Installing DLC on HPC

0. Before you can do anything with the HPC, you'll need to set up your HPC accounts on Quartz

1. Log onto your favorite computer (e.g., quartz.uit.iu.edu)

   • Graphically: 

     1. go to https://red.uits.iu.edu

     2. Links to an external site.

     3. sign in with your IU username and password

     4. Double click on 'terminal' icon 

   • In a terminal

     1. Open a terminal

     2. ssh <yourIUusername>@quartz.uits.iu.edu

     3. Enter your IU password when prompted for a password

2. Create a link in your home directory to the where you'll be installing everything

   • [<yourname>@i51 Quartz]$ ln -s /geode2/projects/iu/BL-PBS-P426/2024-01-P426/$USER P426

3. Navigate to that directory

   • [<yourname>@i51 Quartz]$ cd P426

4. Prepare terminal to use Python

   • [<yourname>@i51 P426]$ module load python

5. Download a copy of DeepLabCut from github

[<yourname>@i51 P426]$ git clone https://github.com/DeepLabCut/DeepLabCut.git

5. • 
     

   • Links to an external site.

5. Create a Python virtual environment into which you will install DeepLabCut

   • [<yourname>@i51 P426]$ python -m venv ~/pvenv

6. Activate the virtual environment that you just created

   • [<yourname>@i51 P426]$ source ~/pvenv/bin/activate

7. Install the Jupyter Notebook package for Python

   • (pvenv) [<yourname>@i51 P426]$ pip install notebook

8. Install the video editing package ffmpeg

   • (pvenv) [<yourname>@i51 P426]$ pip install ffmpeg

9. Install deeplabcut itself with the gui and tensorflow packages included (** be patient, this step takes ~15 min)

   • (pvenv) [<yourname>@i51 P426]$ pip install deeplabcut[gui,tf]

10. Clean up and leave

    • (pvenv) [<yourname>@i51 P426]$ deactivate