krank

krank (comparative kränker, superlative am kränksten)

1. sick; ill
2. (slang) excellent

— Wiktionary

Turn the krank on your data reduction tasks with the magic of containers.

Usage via Docker

TODO

Usage on UA HPC (Singularity)

0. Log in to Ocelote or El Gato
1. module load singularity to make the singularity command available
2. Request a large temporary workspace with xdisk -c create -m 1000 and then cd /xdisk/$USER so that the image builds outside your (somewhat small) home directory quota
3. singularity build krank.img docker://magaox/krank
4. Copy the images you want to analyze into /xdisk/$USER with rsync (e.g. rsync ./data filexfer.hpc.arizona.edu:/xdisk/yournetid/data)

Weird quirks

• UA HPC has a storage quota and a file count quota. Trying to retain intermediate files will quickly exhaust the latter, so be sure to delete those after combining.
• Singularity only has two (useful) users, root at build time (as whom all build commands are run) and $USER (i.e. you) at run time.
• UA-specific HPC network filesystem mount points are present as empty directories in the image to silence Singularity warnings (and let you access HPC shares when run on UA HPC)

Development

Inspecting the image

• In Singularity: singularity shell krank.img
• In Docker: docker run -it magaox/krank bash (After commenting out the entrypoint and rebuilding)

Adding to the Docker image

0. Get access to https://hub.docker.com/r/magaox/krank/
1. Install Docker Community Edition locally
2. git clone this repository
3. ./build.sh
4. ./push.sh
5. git commit and git push when it's all nice and kentucky

Reference

• Dockerfile documentation
• UA HPC Singularity tutorials