Getting AbiPy ¶

Stable version ¶

The version at the Python Package Index (PyPI) is always the latest stable release that can be installed in user mode with:

pip install abipy --user

Note that you may need to install some optional dependencies manually. In this case, please consult the detailed installation instructions provided in the pymatgen howto to install these optional packages and then follow the instructions in the How to install HDF5/Netcdf4 and the python bindings section.

The installation process is greatly simplified if you install the required packages through the Anaconda distribution. We routinely use conda to test new developments with multiple Python versions and multiple virtual environments. The anaconda distribution already provides the most critical dependencies (numpy, scipy, matplotlib, netcdf4-python) in the form of pre-compiled packages that can be easily installed with e.g.:

conda install numpy scipy netcdf4

Additional information on the steps required to install AbiPy with anaconda are available in the Anaconda Howto howto as well as in the conda-based-install section of the pymatgen documentation.

We are also working with the spack community to provide packages for AbiPy and Abinit in order to facilitate the installation on large supercomputing centers.

Advanced users who need to compile a local version of the python interpreter and install the AbiPy dependencies manually can consult the How to compile the Python interpreter document.

Optional dependencies ¶

Optional libraries that are required if you need certain features:

ipython

Required to interact with the AbiPy/Pymatgen objects in the ipython shell (strongly recommended, already provided by conda).

jupyter and nbformat

Required to generate jupyter notebooks. Install these two packages with conda install jupyter nbformat or use pip. To use jupyter you will also need a web browser to open the notebook. (recommended)

Anaconda Howto ¶

Download the anaconda installer from the official web-site. by choosing the version that matches your OS You may want to use the wget utility to download the anaconda script directly from the terminal (useful if you are installing anaconda on a cluster).

Run the bash script in the terminal and follow the instructions. By default, the installer creates the anaconda directory in your home. Anaconda will add one line to your .bashrc to enable access to the anaconda executables. Once the installation is completed, execute:

source ~/anaconda/bin/activate base

to activate the base environment. The output of which python should show that you are using the python interpreter provided by anaconda.

Use the conda command-line interface to install the packages not included in the official distribution. For example, you can install pyyaml and netcdf4 with:

conda install pyyaml netcdf4

Remember that if a package is not available in the official conda repository, you can always download the package from one of the conda channels or use pip install if no conda package is available.

Fortunately there are conda channels providing all dependencies needed by AbiPy. Now add conda-forge to your conda channels with:

conda config --add channels conda-forge

This is the channel from which we will download pymatgen, abipy and abinit.

Finally, install AbiPy with:

conda install abipy

Once you have completed the installation of AbiPy and pymatgen, open the ipython shell and type:

# make sure spglib library works
import spglib

# make sure pymatgen is installed
import pymatgen

from abipy import abilab

to check the installation.

Note that one can use conda to create different environments with different versions of the python interpreter or different libraries. Further information are available on the conda official website. Using different environments is very useful to keep different versions and branches separate.

Developmental version ¶

Getting the developmental version of AbiPy is easy. You can clone it from our github repository using:

git clone https://github.com/abinit/abipy

After cloning the repository, type:

python setup.py install

or alternately:

python setup.py develop

to install the package in developmental mode (Develop mode is the recommended approach if you are planning to implement new features. In this case you may also opt to first fork AbiPy on Git and then clone your own fork. This will allow you to push any changes to you own fork and also get them merged in the main branch).

The documentation of the developmental version is hosted on github pages.

The Github version include test files for complete unit testing. To run the suite of unit tests, make sure you have pytest installed and issue:

pytest

in the AbiPy root directory.

Note that several unit tests check the integration between AbiPy and Abinit. In order to run the tests, you need a working set of Abinit executables and a manager.yml configuration file. For further information on the syntax of the configuration file, please consult the TaskManager section.

A pre-compiled sequential version of Abinit for Linux and OSx can be installed directly from the abinit-channel with:

conda install abinit -c abinit

Examples of configuration files to configure and compile Abinit on clusters can be found in the abiconfig package.

Contributing to AbiPy is relatively easy. Just send us a pull request. When you send your request, make develop the destination branch on the repository AbiPy uses the Git Flow branching model. The develop branch contains the latest contributions, and master is always tagged and points to the latest stable release.

If you choose to share your developments please take some time to develop some unit tests of at least the basic functionalities of your code

How to compile the Python interpreter ¶

This section discusses how to install a local version of the python interpreter as well as the most important dependencies needed by AbiPy. This approach may be needed if you want to use AbiPy on a machine (e.g. a cluster) in which you don’t have root privileges and the version of the python interpreter is too old or if for some reasons you prefer not to use anaconda. In this case you cannot use a virtual environment on top of the preexisting python library.

First of all, you have to create a new directory containing your python interpreter as well as as the libraries and the other executables needed by AbiPy. Let’s assume we decided to create this directory inside $HOME and let’s call it local:

mkdir $HOME/local

Now change your ~/.bashrc file and add the following three lines:

export PATH=$HOME/local/bin:$PATH
export LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH
export C_INCLUDE_PATH=$HOME/include/:$C_INCLUDE_PATH

so that other scripts and tools will know where to find the new binaries/libraries/include files they need.

Get the python tarball from the python official site and unpack it. Configure the package with the --prefix option and compile the code (use the -j option to speedup the compilation with threads):

./configure --prefix=$HOME/local
make -j4

If you plan to use graphical tools you need to make sure that the Tkinter graphical backends is installed and functional at the time of compilation of python, see below.

At the end, you should get the list of modules that could not be built because your system does not provide the required libraries. The installation should be OK for AbiPy if you get:

Python build finished, but the necessary bits to build these modules were not found:
_sqlite3           bsddb185           dl
imageop            sunaudiodev
To find the necessary bits, look in setup.py in detect_modules() for the module's name.

If, on the other hand, python has been built without bz2 or _tkinter you are in trouble because these packages are required.

bz2 is more fundamental than _tkinter because it is used to compress/uncompress files. AbiPy/Pymatgen won’t work without bz2 and you have to install the bzip library with the C headers. The source code is available from bzip.org See also this post on stackoverflow.

Tkinter is less important than bz2 but without it you won’t be able to use the matplotlib graphical back-end. If you want matplotlib with the Tk back-end, you have to install Tk/Tcl. Get the tarball from the tcl.tk site, configure with --prefix and make && make install as usual. Then reconfigure python.

Once you have solved the problem with the missing modules, you can run the tests with:

make test

and install the python interpreter with:

make install

Now we have our python interpreter installed in $HOME/local:

which python
$HOME/local/bin/python

but we still need to install easy_install and pip so that we can automatically download and install other python packages.

To install easy_install:

wget https://bootstrap.pypa.io/ez_setup.py -O - | python

which easy_install
$HOME/local/bin/easy_install

For more info, consult the setuptools page

Now use easy_install to install pip:

easy_install pip

# Upgrade setuptools with
pip install setuptools --upgrade

Henceforth we can start to use pip to install the python modules. Start with cython and numpy:

pip install cython
pip install numpy

The installation of scipy is more complicated due to the need for the BLAS and LAPACK libraries. Try first:

pip install scipy

If the installer does not find BLAS/LAPACK in your system, consult the scipy documentation.

How to install HDF5/Netcdf4 and the python bindings ¶

Obtain the latest HDF5 software from the official hd5 web-site. Configure the package with --enable-hl --enable-shared and the --prefix option as usual. Build and install with:

make
make install

Finally define the environment variable $HDF5_DIR with:

export HDF5_DIR=$HOME/local

Get the latest stable netCDF-C release from this page. Configure with:

configure --prefix=$HOME/local --enable-netcdf-4 --enable-shared \
  CPPFLAGS="-I$HDF5_DIR/include" LDFLAGS="-L$HDF5_DIR/lib"

Build and install with make && make install Define the environment variable $NETCDF4_DIR:

export NETCDF4_DIR=$HOME/local

Now we can download and install the python interface with:

pip install netcdf4

You may want to consult the official netcdf4-python documentation.

Troubleshooting ¶

unknown locale: UTF-8 ¶

If python stops with the error message:

"ValueError: unknown locale: UTF-8"

add the following line to your .bashrc file inside your $HOME (.profile if MacOSx):

export LC_ALL=C

reload the environment with source ~/.bashrc and rerun the code.

netcdf does not work ¶

The version of hdf5 installed by conda may not be compatible with python netcdf. Try the hdf5/netcdf4 libraries provided by conda forge:

conda uninstall hdf4 hdf5
conda config --add channels conda-forge
conda install netcdf4

These packages are known to work on MacOsX:

conda list hdf4
hdf4                      4.2.12                        0    conda-forge
conda list hdf5
hdf5                      1.8.17                        9    conda-forge
conda list netcdf4
netcdf4                   1.2.7               np112py36_0    conda-forge

UnicodeDecodeError ¶

Python2.7 raises an UnicodeDecodeError: ‘ascii’ codec can’t decode byte … when trying to open files with abiopen. Add

import sys
reload(sys)
sys.setdefaultencoding("utf8")

at the beginning of your script.