Welcome to PSYDAC

PSYDAC is a Python 3 Library for isogeometric analysis.

Table of contents

• Requirements
• Python setup and project download
• Installing the library
• Uninstall
• Running tests
• Speeding up Psydac's core
• User Documentation
• Code Documentation

Requirements

Psydac requires a certain number of components to be installed on the machine:

• Fortran and C compilers with OpenMP support
• OpenMP library
• BLAS and LAPACK libraries
• MPI library
• HDF5 library with MPI support

The installations instructions depend on the operating system and on the packaging manager used.

Linux Debian-Ubuntu-Mint

To install all requirements on a Linux Ubuntu operating system, just use APT, the Advanced Packaging Tool:

sudo apt update
sudo apt install python3 python3-dev python3-pip
sudo apt install gcc gfortran
sudo apt install libblas-dev liblapack-dev
sudo apt install libopenmpi-dev openmpi-bin
sudo apt install libomp-dev libomp5
sudo apt install libhdf5-openmpi-dev

macOS

To install all the requirements on a macOS operating system we recommend using Homebrew:

brew update
brew install gcc
brew install openblas
brew install lapack
brew install open-mpi
brew install libomp
brew install hdf5-mpi

Other operating systems

Please see the instructions for the pyccel library for further details.

Python setup and project download

We recommend creating a clean Python virtual environment using venv:

python3 -m venv <ENV-PATH>

where <ENV-PATH> is the location to create the virtual environment. (A new directory will be created at the required location.)

In order to activate the environment from a new terminal session just run the command

source <ENV-PATH>/bin/activate

One can clone the Psydac repository at any location <ROOT-PATH> in the filesystem which does not require administrator privileges, using either

git clone https://github.com/pyccel/psydac.git

or

git clone git@github.com:pyccel/psydac.git

The latter command requires a GitHub account.

Installing the library

Psydac depends on several Python packages, which should be installed in the newly created virtual environment. These dependencies can be installed from the cloned directory <ROOT-PATH>/psydac using

export CC="mpicc"
export HDF5_MPI="ON"
export HDF5_DIR=/path/to/parallel/hdf5

python3 -m pip install --upgrade pip
python3 -m pip install -r requirements.txt
python3 -m pip install -r requirements_extra.txt --no-build-isolation

where the HDF5_DIR environment variable should store the absolute path to the installation point of your parallel HDF5 library, which can be found with

h5pcc -showconfig

or (on macOS)

brew info hdf5-mpi

At this point the Psydac library may be installed in standard mode, which copies the relevant files to the correct locations of the virtual environment, or in development mode, which only installs symbolic links to the Psydac directory. The latter mode allows one to effect the behavior of Psydac by modifying the source files.

• Standard mode:

  python3 -m pip install .

• Development mode:

  python3 -m pip install --editable .

Uninstall

• Whichever the install mode:

  python3 -m pip uninstall psydac

Running tests

export PSYDAC_MESH_DIR=/path/to/psydac/mesh/
python3 -m pytest --pyargs psydac -m "not parallel"
python3 /path/to/psydac/mpi_tester.py --pyargs psydac -m "parallel"

Speeding up Psydac's core

Some of the low-level functions in psydac are written in python in a way that can be accelerated by pyccel. Currently, all of those are in psydac/core/kernels.py, psydac/core/bsplines_pyccel.py and psydac/linalg/kernels.py.

cd path/to/psydac/core
pyccel kernels.py --language fortran
pyccel bsplines_pyccel.py --language fortran

cd ../linalg
pyccel kernels.py --language fortran

User documentation

• Output formats
• Notebook examples
• Other examples

Code documentation

Find our latest code documentation here.

Mesh Generation

After installation, a command psydac-mesh will be available.

Example of usage

psydac-mesh -n='16,16' -d='3,3' square mesh.h5