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cleanup is not inhibited after errors
Issue #276
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SimFactory should detect if qsub or qstat failed, or if the corresponding patterns didn't match. In this case, there should be an error message alerting the user.
In this case, cleanup should not automatically clean up the simulations, since it cannot detect whether the restarts are finished. ("cleanup --force" should probably still work.)
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This has been implemented. I've added a new job_status - E. How this works is the first thing GetJobStatus does is analyzed the output it received to look of the job_id exists somewhere in the output. If it finds the job id, but then is unable to match any of the regular expressions to determine exactly what the job status is, it is assigned this 'E' status, and the then simfactory won't do anything with the job unless --force is specified. This will stop simfactory from accidentally cleaning up an active simulation if for some reason it can't correctly detect its status.
This is a good idea, btw. Thank you!