The default MySQL setting AUTOCOMMIT=1 can impose performance limitations on a busy database server. Where practical, wrap several related DML operations into a single transaction, by issuing SET AUTOCOMMIT=0 or a START TRANSACTION statement, followed by a COMMIT statement after making all the changes.

InnoDB must flush the log to disk at each transaction commit if that transaction made modifications to the database. When each change is followed by a commit (as with the default autocommit setting), the I/O throughput of the storage device puts a cap on the number of potential operations per second.

Avoid performing rollbacks after inserting, updating, or deleting huge numbers of rows. If a big transaction is slowing down server performance, rolling it back can make the problem worse, potentially taking several times as long to perform as the original DML operations. Killing the database process does not help, because the rollback starts again on server startup.

To minimize the chance of this issue occurring: increase the size of the buffer pool so that all the DML changes can be cached rather than immediately written to disk; set innodb_change_buffering=all so that update and delete operations are buffered in addition to inserts; and consider issuing COMMIT statements periodically during the big DML operation, possibly breaking a single delete or update into multiple statements that operate on smaller numbers of rows.

To get rid of a runaway rollback once it occurs, increase the buffer pool so that the rollback becomes CPU-bound and runs fast, or kill the server and restart with innodb_force_recovery=3, as explained in Section 13.6.7.1, “The InnoDB Recovery Process”.

This issue is expected to be less prominent in MySQL 5.5 and up, or in MySQL 5.1 with the InnoDB Plugin, because the default setting innodb_change_buffering=all allows update and delete operations to be cached in memory, making them faster to perform in the first place, and also faster to roll back if needed. Make sure to use this parameter setting on servers that process long-running transactions with many inserts, updates, or deletes.

If you can afford the loss of some of the latest committed transactions if a crash occurs, you can set the innodb_flush_log_at_trx_commit parameter to 0. InnoDB tries to flush the log once per second anyway, although the flush is not guaranteed. Also, set the value of innodb_support_xa to 0, which will reduce the number of disk flushes due to synchronizing on disk data and the binary log.

When rows are modified or deleted, the rows and associated undo logs are not physically removed immediately, or even immediately after the transaction commits. The old data is preserved until transactions that started earlier or concurrently are finished, so that those transactions can access the previous state of modified or deleted rows. Thus, a long-running transaction can prevent InnoDB from purging data that was changed by a different transaction.

When rows are modified or deleted within a long-running transaction, other transactions using the READ COMMITTED and REPEATABLE READ isolation levels have to do more work to reconstruct the older data if they read those same rows.

When a long-running transaction modifies a table, queries against that table from other transactions do not make use of the covering index technique. Queries that normally could retrieve all the result columns from a secondary index, instead look up the appropriate values from the table data.