CREATE TABLE t1 (x INT NOT NULL UNIQUE KEY) ENGINE=InnoDB; INSERT INTO t1 VALUES(5); SET GLOBAL innodb_log_checkpoint_now=TRUE; SET DEBUG_SYNC='commit_cache_rebuild SIGNAL ready WAIT_FOR finish'; ALTER TABLE t1 ADD PRIMARY KEY(x); connect con1,localhost,root,,; SET DEBUG_SYNC='now WAIT_FOR ready'; SET GLOBAL innodb_log_checkpoint_now=TRUE; SET DEBUG_SYNC='now SIGNAL finish'; disconnect con1; connection default; SHOW CREATE TABLE t1; Table Create Table t1 CREATE TABLE `t1` ( `x` int(11) NOT NULL, PRIMARY KEY (`x`), UNIQUE KEY `x` (`x`) ) ENGINE=InnoDB DEFAULT CHARSET=latin1 DROP TABLE t1; SET DEBUG_SYNC='RESET';