components: coreNEURON
• vendoring: external
• stage(s): build
• build configuration: NRN_ENABLE_CORENEURON=ON, CORENRN_ENABLE_GPU=ON
• supported platforms: Linux
• other dependencies:
  • NVHPC

xfonts

• type: font
• version(s):
• NEURON components: GUI
• vendoring: external
• stage(s): runtime
• build configuration: NRN_ENABLE_INTERVIEWS=ON
• supported platforms: Linux
• other dependencies:
  • X11
• external resources:
  • Debian package: https://packages.debian.org/stable/xfonts-100dpi
  • Ubuntu package: https://launchpad.net/ubuntu/noble/amd64/xfonts-100dpi
  • Fedora package: https://packages.fedoraproject.org/pkgs/xorg-x11-fonts/xorg-x11-fonts-100dpi/

[nrnhines]

NEURON GUI sometimes gives the complaint

nrniv: unable to open font "*helvetica-medium-r-normal*--14*", using "fixed"

For ubuntu the solution is

sudo apt install xfonts-100

and one must logout and log back in.

For fedora, the package is https://packages.fedoraproject.org/pkgs/xorg-x11-fonts/xorg-x11-fonts-100dpi/

[JCGoran]

Thanks, added.