In late 2021, Singularity underwent a rebranding to Apptainer, changing the command keyword from
apptainer, though the majority of subsequent commands and options retained their functionality. (Learn more about the changes in the tutorial Apptainer, the container system for secure HPC.)
Before diving into container tasks on HPC infrastructure:
- ensure you checked the available module using the commands:
module avail apptainer module avail singularity
- load a module of your choice:
module load apptainer/<version> # e.g., module load apptainer/1.1.9-py310-wsbt4ge
- and consistently use the appropriate keyword for your commands (in this example: apptainer).
Apptainer is the recommended module for container management, and users are advised to transition to it for enhanced functionality and support.
Singularity on your Mac via Vagrant
This recipe demonstrates how to run Singularity on your Mac via Vagrant and Ubuntu. The recipe requires access to brew which is a package installation subsystem for OS X. This recipe may take anywhere from 5-20 minutes to complete.
Note: this content was taken directly from http://singularity.lbl.gov/install-mac#setup which no longer exists.
First, install brew if you do not have it already.
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
Next, install Vagrant and the necessary bits.
brew cask install virtualbox brew cask install vagrant brew cask install vagrant-manager
Option 1: Singularityware Vagrant Box We are maintaining a set of Vagrant Boxes via Vagrant Cloud, one of Hashicorp many tools that likely you’ve used and haven’t known it. The current stable version of Singularity is available here:
singularityware/singularity-2.4 For other versions of Singularity see our Vagrant Cloud repository.
mkdir singularity-vm cd singularity-vm
Note that if you have installed a previous version of the vm, you can either destroy it first, or create a new directory.
Then issue the following commands to bring up the Virtual Machine:
vagrant init singularityware/singularity-2.4 vagrant up vagrant ssh You are then ready to go with Singularity 2.4! vagrant@vagrant:~$ which singularity /usr/local/bin/singularity vagrant@vagrant:~$ singularity --version 2.4-dist vagrant@vagrant:~$ sudo singularity build growl-llo-world.simg shub://vsoch/hello-world Cache folder set to /root/.singularity/shub Progress |===================================| 100.0% Building from local image: /root/.singularity/shub/vsoch-hello-world-master.simg Building Singularity image... Singularity container built: growl-llo-world.simg Cleaning up... vagrant@vagrant:~$ ./growl-llo-world.simg RaawwWWWWWRRRR!!
Note that when you do vagrant up you can also select the provider, if you use vagrant for multiple providers. For example:
vagrant up --provider virtualbox although this isn’t entirely necessary if you only have it configured for virtualbox.
Option 2: Vagrant Box from Scratch (more advanced alternative) If you want to get more familiar with how Vagrant and VirtualBox work, you can instead build your own Vagrant Box from scratch. In this case, we will use the Vagrantfile for bento/ubuntu-16.04, however you could also try any of the other bento boxes that are equally delicious. As before, you should first make a separate directory for your Vagrantfile, and then init a base image.
mkdir singularity-2.4 cd singularity-2.4 vagrant init bento/ubuntu-16.04
Next, build and start the vagrant hosted VM, and you will install Singularity by sending the entire install script as a command (with the -c argument). You could just as easily shell into the box first with vagrant ssh, and then run these commands on your own. To each bento, his own.
vagrant up --provider virtualbox # Run the necessary commands within the VM to install Singularity vagrant ssh -c /bin/sh <<EOF sudo apt-get update sudo apt-get -y install build-essential curl git sudo man vim autoconf libtool git clone https://github.com/singularityware/singularity.git cd singularity ./autogen.sh ./configure --prefix=/usr/local make sudo make install EOF
At this point, Singularity is installed in your Vagrant Ubuntu VM! Now you can use Singularity as you would normally by logging into the VM directly
Remember that the VM is running in the background because we started it via the command vagrant up. You can shut the VM down using the command vagrant halt when you no longer need it.