Hacks

Here are some useful hacks for dealing with common ChRIS problems. These violate best practices. You didn't hear it from me!

Modifying Read-Only Plugin Properties

OOMKilled is a frustrating problem in ChRIS. Setting memory_limit for plugin instances can be tedious, furthermore it can't even be set for plugin instances created by a workflow.

The proper way to fix these problems is to delete the plugin then re-upload it. Alternatively, plugin properties can be modified in-place using the Django shell.

The min_memory_limit of a plugin can be increased using the Django shell. First, open a Django Python shell, e.g.

kubectl exec -it -n chris deploy/chris-server -- python manage.py shell

Then find your plugin and customize it to your heart's content, though be mindful of how modification can break things for your users, and can violate reproducibility.

from plugins.models import Plugin
p = Plugin.objects.get(dock_image='fnndsc/pl-nii2mnc:1.1.0')
p.min_memory_limit = 2048
p.save()