Support singularity as an alternative do docker

[dprananto]

Hi,
I am trying to run Ubermag on an HPC via a Jupyter-Notebook container pulled from the docker-hub using Singularity.
I followed the Conda installation procedure written on the Ubermag website and tested the installation on the Terminal without a problem. However, when I tried running Ubermag on the Jupyter Notebook, ubermag packages could not run at all. I thought that the problem was on the environment, so I installed ipykernel and was able to run the ubermag package but failed when I tried to drive the system with an error showing that it could not find OOMMF.
I would appreciate it if you can help with this issue.

[lang-m]

Hi @dprananto , could please try the following code snippet (right after the import):

import oommfc as oc
oc.runner.docker_exe = 'singularity'

(I don't have Singularity so can't test this right now; please report any outcome, success or failure)

[dprananto]

Hi @lang-m, it runs successfully without error at this stage

But still have the same error when I drive the system

[lang-m]

Please follow the steps explained in https://ubermag.github.io/documentation/notebooks/ubermagutil/logging.html and run oommfc.runner.autoselect_runner() with debug logging enabled and report the output. That should hopefully tell us why it cannot use Singularity.

[dprananto]

Here is the output after I activated the debug login

[lang-m]

Looking at this in more detail it turns out that the command line interface of docker and singularity are too different, so singularity is currently not supported.

So you will need to install OOMMF using a different method. You could in principle either install it via conda (there is a package on conda-forge, https://anaconda.org/conda-forge/oommf) or compile it yourself. Instructions to compile it yourself and then use it with Ubermag can be found here: https://ubermag.github.io/installation.html#advanced-installation and here: https://github.com/fangohr/oommf?tab=readme-ov-file#clone-and-build-oommf-from-source