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Postgkyl install

Important

git clone https://github.com/ammarhakim/postgkyl.git
cd postgkyl
conda env create -f environment.yml
conda activate pgkyl
pip install -e .

Postgkyl installation can be split to two steps:

  1. Setting up Python environment
  2. Installing Postgkyl from its repository

The following Python packages are required:

  • adios21
  • click
  • matplotlib
  • msgpack-python
  • numpy
  • pytest
  • scipy
  • sympy
  • pytables

For installation and management of these dependencies we recommend the Conda package manager (more precisely the lightweight miniconda version).

Important

The python version of one of the dependencies, ADIOS 2, requires Python 3.11 or higher. Therefore, Postgkyl Conda packages are currently available only for these versions.

Users that installed Posgkyl prior to 2023/08/30 are advised to either create a fresh Python 3.11 environment or reinstall their Conda.

The packages can then be either installed manually or use the prepared environment.yml in the Postgkyl repository. One needs to first clone the repository

git clone https://github.com/ammarhakim/postgkyl.git

navigate to the directory and create a new conda environment

conda env create -f environment.yml

The Postgkyl environment can then be activated using

conda activate pgkyl

and deactivate with

conda deactivate

Note

Managing a significant number of dependencies can easily become very complicated and conflicts may arise. Therefore, we generally recommend using separate conda environments for individual projects.

Note that in order to use environments, conda needs to be initialized. This is the last step of the conda installation, but the current default behavior is _not to perform the initialization. It can be done afterwards using conda init [shell name], e.g., conda init fish with the fantastic fish shell.

When creating a new environment for Postgkyl, one can easily rename it

conda env create -f environment.yml -n custom_name

Or, alternatively, simply try to update the current active environment

conda env update -f environment.yml

Finally, conda can be used to install dependencies without the use of environments

conda install --file requirements.txt

With the dependencies set up and the repository cloned, both the Postgkyl Python module and the command line tool are installed using pip

pip install -e .

Note

Assuming the Conda has been set properly, the pip command above will install both the Python module and the command line tool; no modification of the PYTHOPATH is required! In case Postgkyl was previously used with PYTHONPATH, we strongly recommend removing all entries from there.

  1. Adios 2 is only needed for the production version of Gkeyll. Developers strictly using only the GkeyllZero layer do not need this package.↩