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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determine the time zone when building a singularity image

I am trying to build an image using singularity. in one step I have to run a R script to do so, in the recipe file I need to install R and I did using the following command: apt-get install -y systemd systemd-sysv gdebi-core procps libssl1.1 ed wget…
user10657934
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Singularity keeps getting errors when trying to install TF2

I am trying to make a new Singularity using a recipe but it keeps failing. I have it linked to my github so when I commit it it will automatically be built and compile so that part works fine. However it keep giving me an error like this. pip3…
MNM
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Missing required packages in Ubuntu 18.04 pcc64el

starting from IBM's PowerAI TensorFlow docker container I try building a singularity container with additional packages on my Power 9 (ppc64el plattform). Using apt to install packages I get a lot of missing packages with prevents me from installing…
Deyid
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How to provide singularity images where users can add a custom set of software from a catalogue provided by us

We want to improve the reproducibility of the analyses at our institute. To this effect, we contemplate on implementing a system based on Singularity. The idea is that at the beginning of the analysis, the user can choose a machine configuration…
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Vocabulary for a script that is expected to produce the same output no matter where it is run

I'd like some advice on what vocabulary to use to describe the following. Having the right vocabulary will allow me to search for tools and ideas related to the concept I'd like to say a script is SomeWord if it is expected to produce the same…
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Singularity Could not virtualize file system namespace: Operation not permitted

I'm trying to run Singularity container inside Docker container from following Dockerfile (command to build: docker build -f ./Dockerfile -t rocker-singularity .): FROM rocker/rstudio-stable:3.5.1 RUN apt-get update && apt-get install -y \ gcc…
Taz
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How to replace args from docker to singularity?

I am trying to pull a docker image but have to use singularity. How can I do this? Here is the script I am running. cp -rp ~/adversarial-policies/ $SLURM_TMPDIR cd adversarial-policies/ singularity pull…
cstewa26
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Is it possible to build containers from within a container on a system where I am not admin?

I would like to build singularity recpies locally, rather than relying on Singularity hub and wasting my limited daily build quota on fixing stupid syntax errors. However, I am not admin on the machine where I will be running the containers. I…
hbraunDSP
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Download Singularity images for local builds

I have a system that has no connection to the internet but does have local mirrors of the OS package manager repos, PyPI, Conda, etc. I'd like to build Singularity images on this system. It looks like the localimage bootstrap agent was designed…
Daniel Standage
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Building singularity image: "Failure while installing base packages"

When trying to build the Singularity image for this package: https://bitbucket.org/MAVERICLab/vcontact2.git I get: {cut} I: Configuring login... I: Configuring adduser... I: Configuring apt... I: Configuring util-linux... I: Configuring mount... I:…
Andrea T.
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nvidia-smi not working after installing driver in a singularity container

I use singularity and I need to install a nvidia driver in my singularity container to do some deep learning with a gtx 1080. This singularity image is created from a nvidia docker from here: https://ngc.nvidia.com/catalog/containers/nvidia:kaldi…
Antoine V
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Singularity exclude some directory

singularity -B is used to mount some directories so that those directories can be used inside the singularity container. However, there are some directories that I would like to exclude. For example, I would like to use singularity shell -B /foo/…
Tong Qiu
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Compiling using gcc compiler inside docker/singularity image from outside

I want to use gcc in docker/singularity image to compile a program. Using local gcc, I use gcc tc.c -I PATH_TO_LIB without any error. To use the gcc in the image, I use the following command line. singularity exec gcc_5.1.0.sif gcc tc.c -I…
Amin
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How to use change directory CD and source commands in a singularity recipe

I am trying to create a singularity container for simulating the Emika Franka robot. For this, I need to use catkin to build the moveit examples and the panda_config from the GitHub repositories. However, I keep running into some troubles because of…
rickstaa
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Singularity-container: how to implement significant changes to source in setup?

The aim is to create a singularity container with Feynhiggs/Higgsbounds/HiggsSignal/2HDMC/SusHi running together peacefully. They are a powerful combination, but fiddly to set up. I would like to be able to offer this container as a way to replicate…
Clumsy cat
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