InnoDB detects deadlocks. Deadlocks are those nasty situations, when transaction 1 tries to acquire locks A and B, whereas transaction 2 tries to acquire locks B and A at the same time. As both are stubborn, InnoDB will decide simply to terminate one of them. If it wouldn’t do that, both transactions would have to wait until lock_wait_timeout to expire otherwise. There is a big chance that longer the transaction is, more likely it is to cause deadlocks. Deadlock detection kind of helps, then, but… at certain costs.
Transaction 1 and 2 case is way too easy, try adding few hundred transactions that contend over same set of locks. To do that, InnoDB deadlock monitor will recursively brute-force lock graph, until it hits a 200-transaction-long chain (it will say it is a deadlock), or until it runs out of paths to check. Still, with the power of modern hardware that will still be milliseconds.
Unfortunately, InnoDB will also hold kernel_mutex at that time, so lots and lots of InnoDB operations will not happen at that time. To be exact, InnoDB will rarely do anything else, while deadlock check is happening.
To illustrate that, I have a very simple testcase (that in certain conditions stalls the server for half an hour, even if it is not being ran):
UPDATE t1 SET b=b+1 WHERE a=1;
With few threads it executes nearly 20000 times a second on my desktop machine. With ten threads it executes 14000/s. With 50 threads it is only 3000/s. With 100 threads it falls down to 639 operations a second. At 140 threads it is already just 266.
I built InnoDB without deadlock detection (tiny tiny patch), and tried same test. Similar performance with 10 threads, still doing 10000 operations a second at 100 threads:
Though I illustrated edge case here, its purity actually didn’t show how bad this can go – this situation can happen not only because of high contention on single row, but simply because someone holds up the row lock for a bit too long (there’s always that sleep between UPDATE and COMMIT, too). It can take a single transaction to cause a lock convoy, and once transactions queue up, and update rate falls down below 100/s, all MySQL will be doing is checking for deadlocks, even if they never happen.
On many systems deadlock detection is causing way more issues, than lack of it would. Most deadlocks happen on transactions that are somewhere in the middle of their lock wait anyway :)
There’s some discussion about it at MySQL Bug#49047