Questions tagged [singularity-container]

For questions about programmatic problems relating to the Singularity scientific computing container solution.

Singularity is a container solution created by necessity for scientific and application driven workloads. Singularity provides four primary functions (taken from the preceding link):

  1. Mobility of compute: the ability to define, create and maintain a workflow and be confident that the workflow can be executed on different hosts, operating systems (as long as it is Linux) and service providers.
  2. Reproducibility: once a contained workflow has been defined, the container image can be snapshotted, archived, and locked down such that it can be used later and you can be confident that the code within the container has not changed.
  3. User freedom: users can define their own working environment and literally copy that environment image (single file) to a shared resource, and run their workflow inside that image.
  4. Support on existing traditional HPC: Singularity supports existing and traditional HPC resources as easily as installing a single package onto the host operating system. Custom configurations may be achieved via a single configuration file, and the defaults are tuned to be generally applicable for shared environments.
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How to create an x server with Singularity

Overall, I am trying to render images using Unity on a remote cluster. The cluster does not have an X server; I don't have sudo permissions, or can start a Docker container, but I can start a Singularity container. My plan is to create a container…
guhur
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Build singularity image file from a singularity-vagrant-box

Everything is inside the title. I have a singularity vagrant box setup on my computing, and I'm looking for a way to generate a .sif (singularity image file) from it. Do you know if that is possible ? My vagrant-vm is on windows10. Any advice or…
Hedwin Bonnavaud
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File exists in Singularity container but produces No such file error upon exec

Despite being able to see a file within a container I'm not able to find it on Singularity -s exec. First, we will build the image and investigate the location of the Python script fasta_generate_regions.py: $ sudo docker pull…
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running `exec` programmatically from a bash script

I want to execute a command in various images. I use a simple for bash loop. for i in `ls *.sif` do singularity exec $i cat /etc/os-release done I expect the script to print the os-release information for ALL images in that directory. Instead,…
Amin
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How can I start a named instance of a container in Singularity?

I need to start many containers using Singularity. If I don't assign them a name, it will be difficult to keep track of them. I could store the correspondence between their IDs and what they do in an external file, but it's cumbersome. I need…
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