I've written before about how to figure out which connection is holding the InnoDB locks for which other connections are waiting. In other words, how to figure out who's blocking you from getting work done. The short and sweet: turn on the InnoDB lock monitor and use innotop to look at the locks held and waited-for. This has some disadvantages, so I made a patch to solve the issue the way I like it. The result is significantly more ability to find and solve InnoDB lock wait issues.