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Building Conda environments in Apptainer

Apptainer is a containerization technology forked from Singularity. It's free, open source and compatible with Docker and Singularity images. This has the advantage of keeping all of your Conda environment programs in one convienent file and avoiding conflicts and problematic conflicts with other Conda environments on the same machine.

Apptainer containers are built from a definition file, let's start with this example below:

Bootstrap: docker
From: continuumio/miniconda3

%post -c /bin/bash
    # Update and install system wide software here
    apt-get update -y
    # if you need apt packages install them here
    # apt-get install <package>

    # install conda stuff here, numpy just for example
    conda install -y numpy

%environment
    # Ensure Conda environment is in the PATH
     PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH"
     source /opt/conda/etc/profile.d/conda.sh
     conda activate base

Save this file to MyCondaEnv.def on a machine with Apptainer installed. HPC1 is a fine place to do this as we have Apptainer available there for building images. You can also do it on your local machine and upload the resulting SIF file to HPC1 at a later date.

Now is time to build the image:

apptainer build --fakeroot MyCondaEnv.sif MyCondaEnv.def

This may take a minute or two. 

After it has successfully finished you'll be left with the MyCondaEnv.sif file. This is where the actual Conda binaries and packages are stored. Once created it cannot be modified and has to be rebuilt if you want to add a new package. 

Now you can run the Apptainer image and interact with your data in one of two primary ways. Firstly through apptainer exec:

apptainer exec MyCondaEnv.sif conda list

Where everything after the SIF file will be run inside the container. This prints a list of installed conda packages. Alternatively you can use apptainer run and it will drop you into a shell on the container.

[lh59281@hpc2 ~]$ apptainer run MyCondaEnv.sif
(base) ls
AstroInteractives  Pictures           apptainer_test.sh                gauss_test.log       jupyter2                   jupyternoRoot.def  other_data       processing        test_mpi
Desktop            Public             conda.def                        gpu_test.bsh         jupyterhub.sqlite          lh59281_lambda     output-9604.log  shiny-server.def  test_mpi.c
Documents          Rstudionoroot.def  datascience-notebook_latest.sif  hello_mpi.bsh        jupyterhub_cookie_secret   lh59281_proj       output-9605.log  shiny-server.sif  test_torch.py
Downloads          Templates          error-9604.log                   hello_world.bsh      jupyterlab.def             lh59281_proj.      pc               slurm-9603.out
Music              Untitled.ipynb     error-9605.log                   hello_world_noa.bsh  jupyterlab.sif             miniconda.sif      pi.bsh           slurm-9608.out
OpenFOAM           Videos             gauss_test.com                   jupyter-astronomy    jupyternoRoot-startup.def  ondemand           pi.c             slurm-9609.out
(base)

 

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