occasional slow UPDATE using primary key - mysql

Question

I have an InnoDB table in MySQL 5.5.53 where simple updates like
UPDATE mytable SET acol = 'value' WHERE id = 42;
hang for several seconds. id is the primary key of the table.
If I enable query profiling using
SET profiling = 1;
then run the query and look at the profile, I see something like:
show profile;
+------------------------------+----------+
| Status | Duration |
+------------------------------+----------+
| starting | 0.000077 |
| checking permissions | 0.000008 |
| Opening tables | 0.000024 |
| System lock | 0.000008 |
| init | 0.000346 |
| Updating | 0.000108 |
| end | 0.000004 |
| Waiting for query cache lock | 0.000002 |
| end | 3.616845 |
| query end | 0.000016 |
| closing tables | 0.000015 |
| freeing items | 0.000023 |
| logging slow query | 0.000003 |
| logging slow query | 0.000048 |
| cleaning up | 0.000004 |
+------------------------------+----------+
That is, all the time is spent in end.
The documentation says:
end
This occurs at the end but before the cleanup of ALTER TABLE, CREATE VIEW, DELETE, INSERT, SELECT, or UPDATE statements.
How can such a simple statement spend such a long time in this state?

Answer 1

It turns out that the problem is the query cache.
If I disable it with
SET GLOBAL query_cache_size = 0;
SET GLOBAL query_cache_type = 0;
the problem goes away.
It must be invalidating query cache entries that causes the query to hang for such a long time.