hpc_suite

hpc_suite is a python package for working with data on high performance computing (HPC) systems.

Installation via pip

Install hpc_suite using pip (if using a shared machine, add the --user argument after install)

pip install hpc_suite

Updating

Update the code using pip (if using a shared machine, add the --user argument after install)

pip install hpc_suite --upgrade

Installation with pip editable install

Only do this if you are developing (i.e. changing) the code.

Clone a copy of this repository, preferably while within a directory called git

mkdir -p git; cd git
git clone https://gitlab.com/chilton-group/hpc_suite

Navigate to the package directory

cd hpc_suite/packages

and install the package in editable mode (if using a shared machine, add the --user argument after install)

pip install -e .

When you're done developing (i.e. your changes have been merged to the master), or if you just want to use the current release version of the package, uninstall using pip

pip uninstall hpc_suite

and follow the Installation via pip instructions above.

Building a .whl file (Advanced)

Only do this if you are told to.

To build a copy of the hpc_suite .whl file, move to the package directory.

Now run

./build_binaries.sh

Then install the .whl file with pip (if using a shared machine, add the --user argument after install)

pip install dist/*.whl

Documentation

The documentation for this package is hosted by gitlab, and is automatically generated whenever new code is committed to the main branch. The automatic generation of this documentation relies on a common layout for comments and docstrings within the code, see contributing for more information.

Development

Before making changes to this repository, please follow the steps outlined in the Chilton group wiki.

Bugs

If you believe you have a bug, please check that you are using the most up to date version of the code.

If that does not fix the problem, please create an issue on GitLab detailing the following:

• The commands you entered
• The error message

Remember to simplify the problem as much as possible in order to provide a minimum working example, e.g. an example for a small molecule rather than one with 100000 atoms.

Then, look at the code, try and figure out what you think is wrong if possible, and include this in your issue.