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@gizmok13:~$ ml Singularity petersen@rhinok13:~$ singularity exec ~/ubuntu-python.sif python3 /fh/fast/.../script.py
We are loading the Singularity module on
Gizmo and run python3 with a script residing in
Fast File. The python3 binary is not executed on
Gizmo but Singularity is using python3 from inside the ubuntu-python.sif 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)
As singularity may affect the stability of a compute system to which many users are logged in at the same time, SciComp does not allow Singularity on the
Rhino login nodes. Please use the
grabnode command to get an interactive session on one of the compute nodes.
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 build command (make sure you run
ml Singularity before):
petersen@gizmok13:~$ ml Singularity petersen@gizmok13:~$ singularity build docker://ubuntu:latest INFO: Converting OCI blobs to SIF format INFO: Starting build... Getting image source signatures Copying blob 5bed26d33875 done Copying blob f11b29a9c730 done Copying blob 930bda195c84 done Copying blob 78bf9a5ad49e done Copying config 84d0de4598 done Writing manifest to image destination Storing signatures 2020/03/29 09:01:54 info unpack layer: sha256:5bed26d33875e6da1d9ff9a1054c5fef3bbeb22ee979e14b72acf72528de007b 2020/03/29 09:01:55 info unpack layer: sha256:f11b29a9c7306674a9479158c1b4259938af11b97359d9ac02030cc1095e9ed1 2020/03/29 09:01:55 info unpack layer: sha256:930bda195c84cf132344bf38edcad255317382f910503fef234a9ce3bff0f4dd 2020/03/29 09:01:55 info unpack layer: sha256:78bf9a5ad49e4ae42a83f4995ade4efc096f78fd38299cf05bc041e8cdda2a36 INFO: Creating SIF file... INFO: Build complete: ubuntu_latest.sif
Now you can just use any tool inside the singularity container using the exec command shown above or you shell into the container by invoking bash to see what’s in there:
petersen@gizmok13:~$ singularity exec ubuntu_latest.sif bash petersen@ubuntu_latest.sif>
access to storage on /fh/fast and /fh/scratch inside Singularity containers
When running Singularity containers you automatically have access to your home directory on Gizmo nodes. However you may not see the file systems under /fh/ (fast, scratch). The reason is that the container requires empty directories
/fh/scratch which allow Singularity to pass through the mount points to storage. Please create these empty directories inside your docker container before you pull it using singularity
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 (root access needed)
You can create custom or writable singularity containers, please refer to the Singularity user guide:
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
SciComp to request assistance and discuss which environment is best for your needs.
Updated: March 30, 2020Edit this Page via GitHub Comment by Filing an Issue Have Questions? Ask them here.