WESTPA Workshop 2024 Tutorial Files

https://www.github.com/westpa/westpa-workshop2024-tutorials

A repository with WESTPA Workshop 2024 Tutorial Files

Companion software documentation

• WEDAP : For Weighted Ensemble Data Analysis and Plotting
• LPATH : Linguistics Pathway Analysis of Trajectories with Hierarchical clustering
• westpa.analysis : An API to facilitate the analysis of WESTPA simulation data
• msm_we : For building haMSMs of your WE simulation data

Quick Start Guide

• Video Guide: https://youtu.be/iU_cUbZDvfU

Logging in

1. Go to https://jupyter.crc.pitt.edu

• Login with your Pitt ID/Password
• Click "Start Server"
• Select the "WESTPA 12-core 6 hours"

Setting up files and stuff

2. Open a terminal and run the following:

• git clone https://github.com/westpa/h2p-quickstart
• source h2p-quickstart/run_bash.sh
• Refresh your browser page
• If Firefox, make sure Enhanced Tracking Protection is off (little shield icon next to URL)

Activating environment

3. After everything is done, you should be in $TMPDIR/westpa-workshop2024-tutorials

• A virtual environment called westpa-workshop2024 is made in ~/
• To use venv, select the correct kernel (Top right of Notebook) or run source ~/h2p-quickstart/activate_env.sh (Terminal)

Notes:

• Everything in $TMPDIR will be deleted when your session terminates (TIMEOUT, SLURM job deleted/canceled and/or by clicking “Stop my server” on the CRC website)
• You can reconnect even when your browser disconnects (nothing deleted)
• Your environment (built in ~/) will be preserved. Run source ~/h2p-quickstart/activate_env.sh (Sets environment variables and activates environment: westpa-workshop2024/bin/activate, clones this repository into $TMPDIR if doesn't exist).
• If the kernel is acting weird (can't import things even after kernel restart), just stop your server and restart. (File --> Hub Control Panel --> Stop My Server). Run source ~/h2p-quickstart/activate_env.sh to reclone the repository + activate environment.

• https://pitt.zoom.us/j/94041061817 • Meeting ID: 940 4106 1817 • Passcode: 12345

• Backup:

• Run on Google Colab: https://colab.research.google.com/
• File -> Open Notebook, paste GitHub Link. Select Notebook.
• Notebooks: https://github.com/westpa/westpa-workshop2024-tutorials