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...
#Apptainer
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
@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 :awesome:
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.
🎩✨ 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: Application Containers for Linux
#HackerNews #Apptainer #Application #Containers #Linux #Technology #OpenSource
@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.
#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 :nixos: #nix flakes or #apptainers or whatever floats your boat to do proper pinning of an environment - where you can pin your package manager itself.
@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.
@cliffwade Morning, Cliff. We're getting a new roof as we speak. Hopefully will be done by 6pm tonight. I’ll be shipping some NASA code via #Apptainer to Oxford University after tracking down some bugs in both apptainer and the code itself. I'll spend the weekend studying up a bit to upgrade my #HamRadio license and thinking about how to improve my wireless communications class for next semester. There will be the occasional beer sprinkled in for relaxation.
Building an #Apptainer container for our colleagues in Oxford. The task is made much more pleasant by the awesome weather and a bottle of #Jever Pilsener. It’s very nice outside sitting on the deck.
Today I tried out #AMD #Instinct #MI300a for my existing Deep Learning pipeline. Good news: It worked out of the box. Bad news: For some reason it could not beat my local #Nvidia #1080ti...
After trying all sorts of #ROCM installation methods via prebuild wheels, #apptainer images etc I tried #nanogpt by @karpathy and sure enought: The gpt code ran approx 2x faster than on a #a100 ... I hope that this is due to my programming skills. Not AMD prefering #transformers over #CNNs ...
Apptainer で OpenFold を実行してタンパク質の立体構造予測を試してみた
https://dev.classmethod.jp/articles/getting-started-with-openfold-using-apptainer/
#dev_classmethod #Bioinformatics #Amazon_EC2 #AWS #Apptainer
guix crash course
#ThisMonthInFluiddyn - Nov 2024 edition
* #FluidDyn, #FluidSim, #FluidImage now works with #numpy 2 and #mpi4py 4.0.
* #Spack packaging recipes
https://foss.heptapod.net/fluiddyn/fluiddyn/-/tree/branch/default/misc/spack?ref_type=heads
* #Apptainer and #Guix packaging for FluidSim
https://foss.heptapod.net/fluiddyn/fluidsim/-/tree/branch/default/doc/apptainer?ref_type=heads
* Basic support for #Jax is part of #Transonic with v0.7.x
* #FluidImage v0.5.x has a number of improvements, such as work towards matching #UVmat (the MATLAB #PIV suite), new executors and a command `fluidimage-mean`
Apparently you can apptainer/singularity build docker-daemon://some-image to force a sif container to be built from your local docker installation rather than pulling it from the internet!
In the rare case when you have both docker and apptainer on the same machine, anyway.
Do you want to run the #GROBID PDF-to-#TEI conversion library/server with #Apptainer, for example for #ReferenceExtraction? There was a problem converting the #Docker image, but here's how to solve the problem: https://github.com/kermitt2/grobid/issues/1150#issuecomment-2350942263
The challenge today is to make #genAI converting a Dockerfile to an Apptainer/Singularity file.
I think I could abuse it quite heavily 😅
#HPC #SLURM #apptainer #singularity #Docker #dockerfile #challengeaccepted #devops #datascience #OpenScience
Apptainer - Docker der Wissenschaft
Zur Replikation und Kapselung von Laufzeitumgebungen ist Apptainer die Lösung innerhalb der Computerwissenschaft.
#Apptainer #Wissenschaft #Linux #Replikation #Container #Docker #Linux
@mdziemann Nice! Consider exploring #Apptainer , it's compatible, the images are read only, and do not require root (essential on scientific computing clusters) https://apptainer.org/
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