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.
365 questions
0
votes
0 answers

Pick a specific CUDA version to use inside Singularity 3.6 container

I am working on a POC of running tensorflow container via Singularity 3.6. I have a requirement that the user may need to pick an older version of CUDA which are available in a customized location rather than the system installed one. I read the 3.6…
klin
  • 9
  • 1
0
votes
1 answer

Run conda 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
  • 184
  • 2
  • 10
0
votes
1 answer

Installing Anaconda On Linux If Miniconda already installed

I am using a CentOs Distribution of Linux and have miniconda already installed along with conda environments that I created with it. I am trying to install anaconda now. Do I have to uninstall miniconda first? I have some environments that I…
stjil
  • 11
  • 2
0
votes
1 answer

Different behavior of Singularity image on different machines?

I try to run my python3 based Singularity image on a remote machine, but I get the following error that I do not get with other machines: singularity exec --nv --no-home --bind data/:/data/ image/ scripts/train.sh + singularity exec --nv --no-home…
arthur.sw
  • 11,052
  • 9
  • 47
  • 104
0
votes
1 answer

Problem to extend a Singularity image from an existing docker image

I try to extend the pytorch docker image with my definition file nnunet.def: Bootstrap: docker From: pytorch/pytorch:1.4-cuda10.1-cudnn7-runtime %post git clone https://github.com/NVIDIA/apex cd apex pip install -v --no-cache-dir…
arthur.sw
  • 11,052
  • 9
  • 47
  • 104
0
votes
1 answer

Singularity Recipe: How to access executable within container?

I am a beginner with Singularity. What I want to achieve in the long run: I have a programming project with a long lists of dependencies, and I want to be able to give the program to other people in my company without there being bugs caused by…
Aziuth
  • 3,652
  • 3
  • 18
  • 36
0
votes
1 answer

Error with pip while building singularity image

I'm trying to build a .simg file from a .recipe. In the recipe I upgraded pip. In the building process I get following error after downloading pytorch: can someone tell me what's wrong with pip? Collecting torch==1.5.1 Downloading…
goodL
  • 1
  • 1
0
votes
2 answers

squashfs error when running singularity after Ubuntu upgrade

Overview: I am working with code in a singularity image on a machine running Ubuntu 18.04. It was working (well, I was debugging the code) as of Tuesday evening on machine A. I ran an update and as of the next day any attempt to run any singularity…
user128029
  • 53
  • 1
  • 7
0
votes
1 answer

Escaping filename spaces with singularity %files directive

I have a file with spaces in its name that I want to copy to my container: %files /tmp/some file with spaces /usr/local/bin I have tried using 1 or 2 backslashes paired with single or double quotes, but the full filename is not recognized. …
HoosierDaddy
  • 720
  • 6
  • 19
0
votes
1 answer

Execute a shell command outside of a sandbox while in a sandbox

I'm using singularity to run python in an environnement deprived of python. I'm also running a mysql instance as explained by the IOWA state university (running an instance of mysql, and closing it when done). For clarity, I'm using a bash script to…
0
votes
1 answer

Running windows .exe in Linux environment (other alternatives to "Wine" and VM)

I have this problem I was trying to solve for quite some time now: I have windows executable that I call from a Python script using (subprocess.run()) as a way of automating my simulations. These simulations take days to complete, so in order to…
user10700438
0
votes
3 answers

How to utilize host caches in a singularity build?

I'm looking for ways to optimize the build time of our singularity HPC containers. I know that I can save some time by building them layer by layer. But still, there is room for optimization. What I'm interested in is using/caching whatever makes…
Martin Pecka
  • 2,953
  • 1
  • 31
  • 40
0
votes
1 answer

singularity run error: No valid /bin/sh in container

I have a singularity image and convert the sig file to a sandbox format. After changing some scripts, a modified new sig file was rebuilt with a sandbox. But when I run the sandbox or sig image, error report like below: ERROR: No valid /bin/sh in…
Ren
  • 21
  • 4
0
votes
1 answer

Running docker pipeline in snakemake using singularity without specifying singularity exec docker://

I'm trying to tie scripts from an existing pipeline on docker into my snakemake pipeline. I have the docker pipeline set up using singularity and it works. For instance, singularity exec docker://mypipeline some_command.sh file.bam…
Delete
  • 11
  • 2
0
votes
0 answers

Snakemake: Singularity parameters --home and --bind set by default but disallowed on HPC

I have already posted this as an issue on Github at https://github.com/snakemake/snakemake/issues/279 but haven't got any response yet. I hope to find help here. Version I am using the following versions on our HPC cluster: Snakemake c5.4.4…
Matthias Munz
  • 3,583
  • 4
  • 30
  • 47