InnoDB slowness

[jesusbagpuss]

Creation/population of some tables is slow in InnoDB.
As some tables are re-created each run (set and grouping tables), these wull use the default MySQL storage engine. This used to be MyISAM, but is now InnoDB.
This can lead to various engines being used e.g.

+--------------------------------+--------+
| TABLE_NAME                     | ENGINE |
+--------------------------------+--------+
| irstats2_browsers              | MyISAM |
| irstats2_cache_set_values      | InnoDB |
| irstats2_countries             | MyISAM |
| irstats2_deposits              | InnoDB |
| irstats2_doc_access            | InnoDB |
| irstats2_doc_format            | InnoDB |
| irstats2_downloads             | MyISAM |
| irstats2_groupings_authors     | InnoDB |
| irstats2_groupings_iau         | InnoDB |
| irstats2_groupings_institution | InnoDB |
| irstats2_groupings_type        | InnoDB |
| irstats2_history               | MyISAM |
| irstats2_internal              | MyISAM |
| irstats2_referrer              | MyISAM |
| irstats2_search_terms          | MyISAM |
| irstats2_sets_authors          | InnoDB |
| irstats2_sets_iau              | InnoDB |
| irstats2_sets_institution      | InnoDB |
| irstats2_sets_type             | InnoDB |
| irstats2_views                 | MyISAM |
+--------------------------------+--------+

The irstats2_cache_set_values, irstats2_groupings_*, and irstats2_sets_* tables do not have a primary key, so record insertion with the InnoDB engine is slower (http://stackoverflow.com/questions/9114209/innodb-inserts-very-slow-and-slowing-down).