- Download the Containers To download the containers from Docker Hub, use the following commands:
docker pull gimel12/aretomo:1.3.4
docker pull gimel12/aretomo:interactive
- Running the Non-Interactive Session To run the AreTomo container in a non-interactive session:
docker run --gpus all --shm-size=1g --ulimit memlock=-1 --ulimit stack=67108864 gimel12/aretomo:1.3.4
- Running the Interactive Session To run the AreTomo container in an interactive session:
docker run --gpus all -it --shm-size=1g --ulimit memlock=-1 --ulimit stack=67108864 gimel12/aretomo:interactive
- Connecting a Volume to the Container To connect a volume from your host machine to the container, use the -v option with the docker run command. This allows the container to access files and directories on the host.
For example, to mount the directory /home/user/data from your host machine to the directory /mnt/data in the container, use the following command:
For the non-interactive container:
docker run --gpus all --shm-size=1g --ulimit memlock=-1 --ulimit stack=67108864 -v /home/user/data:/mnt/data gimel12/aretomo:1.3.4
For the interactive container:
docker run --gpus all -it --shm-size=1g --ulimit memlock=-1 --ulimit stack=67108864 -v /home/user/data:/mnt/data gimel12/aretomo:interactive
In these examples:
/home/user/data is the directory on the host machine. /mnt/data is the directory inside the container where the host directory will be mounted.
Download Containers:
docker pull gimel12/aretomo:1.3.4
docker pull gimel12/aretomo:interactive
Run Non-Interactive Session:
docker run --gpus all --shm-size=1g --ulimit memlock=-1 --ulimit stack=67108864 gimel12/aretomo:1.3.4
Run Interactive Session:
docker run --gpus all -it --shm-size=1g --ulimit memlock=-1 --ulimit stack=67108864 gimel12/aretomo:interactive
Non-Interactive:
docker run --gpus all --shm-size=1g --ulimit memlock=-1 --ulimit stack=67108864 -v /home/user/data:/mnt/data gimel12/aretomo:1.3.4
Interactive:
docker run --gpus all -it --shm-size=1g --ulimit memlock=-1 --ulimit stack=67108864 -v /home/user/data:/mnt/data gimel12/aretomo:interactive
Assuming you have a folder /home/user/data on your host machine containing the pictures to be processed by AreTomo.
- Start the Non-Interactive AreTomo Container Start the AreTomo container with the necessary parameters and mount the data directory:
docker run --gpus all --shm-size=1g --ulimit memlock=-1 --ulimit stack=67108864 -v /home/user/data:/mnt/data --name aretomo-container gimel12/aretomo:1.3.4
In this command:
The -v /home/user/data:/mnt/data option mounts the /home/user/data directory on your host to the /mnt/data directory inside the container. The --name aretomo-container option names the container aretomo-container for easier reference. 2. Running Commands Inside the Container To execute commands inside the running container and process the data, you can use docker exec. Here’s an example of running a command to process the images in the /mnt/data directory:
docker exec -it aretomo-container /usr/local/bin/AreTomo /mnt/data
In this command:
The -it option allows for interactive processes (in case you need to provide input or view output directly). aretomo-container is the name of the running container. /usr/local/bin/AreTomo is the path to the AreTomo executable inside the container. /mnt/data is the directory containing the data to be processed.
Here’s a complete example guide:
Step 1: Start the Container
docker run --gpus all --shm-size=1g --ulimit memlock=-1 --ulimit stack=67108864 -v /home/user/data:/mnt/data --name aretomo-container gimel12/aretomo:1.3.4
Step 2: Execute AreTomo Inside the Running Container
docker exec -it aretomo-container /usr/local/bin/AreTomo /mnt/data