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Research Computing Framework Based on Singularity and Lmod
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README.md

Community Collections (CC)

A Research Computing Framework for Software Sharing

CC allows users to keep up with the latest software on HPC systems and is also a reflection of the community's software interests in sharing common containerized software. Powered by Singularity and Lmod on Linux systems.

Requirements

  • Linux
  • A root-installed Singularity or else we will install one for you, and give you the opportunity to enable it with root
  • On RHEL7 systems, “Development Tools” including the gcc compiler
  • bzip2 for obvious reasons
  • git to get the code
  • wget to get necessary components
  • The cryptsetup package for installing recent versions of Singularity
  • A kernel with user namespaces if you lack root and wish to use Singularity sandbox containers instead of image files

CC has only been tested on Bash shells currently.

Quick Start

See our longer docs here: https://community-collections.github.io/ Otherwise, below is a 'Quick Start'.

Testing as a user with admin privileges

Use the following commands to test the code.

# obtain community collections
git clone http://github.com/community-collections/community-collections
cd community-collections

# optional: clean ups if you intend to start over
./cc clean # only if you are developing and want to delete everything 

# start here for the first time
./cc refresh
# we generate a cc.yaml so please have a look!
#   cc.yaml: remove error notes to build Lmod and Singularity locally if needed
vi cc.yaml 
# run cc refresh again after updating file
./cc refresh

# source initialization, user needs to affirm how cc is loaded into their environment
#   'cc profile' generates profile_cc.sh and adds it to ~/.bashrc (only contains references to Lmod)
./cc profile  
# if you wish to skip bashrc changes and only make the profile_cc.sh, use ./cc profile --no-bashrc
# source the file to enable cc
source profile_cc.sh # or get a new login shell if you said "y" to adding to your bashrc

# cc is live after you source a related file or agree to login shell mods
ml av # cc/conda supplies miniconda; cc/env supplies the conda env; and singularity is available as module

# if you are not root you may need to check if singularity is capable
./cc capable
sudo ./cc enable # sudo is required for sif files (no switch yet to enable sandboxes if you have userns)

# some examples of loading modules, community collections will 'pull' the image with the 
# combined power of Singularity and Lmod !
ml julia      # triggers the example singularity pull from docker
ml tensorflow # pulls a specific version with a suffix (see the default cc.yaml)
ml R          # gets a copy of R from r-base

Version checking and versionless modules are still under development.

Testing in a docker container

This section describes a Docker environment which would be sufficient for supporting CC. The code is currently tested in a Docker container with a very minimal set of requirements:

FROM centos:centos7
RUN yum update -y
RUN yum groupinstall -y 'Development Tools'
RUN yum install -y wget
RUN yum install -y which
RUN yum install -y vim
RUN yum install -y git
RUN yum install -y make
RUN yum install -y bzip2
RUN yum install -y cryptsetup

On a fresh VM with CentOS7:

# as root
yum update -y
yum groupinstall -y 'Development Tools'
yum install -y wget which vim git make bzip2 cryptsetup

Without libtcl or squashfs-tools, the code uses the conda environment to supply these.

Note that very recent testing shows that cryptsetup is now required for later versions of Singularity 3.

Documentation

The documentation source is located in docs/source and can be compiled locally with ./cc docs. Note that the administrators can update the documentation site with the ./cc docs --push command.

Motivation and Citation

A recent PDF should be available here.

Citing our work increases our visibility to our scientific research community!
Please include the following citation in related efforts:

K. Manalo, L. Baber, R. Bradley, Z. You, N. Zhang. "Community Collections: A Framework for Openly Sharing Software Stacks Across Research Computing Centers Using Singularity and Lmod". PEARC19, July 28 - August 1, 2019, Chicago, IL, USA. DOI: 10.1145/3332186.3332199

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