Dedalus is a Python 3 package that includes custom C-extensions (compiled with Cython) and that relies on MPI, FFTW (linked to MPI), HDF5, and a basic scientific-Python stack: numpy, scipy, mpi4py (linked to the same MPI), and h5py.
We recommend using conda to build a Python environment with all the necessary prerequisites, as described in the conda instructions below. This procedure can be easily customized to link to existing MPI/FFTW/HDF5 libraries, which may be preferable when installing Dedalus on a cluster.
Once you have the necessary C dependencies (MPI, FFTW+MPI, and HDF5), as well as Python 3, you should be able to install Dedalus from PyPI or build it from source.
Conda installation (recommended)¶
We recommend installing Dedalus via a conda script that will create a new conda environment with a complete Dedalus installation. The script allows you to link against custom MPI/FFTW/HDF5 libraries or opt for builds of those packages that are available through conda.
Modify the options at the top of the script to changes the name of the resulting conda environment, link against custom MPI/FFTW/HDF5 libraries, choose between OpenBLAS and MKL-based numpy/scipy, and more. Then activate the base conda environment and run the script to build a new conda environment with Dedalus and its dependencies, as requested:
conda activate base bash install_conda.sh
To use Dedalus, you simply need to activate the new environment. You can test the installation works using the command-line interface:
conda activate dedalus python3 -m dedalus test
The Dedalus package within the environment can be updated using pip as described below.
Installing the Dedalus package¶
Once the necessary C dependencies and Python 3 are present, Dedalus can be installed from PyPI or built from source using pip.
Note: the instructions in this section assume the
pip3 command is hitting the right Python 3 installation.
You can check this by making sure that
which pip3 and
which python3 reside in the same location.
If not, you may need to use
python3 -m pip instead of
pip3 in the following commands.
Installing from PyPI¶
We currently only provide Dedalus on PyPI as a source distribution so that the Cython extensions are properly linked to your FFTW/MPI libraries at build-time.
To install Dedalus from PyPI, first set the
MPI_PATH environment variables to the prefix paths for FFTW/MPI and then install using pip:
export FFTW_PATH=/path/to/your/fftw_prefix export MPI_PATH=/path/to/your/mpi_prefix pip3 install dedalus
Building from source¶
Alternately, to build the lastest version of Dedalus from source: clone the repository, set FFTW/MPI paths, and install using pip:
hg clone https://bitbucket.org/dedalus-project/dedalus cd dedalus export FFTW_PATH=/path/to/your/fftw_prefix export MPI_PATH=/path/to/your/mpi_prefix pip3 install .
If Dedalus was installed using the conda script or manually from PyPI, it can be updated pip:
pip3 install --upgrade dedalus
Note: any custom FFTW/MPI paths set in the conda script or during the original installation will also need to be exported for the update command to work.
If Dedalus was built from source, it can be updated by first pulling new changes from the source repository, and then reinstalling with pip:
cd /path/to/dedalus/repo hg pull hg update export FFTW_PATH=/path/to/your/fftw_prefix export MPI_PATH=/path/to/your/mpi_prefix pip3 install --upgrade --force-reinstall .
If Dedalus was installed using pip, it can be uninstalled using:
pip3 uninstall dedalus
Alternative installation procedures¶
Note: We recommend installing Dedalus using conda, as described above. These alternative procedures may be out-of-date and are provided for historical reference and expert use.
This all-in-one installation script will build an isolated stack containing a Python installation and the other dependencies needed to run Dedalus. In most cases, the script can be modified to link with system installations of FFTW, MPI, and linear algebra libraries.
You can get the installation script from this link, or download it using:
and execute it using:
The installation script has been tested on a number of Linux distributions and OS X. If you run into trouble using the script, please get in touch on the user list.
Below are instructions for building the dependency stack on a variety of machines and operating systems:
- Install notes for PSC/Bridges: Intel stack
- Install notes for Compute Canada’s Cedar cluster
- Install notes for MIT Engaging Cluster
- Install notes for CU/Janus
- Install notes for Mac OS X (10.9)
- Install notes for NASA/Discover
- Install notes for NASA/Pleiades
- Install notes for BRC HPC SAVIO cluster
- Install notes for TACC/Stampede
- Install notes for Trestles
Once the dependency stack has been installed, Dedalus can be installed as described above.