In my recent benchmarks for MongoDB, we can see that the two engines WiredTiger and TokuMX struggle from periodical drops in throughput, which is clearly related to a checkpoint interval – and therefore I correspond it to a checkpoint activity.
The funny thing is that I thought we solved checkpointing issues in InnoDB once and for good. There are bunch of posts on this issue in InnoDB, dated some 4 years ago. We did a lot of research back then working on a fix for Percona Server
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