Apptainer is a container environment and a successor to Singularity containers as a part of a rebranding. Apptainer is part of the Linux Foundation and the management organization's website may be found here: https://apptainer.org/
Questions tagged [apptainer]
26 questions
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Apptainer on macOS
I would like to use apptainer for a specific program on my macOS. I have installed apptainer through lima. However, although apptainer is my path, I am still not able to use it.
This is how it looks like now in my…
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R-dependence error in using apptainer to build container
I am using apptainer to build a r-text package container in Ubuntu on a server. Anyone could help? My hardware is Mac pro M1 with MacOS 13.4 (22F66).
My build.def file is as follows. The container is based the docker Ubuntu image. And I am trying to…
AlexGu
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How to use sbatch with a docker container that holds a snakemake pipeline?
I am building a Snakemake pipeline that I am going to put in a container. I want users to be able to pull the container using Apptainer or Docker. I would also like users to be able to run the container locally or using SBATCH. I know that there are…
Sam H
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Apptainer installation with use Windows Subsystem for Linux (WSL)
I am extremely happy user of Windows OS 11 who needs to use Apptainer in my developer work. I am considering two options of apptainer installation/use in Windows:
using Git/VirtualBox/Vagrant/Vagrant Manager
using Windows Subsystem for Linux (WSL…
Andrzej Marciniak
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CuDNN error when running JAX on GPU with apptainer
I have an application written in Python 3.10+ with JAX that I would like to run on GPU. I can run containers on my local computer cluster using apptainer (but not Docker) which has an NVIDIA A40 GPU.
Based on the proposed Dockerfile for JAX I made…
Hylke
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Create Apptainer container with environment.yml without creating a new conda environment within container
Hi so I am trying to create a container with apptainer. The server hosts would like to prevent the creation of conda environments within a container.
However, I only have a environment file. Which would result in the creation of a new…
Janosch
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stdout stderr not captured from binary executed in singularity container
I have a complex HPC (openpbs 20.0.1, Ubuntu 18.04) workflow using a python subprocess to execute qsub which ultimately launches a singularity (3.9.9) container with the exec command to execute a binary with arguments. The complexity is driven by…
Chase Schuette
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Script in apptainer work for one user but stuck for other users in computing clusters
We tried to pull a docker from docker hub and use the apptainer to shell into it and run the script inside the shell.
However, only one user can run the script correctly but others will get stuck after setting the LD variables.
I've added the -X…
zhujh
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Running OpenCV inside Apptainer with GPU support
I'm trying to run a OpenCV application inside an Apptainer container, in a remote machine, passing the --nv flag for granting GPU support. But then I get this error:
import cv2
ImportError: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34` not…
Luiz Tauffer
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apptainer/singularity multi-stage build with different registries
I'm building an apptainer/singularity multi-stage recipe in a gitlab CI environment.
The first step of the recipe is built from an image hosted in a private registry, whereas the second built from an image hosted on dockerhub. Something like this:
#…
Michele
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Restrict network access from Apptainer/Singularity container
Is it possible with Apptainer/Singularity to restrict which network interfaces can be used from within a container?
In my specific use-case I want to allow access to the internet but block access to some SocketCAN interfaces that are available on…
luator
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