INSTALL.rst

Installation of Kwant

Ready-to-use Kwant packages are available for many platforms (like GNU/Linux, Mac OS X, Microsoft Windows). See the installation page of the Kwant website for instructions on how to install Kwant on your platform. This is the recommended way for new users.

The remainder of this section documents how to build Kwant from source. This information is mostly of interest to contributors and packagers.

Generic instructions

Obtaining the source code

Source distributions of Kwant (and Tinyarray) are available at the downloads section of the Kwant website as well as PyPI. The sources may be also cloned directly from the official Kwant git repository.

Prerequisites

Building Kwant requires

• Python 3.6 or above (Kwant 1.1 is the last version to support Python 2),
• NumPy 1.13.3 or newer,
• SciPy 0.19.1 or newer,
• LAPACK and BLAS, (For best performance we recommend the free OpenBLAS or the nonfree MKL.)
• Tinyarray 1.2 or newer,

a NumPy-like Python package optimized for very small arrays,

• An environment which allows to compile Python extensions written in C and C++.

The following software is highly recommended though not strictly required:

• matplotlib 2.1.1 or newer, for the module kwant.plotter and the tutorial,
• SymPy 1.1.1 or newer, for the subpackage kwant.continuum.
• Qsymm 1.2.6 or newer, for the subpackage kwant.qsymm.
• MUMPS, a sparse linear algebra library that will in many cases speed up Kwant several times and reduce the memory footprint. (Kwant uses only the sequential, single core version of MUMPS. The advantages due to MUMPS as used by Kwant are thus independent of the number of CPU cores of the machine on which Kwant runs.)
• The py.test testing framework 3.3.2 or newer for running the tests included with Kwant.

In addition, to build a copy of Kwant that has been checked-out directly from version control, you will also need Cython 0.26.1 or newer. You do not need Cython to build Kwant that has been unpacked from a source .tar.gz-file.

Building and installing Kwant

Kwant can be built and installed following the usual Python conventions by running the following commands in the root directory of the Kwant distribution.

python3 setup.py build
python3 setup.py install

Depending on your system, you might have to run the second command with administrator privileges (e.g. prefixing it with sudo).

After installation, tests can be run with:

python3 -c 'import kwant; kwant.test()'

The tutorial examples can be found in the directory tutorial inside the root directory of the Kwant source distribution.

(Cython will be run automatically when the source tree has been checked out of version control. Kwant tarballs include the Cython-generated files, and cythonization is disabled when building not from git. If ever necessary, this default can be overridden by giving the --cython option to setup.py.)

Build configuration

Kwant contains several extension modules. The compilation and linking of these modules can be configured by editing a build configuration file. By default, this file is build.conf in the root directory of the Kwant distribution. A different path may be provided using the --configfile=PATH option.

This configuration file consists of sections, one for each extension module that is contained in Kwant, led by a [section name] header and followed by key = value lines.

The sections bear the names of the extension modules, for example [kwant.operator]. There can be also a [DEFAULT] section that provides default values for all extensions, also those not explicitly present in the file.

Possible keys are the keyword arguments for distutils.core.Extension (For a complete list, see its documentation). The corresponding values are whitespace-separated lists of strings.

Example build.conf for compiling Kwant with C assertions and Cython's line trace feature:

[DEFAULT]
undef_macros = NDEBUG
define_macros = CYTHON_TRACE=1

Kwant can optionally be linked against MUMPS. The main application of build configuration is adopting the build process to the various deployments of MUMPS. MUMPS will be not linked against by default, except on Debian-based systems when the package libmumps-scotch-dev is installed.

The section [kwant.linalg._mumps] may be used to adapt the build process. (For simplicity and backwards compatibility, [mumps] is an aliases for the above.)

Example build.conf for linking Kwant against a self-compiled MUMPS, SCOTCH and METIS:

[mumps]
libraries = zmumps mumps_common pord metis esmumps scotch scotcherr mpiseq gfortran

The detailed syntax of build.conf is explained in the documentation of Python's configparser module.

Building the documentation

To build the documentation, the Sphinx documentation generator is required with numpydoc extension (version 0.5 or newer), as well as jupyter-sphinx (version 0.2 or newer). If PDF documentation is to be built, the tools from the libRSVG (Debian/Ubuntu package librsvg2-bin) and a Sphinx extension sphinxcontrib-svg2pdfconverter are needed to convert SVG drawings into the PDF format.

As a prerequisite for building the documentation, Kwant must have been built successfully using python3 setup.py build as described above (or Kwant must be already installed in Python's search path). HTML documentation is built by entering the doc subdirectory of the Kwant package and executing make html. PDF documentation is generated by executing make latex followed by make all-pdf in doc/build/latex.

Because of some quirks of how Sphinx works, it might be necessary to execute make clean between building HTML and PDF documentation. If this is not done, Sphinx may mistakenly use PNG files for PDF output or other problems may appear.

Hints for specific platforms

Unix-like systems (GNU/Linux)

Kwant should run on all recent Unix-like systems. The following instructions have been verified to work on Debian 8 (Jessie) or newer, and on Ubuntu 14.04 or newer. For other distributions step 1 will likely have to be adapted. If Ubuntu-style sudo is not available, the respective command must be run as root.

1. Install the required packages. On Debian-based systems like Ubuntu this can be done by running the command

   sudo apt-get install python3-dev python3-setuptools python3-scipy python3-matplotlib python3-pytest python3-sympy g++ gfortran libmumps-scotch-dev

2. Unpack Tinyarray, enter its directory. To build and install, run

   python3 setup.py build
   sudo python3 setup.py install

3. Inside the Kwant source distribution's root directory run

   python3 setup.py build
   sudo python3 setup.py install

By default the package will be installed under /usr/local. Run python3 setup.py --help install for installation options.

Mac OS X: MacPorts

The following instructions are valid for Kwant 1.1 with Python 2.7. They need to be updated for Kwant 1.2. (Help is welcome.)

The required dependencies of Kwant are best installed with one of the packaging systems. Here we only consider the case of MacPorts in detail. Some remarks for homebrew are given below.

1. Install a recent version of MacPorts, as explained in the installation instructions of MacPorts.

2. Install the required dependencies:

   sudo port install gcc47 python27 py27-numpy py27-scipy py27-matplotlib mumps_seq
   sudo port select --set python python27

3. Unpack Tinyarray, enter its directory, build and install:

   python setup.py build
   sudo python setup.py install

4. Unpack Kwant, go to the Kwant directory, and edit build.conf to read:

   [mumps]
   include_dirs = /opt/local/include
   library_dirs = /opt/local/lib
   libraries = zmumps_seq mumps_common_seq pord_seq esmumps scotch scotcherr mpiseq gfortran

5. Then, build and install Kwant.

   CC=gcc-mp-4.7 LDSHARED='gcc-mp-4.7 -shared -undefined dynamic_lookup' python setup.py build
   sudo python setup.py install

You might note that installing Kwant on Mac OS X is somewhat more involved than installing on Linux. Part of the reason is that we need to mix Fortran and C code in Kwant: While C code is usually compiled using Apple compilers, Fortran code must be compiled with the Gnu Fortran compiler (there is no Apple Fortran compiler). For this reason we force the Gnu compiler suite with the environment variables CC and LDSHARED as shown above.

Mac OS X: homebrew

The following instructions are valid for Kwant 1.1 with Python 2.7. They need to be updated for Kwant 1.2. (Help is welcome.)

It is also possible to build Kwant using homebrew. The dependencies can be installed as

brew install gcc python
brew tap homebrew/science
brew tap homebrew/python
brew tap kwant-project/kwant
pip install pytest pytest-runner six
brew install numpy scipy matplotlib

Note that during the installation you will be told which paths to add when you want to compile/link against scotch/metis/mumps; you need to add these to the build.conf file. Also, when linking against MUMPS, one needs also to link against METIS (in addition to the libraries needed for MacPorts).

Microsoft Windows

Our efforts to compile Kwant on Windows using only free software (MinGW) were only moderately successful. At the end of a very complicated process we obtained packages that worked, albeit unreliably. As the only recommended way to compile Python extensions on Windows is using Visual C++, it may well be that there exists no easy solution.

It is possible to compile Kwant on Windows using non-free compilers, however we (the authors of Kwant) have no experience with this. The existing Windows binary installers of Kwant and Tinyarray were kindly prepared by Christoph Gohlke.