Problem statement I have a Python program that needs to launch a number of Singularity containers in parallel. Is it possible to do this, exploiting all of the available hardware, using only built-in libraries (subprocessing, concurrent.futures, etc)? The 'host' script…
In AWS, created a docker image with a python script to print a string(basicprint.py) docker file: FROM python COPY ./basicprint.py ./ CMD ["python", "basicprint.py"] It works fine then saved docker image as .tgz file. copy that .tgz file in to…
I have built a Singularity sandbox container using this command: sudo singularity build --sandbox ubuntu/ library://ubuntu Now, I would like to copy/export this container as a sif file. But I cannot find how to do this in the documentation. Any…
I have been trying to create a Singularity container with libxc and Quantum Espresso 7.0. I started with a definition file I created myself and then used the sudo singularity build --sandbox QE7-libxcm base.def option, followed with sudo singularity shell…
I need to install Cuda, CuDNN, and NCCL in a singularity container to build the MXNET Library for GPU Support. Currently, I have this minimal Definition File: Bootstrap: library From: ubuntu:20.04 %environment export CC=/usr/bin/gcc export CXX=/usr/bin/g++ ... some other stuff…
I am trying to containerize vim along with the plugins. I am using singularity containers. The most important plugin is youcompleteme. My approach to containerizing the plugins is to install vim and clone all the plugins to /etc/vim/plugin and compile…
I tried to pull the latest version of the Singularity image for fmriprep into an HPC, which to my understanding is 21.0.1. I did it using the following bash script: module load singularity singularity pull --name fmriprep_latest.sif docker://poldracklab/fmriprep:latest Unfortunately, for…
I'm trying to install R package A into a Singularity container with R 3.6.0. Package A needs R package B as a dependency. I originally installed package A with version 1 of package B, and things worked fine. Now, however,…
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…
I am trying to build a singularity container, to run a Python script on a CentOS 7-based cluster. The container runs as expected on my host, which I also used to create the container, but fails on the cluster as…