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Installing Conda packages more quickly using Mamba

The ITSR support team often receive tickets from Conda users concerned that creating environments and installing packages is taking quite a long time. Now we have moved to Miniforge exclusively for all Conda usage on Apocrita, the Mamba libsolver is available for all package installs.

What is Mamba?

Anaconda traditionally used conda as its package manager, but over time it became quite slow at resolving dependencies when installing packages. mamba is a re-implementation of conda written in C++ offering the following benefits:

  • parallel downloading of repository data and package files using multi-threading
  • libsolv for much faster dependency solving, a state of the art library used in the RPM package manager of Red Hat, Fedora and OpenSUSE
  • core parts of mamba are implemented in C++ for maximum efficiency

At the same time, mamba utilises the same command line parser, package installation code and transaction verification routines as conda to stay as compatible as possible.

Why Mamba?

Put simply, in a lot of cases mamba is a lot faster at installing packages when compared to conda:

Mamba vs Conda

Installing packages with Mamba

Do not use a login node for creating Conda environments

Creating a Conda environment requires a reasonably large amount of time and memory. Do not use a login node for creating a Conda environment. Please use an interactive qlogin session.

Environment creation is single-core, so 1 core for 1 hour with 8GB RAM is recommended for following the example below:

qlogin -l h_vmem=8G -l h_rt=1:0:0

A popular package with Apocrita users is busco. Using mamba instead of conda, busco takes less than five minutes to install.

So, to use mamba to install busco:

1) Load the miniforge module:

module load miniforge

2) Create a new Conda env (I've called mine busco but it can be called anything you like):

mamba create --quiet --yes --name busco

3) Activate the environment:

mamba activate busco

4) Install busco (version 5.8.2) using mamba:

mamba install bioconda::busco=5.8.2

mamba will now rapidly pull all required dependencies and ask you to confirm the package installation list (which you can do by typing y and pressing Enter). The installation should then complete within just a few minutes, and busco will be available in your env:

(busco) $ busco -v
BUSCO 5.8.2
(busco) $ busco -h
usage: busco -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]
...

Conclusion

You can find more information about mamba on the project's official docs page, as well as on the QMUL Miniforge docs page.

We hope you find these tips useful. As usual, you can ask a question on our Slack channel (QMUL users only), or by sending an email to its-research-support@qmul.ac.uk which is handled directly by staff with relevant expertise.

Title image: Generated using Stable Diffusion
Comparison video: Taken from the Anaconda Blog