singularity-container | 易学教程

How to activate an Anaconda environment in a Singularity recipe

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问题 I am trying to create a singularity image and recipe that will create an anaconda environment and then activate said environment so I can build the python wheel of a project in that environment so it's 100% installed and functional after the singularity build is completed. Bootstrap: docker From: nvidia/cuda:9.0-cudnn7-devel-ubuntu16.04 %environment # use bash as default shell SHELL=/bin/bash # add CUDA paths CPATH="/usr/local/cuda/include:$CPATH" PATH="/usr/local/cuda/bin:$PATH" LD_LIBRARY

Activate conda environment on execution of Singularity container in Nextflow

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问题 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 shub://brucemoran/Singularity:pcgr.centos7 singularity shell brucemoran-Singularity-pcgr.centos7.img #<inside container> source activate pcgr When Nextflow executes I have defined to source activate pcgr which I think should activate the conda env. But I get an unbound variable HOST

Activate conda environment on execution of Singularity container in Nextflow

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bash script to perform action in a singularity container it opens

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问题 I am using the following workflow on RedHat in terminal: open a singularity image: singularity run /mn/sarpanitu/singularity/test/fenics-and-more.img export some display inside the singularity: export DISPLAY=:0.0 export a path to gmsh inside the singularity: export PATH="$HOME/Downloads/gmsh-git-Linux64/bin:$PATH" I want to put everything as a bash script. My first (not working) approach is the following (all in a singularity_script.sh file): #!/bin/bash function singularity_script(){

Is there a “multi-user” Docker mode, e.g. for scientific clusters?

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问题 I want to use Docker for isolating scientific applications for the use in a HPC Unix cluster. Scientific software often has exotic dependencies so isolating them with Docker appears to be a good idea. The programs are to be run as jobs and not as services. I want to have multiple users use Docker and the users should be isolated from each other. Is this possible? I performed a local Docker installation and had two users in the docker group. The call to docker images showed the same results

Is there a “multi-user” Docker mode, e.g. for scientific clusters?

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I want to use Docker for isolating scientific applications for the use in a HPC Unix cluster. Scientific software often has exotic dependencies so isolating them with Docker appears to be a good idea. The programs are to be run as jobs and not as services. I want to have multiple users use Docker and the users should be isolated from each other. Is this possible? I performed a local Docker installation and had two users in the docker group. The call to docker images showed the same results for both users. Further, the jobs should be run under the calling users's UID and not as root. Is such a

Containerize a conda environment in a Singularity container

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问题 I've come across several instances where it would be really helpful to containerize a conda environment for long-term reproducibility. As I'm normally running in high-performance computing systems, they need to be Singularity containers for security reasons. How can this be done? 回答1: First, you'll want to get the environment YML for your particular conda environment. conda activate your_env conda env export > environment.yml Normally, you would just use this as follows: conda env create -f