Installation#


You can install the latest stable release with pip ``` pip install pysif ```

First, clone the repository and move into it 
git clone https://github.com/lucapalmi/sif.git
cd sif

Note

The library requires OpenMP. If you are on macOS, make sure to use a compiler that supports it (e.g. LLVM-Clang or GCC) or install the libomp runtime (brew install libomp)

Dependencies

The library has few, non-vendored dependencies that should be available on your system

  1. fftw3

  2. cmake

  3. hdf5 (optional)

You can install them with any package manager,

# macOS
brew install fftw hdf5 cmake

# Ubuntu / Debian
sudo apt install build-essential cmake libfftw3-dev libhdf5-dev

HPC cluster usage

If you are on an HPC cluster, make sure to load the module files for the dependencies and the compiler.

C library

The library is compiled through CMake. These are the available options

  • SIF_FFTW_THREADING: set the FFTW multi-threading backend to use, either the OpenMP runtime or the pthreads runtime. By default, the backend is set to OpenMP. If you use LLVM-clang (brew install llvm) on macOS, the FFTW OpenMP runtime may cause crashes and/or wrong results; in this scenario, it is suggested to use the pthreads runtime with -DSIF_FFTW_THREADING=threads. Options (omp|threads), default omp.

  • SIF_HDF5_SUPPORT: activates the HDF5 integration. By default, HDF5 is used only if it’s available as a CMake package and is a serial build (no MPI). Options (AUTO|ON|OFF), default AUTO.

  • SIF_NATIVE_ARCH: activates the -march=native compile flag in Release builds. If the compiled library will be used on machines with different architectures, this option should be turned off. Options (ON|OFF), default ON.

HPC cluster usage

If you are on an HPC cluster, check that the login nodes have the same architecture of the compute nodes. If not, compile with -DSIF_NATIVE_ARCH=OFF.

Note

If you are using AppleClang with libomp, make sure to use the option -DOpenMP_ROOT=$(brew --prefix libomp) when configuring the project.

To configure the CMake, run

cmake -B build -DSIF_HDF5_SUPPORT=ON

Then, compile and install with

cmake --build build
cmake --install build

Python package

The python package can be installed with pip.

pip install .

Note

The project’s compile options are set to their default values. If you need to modify them, the standard syntax is

pip install . -C cmake.define.OpenMP_ROOT=$(brew --prefix libomp)