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 build docker image from singularity image

I am currently working on singularity and docker. I am running singularity for MPI environment. I want to use advantages of singularity for MPI but singularity files are very large. So after running the singularity image I want to convert it to…
alex
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R Draws Plots with Rectangles Instead of Text

I'm building a pipeline with snakemake and using conda and singularity environments to ensure reproducibility. I run into an error where the text on my plots is replaced by rectangles After experimenting with the pipeline on Linux and Mac systems…
Tomas Bencomo
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How to run a jupyter notebook using a singularity image?

I have built a singularity image (jupyter.sif) that contains the latest anaconda version and I want to use that to run a jupyter notebook. I would like to run something like this: singularity exec \ --bind /path/outside/image/:/path/inside/image/…
maos.a
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Snakemake Singularity with Local Resources / Questions about Snakemake with --use-singularity

I'm starting to experiment with using containers with Snakemake, and I have a question about what needs to be pre-build into the container and what doesn't. For example: I want to run a python script (stored in workflow_root/scripts/myScript.py,…
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Change singularity home directory to a folder within the container

Background I have a singularity container that was created from a docker image. The docker image has files that are meant to be in the user's home directory (e.g. in $HOME/.files). Because I don't know what the username will be, I put the files in…
alex_danielssen
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Singularity 3.6.2 Installation

I have problems with installation of singularity 3.6.2 in linux mint, I followed the instructions of https://sylabs.io/guides/3.0/user-guide/installation.html. I installed the dependencies and Go. Then I run the command for install the latest…
JocHwo
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Launching a Singularity Container Remotely using Visual Studio Code

I am aware that you can launch docker containers remotely in VSCode. Is it possible to do the same with singularity containers?
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How to change the default prompt in a singularity container

I am creating a Singularity image and I want to have a custom bash prompt, just like I can set a bash prompt as a normal user by setting the variable PS1 in my ~/.bash_profile. But, unfortunately, Singularity does something to enforce its own prompt…
akraf
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MPI in container without MPI on local host

Background: I have successfully created MPI-based applications within a Singularity container and executed them using the hybrid mode recommended by the Singularity documentation. This requires that I have a "compatible" version of MPI installed…
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Activating a conda environment in a singularity recipe

I'm new to singularity and I would like to activate a conda environment (myenv) within a singularity recipe in order to install a package into it (mypkg). I've read some related posts but the answers did not solve my problem although the questions…
RomB
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How can I use a python interpreter in a singularity/docker image in visual studio code

I want to be able to use a python interpreter inside a singularity image from visual studio code. It seems that all of the options to point VSC to python interpreters involve a direct path, but using python within an image requires a…
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Activate conda environment on execution of Singularity container in Nextflow

I am using Singularity containers to run commands from Nextflow workflow management system. I have a conda environment inside Singularity which I can activate when I shell into the container singularity pull…
bruce.moran
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Is it possible to run slurm commands within a singularity container?

I want to go into a container with singularity and then run slurm commands. For example: singularity shell docker://tensorflow/tensorflow:1.0.0-gpu-py3 then within it run the script that I do want to run my script: python tf_test.py the contents…
Charlie Parker
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Use singularity container as python interpreter in Visual Studio Code

I am connecting to an HPC environment through VScode remote ssh and would like to run python code directly in VScode for testing purposes. I would like to set the python interpreter to a singularity container which runs python upon execution. This…
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Is there a way to track singularity containers like "docker ps" without starting as singularity instance?

Is there a way to track running singularity container like "docker ps" ? or singularity logs any start/stop info in somewhere. I have tried the "singularity instance list" command but it doesn't work for the singularity container which doesn't start…
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