mysql 5.6 flushing all dirty pages on ib_logfile rotation creating checkpoint stall
The sentence about requiring a checkpoint before the log file rotation/reuse may have been removed from documentation, but the logic hasn't changed in version 5.6 -- you cannot overwrite log records that belong to not-yet-persisted data, so you have to checkpoint still. The fact that it is happening in your environment indicates that flushing of dirty pages with fuzzy checkpoints is not aggressive enough for your workload.

I'd try raising the innodb_adaptive_flushing_lwm threshold and lowering innodb_max_dirty_pages_pct to make page cleaning more proactive.

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