With changes in Shaheen programming environment, it is sometimes necessary to upgrade python and its dependencies. This implies that all the packages depending on python will also need updating. Conda environment are good up an alternative package management strategy which freezes the runtime environment is containers. This container image should work on Shaheen, Ibex or Neser.
Running rootless containers on Shaheen is easy. Here is an example of cdsapi container which KSL team has created and uploaded in the DockerHub registry for our users.
Pull the Image
Before you run cdsapi as a container job Shaheen, first pull the image on Shaheen filesystem:
module load singularity
singularity pull docker://krccl/cdsapi:0.5.1
The above should produce a file named cdsapi_0.5.1.sif
CDSAPI key file
Create an API Key file needed by cdsapi as you identity for the remote repositories to recognise your account. The API key can be generated by creating an account using the following instruction: https://cds.climate.copernicus.eu/api-how-to
Copy the url and API key and paste in the file /scratch/$USER/cdsapi_rc
Running container job on compute node as batch job
Here is a jobscript that runs cdsapi as a batch job on Shaheen compute node: