Conda environment file not working for Singularity about hpc-container-maker

[samcmill]

Thanks for the issue report @michael-sutherland.

What version of Singularity are you using?

Can you please check whether /var/tmp/environment.yml exists on the host?

Some background: the reason HPCCM uses /var/tmp rather than /tmp is that Singularity mounts /tmp from the host into the container build process. Using /tmp would sometimes result in leftover files from the container build polluting the host /tmp or conflicts between paths with the same name. It looks like Singularity's behavior has changed and (at least as of 3.5.3) it also mounts /var/tmp from the host at build time.

[michael-sutherland]

I'm using singularity version 3.6.4-1.el8.

/var/tmp/environment.yml, does NOT exist on my host (although I see the miniconda installer among other files).

[samcmill]

@michael-sutherland can you please try #333?

Specifically, add hpccm.config.set_working_directory('/') to your script (before the conda building block).

Alternatively, add wd keyword argument to the conda building block:

    stage += hpccm.building_blocks.conda(environment="environment.yml",
                                         eula=True,
                                         ospackages=['wget', 'ca-certificates', 'git'],
                                         wd='/')

[VI-gha]

Another option could be to NOT use a separate environment.yml file but have all the conda channels and conda packages explicitly listed in the same building block using something like:

stage += hpccm.building_blocks.conda(channels=['conda-forge'], packages=['numpy'], eula=True, ospackages=['wget', 'ca-certificates', 'git'])

[samcmill]

Closing as fixed by #333. Please reopen if the issue persists.