You are using a transaction; autocommit does not disable transactions, it just makes them automatically commit at the end of the statement.

What is happening is, some other thread is holding a record lock on some record (you’re updating every record in the table!) for too long, and your thread is being timed out.

You can see more details of the event by issuing a

SHOW ENGINE INNODB STATUS\G 

mysql> set innodb_lock_wait_timeout=100

Query OK, 0 rows affected (0.02 sec)

mysql> show variables like 'innodb_lock_wait_timeout';
+--------------------------+-------+
| Variable_name            | Value |
+--------------------------+-------+
| innodb_lock_wait_timeout | 100   |
+--------------------------+-------+
---------------------------------------------------

Take a look on if your database is fine tuned. Especially the transactions isolation. Isn’t good idea to increase the innodb_lock_wait_timeout variable.

Check your database transaction isolation level in the mysql cli:

mysql> SELECT @@GLOBAL.tx_isolation, @@tx_isolation, @@session.tx_isolation;
+-----------------------+-----------------+------------------------+
| @@GLOBAL.tx_isolation | @@tx_isolation  | @@session.tx_isolation |
+-----------------------+-----------------+------------------------+
| REPEATABLE-READ       | REPEATABLE-READ | REPEATABLE-READ        |
+-----------------------+-----------------+------------------------+
1 row in set (0.00 sec)

You could get improvements changing de isolation level, use the oracle like READ COMMITTED instead REPEATABLE READ (InnoDB Defaults)

mysql> SET tx_isolation = 'READ-COMMITTED';
Query OK, 0 rows affected (0.00 sec)

mysql> SET GLOBAL tx_isolation = 'READ-COMMITTED';
Query OK, 0 rows affected (0.00 sec)

mysql> 
http://stackoverflow.com/questions/5836623/getting-lock-wait-timeout-exceeded-try-restarting-transaction-even-though-im

Lock wait timeout exceeded; try restarting transaction
http://www.tonyspencer.com/2008/10/23/if-you-get-this-in-mysql-lock-wait-timeout-exceeded-try-restarting-transaction/