Using Conda Env inside ozstar

Step 1

In Ozstar terminal interface write the following command to use mamba

  ml mamba

Step 2

By default, Conda places environments in the home directory in ~/.conda. As you create new environments, the home directory disk quota will be exhausted very quickly. To resolve this issue, we recommend changing where conda environments are created:

conda config --env --prepend envs_dirs /path/to/my/project/on/fred/.conda/envs
conda config --env --prepend pkgs_dirs /path/to/my/project/on/fred/.conda/pkgs

Step 3

Finally, create e new environment

conda create -n <env-name>

If you have a .yml file then you can use the following command

conda env create -f environment.yml

More about yml file

Using Apptainer inside ozstar

If you want to use apptainer, in that case, first you have to load the apptainer module by running the following command

ml apptainer 

If you want to access the container shell

apptainer shell your_apptainer.sif

if you want to create an instance of the apptainer then

apptainer instance start your-apptainer.sif your_instance_name

you can check all the instances using

apptainer instance list

To access an instance shell, run

apptainer shell instance://your_instance_name

to stop an instance

apptainer instance stop your_instance_name

To bind

apptainer instance start --bind $HOME/mydata:/data your_apptainer.sif your_instance_name