Installation

The easiest way to install 21cmFAST is to use conda. Simply use conda install -c conda-forge 21cmFAST. With this method, all dependencies are taken care of, and it should work on either Linux or MacOS. If for some reason this is not possible for you, read on.

Dependencies

We try to have as many of the dependencies automatically installed as possible. However, since 21cmFAST relies on some C libraries, this is not always possible.

The C libraries required are:

  • gsl

  • fftw (compiled with floating-point enabled, and --enable-shared)

  • openmp

  • A C-compiler with compatibility with the -fopenmp flag. Note: it seems that on OSX, if using gcc, you will need v4.9.4+.

As it turns out, though these are fairly common libraries, getting them installed in a way that 21cmFAST understands on various operating systems can be slightly non-trivial.

HPC

These libraries will often be available on a HPC environment by using the module load gsl and similar commands. Note that just because they are loaded doesn’t mean that 21cmFAST will be able to find them. You may have to point to the relevant lib/ and include/ folders for both gsl and fftw (these should be available using module show gsl etc.)

Note also that while fftw may be available to load, it may not have the correct compilation options (i.e. float-enabled and multiprocessing-enabled). In this case, see below.

Linux

Most linux distros come with packages for the requirements, and also gcc by default, which supports -fopenmp. As long as these packages install into the standard location, a standard installation of 21cmFAST will be automatically possible (see below). If they are installed to a place not on the LD_LIBRARY/INCLUDE paths, then you must use the compilation options (see below) to specify where they are.

Note

there exists the option of installing gsl, fftw and gcc using conda. This is discussed below in the context of MacOSX, where it is often the easiest way to get the dependencies, but it is equally applicable to linux.

MacOSX

On MacOSX, obtaining gsl and fftw is typically more difficult, and in addition, the newer native clang does not offer -fopenmp support.

For conda users (which we recommend using), the easiest way to get gsl and fftw is by doing conda install -c conda-forge gsl fftw in your environment.

Note

if you use conda to install gsl and fftw, then you will need to point at their location when installing 21cmFAST (see compiler options below for details). In this case, the installation command should simply be prepended with:

LIB=/path/to/conda/env/lib INC=/path/to/conda/env/include

To get gcc, either use homebrew, or again, conda: conda install -c anaconda gcc. If you get the conda version, you still need to install the headers:

xcode-select --install

On older versions then you need to do:

open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_<input version>.pkg

For newer versions, you may need to prepend the following command to your pip install command when installing 21cmFAST (see later instructions):

CFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX<input version>.sdk"

See faqs/installation_faq for more detailed questions on installation. If you are on MacOSX and are having trouble with installation (or would like to share a successful installation strategy!) please see the open issue.

With the dependencies installed, follow the instructions below, depending on whether you are a user or a developer.

For Users

Note

conda users may want to pre-install the following packages before running the below installation commands:

conda install numpy scipy click pyyaml cffi astropy h5py

Then, at the command line:

pip install git+git://github.com/21cmFAST/21cmFAST.git

If developing, from the top-level directory do:

pip install -e .

Note the compile options discussed below!

For Developers

If you are developing 21cmFAST, we highly recommend using conda to manage your environment, and setting up an isolated environment. If this is the case, setting up a full environment (with all testing and documentation dependencies) should be as easy as (from top-level dir):

conda env create -f environment_dev.yml

Otherwise, if you are using pip:

pip install -e .[dev]

The [dev] “extra” here installs all development dependencies. You can instead use [tests] if you only want dependencies for testing, or [docs] to be able to compile the documentation.

Compile Options

Various options exist to manage compilation via environment variables. Basically, any variable with “INC” in its name will add to the includes directories, while any variable with “lib” in its name will add to the directories searched for libraries. To change the C compiler, use CC. Finally, if you want to compile the C-library in dev mode (so you can do stuff like valgrid and gdb with it), install with DEBUG=True. So for example:

CC=/usr/bin/gcc DEBUG=True GSL_LIB=/opt/local/lib FFTW_INC=/usr/local/include pip install -e .

In addition, the BOXDIR variable specifies the default directory that any data produced by 21cmFAST will be cached. This value can be updated at any time by changing it in the $CFGDIR/config.yml file, and can be overwritten on a per-call basis.

While the -e option will keep your library up-to-date with any (Python) changes, this will not work when changing the C extension. If the C code changes, you need to manually run rm -rf build/* then re-install as above.

Logging in C-Code

By default, the C-code will only print to stderr when it encounters warnings or critical errors. However, there exist several levels of logging output that can be switched on, but only at compilation time. To enable these, use the following:

LOG_LEVEL=<log_level> pip install -e .

The <log_level> can be any non-negative integer, or one of the following (case-insensitive) identifiers:

NONE, ERROR, WARNING, INFO, DEBUG, SUPER_DEBUG, ULTRA_DEBUG

If an integer is passed, it corresponds to the above levels in order (starting from zero). Be careful if the level is set to 0 (or NONE), as useful error and warning messages will not be printed. By default, the log level is 2 (or WARNING), unless the DEBUG=1 environment variable is set, in which case the default is 4 (or DEBUG). Using very high levels (eg. ULTRA_DEBUG) can print out a lot of information and make the run time much longer, but may be useful in some specific cases.