ENABLE/DISABLE KEYS lag: how to optimize?
There are some rare occasions when mysqld processes ALTER TABLE ... ENABLE KEYS; and you get Repair by keycache. The real question to ask is Under what circumstances does mysqld perform Repair by keycache ?

According to MySQL Documentation on General Thread States


  Repair with keycache
  
  The repair code is using creating keys one by one through the key cache. This is much slower than Repair by sorting.


There are one or more server variables in the session that could potentially affect this behavior


sort_buffer_size


Independent of Storage Engine
The default is 256K
If this is set to 2M and mysqld needs more that 2M to process a sort operation, the session dumps the 2M it has in the sort buffer to a temporary MyISAM table, then continue processing from there.

innodb_sort_buffer_size


Default: 1M, MinValue: 64K, MaxValue: 64M
Documentation says three buffers of this size are allocated for an ALTER TABLE or CREATE TABLE statement that creates an index.

myisam_sort_buffer_size


Default value is 8M.
Definition : The size of the buffer that is allocated when sorting MyISAM indexes during a REPAIR TABLE or when creating indexes with CREATE INDEX or ALTER TABLE.
If the sort operation needs more than 8M, there is where mysqld will make the session stop doing Repair by sorting and switch to Repair by keycache.



SUGGESTION

Based on the MySQL Documentation on sort_buffer_size


  As of MySQL 5.6.4, the optimizer tries to work out how much space is needed but can allocate more, up to the limit. Before MySQL 5.6.4, the optimizer allocates the entire buffer even if it is not all needed. In either case, setting it larger than required globally will slow down most queries that sort. It is best to increase it as a session setting, and only for the sessions that need a larger size. On Linux, there are thresholds of 256KB and 2MB where larger values may significantly slow down memory allocation, so you should consider staying below one of those values. Experiment to find the best value for your workload. See Section B.5.4.4, “Where MySQL Stores Temporary Files”.


Only sort_buffer_size and myisam_sort_buffer_size can be changed for the session.

If you don't have a lot of memory, change myisam_sort_buffer_size so that a larger temp table can be formed. To set it to 1G in your session, do one of the following before executing a large reindexing:

SET myisam_sort_buffer_size = 1024 * 1024 * 1024;


or

SET SESSION myisam_sort_buffer_size = 1024 * 1024 * 1024;


That way, the temp table on disk will be allowed to grow to 1G. Make sure the folder mapped to tmpdir can hold large temp tables.

If you want 1G as the permanent setting for myisam_sort_buffer_size going forward, do this

STEP #1 : Add this to /etc/my.cnf

[mysqld]
myisam_sort_buffer_size=1G


This will allow connections to have this setting after mysqld is restarted.

STEP #2 : Login to mysql as root@localhost and run

SET GLOBAL myisam_sort_buffer_size = 1024 * 1024 * 1024;


This will enabled new connections to have this setting. Current connections would have to be closed and reopened (perhaps restarting apache/tomcat/Hibernate or whatever web server you are using).

MY OTHER POSTS ON Repair by keycache


May 09, 2012 : ENABLE KEYS on a large table is crashing mysql
May 17, 2013 : MySQL Hanging Completely when `ALTER TABLE... ENABLE KEYS`
Aug 12, 2013 : MySQL MyISAM index causes query to match no rows; indexes disabled, rows match