mirror of https://github.com/phonopy/phono3py.git
Minor update on installation
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Atsushi Togo
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commit
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@ -4,22 +4,42 @@ Installation
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=============
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.. contents::
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:depth: 2
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:depth: 3
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:local:
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System requirement
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-------------------
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**Phono3py-1.11.7 depends on phonopy-1.11.6 or later.** So the
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installation of phonopy before the installation of phono3py is
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Installation of phonopy before the installation of phono3py is
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required. See how to install phonopy at
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https://atztogo.github.io/phonopy/install.html .
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https://atztogo.github.io/phonopy/install.html. Phono3py relies on
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phonopy, so please use the latest release of phonopy when installing
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phono3py.
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From source code
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-----------------
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When installing phono3py using ``setup.py`` from the source code, a
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few libraries are required before running ``setup.py`` script.
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For phono3py, OpenMP library is necessary for the multithreding
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support. In the case of the GNU OpenMP library, the library name may
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be ``libgomp1``. In additon, LAPACK and LAPACKE are also needed. These
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packages are probably installed using the package manager for each
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OS. In the case of ubuntu linux, it would be like::
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support. In additon, BLAS, LAPACK, and LAPACKE are also needed. These
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packages are probably installed using the package manager for each OS
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or conda.
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When using gcc to compile phono3py, ``libgomp1`` is necessary to
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enable OpenMP multithreading support. This library is probably
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installed already in your system. If you don't have it and you use
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Ubuntu linux, it is installed by::
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% sudo apt-get install libgomp1
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Installation of necessary libraries
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Here two ways to install necessary libraries are introduced.
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By Ubuntu package manager
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^^^^^^^^^^^^^^^^^^^^^^^^^^
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In the case of ubuntu linux, it would be like::
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% sudo apt-get install libgomp1 liblapack-dev liblapacke-dev
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@ -44,26 +64,32 @@ it. As an example, the procedure of compiling LAPACKE is shown below.
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BLAS, LAPACK, and LAPACKE, these all may have to be compiled
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with -fPIC option to use it with python.
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Multithreading support
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------------------------
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By conda
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^^^^^^^^^
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Phono3py supports OpenMP multithreading and most users will need it,
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otherwise the calculation may take long time. The library options used
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for GCC, ``-lgomp`` and ``-fopenmp``, are written in ``setup.py``,
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but for the other compilers, you may have to change them. If you need
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to compile without the OpenMP support, you can remove these options in
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``setup.py``.
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The installtion of LAPACKE is easy by conda. It is::
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Install using pip/conda
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------------------------
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% conda install openblas
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PyPI and conda packages are prepared at phonopy and phono3py
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releases. Using these packages, the phonopy and phono3py installations
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are expected to be easily done. For more detail, see
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https://atztogo.github.io/phonopy/install.html .
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or if the python libraries are not yet installed::
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% conda install openblas numpy scipy h5py pyyaml matplotlib
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This openblas package contains BLAS, LAPACK, and LAPACKE.
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..
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Multithreading support
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------------------------
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Phono3py supports OpenMP multithreading and most users will need it,
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otherwise the calculation may take long time. The library options used
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for GCC, ``-lgomp`` and ``-fopenmp``, are written in ``setup.py``,
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but for the other compilers, you may have to change them. If you need
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to compile without the OpenMP support, you can remove these options in
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``setup.py``.
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Building using setup.py
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------------------------
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~~~~~~~~~~~~~~~~~~~~~~~~
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If package installation is not possible or you want to compile with
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special compiler or special options, phono3py is built using
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@ -91,11 +117,11 @@ already a user of phonopy, ``PYTHONPATH`` for the original phonopy
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version has to be removed. The ``PYTHONPATH`` setting depends on
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shells that you use. For example in bash or zsh::
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export PYTHONPATH=~/phono3py-1.11.3/lib/python
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export PYTHONPATH=~/phono3py-1.11.11/lib/python
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or::
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export PYTHONPATH=$PYTHONPATH:~/phono3py-1.11.3/lib/python
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export PYTHONPATH=$PYTHONPATH:~/phono3py-1.11.11/lib/python
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Phono3py command is installed under ``bin`` directory. The location of
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``bin`` directory is depending on ``--user`` or ``--home`` scheme when
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@ -104,3 +130,12 @@ operation system, e.g., ``~/.local/bin`` for Ubuntu linux and
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``~/Library/Python/2.7`` for Mac (& python2.7). In the latter case,
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``bin`` directory is found on the current directory if it was
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``--home=.``.
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Install using pip/conda
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------------------------
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PyPI and conda packages are prepared at phonopy and phono3py
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releases. Using these packages, the phonopy and phono3py installations
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are expected to be easily done. For more detail, see
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https://atztogo.github.io/phonopy/install.html .
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@ -354,6 +354,13 @@ cutoff_frequency = conf['cutoff_frequency']
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symprec = options.symprec
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# Check supercell size
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if supercell_matrix is None:
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print_error_message("Supercell dimension (--dim) has to be specified.")
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if log_level > 0:
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print_end()
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sys.exit(0)
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#################################################
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# Create supercells with displacements and exit #
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#################################################
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18
setup.py
18
setup.py
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@ -82,20 +82,30 @@ elif os.path.isfile("libopenblas.py"):
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extra_compile_args += ['-DMULTITHREADED_BLAS']
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else:
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define_macros += [('MULTITHREADED_BLAS', None)]
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elif platform.system() == 'Darwin':
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# For MacPort
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elif (platform.system() == 'Darwin' and
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os.path.isfile('/opt/local/lib/libopenblas.a')):
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# For MacPort:
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# % sudo port install gcc6
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# % sudo port select --set gcc mp-gcc
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# % sudo port install OpenBLAS +gcc6
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extra_link_args_lapacke = ['/opt/local/lib/libopenblas.a']
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include_dirs_lapacke = ['/opt/local/include']
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library_dirs_lapacke = []
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else:
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elif os.path.isfile('/usr/lib/liblapacke.so'):
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# This is when lapacke is installed on system
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extra_link_args_lapacke = ['-llapacke', '-llapack', '-lblas']
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include_dirs_lapacke = []
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library_dirs_lapacke = []
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else:
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# For conda: Try dynamic link library of openblas
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# % conda install numpy scipy h5py pyyaml matplotlib openblas
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extra_link_args_lapacke = ['-lopenblas']
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include_dirs_lapacke = []
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library_dirs_lapacke = []
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if use_setuptools:
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extra_compile_args += ['-DMULTITHREADED_BLAS']
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else:
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define_macros += [('MULTITHREADED_BLAS', None)]
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## Uncomment below to measure reciprocal_to_normal_squared_openmp performance
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# define_macros += [('MEASURE_R2N', None)]
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