singularity.md

Modify singularity image on a linux platform where you are root

I want to add cdo tools to pynextsim-no-code.sif singularity image. On lgge194 :

• download singularity images : scp [email protected]:/cluster/projects/nn9878k/sim/singularity_image_files/*sif .
• make a sandbox image (writable) from the singularity image : sudo singularity build --sandbox pynextsim_sandbox/ pynextsim-no-code.sif (needs root priviledge)
• open the sandbox : sudo singularity shell --writable pynextsim_sandbox/
• install cdo tools :

    apt install cdo
    exit

• build new container : sudo singularity build pynextsim-cdo pynextsim_sandbox/
• test : singularity shell pynextsim-cdo cdo

For boost library, install with apt-get update; apt-get install libboost-all-dev Test the existence in the shell by typing b2

Turn a docker image into singularity

• where the docker image was built : docker save nextsim > nextsim_image.tar

• On my lgge194 :

    singularity build test.sif docker-archive://pynextsimf_shom_07.tar

• Test with : singularity shell test.sif and inside the container :

cdo
ipython
In [1]: import bamg
In [2]: import mapx
In [3]: import pynextsim
In [4]: import pynextsimf