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After make zpkg commands fail after Synthesis I found this post on stack overflow:
https://stackoverflow.com/questions/55733058/vivado-synthesis-hangs-in-docker-container-spawned-by-jenkins
which seemed to match the problem we have been encountering. When run in docker there is no PID 1 process which automatically cleans up zombie processes. This adds tini to the CI container which will clean up zombie processes.
I have found adding this to the container and running the make zpkg command with tini running as a process subreaper fixes the problem.