Sometimes a MySQL server running InnoDB takes a long time to shut down. The usual culprit is flushing dirty pages from the buffer pool. These are pages that have been modified in memory, but not on disk.
If you kill the server before it finishes this process, it will just go through the recovery phase on startup, which can be even slower in stock InnoDB than the shutdown process, for a variety of reasons.
One way to decrease the shutdown time is to pre-flush the dirty pages, like this:
mysql> set global innodb_max_dirty_pages_pct = 0;
Now run the following command:
$ mysqladmin ext -i10 | grep dirty
| Innodb_buffer_pool_pages_dirty | 1823484 |
| Innodb_buffer_pool_pages_dirty | 1821293 |
| Innodb_buffer_pool_pages_dirty | 1818938 |
And wait until it approaches zero. (If the server is being actively used, it won’t get to zero.)
Once it’s pretty low, you can perform the shutdown and there’ll be a lot less unfinished work to do, so the server should shut down more quickly.