wrappie is a tool for automated deployment of applications using containers, bash wrappers and modules.
Containers are used under the hood while users interact with modules, resulting in the typical user experience of a HPC shared system.

Find it on GitHub

May 2021: the original developers of Singularity have released a tool that includes most (if not all) functionalities of wrappie: Singularity Registry HPC, or shpc. Our team will evaluate this tool prior to further developing wrappie.

• Singularity : template installation script

• A module system, either

  • Environment modules : template installation script
  • Lmod

Lines 20-26 of the wrappie script provide values for the following variables:

• basedir: default base-name for the following two variables
• rootdir: upper level path for the directory tree of packages (containers and wrappers). The tree has the default format: basedir/containers/tool/tag/
• moduledir: upper level path for the directory tree of modules, default format basedir/modulefiles/tool/tag
• workdir: directory(ies) to be bound mounted in containers. Can be comma separated list, only used to display information

You can specify customised values for these variables either in the shell environment, or by editing those lines in wrappie.

Write a text file, e.g. see examples/dummy_list, of this form:

docker://ubuntu:18.04
- ls
- pwd

i.e. containing image addresses, followed by a dashed list of commands you will need to run from that image. If the image has GPU capabilities, just add a dashed item GPU as the first item for the image.
Lines starting with # will be ignored.

Finally run wrappie:

./wrappie examples/dummy_list

At the end of the process (non Pawsey HPC systems only), an output will advise on a couple of variable definitions to be added in your ~/.bash_profile, something like:

For proper functioning of this setup, ensure these two definitions are in your ~/.bash_profile :

##############################
module use [..]
export SINGULARITY_BINDPATH=$SINGULARITY_BINDPATH,[..]
##############################

To install wrappie, a maali cygnet file is available in the extras/ directory.

At runtime, wrappie can recognise if it is being run on Pawsey systems, and adjust the installation paths accordingly:

• for regular users, the basedir will be set to $MYGROUP/software/$PAWSEY_OS
• for super user maali, system paths will be set

Checkout this alternative tool to install containerised applications, including bash wrappers and modules:

• Singularity Registry HPC
• Community Collections
• Quay Containers

• port the code-base to Python
• port package recipes to YAML
• ..

Marco De La Pierre [email protected]
Audrey Stott [email protected]
Sarah Beecroft [email protected]