Installation#

Installation via conda#

Conda is a software package management system. Once the conda system is set-up (see miniforge), the installation of phonopy is super easy for any of Linux, MacOSX, and Windows. Phonopy is installed using conda by

% conda install -c conda-forge phonopy

This phonopy’s conda package is prepared and maintained by Paweł T. Jochym at conda-forge channel (please be aware that this is not a trivial job).

Minimum steps to install and use phonopy via conda#

In the following procedure, conda’s environment (see miniforge) is used not to interfere existing environment (mainly python environment).

% conda create -n phonopy -c conda-forge
% conda activate phonopy
% conda install -c conda-forge phonopy

To exit from this conda’s environment:

% conda deactivate

To use this phonopy, entering this environment is necessary like below.

% conda activate phonopy
(phonopy) % phonopy
        _
  _ __ | |__   ___  _ __   ___   _ __  _   _
 | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
 | |_) | | | | (_) | | | | (_) || |_) | |_| |
 | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
 |_|                            |_|    |___/
                                      2.12.0

Python version 3.9.6
Spglib version 1.16.2


Supercell matrix (DIM or --dim) was not explicitly specified.
By this reason, phonopy_yaml mode was invoked.
But "phonopy_params.yaml", "phonopy_disp.yaml" and "phonopy.yaml" could not be found.
  ___ _ __ _ __ ___  _ __
 / _ \ '__| '__/ _ \| '__|
|  __/ |  | | | (_) | |
 \___|_|  |_|  \___/|_|

Using HDF5 on NFS mounted file system#

Recent hdf5 versions just as installed may not work on NFS mounted file systems. In this case, setting the following environment variable may solve the problem:

export HDF5_USE_FILE_LOCKING=FALSE

Installation from source code#

System requirement#

The procedure to setup phonopy is explained in this section. It is supposed that phonopy is installed on the recent linux distribution like Ubuntu or Fedora with Python version 3.7 or later. Mac OS X users may use conda (conda-forge channel) packages. Windows users should use conda (conda-forge channel) packages as well.

Prepare the following Python libraries:

  • Python (>=3.7) and its header files

  • numpy (>=1.15)

  • matplotlib (>=2.2.2)

  • python-yaml (pyyaml)

  • python-h5py (h5py)

  • spglib

It is recommended to install seekpath to plot phonon band structure:

  • seekpath

Scipy is optional because most of features of phonopy can work without scipy, but scipy is needed for fitting to equations of states for quasi-harmonic phonon calculation.

  • scipy

For the CP2K interface, the following package will be needed to install:

  • cp2k-input-tools

Installing required packages by conda#

The python libraries can be installed using conda. Conda packages are distributed in binary. Minimum setup of conda envrironment is done by miniforge, which is downloaded at https://github.com/conda-forge/miniforge. It is strongly recommended to create conda’s virtual environment by conda create -n <venvname> as written above. The installation of necessary libraries is done as follows:

% conda install -c conda-forge numpy scipy h5py pyyaml matplotlib-base seekpath spglib

A libblas library installed can be chosen among [openblas, mkl, blis, netlib]. If specific one is expected, it is installed by (e.g. openblas)

% conda install -c conda-forge "libblas=*=*openblas"

If you need a compiler,

% conda install -c conda-forge c-compliler

Building using setup.py#

If package installation is not possible or you want to compile with special compiler or special options, phonopy is built using setup.py. In this case, manual modification of setup.py may be needed.

  1. Get the source code from github

    % git clone https://github.com/phonopy/phonopy.git
    % cd phonopy
    % git checkout master
    
  2. Run setup.py script via pip

    % pip install -e . -vvv
    

Under the system with OpenMP library, setting environment variable

export PHONOPY_USE_OPENMP=true

before pip install -e . -vvv will build phonopy with OpenMP support thought the performance improvement is limited for many cases.

Trouble shooting#

Remove previous phonopy installations#

Sometimes previous installations of phonopy prevent from loading newly installed phonopy. In this case, it is recommended to uninstall all the older phonopy packages by

  1. Running pip uninstall phonopy as many times as no phonopy packages will be found. Error message may be shown, but don’t mind it. Similarly do conda uninstall phonopy.

  2. There may still exist litter of phonopy packages. So it is also recommend to remove them if it is found, e.g.:

    % rm -fr ~/.local/lib/python*/site-packages/phonopy*
    

Set correct environment variables PATH and PYTHONPATH

When using conda environment, this information is not applicable.#

In phonopy, PATH and PYTHONPATH play important roles. Of course the information about them can be easily found in internet (e.g. https://en.wikipedia.org/wiki/PATH_(variable)), so you really have to find information by yourself and read them. Even if you can’t understand them, first you must ask to your colleagues or people before sending this unnecessary question (as a researcher using computer simulation) to the mailing list.

The problem appears when phonopy execution and library paths are set multiple times in those environment variable. It is easy to check current environment variables by:

% echo $PATH
% echo $PYTHONPATH

When multiple different phonopy paths are found, remove all except for what you really need. Then logout from the current shell (terminal) and open new shell (terminal) to confirm that the modification is activated.