Does your dataset consist of InnoDB tables with large BLOB data such that the data is stored in external BLOB pages? Was the dataset created in MySQL version 5.1 and below and without using the InnoDB plugin, or with InnoDB plugin but with MySQL version earlier than 5.1.55? If the answer to both the questions are "YES" then it could very well be that you have a hidden corruption lying around in your dataset.
Each day there is probably work done to improve performance of the InnoDB storage engine and remove bottlenecks and scalability issues. Hence there was another one I wanted to highlight: Scalability issues due to tables without primary keys. This scalability issue is caused by the usage of tables without primary keys. This issue typically shows itself as contention on the InnoDB dict_sys mutex. Now the dict_sys mutex controls access to the data dictionary. This mutex is used at various important places throughout the InnoDB code and as such any contention on the dict_sys mutex is going to have a InnoDB system-wide negative affect.
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I have been working with Peter in preparation for the talk comparing the optimizer enhancements in MySQL 5.6 and MariaDB 5.5. We are taking a look at and benchmarking optimizer enhancements one by one. So in the same way this blog post is aimed at a new optimizer enhancement Index Condition Pushdown (ICP). Its available in both MySQL 5.6 and MariaDB 5.5
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