iCAT - Isolated CAT

A docker container for CogStack/MedCAT/HuggingFace development in isolated environments. This is meant for envs that are completely locked-out, everything has to be prebuilt and then moved. It contains the basic tools necessary to interact with the CogStack platform + GPU support + MedCAT + Transformers from HuggingFace.

How to run [with GPU support]

0. Clone the repo and open the destination folder (or run mkdir -p icat/models folder for mounting)
1. To run (and download) the container do:

docker run -t -d --name icat --hostname icat --user icat -p 8888:8888 --gpus all --mount type=bind,source="$(PWD)/icat/models",target=/home/icat/models --mount source=data,target=/data --mount source=projects,target=/home/icat/projects rattel/icat:latest zsh

2. If you do not want GPU support, remove the --gpus all and run
3. Connect to the container using docker exec -it icat zsh
4. Activate the environment source /home/icat/.venv/play/bin/activate
   • Jupyter: First set the password with jupyter notebook password and second, run using nohup jupyter notebook --ip 0.0.0.0 &. Now it will be available at <server_ip>:8888
5. If the container stops and you want to start it again, use: docker start icat

How to Build

1. Clone the repository
2. Run docker-compose -f docker-compose-build.yml build
3. Push to docker Hub or save to a file

Current status

• Starts from a pytorch/cuda image
• Basic ubuntu packages pre-installed
• Configuration for vim and zsh
• Base python requirements for CogStack/MedCAT/HuggingFace pre-installed
• Volumes for data, models and projects
• Open ports for jupyter notebooks (8888)
• Pre-downloaded GPTv2 and BERT models

This is very experimantal