Random insertions into or deletions from a secondary index may cause the index to become fragmented. Fragmentation means that the physical ordering of the index pages on the disk is not close to the index ordering of the records on the pages, or that there are many unused pages in the 64-page blocks that were allocated to the index.

One symptom of fragmentation is that a table takes more space than it “should” take. How much that is exactly, is difficult to determine. All InnoDB data and indexes are stored in B-trees, and their fill factor may vary from 50% to 100%. Another symptom of fragmentation is that a table scan such as this takes more time than it “should” take:

SELECT COUNT(*) FROM t WHERE a_non_indexed_column <> 12345;

The preceding query requires MySQL to scan the clustered index rather than a secondary index. Most disks can read 10MB/s to 50MB/s, which can be used to estimate how fast a table scan should be.

To speed up index scans, you can periodically perform a “null” ALTER TABLE operation, which causes MySQL to rebuild the table:

ALTER TABLE tbl_name ENGINE=INNODB

Another way to perform a defragmentation operation is to use mysqldump to dump the table to a text file, drop the table, and reload it from the dump file.

If the insertions into an index are always ascending and records are deleted only from the end, the InnoDB filespace management algorithm guarantees that fragmentation in the index does not occur.