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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 3.5 or higher. Python 2.7 is also supported.

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

  • gsl-1.16 or higher.
  • python-numpy

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

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

Now use pip to download and install the pymoose.

$ 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 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.

Notes

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

$ sudo pip install python-libsbml