Installation¶

gsd binaries are available in the glotzerlab-software Docker/Singularity images and in packages on conda-forge and PyPI. You can also compile gsd from source, embed gsd.c in your code, or read gsd files with a pure Python reader pygsd.py.

Binaries¶

Conda package¶

gsd is available on conda-forge on the linux-64, linux-aarch64, linux-ppc64le, osx-64, osx-arm64 and win-64 platforms. To install, download and install miniforge or miniconda Then install gsd from the conda-forge channel:

$ conda install -c conda-forge gsd

Singularity / Docker images¶

See the glotzerlab-software documentation for instructions to install and use the containers.

PyPI¶

Use pip to install gsd:

$ python3 -m pip install gsd

Note

On some platforms, such as macOS with Apple silicon, pip’s default options may fail to install gsd or its dependencies. You can force pip to build these packages one at a time from source:

$ python3 -m pip install cython
$ python3 -m pip install --no-binary :all: --no-use-pep517 numpy
$ python3 -m pip install --no-binary :all: --no-use-pep517 gsd

Compile from source¶

Obtain the source¶

Download source releases directly from the web: https://glotzerlab.engin.umich.edu/downloads/gsd

$ curl -O https://glotzerlab.engin.umich.edu/downloads/gsd/gsd-v2.4.2.tar.gz

Or, clone using git:

$ git clone https://github.com/glotzerlab/gsd

Configure a virtual environment¶

When using a shared Python installation, create a virtual environment where you can install gsd:

$ python3 -m venv /path/to/environment

Activate the environment before configuring and before executing gsd scripts:

$ source /path/to/environment/bin/activate

Note

Other types of virtual environments (such as conda) may work, but are not thoroughly tested.

Install Prerequisites¶

gsd requires:

C compiler (tested with gcc 7-10, clang 6-11, vs2017-2019)
Python >= 3.6
numpy >= 1.9.3
Cython >= 0.22

Additional packages may be needed:

pytest >= 3.9.0 (unit tests)
Sphinx (documentation)
IPython (documentation)
an internet connection (documentation)
CMake (for development builds)

Install these tools with your system or virtual environment package manager. gsd developers have had success with pacman (arch linux), apt-get (ubuntu), Homebrew (macOS), and MacPorts (macOS):

$ your-package-manager install ipython python python-pytest python-numpy cmake cython python-sphinx python-sphinx_rtd_theme

Typical HPC cluster environments provide Python, numpy, and cmake via a module system:

$ module load gcc python cmake

Note

Packages may be named differently, check your system’s package list. Install any -dev packages as needed.

Tip

You can install numpy and other python packages into your virtual environment:

python3 -m pip install numpy

Install with setuptools¶

Use pip to install the python module into your virtual environment:

$ python3 -m pip install .

Build with CMake for development¶

You can assemble a functional python module in the build directory. Configure with CMake and compile with make.

$ mkdir build
$ cd build
$ cmake ../
$ make

Add the build directory path to your PYTHONPATH to test gsd or build documentation:

$ export PYTHONPATH=$PYTHONPATH:/path/to/build

Run tests¶

Use pytest to execute unit tests:

$ python3 -m pytest --pyargs gsd

Add the --validate option to include longer-running validation tests:

$ python3 -m pytest --pyargs gsd -p gsd.pytest_plugin_validate --validate

Build user documentation¶

Build the user documentation with Sphinx. IPython is required to build the documentation, as is an active internet connection. First, you need to compile and install gsd. If you compiled with CMake, add gsd to your PYTHONPATH first:

$ export PYTHONPATH=$PYTHONPATH:/path/to/build

To build the documentation:

$ cd /path/to/gsd
$ cd doc
$ make html
$ open _build/html/index.html

Using the C library¶

gsd is implemented in a single C file. Copy gsd/gsd.h and gsd/gsd.c into your project.

Using the pure python reader¶

If you only need to read files, you can skip installing and just extract the module modules gsd/pygsd.py and gsd/hoomd.py. Together, these implement a pure Python reader for gsd and HOOMD files - no C compiler required.