CellModeller is a multicellular modelling framework created by Tim Rudge, PJ Steiner, and Jim Haseloff, University of Cambridge. This docker hub image is an attempt to simplify the process of deploying the graphical user interface of CellModeller with a very few steps. The image has been built by extensively modifying the nvidia/opengl ubuntu 18.04 docker hub image with several other essential packages. Currently this works only with NVIDIA GPUs but AMD GPU support is also a work in progress.
Make sure you have installed the Nvidia Drivers(>=v390) on your Linux system. Here is a distribution wise coverage. You would also require the Nvidia Runtime Container Toolkit. The installation steps are described here based on different distros.
Install Docker. On Ubuntu, you can run the following steps:
sudo apt update
sudo apt install docker.io
After installation, run:
sudo groupadd docker
It may already exist after Docker was installed. Nevertheless, add your Linux username to the group:
sudo usermod -aG docker $USER
Reboot the system.
Make sure you can run Docker as non-root user:
docker run hello-world
Run Docker on every boot so you wouldn't need to do that whenever you run CellModeller:
sudo systemctl enable docker
The following command has to be run on the host system's terminal:
mkdir -p ~/cellmodeller/data
You will be able to access this inside your CellModeller container as /data.
Permit your Linux username on the local machine to connect to the X windows display with the following command:
xhost +local:username
With the following command you can now directly run the GUI in one go:
docker run --rm -it --gpus all -v /tmp/.X11-unix:/tmp/.X11-unix -v ~/cellmodeller/data:/data --name cmgui avimanyu786/cellmodeller:4.3.1
To check the dev branch, use the dev tag instead of 4.3.1 in the above command.
The first run will take some time as it would download the new image. If you close the GUI window after it finally launches, running the cmgui command in the container's terminal can bring it up again.
For batch mode, use python CellModeller/Scripts/batch.py <model file name>. You can launch them from /data through the container which is nothing but /home/username/cellmodeller/data on your host system.
In case you have more than one GPU on your system and want to run CellModeller on a specific GPU device, you would have to change the --gpus all flag to --gpus 0, 0,1 and so on being the specific Nvidia GPUs.
When you want to quit the session, simply type exit in the container's terminal and you will come back to your host terminal session.
Remove the previously allotted permissions with:
xhost -local:username
Reown the root owned directories inside ~/cellmodeller/data as your Linux username with:
sudo chown -R username:username ~/cellmodeller/data/
This container was built with several attempts, tweaks and modifications. Hope this container image makes it much easier for you to deploy, use or develop the framework.