Installation

Installation of phonopy before the installation of phono3py is required. See how to install phonopy at https://atztogo.github.io/phonopy/install.html. Phono3py relies on phonopy, so please use the latest release of phonopy when installing phono3py.

Installation using conda

Using conda is the easiest way for installation of phono3py if you are using usual 64 bit linux system. The conda packages for 64bit linux are also found at atztogo channel:

% conda install -c atztogo phono3py

All dependent packages are installed simultaneously.

Installation using pip

PyPI packages are prepared for phonopy and phono3py releases. When installing with PyPI, setup.py is executed locally to compile the part of the code written in C, so a few libraries such as lapacke must exist in the system. Those necessary libraries are explained in the next section.

Installation from source code

When installing phono3py using setup.py from the source code, a few libraries are required before running setup.py script.

For phono3py, OpenMP library is necessary for the multithreding support. In additon, BLAS, LAPACK, and LAPACKE are also needed. These packages are probably installed using the package manager for each OS or conda.

When using gcc to compile phono3py, libgomp1 is necessary to enable OpenMP multithreading support. This library is probably installed already in your system. If you don’t have it and you use Ubuntu linux, it is installed by:

% sudo apt-get install libgomp1

Installation of LAPACKE

LAPACK library is used in a few parts of the code to diagonalize matrices. LAPACK*E* is the C-wrapper of LAPACK and LAPACK relies on BLAS. Both single-thread or multithread BLAS can be used in phono3py. In the following, multiple different ways of installation of LAPACKE are explained.

MKL LAPACKE (with multithread BLAS)

Phono3py can be compiled with MKL for using LAPACKE. If setup.py finds the file named mkl.py, the contents of mkl.py is read and those are included in the compilation setting. For example, the following setting prepared as mkl.py seems working on Ubuntu 16.04 system:

intel_root = "/opt/intel/composer_xe_2015.7.235"
mkl_root = "%s/mkl" % intel_root
compiler_root = "%s/compiler" % intel_root

mkl_extra_link_args_lapacke = ['-L%s/lib/intel64' % mkl_root,
                               '-lmkl_rt']
mkl_extra_link_args_lapacke += ['-L%s/lib/intel64' % compiler_root,
                                '-lsvml',
                                '-liomp5',
                                '-limf',
                                '-lpthread']
mkl_include_dirs_lapacke = ["%s/include" % mkl_root]

This setting considers to use icc but it may be compiled with gcc. With gcc, the compiler related setting shown above (i.e., around compiler_root) is unnecessary. To achieve this installation, not only the MKL library but also the header file are necessary. The libraries are linked dynamically, so in most of the cases, LD_LIBRARY_PATH environment variable has to be correctly specified to let phono3py find those libraries.

OpenBLAS provided by conda (with multithread BLAS)

The installtion of LAPACKE is easy by conda. It is:

% conda install openblas

or if the python libraries are not yet installed:

% conda install openblas numpy scipy h5py pyyaml matplotlib

This openblas package contains BLAS, LAPACK, and LAPACKE. When this libopenblas is linked and the else statement of the C macro definition section in setup.py is executed, the following macro are activated:

if use_setuptools:
    extra_compile_args += ['-DMULTITHREADED_BLAS']
else:
    define_macros += [('MULTITHREADED_BLAS', None)]

Netlib LAPACKE provided by Ubuntu package manager (with single-thread BLAS)

In the versions of Ubuntu-12.10 or later, LAPACKE (http://www.netlib.org/lapack/lapacke.html) can be installed from the package manager (liblapacke and liblapacke-dev):

% sudo apt-get install liblapack-dev liblapacke-dev

Compiling Netlib LAPACKE

The compilation procedure is found at the LAPACKE web site. After creating the LAPACKE library, liblapacke.a (or the dynamic link library), setup.py must be properly modified to link it. As an example, the procedure of compiling LAPACKE is shown below.

% tar xvfz lapack-3.6.0.tgz
% cd lapack-3.6.0
% cp make.inc.example make.inc
% make lapackelib

BLAS, LAPACK, and LAPACKE, these all may have to be compiled with -fPIC option to use it with python.

OpenBLAS provided by MacPorts (with single-thread BLAS)

MacPorts, the OpenBLAS package contains not only BLAS but also LAPACK and LAPACKE in libopenblas.

Building using setup.py

If package installation is not possible or you want to compile with special compiler or special options, phono3py is built using setup.py. In this case, manual modification of setup.py may be needed.

  1. Download the latest source code at

    https://pypi.python.org/pypi/phono3py

  2. and extract it:

    % tar xvfz phono3py-1.11.13.39.tar.gz
    % cd phono3py-1.11.13.39
    

    The other option is using git to clone the phonopy repository from github:

    % git clone https://github.com/atztogo/phono3py.git
    % cd phono3py
    
  1. Set up C-libraries for python C-API and python codes. This can be done as follows:

    Run setup.py script:

    % python setup.py install --user
    
  2. Set $PATH and $PYTHONPATH

    PATH and PYTHONPATH are set in the same way as phonopy, see https://atztogo.github.io/phonopy/install.html#building-using-setup-py.

Installation on macOS

macOS users may be able to install phonopy and phono3py on recent macOS. But it requires a basic knowledge on UNIX and python. So if you are afraid of that, please prepare a computer or a virtual machine with a normal linux OS such as Ubuntu-linux-64bit 14.04 or 16.04.

If you think you are familiar with macOS, unix system, and python, the recommended installation process is written at https://atztogo.github.io/phonopy/MacOSX.html, which is more-or-less the same as phonopy, but with openblas, too. An example of the procedure is summarized in the next section.

An example of installation process

  1. Download miniconda package

    Miniconda is downloaded at https://conda.io/miniconda.html.

    For usual 64-bit Linux system:

    % wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
    

    For macOS, it is assumed that gcc compiler is installed on your system. The compiler such as default clang on macOS can’t handle OpenMP, so it can’t be used. The gcc compiler may be installed using homebrew, e.g.:

    % brew install gcc
    

    or using MacPort, e.g.:

    % sudo port install gcc7 wget
    

    where wget is optional. Then download using wget:

    % wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
    
  2. Install conda packages

    It is supposed to have the following environment variable:

    export PATH=~/.miniconda3/bin:$PATH
    

    Then install and update conda:

    % bash miniconda.sh -b -p $HOME/.miniconda3
    % conda update conda
    

    The necessary python libraries and openBLAS are installed by:

    % conda install numpy scipy h5py pyyaml matplotlib openblas
    

    Install the latest phonopy and phono3py:

    % export CC=gcc # only for macOS (macport), CC=gcc-7 for homebrew
    % git clone https://github.com/atztogo/phonopy.git
    % cd phonopy
    % python setup.py install --user
    % cd ..
    % git clone https://github.com/atztogo/phono3py.git
    % cd phono3py
    % python setup.py install --user
    % cd ..
    

    Environment variables PATH and PYTHONPATH must be set appropriately to use phono3py. See see https://atztogo.github.io/phonopy/install.html#building-using-setup-py and https://atztogo.github.io/phonopy/install.html#set-correct-environment-variables-path-and-pythonpath.

Multithreading and its controlling by C macro

Phono3py uses multithreading concurrency in two ways. One is that written in the code with OpenMP parallel for. The other is achieved by using multithreaded BLAS. The BLAS multithreading is depending on which BLAS library is chosen by users and the number of threads to be used may be controlled by the library’s environment variables (e.g., OPENBLAS_NUM_THREADS or MKL_NUM_THREADS). In the phono3py C code, these two are written in a nested way, but of course the nested use of multiple multithreadings has to be avoided. The outer loop of the nesting is done by the OpenMP parallel for code. The inner loop calls LAPACKE functions and then the LAPACKE functions call the BLAS routines. If both of the inner and outer multithreadings can be activated, the inner multithreading must be deactivated at the compilation time. This is achieved by setting the C macro MULTITHREADED_BLAS, which can be written in setup.py. Deactivating the multithreading of BLAS using the environment variables is not recommended because it is used in the non-nested parts of the code and these multithreadings are unnecessary to be deactivated.

Trouble shooting

  1. Phonopy version should be the latest to use the latest phono3py.
  2. There are other pitfalls, see https://atztogo.github.io/phonopy/install.html#trouble-shooting.