Show threadChristian Meesters4d ago

Which new features did I like the most?

Well, there are so many, it merits a preprint for which @egonw already lend tremendous support.

Anyway, here are my favourites:
- #Snakemake tracks all #metadata during the workflow execution. This caused many(!) file access requrests. Now, we have a SQLite-DB for that purpose, thereby lifting quite some overhead.
- containerizing workflows to a Dockerfile was possible for long time. With "--containerize apptainer" there is direct support for #apptainer
- when a workflow is aborted abruptly it cannot delete its lockfile. Now running `--unlock` will not require calculating the DAG any more.

Oh, there is much, much more. But the Changelog is already linked.

#SnakemakeHackathon2026

Ricardo Barros LourençoFeb 12
For those doing #HPC #DL model trainings, I need some suggestions. I want to use #horovod in a multi-gpu, multimode setting, but using #Apptainer (or #Docker) containers, due to cluster policy issues. Any reference to share? Issue here: github.com/horovod/horo...
Reference for multigpu HPC model training using docker /singularity · horovod horovod · Discussion #4316

Hi everyone! I'm looking for a reference implementation. In my situation, I want to run a multinode, multigpu model training, based in containers (preferably Singularity, but Docker can be ok). It'...

GitHub
Galaxy-Team der Uni FreiburgOct 16

Galaxy can be adjusted for sensitive data.
In the Netherlands, a GDPR-compliant Galaxy clone runs in an isolated network, converting Toolshed tools to Apptainer containers—secure, auditable, and reproducible.
Read more: https://galaxyproject.org/news/2025-01-20-esg-w-p5/

#UseGalaxy #GalaxyProject #UniFreiburg #EOSC #EuroScienceGateway #SensitiveData #GDPR #PrivacyByDesign #ReproducibleResearch #Bioinformatics #Apptainer #DataGovernance #Netherlands

Galaxy instance for sensitive data running in isolated network environ

GDPR-compliant Galaxy clone in isolated environment

Show threadchrisOct 15
@gnulinux Danke für den podcast zu #Apptainer :) Gab mir als früher intensiver Nutzer von #hpc einen informativen Einblick, was aus Singularity entstanden ist, und zu den aktuellen Möglichkeiten mit containern und wissenschaftlichem Rechnen 
Jens HannemannJul 19, 2025

My head hurts. Doing a deep-dive into containerization/VM with #Jenkins. So many options. I think I'll give #LXD a shot. But frankly, since my #OpenMPI program is already containerized via #Apptainer, I'll just go ahead and build on the (fairly powerful) Jenkins host for now, just to get the pipeline built as a proof of concept.

Time for an adult beverage.

N-gated Hacker NewsJun 26, 2025
🎩✨ Behold, the marvel of Apptainer: the magical name change from #Singularity that will revolutionize your Linux container universe by... being exactly like every other container system but with more labels. 🌟🔒 Rejoice as your software components remain safely ensconced in their digital dungeons, as you navigate the labyrinthine #GitHub to inspect your secured, portable future. 🤖🔍
https://apptainer.org/ #Apptainer #LinuxContainers #SoftwareDevelopment #HackerNews #ngated
Apptainer - Portable, Reproducible Containers

Apptainer is an open source container platform designed to run complex applications on high-performance computing (HPC) clusters in a simple, portable, and reproducible way.

Hacker NewsJun 26, 2025

Apptainer: Application Containers for Linux

https://apptainer.org/

#HackerNews #Apptainer #Application #Containers #Linux #Technology #OpenSource

Apptainer - Portable, Reproducible Containers

Apptainer is an open source container platform designed to run complex applications on high-performance computing (HPC) clusters in a simple, portable, and reproducible way.

Show threadJens HannemannJun 10, 2025
@beardedtechguy Doing some literature review for a grant application and trying to figure out how to do SCIF apps in #Apptainer. They're jackhammering the hell out of the pavement in front of my office, so I sought refuge in the student center's Starbucks.
Show threadYann Büchau May 31, 2025
#Python #poetry (and #uv I guess) is NOT a comprehensive tool to pin your environment! It is JUST a tool to help you manage some downstream Python packages, that's it. Use something more powerful like  #nix flakes or #apptainer​s or whatever floats your boat to do proper pinning of an environment - where you can pin your package manager itself.
Show threadJens HannemannMay 27, 2025

@beardedtechguy Welcome back! And I guess congratulations are in order

Grading and accreditation work are done here, too, for now. I’m currently picking up my NASA work again, building an #Apptainer container to be shipped to Oxford University. Also getting ready to upgrade my #HamRadio license and working on improving my wireless communications class for next semester.