Non pre-emptible gVCF combiner jobs #1096
Merged
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By default this makes the Combiner host job non-preemptible. This alters the scheduling behaviour, and prevents the top level job being preempted/replaced. The quirk is this:
worst case scenario here: https://batch.hail.populationgenomics.org.au/batches/588549/jobs/1 - multiple sporadic preemptions and a really muddy job history. The final job didn't appear to get close to a conclusion.
This change makes the single host/driver job non-spot to prevent preemption, which doesn't stop QOB jobs being preempted, but does stop multiple versions of the same batch being started. This job is relatively low-resource, so even a non-spot instance should represent a negligible cost relative to the gVCF combining.
Tagging @katiedelange and @Alexander-Stuckey as an FYI - this preemption/combiner duplication has been pretty frequent lately, and could easily happen in the PA pipeline