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Commit 76459aa4 authored by Michael Wimmer's avatar Michael Wimmer Committed by Christoph Groth
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add Mac OSX instructions for installing from package, update the Mac from source instructions

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=============================
Building and installing Kwant
=============================
================
Installing Kwant
================
Kwant can be installed either using some prepared packages (on Linux, Mac OSX,
and Windows), or it can be built and installed from source.
Installation from packages is in general advisable, especially for novice
users. Expert users may find it helpful to build Kwant from source, as this
will also allow them to customize Kwant to use certain optimized versions of
libraries.
******************************
Installing Kwant from packages
******************************
Mac OSX
=======
There is a number of different package managers for bringing software
from the Unix/Linux world to Mac OSX. Since the community is quite
split, we provide kwant and its dependencies both via the `MacPorts
<http://www.macports.org>`_ and `homebrew <http://brew.sh>`_ systems.
MacPorts
--------
MacPorts is a full-fledged package manager that recreates a whole Linux-like
environment on your Mac. It requires little choices to be made by the user,
and allows for the simplest way to install kwant.
In order to install kwant, you have to
1. Install a recent version of MacPorts, as explained in the
`installation instructions of MacPorts
<http://www.macports.org/install.php>`_.
In particular, as explained there, you will have to install also a
few prerequisites, namely
* the Xcode developer tools (compiler suite for Mac OSX) from
`<http://developer.apple.com/downloads>`_. You need an Apple ID to
download: Note that if you have one already from using the App store
on the Mac/Ipad/Iphone/... you can use this one. You will also need the
command line tools: Within Xcode 4, you have to download them by going to
`Xcode->Preferences`, click on `Download`, go to `Components`,
select `Command Line Tools` and click on `Install`. Alternatively, you can
also directly download the command line tools from the
Apple developer website.
* if you have MacOSX 10.8 or higher, the X11 server from the
`XQuartz project <http://xquartz.macosforge.org>`_.
2. After the installation, open a terminal and execute ::
echo http://dl.dropboxusercontent.com/u/769003/ports.tar | sudo tee -a /opt/local/etc/macports/sources.conf >/dev/null
(this adds the kwant MacPorts download link
`<http://dl.dropboxusercontent.com/u/769003/ports.tar>`_ at the end of the
``sources.conf`` file.)
3. Execute ::
sudo port selfupdate
4. Now, install kwant and its prerequisites ::
sudo port install py27-kwant
5. Finally, we choose python 2.7 to be the default python ::
sudo port select --set python python27
After that, you will need to close and reopen the terminal to
have all changes in effect.
Notes
.....
* If you have problems with macports because your institution's firewall
blocks macports (more precisely, the `rsync` port), resulting in
errors from ``sudo port selfupdate``, follow
`these instructions <https://trac.macports.org/wiki/howto/PortTreeTarball>`_.
* Of course, if you already have macports installed, you can skip step 1
and continue with step 2.
homebrew
--------
homebrew is a recent addition to the package managers on Mac OSX. It is
more lightweight, tries to be as minimalistic as possible and give the user
more freedom. Because of that, it requires a little more experience on
the user side compared to MacPorts. The requirements are moderate though,
if you know how to add directories to the ``$PATH`` variable for your shell,
you are safe.
1. Open a terminal and install homebrew as described on the `homebrew
homepage <http://brew.sh>`_ (instructions are towards the end of
the page)
2. Run ::
brew doctor
and follow its directions. It will ask for a few prerequisites to be
installed, in particular
* the Xcode developer tools (compiler suite for Mac OSX) from
`<http://developer.apple.com/downloads>`_. You need an Apple ID to
download: Note that if you have one already from using the App store
on the Mac/Ipad/Iphone/... you can use this one. Note that downloading
the command line tools (not the full Xcode suite) suffices. If you have
the full Xcode suite installed, you might need to download the command
line tools manually if you have version 4 or higher. In this case
go to `Xcode->Preferences`, click on `Download`, go to `Components`,
select `Command Line Tools` and click on `Install`.
* although `brew doctor` might not complain about it right away,
while we're at it, you should also install the X11 server from the
`XQuartz project <http://xquartz.macosforge.org>`_ if you have Mac
OSX 10.8 or higher.
3. Add permanently ``/usr/local/bin`` before ``/usr/bin/`` in the ``$PATH$``
environment variable of your shell, for example by adding ::
export PATH=/usr/local/bin:$PATH
at the end of your ``.bash_profile`` or ``.profile``. Then close
the terminal Terminal and reopen it again.
4. Install a few prerequisites ::
brew install gfortran python
5. Add additional repositories ::
brew tap homebrew/science
brew tap samueljohn/python
brew tap michaelwimmer/kwant
6. Install kwant and its prerequisites ::
pip install nose
brew install numpy scipy matplotlib
brew install kwant
Notes
.....
- If something does not work as expected, use ``brew doctor`` for
instructions (it will find conflicts and things like that).
- As mentioned, homebrew allows for quite some freedom. In particular,
if you are an expert, you don't need necessarily to install
numpy/scipy/matplotlib from homebrew, but can use your own installation.
The only prerequisite is that they are importable from python. (the
kwant installation will in any case complain if they are not)
- In principle, you need not install the homebrew python, but could use
Apple's already installed python. Homebrew's python is more up-to-date,
though.
*****************************************
Building and installing Kwant from source
*****************************************
Prerequisites
=============
......@@ -122,87 +281,63 @@ and select the "libblas.so.3gf" alternative when prompted by the second command.
Mac OS X
--------
These instructions were verified in April 2013 under Mac OS X 10.8.2
The instructions also include installing MUMPS for optimal performance
of Kwant. If you choose to omit MUMPS, you can skip over the optional
steps 3 and 5.
The required dependencies of kwant are best installed with one of the packaging
systems. Here we only consider the case of `MacPorts
<http://www.macports.org>`_ in detail. Some remarks for homebrew are given
below.
1. Install the current version of `MacPorts
<http://www.macports.org/>`_. As a prerequisite, you will also
have to install a current version of Xcode (Apple's developer
tools). For that, follow the `installation instructions of MacPorts
<http://www.macports.org/install.php>`_. (Note that you will need an
account with Apple to download the latest version of Xcode).
1. In order to set up MacPorts or homebrew, follow steps 1 - 3 of
the respective instructions of `MacPorts`_
2. Install the required packages::
2. Install the required dependencies::
sudo port install gcc48
sudo port install python27
sudo port install gcc47 python27 py27-numpy py27-scipy py27-matplotlib mumps_seq
sudo port select --set python python27
sudo port install py27-numpy py27-scipy py27-cython py27-matplotlib
3. (OPTIONAL) For the best performance, install also the MUMPS library and its
prerequisites.
* Download `METIS <http://glaros.dtc.umn.edu/gkhome/metis/metis/overview>`_.
You need to download version 4.0.3 from the METIS `download page
<http://glaros.dtc.umn.edu/gkhome/fsroot/sw/metis/OLD>`_ (the newer
versions have an incompatible interface).
In order to compile metis, edit the corresponding lines in
``Makefile.in`` such that they read::
CC = gcc-mp-4.8
COPTIONS = -fPIC
LDOPTIONS = -fPIC
Then, execute ``make``.
* Download `MUMPS <http://graal.ens-lyon.fr/MUMPS/>`_. In order to install
it, copy ``Make.inc/Makefile.gfortran.SEQ`` to ``Makefile.inc``, and
edit in it the corresponding lines such they read::
LMETISDIR = <metisdir>
LMETIS = -L$(LMETISDIR) -lmetis
ORDERINGSF = -Dpord -Dmetis
CC = gcc-mp-4.8
FC = gfortran-mp-4.8
FL = gfortran-mp-4.8
LIBBLAS = -lblas
OPTF = -O -DALLOW_NON_INIT -fPIC
OPTL = -O -fPIC
OPTC = -O -fPIC
where ``<metisdir>`` is the directory of METIS.
Then, execute ``make all``.
4. Unpack Tinyarray, enter its directory, build and install::
3. Unpack Tinyarray, enter its directory, build and install::
python setup.py build
sudo python setup.py install
5. (OPTIONAL) To make Kwant use MUMPS, go to the Kwant directory, and
edit ``build.conf`` to read::
5. Unpack Kwant, go to the Kwant directory, and edit ``build.conf`` to read::
[lapack]
extra_link_args = -Wl,-framework -Wl,Accelerate
[mumps]
include_dirs = <mumpsdir>/include
library_dirs = <mumpsdir>/lib <mumpsdir>/libseq <metisdir>/
libraries = zmumps mumps_common pord metis mpiseq
where ``<mumpsdir>`` and <metisdir>`` are the driectories of the previously
installed MUMPS and METIS.
include_dirs = /opt/local/include
library_dirs = /opt/local/lib
libraries = zmumps_seq mumps_common_seq pord_seq esmumps scotch scotcherr mpiseq gfortran
6. Then, build and install Kwant. ::
python setup.py build
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 OSX 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.
Notes on homebrew
.................
It is also possible to build kwant using homebrew. The dependencies can be
installed as ::
brew install gfortran python
brew tap homebrew/science
brew tap samueljohn/python
brew tap michaelwimmer/kwant
pip install nose
brew install numpy scipy matplotlib
brew install mumps_seq
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
-----------------
......
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