Large long-running reporting queries are causing very slow new mysql connections Usually, mysql's connecton time is in the 0.001 second range. However, when I run a large reporting query (that spans multiple tables with aggregates), I get tons of warnings saying that new mysql connections are taking between .5 and 2 seconds just to connect! Why would a single large query affect connection times so much?

Doing research online, I can't seem to find which mysql settings would need to be tweaked to mitigate the issue.

I'm on MySQL 5.6, using all InnoDB tables.
It's look like your reporting query lock for a while the tables needed by general queries.

There is no general recipe for such cases and you have to refactor your reporting to avoid locking. Sometimes you can achieve this with splitting one big query into the series of smaller ones. Sometimes the good approach is to copy some tables for exclusive use by report generator. Sometimes it is something else. All depends on the your DB scheme.