Over the last month or so, we noticed steady week-over-week rises in overall MySQL query time. A poorly-performing database makes for a slow site and a slow site makes for a terrible experience, so we dug in to see what was going on.

The investigation is probably more interesting than the actual solution. We started with the most basic things: taking a look at long-running queries, database size, indexes. Nothing in that was especially fruitful.

We turned to some extremely helpful open source tools from Percona to figure out what was going on. I set up pt-stalk to trigger alerts and dumps of diagnostic data whenever MySQL’s running thread count got inordinately high. We sent stats about frequency of pt-stalk triggers to our Graphite instance, and I set up an alert in our Campfire that audibly pinged me on every trigger. The constant sound of the “submarine” alert in my Campfire client was driving me to Poe-esque insanity, so I was doubly motivated to fix this.

With more investigation, we were able to rule out a number of other potential causes, including physical problems on the machine, network issues, and IO issues. Naturally, the submarine noises kept going off, and at one point I may or may not have heard Sean Connery say “Give me a ping, Vasily. One ping only, please.”

Luckily, I noticed pt-stalk data dumps and SHOW ENGINE INNODB STATUS revealing hundreds of these bad things:

--Thread 140164252591872 has waited at trx/trx0trx.c line 807 for 1.0000 seconds the semaphore:
Mutex at 0x24aa298 '&kernel_mutex', lock var 0

Issues in MySQL 5.1 and 5.5 (we run 5.1 for now) with kernel_mutex around transactions have been known for some time. They have also been known to my friend and increasingly well-regarded yoga expert @jamesgolick, who last year wrote about the exact issue we were encountering.

So we took a page from Golick’s work and from our own thinking on the issue, and went forward with the switch from stock malloc to TCMalloc.

Different allocators are good at different things, and TCMalloc (available as part of gperftools) is particularly good at reducing lock contention in programs with a lot of threads. So @tmm1 dropped in a straight-forward export LD_PRELOAD="/usr/lib/libtcmalloc_minimal.so", and with a database restart we were off to the races.

Good things happened. After the switchover, those pt-stalk triggers declined to about 1/7th of their original frequency, and the previously-seen contention dropped significantly. I had expected at best a stop in rising query times with this change, but we ended up with something much better — a rather shocking 30 percent improvement in query performance across the board and a general decline in spikes.

I allowed myself a small celebration by reading The Raven in silence and enjoying a non-trivial amount of Nutella.