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Singularity
Singularity is a container platform, perhaps the most well-supported Docker alternative. It allows you to run containers that package up pieces of software in a way that is portable and reproducible. You can build a container using Singularity on your laptop, self-managed desktop or a virtual machine and then run it on a DICE desktop or server or even move it to the cloud or a HPC cluster.
Singularity is currently available on all Ubuntu Teaching Cluster nodes (landonia nodes)
Full documentation can be found here: Singularity user's guide
Using Singularity on DICE
Singularity is only available on DICE Ubuntu.
Check that Singularity is installed by simply using:
singularity --version
If this returns command not found
please raise a ticket requesting for its installation on your DICE machine.
The most common usage of singularity is to download pre-built images from an external resource like the Container Library or Docker Hub. You can use search
command to locate groups, collections, and containers of interest on the Container Library.
This will output an extensive list of all containers on the Container Library built around tensorflow.
singularity search tensorflow
You can use the pull
command to download pre-built images.
singularity pull library://lolcow
for Container Library images or
singularity pull docker://sylabsio/lolcow
for Docker Hub images
Singularity and AFS
When pulling images from Container Library a single image file (.sif
) is downloaded. When pulling images from Docker Hub the image will be built on the fly. For this reason Singularity uses temporary and cache folders. As the default location for these folders is inside your home folder (~/.singularity
) this might result in running out of AFS space. Singularity offers a solution to this by using two environmental variables SINGULARITY_TMPDIR
and SINGULARITY_CACHEDIR
. Please consider adding these to your .brc
or .bashrc
file. The below is just an example:
export SINGULARITY_TMPDIR=/disk/scratch/singularity/temp export SINGULARITY_CACHEDIR=/disk/scratch/singularity/cache
Interacting with images
The shell
command allows you to spawn a new shell within your container and interact with it as though it were a small virtual machine.
singularity pull library://lolcow singularity shell lolcow_latest.sif Singularity>
The change in prompt indicates that you have entered the container.
Once inside of a Singularity container, you are the same user as you are on the DICE machine.
The exec
command allows you to execute a custom command within a container by specifying the image file. For instance, to execute the cowsay program within the lolcow_latest.sif
container:
singularity exec lolcow_latest.sif cowsay moo _____ < moo > ----- \ ^__^ \ (oo)\_______ (__)\ )\/\ ||----w | || ||
Singularity containers contain runscripts. These are user defined scripts that define the actions a container should perform when someone runs it. The runscript can be triggered with the run command, or simply by calling the container as though it were an executable. Both commands below will give the same result.
singularity run lolcow_latest.sif
or
./lolcow_latest.sif
Working with files
By default Singularity bind mounts your home folder, /tmp
and current working directory into the container at runtime. You can specify additional directories to bind mount into your container with the --bind
option. e.g:
singularity shell lolcow_latest.sif Singularity> ls /disk/scratch ls: cannot access '/disk/scratch': No such file or directory Singularity> exit singularity shell --bind /disk/scratch lolcow_latest.sif Singularity> ls /disk/scratch/ lost+found miniconda3
Working with GPUs
Singularity does not bind GPU(s) to containers by default. Please use --nv
parameter to do so.
singularity shell --nv lolcow_latest.sif Singularity> nvidia-smi Thu Jun 30 13:39:59 2022 +-----------------------------------------------------------------------------+ | NVIDIA-SMI 470.129.06 Driver Version: 470.129.06 CUDA Version: 11.4 | |-------------------------------+----------------------+----------------------+ | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | (...) | No running processes found | +-----------------------------------------------------------------------------+
Build images from scratch
To build containers requires a machine you have root privileges for. As this is not the scope of this quick start guide please refer to Singularity user's guide.
For any issues or further help please use the computing support form.