withoverlay

A bash wrapper to run singularity commands and capture filesystem information in an overlay

This is withoverlay 1.0 by Pierre Rioux

Usage: withoverlay [-v] overlaypath[=overlaysize] containerimage command [args]

This program will run command (and args) from within a singularity container with a writable overlay to capture results. Files created while the command run will only end up in the overlay if they are not in one of the pre-mounted singularity paths (typically: the HOME directory and /tmp). Overlays cover the entire file system down from the root, /, but typically the only writable place is directlry under "/home", so programs should store persistent data in "/home/choosethis".

Requirements:

Singularity 3.2 or better is absolutely necessary.

Options:

• -v

Make this program a bit more verbose. Normally the program is silent about all its activities and will only print whatever output the command produces. Note that the initial creation of the overlay can take some time, so it recommanded to use the verbose option with it. That way the user can see the progress of this phase.

Arguments:

overlaypath

The path to an overlay file; if the file doesn't exist it will be created, provided a suffix "=overlaysize" is provided. If the overlay file exists, the suffix will be ignored. The value is a size in gigabytes, e.g hello.img=20 means use the file 'hello.img' and create it with a size of 20 gigabytes if needed.

containerimage

The path to a singularity container image to use to run your command.

command [args]

A command or program with arguments. Note that the command will be passed as-is to the 'singularity exec' command, and handling of single quoted or double quoted arguments is tricky. It is better to wrap any complex set of commands within a shell wrapper and execute that wrapper as a single command instead.

Two special commands are supported:

getlog

This will print a log of the activity (mostly commands) that were used through this program (maintained internally in the overlay in path $INTERNAL_LOG).

addlog words words words

This will add a log message with words words words.

Examples:

  # Just create a 1G overlay, don't run anything in it yet:
  withoverlay -v ~/base.img=1  centos.img true
  withoverlay    ~/base.img=1  centos.img getlog # the '=1' will be ignored here

  # Run some commands and store data in the overlay:
  withoverlay -v ~/data.img=10 centos.img bash -c 'mkdir /home/hello;uptime >/home/hello/uptime'
  withoverlay    ~/data.img    centos.img cat /home/hello/uptime
  withoverlay    ~/data.img    centos.img addlog this is great
  withoverlay    ~/data.img    centos.img getlog

  # Another abstract example
  withoverlay hello.img=5 planet.img planet_maker --name pluto --distance 5.5h
  withoverlay hello.img=5 planet.img moon_maker   --name charon --parent pluto
  withoverlay hello.img=5 planet.img getlog

Notes

Do not run this on MacOS; before the script is even able to crash when it attempts to run singularity, it will have created the empty placeholder file for the overlay filesystem, and since MacOS doesn't support sparse files (or at least, the commands here do not create a file with holes), you'll end up with a huge chunk of your disk space missing.

Author

Pierre Rioux July 2019