Questions tagged [singularity-containers]

Singularity is a container platform created to run complex applications on HPC clusters in a simple, portable, and reproducible way. Singularity is an open-source project, with a friendly community of developers and users. The user base continues to expand, with Singularity now used across industry and academia in many areas of work.

Singularity is a container platform. It allows you to create and run containers that package up pieces of software in a way that is portable and reproducible. You can build a container using Singularity on your laptop, and then run it on many of the largest HPC clusters in the world, local university or company clusters, a single server, in the cloud, or on a workstation down the hall. Your container is a single file, and you don’t have to worry about how to install all the software you need on each different operating system.

Singularity was created to run complex applications on HPC clusters in a simple, portable, and reproducible way. First developed at Lawrence Berkeley National Laboratory, it quickly became popular at other HPC sites, academic sites, and beyond. Singularity is an open-source project, with a friendly community of developers and users. The user base continues to expand, with Singularity now used across industry and academia in many areas of work.

More information at https://sylabs.io/.

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How to run a conda command inside singularity?

I would like to run a conda command with singularity. The command is: singularity exec ~/dockerimage.sif conda It yields an error: /.singularity.d/actions/exec: 9: exec: conda: Permission denied Here is my dockerfile: FROM ubuntu:20.04 ARG…
bmv
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strip could not create temporary file to hold stripped copy: cause of error unknown

I am trying to run a singularity container on a CentOS7 host, which contains an application with Qt5 dependencies. I am experiencing a error where libQt5Core.so.5 can not be used because of an incompatibility with the linux kernel version of…
Paidoo
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Singularity container best practice - install libraries inside or outside of container?

I am building a singularity container for my project. My project has a bunch of dependencies like python libraries and a simulator program. Should I install these libraries and the simulator program inside of the container, or should I download them…
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Singularity exec gives environment error when running python script, but the python script can be run interactively fine

When running these two commands sequentially in a terminal, singularity run /home/___/singularity_containers/singularity_container.simg bash python3 /home/__/__/___/src/python_file.py Everything executes correctly, but when trying to run this from…
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How to run singularity container and python code from within the singularity container in a shell script?

I am trying to start a singularity container and then run a python script from within that container. The commands work individually if I run them outside, but as soon as I put them in a shell script and run the shell script, the python script does…
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How to set a relative soft link using $SINGULARITY_ROOTFS in the setup part of the Singularity recipe file?

I'm trying to create soft link in the %setup section of the Singularity recipe file. If the link is relative, it does not work. For example: ln -s ${SINGULARITY_ROOTFS}../python2/2.7.5a ${SINGULARITY_ROOTFS}/usr/pkgs/python/2.7.5 It…
vesii
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