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draeger-lab / ModelPolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
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Running with docker-compose run -u $(id -u):$(id -g) potentially locks up execution #98

Closed mephenor closed 3 months ago

mephenor commented 4 years ago

Running the docker container as non-root consistently produces May 13, 2020 6:47:47 AM java.util.prefs.FileSystemPreferences checkLockFile0ErrorCode --- WARNING: Could not lock User prefs. Unix error code 2. May 13, 2020 6:47:47 AM java.util.prefs.FileSystemPreferences syncWorld --- WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. after random intervals of time, which potentially locks up the process indefinitely.

Creating .java/.userPrefs and .java/.systemPrefs within the container does not seem to work.

Schmoho commented 3 months ago

I don't see why there is a reason to run as non-root. This is current Docker best practice: https://docs.docker.com/engine/security/userns-remap/