Singularity is a technology to run software containers (think Docker containers) in an High-Performance Computing environment. The most striking difference in comparison to Docker is that running these singularity containers do not need root rights.
Singularity is a software system that is in development. SURFsara aims to keep the version of singularity on our systems at the latest stable release. To keep our documentation up to date we decided to give some guidelines and do not provide in-depth generic information, but there are links to find this information. We guarantee no backward compatibility when singularity is upgraded.
- Access to Snellius, Grid or Lisa system
- Access to a Linux system with root rights
Build and install Singularity
In case you want to use Singularity on your Fedora (Linux) workstation, you can then install Singularity with the command
sudo dnf install singularity. Ubuntu does not have Singularity included in the main software repositories. For manual builds, you can check the documentation. This can be done for example on your own machine, or on a virtual environment, either at your local computer, at SURF HPC Cloud, or at another Cloud resource provider. Administrative privileges are necessary to install the software. However, you can also use the container build nodes on Snellius.
Container build nodes (Snellius)
On Snellius we have a Singularity build partition called "cbuild". The nodes in this partition are configured to allow the building of containers without root privileges.
In case you need a customized image and want to build your own. You can then check the documentation to see the lolcow example as a Singularity definition file. In order to build the lolcow image without root privileges, use the nodes in the "cbuild" partition on Snellius.
When your Singularity definition file is ready to be built, you must use the
--fakeroot switch, e.g.
Once the build is finished, you can run the container with
Get and run an image from Docker Hub
It is possible to convert a Docker container to the Singularity format, make sure you use the "cbuild" partition on Snellius for this. Otherwise you will run into errors related to missing privileges. E.g. to pull in an image from Docker Hub with
and then run it with
To run a container interactivly, pull in an image with e.g.
And then enter the container with
Or run a single command with
By default, the $HOME directory will be bound to your image. Changes made inside the image to the files that are bound also take effect outside the container. Deleting, creating and modifying files in your image's home directory removes also the files from the host itself. Changes inside the image made to the image itself (not to the directories that are bound) will not be saved and you will not have root rights inside the container. To make permanent adjustments continue reading in the post hoc adjustments section.
Build an image with a Singularity definition file
Convert from local existing Docker images.
Docker is not installed or used on Snellius and Lisa. The following is possible when Docker and Singularity are installed on a host. Current local Docker images can be shown with
sudo docker images where you can find the ID or IMAGE ID
To convert the image you need to set up a local Docker registry
tag the wanted images and push it to the registry
Now you can use singularity to pull the images from your private local registry. The registry has no encryption and we must tell singularity to ignore lack of https with the prefix "SINGULARITY_NOHTTPS=true"
Stop the docker registry and clean up
Post hoc image adjustments
When you need to install additional software or change some settings you can execute commands using shell commands inside the image.
Keep in mind that you will need root permissions for these operations. Which you do not have on Snellius/Lisa.
First step is to convert the compressed image into a uncompressed format in a folder structure (called a sandbox)
To keep the image persistent use the
--writeable option. e.g.
Exiting the image can be done by exiting the shell with the
After editing you compress the sandbox to ensure portability and ease of use with
Fine-tune for NIKHEF systems
To ensure you can reach data in scratch on NIKHEF systems while working on the grid you need to create a directory with the same name inside your image. This is also done with the following one-liner:
Upload your image to our systems
After bootstrap has been completed on your system and tests have been done locally it is time to move the image to one of the SURFsara systems. The various systems have different best practices on where to put your image.
From your local system, you can do a SCP to Snellius, Lisa, or Grid with the following command the image will be placed in your home directory.
Or while using the Grid distribute it via Softdrive (cvmfs):
And publish with with
Use your singularity image
First create a directory on the scratch-shared part of the scratch file system ( NOTE: of course there are a lot of other ways to use your image, we just give one example ).
Copy the image to the newly created scratch shared directory.
Go into the newly created directory
Start an interactive container sesion (you need to be on a compute node in order to access singularity).
Jump into the scratch directory
copy your image to the scratch space
When you start a job you start by default in the scratch dir (
$TMPDIR) and there is no need to switch to another directory. Images are automaticly cached by the cvmfs filesystem and there is no need to copy them to the scratch (
How do I set the
$PATH variable is taken from host environment. You can add a path to $PATH with
To make the PATH persistent in your image, add the export PATH line to "/environment" inside the container
My image is too large, can I make it smaller?
This is most likely caused by the software that was needed to build the software. Think of compilers, development headers and source code.
To make the image smaller you can best uninstall these packages and source code compress the package. Hereby an example which works on a ubuntu based container.
Detect and remove the largest packages
Before we can edit the image we need to convert it to an editable sandbox format
Then bash inside your sandbox with sudo rights:
To detect the largest packages we run the following one-liner which prints package size and sort them by size (from small to big)
Then we select the big package, which are not needed at runtime. This depends on your software stack but in general, it is save to remove gcc, clang, and *-dev packages.
Also, remove the unneeded old packages and removing the cache of apt might help to clean the container.
Compress the image
After cleaning the container can converted back to a compressed format with
Why is the
--pwd $PWD option necessary?
By default, Singularity makes the current working directory in the container the same as on the host. For resolving the current working directory, Singularity looks up the physical absolute path (see
man pwd for more info). However, many directories on our systems are symbolic links and the current working directory would resolve different than expected. This results that your files are not were you expected them to be (combined with some warning messages).
I do not like Docker, is there an alternative?
Yes, there is! You can write a Singularity bootstrap file (or convert Dockerfile to Singularity bootstrap).
A singularity bootstrap file is a recipe to create a singularity image (or Singularities counterpart of a Dockerfile).
Information about writing a Singularity bootstrap file can be found at https://www.sylabs.io/guides/3.0/user-guide/definition_files.html.
You can use Singularity build command to convert containers between the formats supported by Singularity.
When I use Singularity, I get an "LD_PRELOAD error". Is this affecting my runs and how can avoid it?
This error is caused by the XALT tool we use to monitor software usage on the system. The error does not impact the correct execution of Singularity, but it is printed every time you run a command interactively within the container.
In order to stop Singularity to print this error, you need to unset the LD_PRELOAD variable outside the container with the command:
This will prevent XALT to track your usage, so please use this only if directly affect your work with Singularity.