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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Getting "buffer overflow detected" when trying to run NVIDIA FleX

I have been using Singularity 2.6 for a while and recently upgraded my Singularity to 3.0 (I cannot upgrade to 3.0.3 for technical reasons). Using Singularity 3.0 I build my new container with the same exact definition file that I used to build my…
Amir
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Capturing log files generated by cmake within singularity image before the image cleans up after failed build

I'm building an application using a Singularity (v. 2.5.1) recipe file. At some point it fails during the build, cmake fails and writes a errors to a log file within the singularity image. To build the image : sudo…
irritable_phd_syndrome
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How can I run docker image using singularity?

I would like to run a docker image with singularity (I have never used either). The person who made the docker image suggested to locate the terminal shell to the location where the files (that are used as input for the docker image) are located and…
Pivi
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How to start a VM in a Singularity container?

So I want to spit up a Windows.iso I have on a cluster node using Singularity images. I tried VirtualBox yet got this exception: ingularity virtualbox:~> virtualbox WARNING: The vboxdrv kernel module is not loaded. Either there is no module …
DuckQueen
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how to detach singularity container gracefully?

Depending of the type of container you use C-p C-q or C-ad works most of time but does not seems to make the trick to detach the container gracefully.
aurelien
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Singularity - Centos7 - Permission

i use singularity on Centos7 system, but i block on incomprehensible like-permission problem. (It's a centrifuge/recentrifuge container made by myself that perfectly working on Ubuntu system) command singularity exec…
DalinDad
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Segmentation violation in Singularity Container with matlab

For deployment on a cluster i am packaging a academic software called leverjs inside a Singularity container. It comes with prebuild Matlab packages that get run from the software. I have installed the Matlab runtime R2017b, leverjs and all…
cwlkr
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Tab completion inside singularity bash shell

I am using a singularity container created from a docker ubuntu:xenial base image. When I get into the shell using this command - singularity shell --bind /path/to/inputs:/mnt3,/path/to/outputs:/mnt2 /singularity_docker_xenial_image.img 1) the tab…
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ERROR : Base home directory does not exist within the container with Singularity container

I have built a sandbox singularity container on a server where I have full permissions: sudo singularity build --sandbox myimage myrecipe. I moved it to another server. When I run: singularity shell myimage I get access to the shell. But, when I…
Monica Heddneck
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Singularity & Snakemake - MissingOutputException

I am combining Singularity & Snakemake to create a workflow for some sequencing data. I modeled my pipeline after this git project https://github.com/sci-f/snakemake.scif. The version of the pipeline that does not use Singularity runs absolutely…
dddxxx
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Singularity ERROR : Failed to mount image in (read only): Invalid argument

I try to build a singularity image from a docker image located on dockerhub. singularity build pcgr.simg docker://sigven/pcgr:0.5.3 Then when I try yo execute it : singularity exec pcgr.simg ls It gives me this error : ERROR : Failed to mount…
Nicolas Rosewick
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meteor specify working directory in container

I'm trying to install a meteor application inside a container (singularity), but when I start the application it wants to write to a read only part of the image. Is it possible to specify a working directory different from the application directory?…
landge
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Necessary libraries for openMPI and Singularity software containers?

Question For deployment of singularity software containers on HPC systems, is it better to copy from host, bind to host, or install during bootstrap relevant HPC libraries into the container? If strategy 1. or 2. are generally recommendable, how…
Niels
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Singularity image size and internal disk usage ( du ) mismatch

I wanted to ask for clarification regarding disk usage ( du ) within a singularity image and the apparent mismatch I'm seeing. For example: If I list the container image information: ls -s --block-size=M container.sif 428M container.sif The image…
drrio
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Failed to create user namespace

I installed singularity and nextflow in a docker image, I wanted to launch the singularity pcm image, with this command : nextflow pcm.nf --allow-setuid --in example/example_proteome.faa --out result -w work/ -with-singularity pcm_202010.img Please…
SAAD
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