UbuntuBuild.md

Building MOOSE on Ubuntu (possibly in WSL)

0. Install GNU build tools

sudo apt install build-essential

Building with system Python

1. Install the dependencies

sudo apt-get install ninja meson pkg-config python-pip python-numpy libgsl-dev g++ pybind11 
pip install meson-python
pip install python-libsbml
pip install pyneuroml
pip install vpython

2. Now use pip to download and install pymoose from the github repository.

$ pip install git+https://github.com/BhallaLab/moose-core --user

Building with conda or variants

1. Install conda/mamba/micromamba (in all the commands below conda can be replaced by mamba or micromamba respectively). See https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html to find how to install conda or its variants.

2. Create an environment with required packages

conda create -n moose ninja meson meson-python gsl hdf5 numpy matplotlib vpython doxygen pybind11[global] pkg-config -c conda-forge

3. Activate the environment

conda activate moose

After the above steps, for both system Python and conda environment

4. Clone moose-core source code using git

    $ git clone https://github.com/BhallaLab/moose-core --depth 50 

5. Build moose

cd moose-core

meson setup --wipe _build --prefix=`pwd`/_build_install -Duse_mpi=false -Dbuildtype=release
ninja -v -C _build 
meson install -C _build

This will create moose module inside moose-core/_build_install directory. To make moose importable from any terminal, add this directory to your PYTHONPATH environment variable. For standard installation you can simply run pip install . in the moose-core directory.

Meson provides many builtin options: https://mesonbuild.com/Builtin-options.html. Meson options are supplied in the command line to meson setup in the format -Doption=value.

• Buildtype

  If you want a developement build with debug enabled, pass -Dbuildtype=debug in the meson setup ... command line.

  meson setup --wipe _build --prefix=`pwd`/_build_install -Duse_mpi=false -Dbuildtype=debug -Ddebug=true
  

  You can either use buildtype option alone or use the two options debug and optimization for finer grained control over the build. According to meson documentation -Dbuildtype=debug will create a debug build with optimization level 0 (i.e., no optimization, passing -O0 -g to GCC), -Dbuildtype=debugoptimized will create a debug build with optimization level 2 (equivalent to -Ddebug=true -Doptimization=2), -Dbuildtype=release will create a release build with optimization level 3 (equivalent to -Ddebug=false -Doptimization=3), and -Dbuildtype=minsize will create a release build with space optimization (passing -Os to GCC).

• Optimization level

  To set optimization level, pass -Doptimization=level, where level can be plain, 0, g, 1, 2, 3, s.

6. For a Python development build so that your edits to the Python source code are included, run:

python -m pip install --no-build-isolation --editable .

7. To build a wheel (for distribution), run pip wheel command in the moose-core directory:

 pip wheel -w dist .

This weel create the pymoose-{version}-{python}-{abi}-{os}_{arch}.whl wheel file in the moose-core/dist directory. This can installed with

pip install dist/pymoose-{version}-{python}-{abi}-{os}_{arch}.whl

Development build with meson and ninja

pip builds pymoose with default options, it runs meson behind the scene. If you are developing moose, want to build it with different options, or need to test and profile it, meson and ninja based flow is recommended.

Install the required dependencies and download the latest source code of moose from github.

    $ git clone https://github.com/BhallaLab/moose-core --depth 50 
    $ cd moose-core
    $ meson setup --wipe _build --prefix=`pwd`/_build_install -Duse_mpi=false -Dbuildtype=release
    $ ninja -v -C _build 
	$ meson install -C _build

This will build moose, in moose-core/_build directory and install it as Python package in the moose-core/_build_install directory.

To rebuild, delete the _build directory and the generated _build_install/ directory and continue the steps above starting with meson setup ....

To make in debug mode replace the option -Dbuildtype=release with -Dbuildtype=debug