singularity
9 posts
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Running AlphaFold3 and OpenFold3 protein-ligand structure prediction on SDSC Expanse
I built two self-contained, reproducible projects that run realistic (non-toy) protein structure prediction on a single SDSC Expanse GPU node: one with DeepMind AlphaFold3 (via nf-core/proteinfold) and one with the fully open OpenFold3 (MCL1 protein-ligand ensemble).
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Building Singularity containers with Conda environments from requirements.txt
This post introduces a method for building Singularity containers that include a Conda environment based on a requirements.txt file. This approach provides a reproducible and portable environment for any Python project.
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Build and host Singularity containers on GitHub
I present a demo repository configured to build Singularity containers using Github actions and then host them using the Github container registry:
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Singularity on Expanse tutorial
As one of my last tasks in XSEDE, I updated and improved the tutorial about running Singularity containers in the HPC system Espanse at my institution the San Diego Supercomputer Center.
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PEARC18 paper on deploying Jupyterhub at scale on XSEDE
Bob Sinkovits and I are presenting a paper at PEARC18 about: "Deploying Jupyter Notebooks at scale on XSEDE resources for Science Gateways and workshops"
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Updated Singularity images for Comet
Back in January 2017 I wrote a blog post about running Singularity on Comet. I recently needed to update all my container images to the latest scientific python packages, so I also took the opportunity to create both a Docker auto-build repository on DockerHub and a SingularityHub image.
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How to modify Singularity images on a Supercomputer
Singularity allows to run your own OS within most Supercomputers, see my previous post about Running Ubuntu on Comet via Singularity
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Deployment of Jupyterhub with Globus Auth to spawn notebook on Comet in Singularity containers
Follow the instructions at to build images from the ubuntuanacondajupyterhub.def and centosanacondajupyterhub.def definition files, or use the containers I have already built on Comet:
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Run Ubuntu in HPC with Singularity
If your answer to any of those question is yes, read on! Otherwise, well, still read on, it's awesome! Singularity