Docker can only run containers as root so we cannot use them in shared multi-user environments such as
Gizmo with shared storage such as
/fh/scratch. Singularity can import Docker containers and run them.
Singularity containers can run under any user account once created. This is possible:
petersen@gizmof13:~$ ml Singularity petersen@rhinof13:~$ singularity exec ~/ubuntu-python.simg python3 /fh/fast/_HDC/team/SciComp/script.py
We are loading the singularity lmod environment on
Gizmo and are then running python3 with a script residing in
Fast. The python3 binary is not executed on
Gizmo but Singularity is using python3 from inside the ubuntu-python.img container which is stored in my home directory. This process allows us to package entire pipelines in containers and integrate them seamlessly in HPC workflows as
/fh are always read from the
Gizmo environment outside the container.
Preparing Singularity and a workaround (DO NOT USE IT ON RHINO)
Before you use Singularity please let
SciComp know the users in your group and the PI folder you will be working with, otherwise you will get this error which also affects others.
$ singularity run container.simg ERROR : There was an error binding the path /app: Too many levels of symbolic links ABORT : Retval = 255
You should only use Singularity on a
Gizmo node and never on
SciComp will only allow users to run Singularity who are able to follow this guidance consistently.
Using Docker Containers with Singularity
Docker containers are the predominant storage format for containerized workflows and it is important to know that Singularity can easily import Docker containers. To create a new container from a Docker image on DockerHub you just need to run the
singularity pull command (make sure you run
ml Singularity before):
petersen@gizmof13:~$ ml Singularity petersen@gizmof13:~$ singularity pull docker://ubuntu:latest WARNING: pull for Docker Hub is not guaranteed to produce the WARNING: same image on repeated pull. Use Singularity Registry WARNING: (shub://) to pull exactly equivalent images. Docker image path: index.docker.io/library/ubuntu:latest Cache folder set to /home/petersen/.singularity/docker Importing: base Singularity environment Exploding layer: sha256:84ed7d2f608f8a65d944b40132a0333069302d24e9e51a6d6b338888e8fd0a6b.tar.gz . . Exploding layer: sha256:e9055237d68d011bb90d49096b637b3b6c5c7251f52e0f2a2a44148aec1181dc.tar.gz Exploding layer: sha256:c6a9ef4b9995d615851d7786fbc2fe72f72321bee1a87d66919b881a0336525a.tar.gz WARNING: Building container as an unprivileged user. If you run this container as root WARNING: it may be missing some functionality. Building Singularity image... Singularity container built: ./ubuntu-latest.simg Cleaning up... Done. Container is at: ./ubuntu-latest.simg
Now you can just use any tool inside the singularity container using the exec command shown above or you shell into the container to see what’s in there:
petersen@gizmof13:~$ singularity run ./ubuntu-latest.simg WARNING: Failed to open directory '/fh/fast/xyz' WARNING: Failed to open directory '/fh/fast/abc' WARNING: Failed to open directory '/fh/fast/klm' WARNING: Failed to open directory '/home/xyz' WARNING: Failed to open directory '/home/abc' WARNING: Non existent bind point (directory) in container: '/app' WARNING: Non existent bind point (directory) in container: '/fh' email@example.com>
You will get an error message which means that empty folders inside the container for mount points /app and /fh are not created yet. You can address this by creating these folders in the docker container you pull from DockerHub. There are also some warnings like
WARNING: Failed to open directory You can ignore those warnings.
Tuning your Environment
Singularity uses settings from the home directory of the invoking user on the host system, for example .bashrc. The recommended settings for ~/.bashrc: check for a Singularity symlink at the root or a SINGULARITY_NAME env var. In some cases you want bash to behave differently if you are inside a container. You can put this into ~/.bashrc.
if [ -L '/singularity' ]; then PS1='\u@$SINGULARITY_CONTAINER> ' export PROMPT_COMMAND='' else PS1='' fi
Creating custom Singularity Containers for Docker Images
Sometimes you would like a larger Singularity container than your docker container and/or customize your singularity container after the fact. (This should be the exceptions as we want to use docker containers in most cases.
If you have root access (
SciComp staff) you can use the esudo wrapper (yes, use esudo wrapper instead of sudo!) to open the image as root in write mode to create the 2 empty folders to mount file systems.
petersen@gizmof13:~$ singularity create --size 2048 ubuntu-1404.img petersen@gizmof13:~$ singularity import ubuntu-1404.img docker://ubuntu:trusty petersen@gizmof13:~$ esudo singularity shell -w ubuntu-1404.img WARNING: Non existant bind point (directory) in container: '/app' WARNING: Non existant bind point (directory) in container: '/fh' Singularity: Invoking an interactive shell within container... Singularity ubuntu-1404.img:~> mkdir /app /fh
SciComp’s Singularity install is configured to allow access to mounted file systems at
/mnt, this is set in
singularity.conf, for example these 3 lines were added to
bind path = /app bind path = /fh bind path = /mnt
You might see this intermittent Error with Singularity:
ERROR : Could not open image /fh/fast/.......: Too many levels of symbolic links
the gory details are reported here: https://github.com/sylabs/singularity/issues/2556
Workaround: You have not notified SciComp that you want to use this folder with Singularity. Please do so ASAP
SciComp to request assistance and discuss which environment is best for your needs.