googlegenomics / gcp-deepvariant-runner

This repository contains a docker container that runs DeepVariant on the Google Cloud Platform.
Apache License 2.0
2 stars 6 forks source link

Revert "Avoid non-preemptible retries when '--preemptible' (#18)" #24

Closed samanvp closed 5 years ago

samanvp commented 5 years ago

This reverts commit 72d3f90713caacd43f624d4ff9c2ef8117ceaf79. Why: without non-preemptive retries, especially when we use many workers for make_examples stage such as 64 or 128, there is a high chance one of the workers get preempted more than --attempts. This will cause the whole operation fail.

A more efficient recovery would be to have a final retry using non-preemtpive worker to avoid wasting all work done by other workers.