UW Molecular Engineering and Materials Center (MEMC) Research Experience for Undergraduates (REU) Workshop Materials
We will be using UW-IT Research Computing's implementation of Open OnDemand (OOD) for this training series. OOD is a web-based portal that provides an integrated, single access point for access to the Hyak Klone HPC Cluster. OOD provides a graphical user interface (GUI) as an alternative to the command line that simplifies the process of submitting jobs, managing files, launching applications, and monitoring job status. Access our implementation at https://ondemand.hyak.uw.edu/.
In order to access OOD you need to have an account on the Hyak cluster. If you don't have an account, check out our documentation here.
Introductory materials include:
- 00-connect-vpn.ipynb - Instructions for connecting to the UW VPN. A VPN connection is required for using Open OnDemand outside of the UW campus network.
- 01-start-jupyter.ipynb - Instructions for launching a JupyterLab session on Hyak's OOD platform.
- 02-introduction.ipynb - An introduction to Jupyter Notebooks.
- Jupyter notebooks were adapted from Software Carpentry's "Plotting and Programming in Python" and "Programming with Python".
- Notebooks starting 01-08 can be followed workbook style by running the code blocks to demonstrate presented concepts. This set of Notebooks excludes the solutions to the Exercises.
- Notebooks starting S01-S08 are duplicates of the Notebooks starting 01-08, but this set of Notebooks include the solutions to the Exercises.
- The notebooks are meant to be a resource for your reference after the workshop has concluded. The workshop will be a hands on coding demonstration. The notebooks include additional practice exercises.
- Learning materials were adapted from "Plotting and Programming in Python" by Software Carpentry and "Python Data Science Handbook" by Jake VanderPlas.
- Notebook starting 00-02 can be followed workbook style by running the code blocks to demonstrate presented concepts.
- Notebook starting S00-S02 are duplicates of the Notebooks starting 00-02, with the solutions to the Exercises included.
- The notebooks are meant to be a resource for your reference after the workshop has concluded. The workshop will be a hands on coding demonstration. The notebooks include additional practice exercises.
- analysis sub-directory
- Complete Jupyter Notebook
- Jupyter Notebook with "TODO" or in-session code boxes for demonstration.
License information:
- Some of the data and exercises used are under the Copyright of Software Carpentry and are made available under the Creative Commons Attribution license (CC BY 4.0).