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INSTALL.md

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Building MOOSE

To build MOOSE from source, you need cmake and python-setuptools. We recommend to use Python 3.8 or higher.

Before running the following command to build and install, make sure that followings are installed.

  • gsl-1.16 or higher.
  • python-numpy
  • pybind11 (if the setup fails to find pybind11, try running pip install pybind11[global])

On Ubuntu-16.04 or higher, these dependencies can be installed with:

sudo apt-get install python-pip python-numpy cmake libgsl-dev g++ pybind11

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

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

Using cmake (For developers)

pip builds pymoose with default options, it runs cmake behind the scene. If you are developing moose, build it with different options, or needs to test and profile it, cmake 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
$ mkdir _build
$ cd _build
$ cmake ..
$ make -j3  
$ ctest -j3 --output-on-failure

This will build moose, ctest will run few tests to check if build process was successful.

To rebuild, delete the _build directory and the generated _temp__build/ directory and recreate the _build directory:

$ cd ..; rm -rf _build; rm -rf _temp__build

and continue the steps following that described above.

To make in debug mode use: $ cmake -DCMAKE_BUILD_TYPE=Debug ..

To make in debug mode with optimization turned off, use: $ cmake -DCMAKE_BUILD_TYPE=Debug
-DCMAKE_C_FLAGS_DEBUG="-g -O0"
-DCMAKE_CXX_FLAGS_DEBUG="-g -O0" ..

To make with profiling: $ cmake -DGPROF=ON -DCMAKE_BUILD_TYPE=Debug ..

To make with NSDF support (requires installation of libhdf5-dev): $ cmake -DWITH_NSDF=ON ..

To install MOOSE into non-standard directory, pass additional argument -DCMAKE_INSTALL_PREFIX=path/to/install/dir to during configuration. E.g.,

$ mkdir _build && cd _build # inside moose-core directory. $ cmake -DCMAKE_INSTALL_PREFIX=$HOME/.local .. $ make && make install

Will build and install pymoose to ~/.local.

To use a non-default python installation, set PYTHON_EXECUTATBLE=/path/to/python e.g.,

$ cmake -DPYTHON_EXECUTABLE=/opt/bin/python3 ..

Post installation

Now you can import moose in a Python script or interpreter with the statement:

>>> import moose
>>> moose.test()   # will take time. Not all tests will pass.

Uninstall

To uninstall moose, run

$ pip uninstall pymoose

If you are building moose from source, make sure to get out of the source directory, or you may encounter a message like this:

Found existing installation: pymoose {version}
Can't uninstall 'pymoose'. No files were found to uninstall.

Notes

  • SBML support is enabled by installing python-libsbml. Alternatively, it can be installed by using python-pip

    $ sudo pip install python-libsbml