Talk:SW:Singularity

j-perdue random links for 8/10/2018

Placeholder

To be added to SW:Singlularity:Examples or something.... just a placeholder for now to dump all my URLs at home for access at work:

https://github.com/singularityware/singularity/issues/1076

https://github.com/singularityware/singularity/issues/1165

http://singularity.lbl.gov/quickstart#build-images-from-scratch

https://hub.docker.com/_/fedora/

https://github.com/NIH-HPC/singularity-examples/blob/master/torch/Singularity.torch

https://www.sylabs.io/docs/

history

• random notes from .bash_history on hprclab2

[j-perdue@hprclab2 ~]$ history | grep docker
  460  git clone https://github.com/fedora-cloud/docker-brew-fedora.git
  466  less prep-docker-brew-branch.sh 
  468  ./prep-docker-brew-branch.sh 28
  470  sudo docker pull fedora:28
  472  sudo docker run --rm -ti fedora:28 bash
  484  sudo docker run  -ti fedora:28 bash
  494  sudo docker run  -ti fedora:28 bash
  495  man docker
  496  man docker-run
  497  sudo docker build --writable Fedora28.img fedora:28 
  515  sudo singularity build --writable FedoraLatest.img docker://fedora:latest
  516  sudo singularity build --writable Fedora28.img docker://fedora:28
  523  # sudo singularity build --writable --size Fedora28.img docker://fedora:28
  541  history | grep docker
[j-perdue@hprclab2 ~]$ history | grep singularit
  510  sudo singularity build --writable Fedora28.img fedora:28 
  511  sudo singularity build --writable Fedora28.img fedora:27
  512  sudo singularity build --writable Fedora28.img 
  XXX  sudo singularity shell --writable Fedora28-HPRCLAB.img

nearing in on objective

The objective in this case is a Fedora28-HPRCLAB.img file:

1. that we can provide to users, a Singularity .img file (self-contained), for them to update as needed (as root on their own workstations) that also runs on our clusters
2. is already populated with HPRCLAB RPMs
3. has plenty of disk space for the user to add files (as non-root) while on the cluster

Latest go around looks like this:

1) create a (--writeable) Singularity sandbox from docker://fedora:28 (called mysandbox below... a directory) 2) run 'sudo singularity shell" on sandbox to populate (JKP: need to check if sudo is necessary here) 3) populate the sandbox with all the RPMs (probably requires sudo above) and users (again sudo) 4) once you are happy with that, time to make an .img 5) singularity image.create myimage # create .img file 6) singularity image.expand -s 20480 # expand to 20GB (works because there is no real file system yet) 7) sudo tar -cvf - -C mysandbox/ . | sudo singularity image.import 10g.img # see the last/tar example in 'singularity image.import --help'