From Sources

From-source installation is directed at those, who wish to carry out 13C-MFA on complex models and heavy machinery or develop new features associated with labeling simulation. This approach is arguably the most difficult, but allows to get every ounce of performance out of 13CFLUX. Only installing the C++ backend itself is only recommended for benchmarking and development, since it does not offer an higher-level function such optimization or inference.

As prerequisite, you need to install

  • C++17 capable compiler (supported: gcc, clang)

  • CMake (>= 3.18)

  • Boost: log, date time, unit test framework (>= 1.65, build with -fPIC)

  • FluxML (with –enable-pic to build the Python package)

  • SUNDIALS (>= 6.6.0, < 7.0.0)

  • OpenMP (>= 3.0, optional)

  • Python dev tools (>= 3.9, only required to build the Python package)

  • ipopt (>= 3.11, only required to build the Python package)

Python package

The most difficult task is to install boost with position-independent code. Unfortunately, this is a requirement by pybind. For more information, consider this StackOverflow thread. Having installed the prerequisites, a simple

pip install .

in the source directory should suffice.

Only C++ backend

Create a build directory for cmake in the top source directory:

mkdir build && cd build

In the build directory run

cmake ..

to configure CMake. You can supply this call with -DBUILD_TESTS=ON to enable testing or -DBUILD_NATIVE=ON to optimize the binary to the compilation machine.

After that you can build 13CFLUX with

sudo make install