diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index 6f9aac49..3a412a06 100644 Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ diff --git a/.doctrees/install.doctree b/.doctrees/install.doctree index 25e06d7d..a677603f 100644 Binary files a/.doctrees/install.doctree and b/.doctrees/install.doctree differ diff --git a/_sources/install.md b/_sources/install.md index 13c965f3..6ff25900 100644 --- a/_sources/install.md +++ b/_sources/install.md @@ -61,6 +61,7 @@ See an example at {ref}`install_an_example`. In the standard output, flags and libraries found by cmake are shown. Please carefully check if those configurations are expected ones or not. +(install_without_lapacke)= ### Building without linking LAPACKE **Experimental** @@ -118,7 +119,14 @@ wrong python libraries can be imported. For x86-64 system: ```bash - % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler cxx-compiler "libblas=*=*mkl" spglib mkl-include cmake + % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler cxx-compiler cmake spglib + ``` + + Unless {ref}`install_without_lapacke`, the following packages will be + necessary to compile phono3py: + + ```bash + % conda install "libblas=*=*mkl" mkl-include ``` A libblas library can be chosen among `[openblas, mkl, blis, netlib]`. If @@ -128,20 +136,21 @@ wrong python libraries can be imported. % conda install "libblas=*=*openblas" ``` - For macOS ARM64 system, currently only openblas can be chosen: + For macOS ARM64 system: ```bash - % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler cxx-compiler spglib cmake openblas + % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler cxx-compiler spglib cmake ``` - Note that using hdf5 files on NFS mounted file system, you may have to disable - file locking by setting + Unless {ref}`install_without_lapacke`, the following package will be + necessary to compile phono3py: ```bash - export HDF5_USE_FILE_LOCKING=FALSE + % conda install openblas ``` - Install the latest phonopy and phono3py from github sources: + The latest phonopy and phono3py are obtained from github, and they are + compiled and installed by: ```bash % mkdir dev @@ -154,20 +163,29 @@ wrong python libraries can be imported. % pip install . -vvv ``` - The editable install (`pip install -e`) may not work depending on the - computer environment. The conda packages dependency can often change and this - recipe may not work properly. So if you find this instruction doesn't work, - it is very appreciated if letting us know it in the phonopy mailing list. +## Dependent libraries + +### OpenMP + +#### GCC on Ubuntu + +With system provided gcc, `libgomp1` may be 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: + +```bash +% sudo apt-get install libgomp1 +``` (install_lapacke)= -## Installation of LAPACKE +### 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. -### OpenBLAS provided by conda +#### OpenBLAS provided by conda The installation of LAPACKE is easy by conda. It is: @@ -175,7 +193,7 @@ The installation of LAPACKE is easy by conda. It is: % conda install -c conda-forge openblas ``` -### Netlib LAPACKE provided by Ubuntu package manager (with single-thread BLAS) +#### Netlib LAPACKE provided by Ubuntu package manager (with single-thread BLAS) LAPACKE (http://www.netlib.org/lapack/lapacke.html) can be installed from the Ubuntu package manager (`liblapacke` and `liblapacke-dev`): @@ -184,7 +202,17 @@ Ubuntu package manager (`liblapacke` and `liblapacke-dev`): % sudo apt-get install liblapack-dev liblapacke-dev ``` -(install_openmp)= +## Using HDF5 files on NFS mounted file system + +If you are using HDF5 files on an NFS-mounted file system, you might need to +disable file locking. This can be done by setting the following environment +variable: + +```bash +export HDF5_USE_FILE_LOCKING=FALSE +``` + + ## Trouble shooting diff --git a/install.html b/install.html index d5b0ec43..dbe2952f 100644 --- a/install.html +++ b/install.html @@ -312,15 +312,19 @@

Contents

  • Installation instruction of latest development version of phono3py
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  • Installation of LAPACKE