Quick Start#
This page is under development
Tip
For using MolSSI-AI Container Hub, a basic familiarity with Docker or Apptainer will be helpful but not necessary. Make sure you take a glance at the Installations page.
Check the Docker documentation if you are unfamiliar with the Docker. The documentation offers a nice tutorial series to get you up and running, quickly.
Structure of MolSSI-AI Container Hub#
The Molssi Container Hub provides three ingredients for each containerized software:
Image recipie
Container repository
Image catalog
Let’s focus on a specific software, say, MOPAC to see how the aforementioned ingredients come into play.
In order to be able to use MOPAC, one normally needs to install it on the host machine first. This can be done either by building MOPAC from the source repository or via graphical installer. One can also use Conda or Fedora package managers or download MOPAC from Google Play Store. Each route has its complexity and might be suitable for one operating system or another.
One of the benefits of using Docker or Apptainer is that once you have either of them on your machine, you are set to use any containerized software including those listed in the MolSSI Container Hub without having to install anything else or try figuring out and meeting their dependencies.
Image Recipes#
For each containerized software, including MOPAC, we provide an image recipe which tells you how we build the software inside an isolated environment (container). For simplicity, think of containers as an entity similar to a portable virtualenv or Conda environment and the image recipe similar to an environment YAML file. Since the software is isolated in its own filesystem, you can run it on a variety of operating systems in a reproducible manner.
Tip
Once you are comfortable with Docker, you can write your own image recipes or fine-tune those available from the MolSSI Container Hub towards your needs.
Container Repositories#
Container repository is a place we build and then register our ready-to-use containers on. Container repository is an entity similar to PyPI which is a repository for software written in Python: you can search through the repository, find your software and fetch it into your system to use using a command such as pip install …. There can be a variety of container repositories within a container registry. Docker Hub is an example of a container registry and the one we use it to publish our containerized software. You can use the following command to fetch the latest version of MOPAC image into your machine
docker pull molssi/mopac220-mamba141:latest
Once you have downloaded the image on your machine, you can use it via the following command
docker run --rm -it molssi/mopac220-mamba141:latest /bin/bash
which creates a temporary Docker container and allows you to get access to it through an interactive
PuTTY bash session. Think of this step as running a conda activate <env> command. You can now
work with your terminal interactively as if you have MOPAC installed on your system. Just run a
mopac --version command to test it.
Note
The docker run command will use your existing docker image to create the temporary environment
for you. If the image does not exist on your machine, the docker run command will fetch the
image for you from the repository before running the container. Once you exit from the container
environment, it is automatically destroyed like it never existed!
Tip
If you want to retain your environment, you can remove the --rm flag from your run command.
Image Catalogs#
Image catalogs are auto-generated documentation pages for all information you need about a containerized software: the developers, the source repository, the links to the container regiestry, image recipes etc. As an example, you can see in the MOPAC catalog that we have also included the Docker commands that you will need to pull/run the containers from their repository.
Thus, when you want to use any containerized software listed on the MolSSI Container Hub, the fastest way might be to just go to the documentation page, search for your favorite containerized software, nativate to its catalog page and copy-paste the Docker command in a terminal to use the software.