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Singularity v3.0 was completely re-written in Go. We will need to install the Go language so that we can compile Singularity. This procedure consists of downloading Go in a compressed archive, extracting it to /usr/local/go and placing the appropriate directory in our PATH. For more details, check out the Go Downloads page.

If everything went according to plan, you now have a working installation of Singularity.Simply typing singularity will give you a summary of all the commands you can use.Typing singularity help will give you more detailed information about running an individual command.

Being able to specify download locations allows you to keep the local set of images organised and tidy, by making use of a directory tree. It also allows for easy sharing of images within your team in a shared resource. In general, you will need to specify the location of the image upon execution, e.g. by defining a dedicated variable:

The default directory location for the image cache is $HOME/.singularity/cache. This location can be inconvenient in shared resources such as HPC centres, where often the disk quota for the home directory is limited. You can redefine the path to the cache dir by setting the variable SINGULARITY_CACHEDIR.

Dear Community,I am trying to download the .sif file to install the singularity most updated fmriprep environment (20.2.7 or 21.0.1). I work on a HPC and so to my (limited) understanding, I have to download it using singularity (and not with other commands).

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I have a system that has no connection to the internet but does have local mirrors of the OS package manager repos, PyPI, Conda, etc. I'd like to build Singularity images on this system. It looks like the localimage bootstrap agent was designed specifically for this use case, but how would I download the base image from which to build my images? From an internet-connected machine, can I download an "official" base image from SyLabs, Singularity Hub, or somewhere else in my browser without installing Singularity?

Singularity version < 2.5.In this case, start with a machine (e.g., your personal computer) with Docker installed.Use docker2singularity tocreate a singularity image.You will need an active internet connection and some time.

Setting up a functional execution framework with Singularity might be tricky in someHPC systems.Please make sure you have read the relevant documentation of Singularity, and checked all the defaults and configuration in yoursystem.The next step is checking the environment and access to fMRIPrep resources, usingsingularity shell.

The system administrator can also define what is added to a container. This is important on campus HPC systems that often have a /scratch or /xdisk directory structure. By editing the /etc/singularity/singularity.conf a new path can be added to the system containers.

We also need to initialise your environment to make Singularity available. NeSI maintains up-to-date versions of Singularity as software modules on Mahuika. Load the latest Singularity and check the version. Note that the singularity command includes extensive self-documentation::

For the ERNZ20 tutorial we have prepared some of the bigger images to be downloaded in a specific directory - /nesi/nobackup/nesi99991/ernz20-containers/demos/sif/. Create the following symbolic link to be able to use them. Normally downloading the required images will take up to an hour.

Being able to specify download locations for the container images allows you to keep your local set of images organised and tidy, by making use of a directory tree. It also allows for easy sharing of images within your team in a shared resource.

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Singularity is installed on CARC systems as an RPM package outside of the software module system, so there is no need to load a module in order to use it. Instead, you can directly use the singularity commands. Please note that the commands that require sudo will not be available to you on CARC systems.

To get a container image for use on CARC systems, you can either pull (i.e., download) pre-built container images into one of your directories or externally build a custom container image from a definition file and then transfer it to one of your directories.

When pulling containers, Singularity will create a ~/.singularity/cache directory by default to store cache files, which can quickly use a lot of storage space. We recommend changing this location to a directory with more storage space (e.g., one of your scratch directories) by setting the environment variable SINGULARITY_CACHEDIR. For example:

If you have identified a pre-built container image from a registry that includes all the software you need, then you can download this image into one of your directories using the singularity pull command.

The easiest way to build containers externally for use on CARC systems is to use the cloud-based Singularity Remote Builder, which is integrated with the Singularity Cloud Library. To use this service, you can sign in with your GitHub, GitLab, Google, or Microsoft account. Currently, you are limited to 11 GB of free storage for your container builds. Once signed in, you can submit a definition file to the remote builder and it will build the image and provide a build log. Assuming the build is successful, you can then pull the container image directly to one of your directories on CARC systems with the provided pull command. Instead of using the web interface, you can also create definition files and build remotely from CARC systems by using the singularity build --remote command. 2b1af7f3a8