A fresh pair of logs is needed for the variable 'innodb_log_block_size' to be changed, which means a clean restart and removal of the old logs. Here is how I tested it: [root@ovaistariq-net mysql-test]# ./mtr --start-and-exit Logging: ./mtr --start-and-exit 120922 13:38:24 [Note] Flashcache bypass: disabled 120922 13:38:24 [Note] Flashcache setup error is : ioctl failed 120922 13:38:24 [Note] Plugin 'FEDERATED' is disabled. MySQL Version 5.5.23 Checking supported features... - skipping ndbcluster - SSL connections supported Using suites: main,sys_vars,binlog,federated,rpl,innodb,perfschema Collecting tests... vardir: /work/sources/percona-server/5.5.23-25.3/Percona-Server/mysql-test/var Removing old var directory... Creating var directory '/work/sources/percona-server/5.5.23-25.3/Percona-Server/mysql-test/var'... Installing system database... Using server port 59141 ============================================================================== TEST RESULT TIME (ms) or COMMENT -------------------------------------------------------------------------- worker[1] - 'localhost:13000' was not free worker[1] Using MTR_BUILD_THREAD 301, with reserved ports 13010..13019 worker[1] mysql-test-run: WARNING: running this script as _root_ will cause some tests to be skipped worker[1] Started [mysqld.1 - pid: 10340, winpid: 10340] worker[1] Using config for test main.1st worker[1] Port and socket path for server(s): worker[1] mysqld.1 13010 /work/sources/percona-server/5.5.23-25.3/Percona-Server/mysql-test/var/tmp/mysqld.1.sock worker[1] Server(s) started, not waiting for them to finish [root@ovaistariq-net mysql-test]# ../client/mysql -S ./var/tmp/mysqld.1.sock Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 1 Server version: 5.5.23-rel25.3-log Percona Server with XtraDB (GPL), Release rel25.3, Revision 240 Copyright (c) 2000, 2011, Oracle and/or its affiliates. All rights reserved. Oracle is a registered trademark of Oracle Corporation and/or its affiliates. Other names may be trademarks of their respective owners. Type 'help;' or '\h' for help. Type '\c' to clear the current input statement. mysql> select @@innodb_log_block_size; +-------------------------+ | @@innodb_log_block_size | +-------------------------+ | 512 | +-------------------------+ 1 row in set (0.00 sec) mysql> set global innodb_log_block_size=4*1024; ERROR 1238 (HY000): Variable 'innodb_log_block_size' is a read only variable mysql> Bye [root@ovaistariq-net mysql-test]# vim ./var/my.cnf innodb_log_block_size=4096 [root@ovaistariq-net mysql-test]# ../client/mysqladmin -S ./var/tmp/mysqld.1.sock shutdown 120922 13:58:31 [Note] /work/sources/percona-server/5.5.23-25.3/Percona-Server/sql/mysqld: Normal shutdown 120922 13:58:31 [Note] Event Scheduler: Purging the queue. 0 events 120922 13:58:32 InnoDB: Starting shutdown... 120922 13:58:35 InnoDB: Shutdown completed; log sequence number 12599894 120922 13:58:35 [Note] /work/sources/percona-server/5.5.23-25.3/Percona-Server/sql/mysqld: Shutdown complete [root@ovaistariq-net mysql-test]# /work/sources/percona-server/5.5.23-25.3/Percona-Server/sql/mysqld --defaults-group-suffix=.1 --defaults-file=/work/sources/percona-server/5.5.23-25.3/Percona-Server/mysql-test/var/my.cnf --user=root --log-output=file --default-storage-engine=MyISAM --loose-skip-log-bin --core-file --loose-debug-sync-timeout=300 & [1] 10397 [root@ovaistariq-net mysql-test]# 120922 13:58:40 [Note] Flashcache bypass: disabled 120922 13:58:40 [Note] Flashcache setup error is : ioctl failed 120922 13:58:40 [Note] Plugin 'FEDERATED' is disabled. InnoDB: Warning: innodb_log_block_size has been changed from default value 512. (###EXPERIMENTAL### operation) InnoDB: The log block size is set to 4096. 120922 13:58:40 InnoDB: The InnoDB memory heap is disabled 120922 13:58:40 InnoDB: Mutexes and rw_locks use GCC atomic builtins 120922 13:58:40 InnoDB: Compressed tables use zlib 1.2.3 120922 13:58:40 InnoDB: Using Linux native AIO 120922 13:58:40 InnoDB: Initializing buffer pool, size = 32.0M 120922 13:58:40 InnoDB: Completed initialization of buffer pool 120922 13:58:40 InnoDB: highest supported file format is Barracuda. InnoDB: No valid checkpoint found. InnoDB: If this error appears when you are creating an InnoDB database, InnoDB: the problem may be that during an earlier attempt you managed InnoDB: to create the InnoDB data files, but log file creation failed. InnoDB: If that is the case, please refer to InnoDB: http://dev.mysql.com/doc/refman/5.5/en/error-creating-innodb.html 120922 13:58:40 [ERROR] Plugin 'InnoDB' init function returned error. 120922 13:58:40 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed. 120922 13:58:40 [Warning] /work/sources/percona-server/5.5.23-25.3/Percona-Server/sql/mysqld: unknown variable 'loose-debug-sync-timeout=300' 120922 13:58:40 [Note] Event Scheduler: Loaded 0 events 120922 13:58:40 [Note] /work/sources/percona-server/5.5.23-25.3/Percona-Server/sql/mysqld: ready for connections. Version: '5.5.23-rel25.3-log' socket: '/work/sources/percona-server/5.5.23-25.3/Percona-Server/mysql-test/var/tmp/mysqld.1.sock' port: 13010 Percona Server with XtraDB (GPL), Release rel25.3, Revision 240 [root@ovaistariq-net mysql-test]# ../client/mysql -S ./var/tmp/mysqld.1.sock Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 1 Server version: 5.5.23-rel25.3-log Percona Server with XtraDB (GPL), Release rel25.3, Revision 240 Copyright (c) 2000, 2011, Oracle and/or its affiliates. All rights reserved. Oracle is a registered trademark of Oracle Corporation and/or its affiliates. Other names may be trademarks of their respective owners. Type 'help;' or '\h' for help. Type '\c' to clear the current input statement. mysql> show engines; +--------------------+---------+----------------------------------------------------------------+--------------+------+------------+ | Engine | Support | Comment | Transactions | XA | Savepoints | +--------------------+---------+----------------------------------------------------------------+--------------+------+------------+ | FEDERATED | NO | Federated MySQL storage engine | NULL | NULL | NULL | | MRG_MYISAM | YES | Collection of identical MyISAM tables | NO | NO | NO | | MyISAM | DEFAULT | MyISAM storage engine | NO | NO | NO | | BLACKHOLE | YES | /dev/null storage engine (anything you write to it disappears) | NO | NO | NO | | CSV | YES | CSV storage engine | NO | NO | NO | | MEMORY | YES | Hash based, stored in memory, useful for temporary tables | NO | NO | NO | | ARCHIVE | YES | Archive storage engine | NO | NO | NO | | PERFORMANCE_SCHEMA | YES | Performance Schema | NO | NO | NO | +--------------------+---------+----------------------------------------------------------------+--------------+------+------------+ 8 rows in set (0.00 sec) mysql> Bye [root@ovaistariq-net mysql-test]# ../client/mysqladmin -S ./var/tmp/mysqld.1.sock shutdown 120922 14:04:11 [Note] /work/sources/percona-server/5.5.23-25.3/Percona-Server/sql/mysqld: Normal shutdown 120922 14:04:11 [Note] Event Scheduler: Purging the queue. 0 events 120922 14:04:11 [Note] /work/sources/percona-server/5.5.23-25.3/Percona-Server/sql/mysqld: Shutdown complete [root@ovaistariq-net mysql-test]# mv ./var/mysqld.1/data/ib_logfile0 ./var/mysqld.1/data/ib_logfile0.bak [root@ovaistariq-net mysql-test]# mv ./var/mysqld.1/data/ib_logfile1 ./var/mysqld.1/data/ib_logfile1.bak [root@ovaistariq-net mysql-test]# /work/sources/percona-server/5.5.23-25.3/Percona-Server/sql/mysqld --defaults-group-suffix=.1 --defaults-file=/work/sources/percona-server/5.5.23-25.3/Percona-Server/mysql-test/var/my.cnf --user=root --log-output=file --default-storage-engine=MyISAM --loose-skip-log-bin --core-file --loose-debug-sync-timeout=300 & [1] 10428 [root@ovaistariq-net mysql-test]# 120922 14:05:25 [Note] Flashcache bypass: disabled 120922 14:05:25 [Note] Flashcache setup error is : ioctl failed 120922 14:05:25 [Note] Plugin 'FEDERATED' is disabled. InnoDB: Warning: innodb_log_block_size has been changed from default value 512. (###EXPERIMENTAL### operation) InnoDB: The log block size is set to 4096. 120922 14:05:25 InnoDB: The InnoDB memory heap is disabled 120922 14:05:25 InnoDB: Mutexes and rw_locks use GCC atomic builtins 120922 14:05:25 InnoDB: Compressed tables use zlib 1.2.3 120922 14:05:25 InnoDB: Using Linux native AIO 120922 14:05:25 InnoDB: Initializing buffer pool, size = 32.0M 120922 14:05:25 InnoDB: Completed initialization of buffer pool 120922 14:05:25 InnoDB: Log file ./ib_logfile0 did not exist: new to be created InnoDB: Setting log file ./ib_logfile0 size to 5 MB InnoDB: Database physically writes the file full: wait... 120922 14:05:26 InnoDB: Log file ./ib_logfile1 did not exist: new to be created InnoDB: Setting log file ./ib_logfile1 size to 5 MB InnoDB: Database physically writes the file full: wait... 120922 14:05:26 InnoDB: highest supported file format is Barracuda. InnoDB: The log sequence number in ibdata files does not match InnoDB: the log sequence number in the ib_logfiles! 120922 14:05:26 InnoDB: Database was not shut down normally! InnoDB: Starting crash recovery. InnoDB: Reading tablespace information from the .ibd files... InnoDB: Restoring possible half-written data pages from the doublewrite InnoDB: buffer... 120922 14:05:26 InnoDB: Waiting for the background threads to start 120922 14:05:27 Percona XtraDB (http://www.percona.com) 1.1.8-rel25.3 started; log sequence number 12603404 120922 14:05:27 [Warning] /work/sources/percona-server/5.5.23-25.3/Percona-Server/sql/mysqld: unknown variable 'loose-debug-sync-timeout=300' 120922 14:05:27 [Note] Event Scheduler: Loaded 0 events 120922 14:05:27 [Note] /work/sources/percona-server/5.5.23-25.3/Percona-Server/sql/mysqld: ready for connections. Version: '5.5.23-rel25.3-log' socket: '/work/sources/percona-server/5.5.23-25.3/Percona-Server/mysql-test/var/tmp/mysqld.1.sock' port: 13010 Percona Server with XtraDB (GPL), Release rel25.3, Revision 240 [root@ovaistariq-net mysql-test]# ../client/mysql -S ./var/tmp/mysqld.1.sock Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 1 Server version: 5.5.23-rel25.3-log Percona Server with XtraDB (GPL), Release rel25.3, Revision 240 Copyright (c) 2000, 2011, Oracle and/or its affiliates. All rights reserved. Oracle is a registered trademark of Oracle Corporation and/or its affiliates. Other names may be trademarks of their respective owners. Type 'help;' or '\h' for help. Type '\c' to clear the current input statement. mysql> select @@innodb_log_block_size; +-------------------------+ | @@innodb_log_block_size | +-------------------------+ | 4096 | +-------------------------+ 1 row in set (0.00 sec) mysql> Bye [root@ovaistariq-net mysql-test]# ../client/mysqladmin -S ./var/tmp/mysqld.1.sock shutdown 120922 14:22:10 [Note] /work/sources/percona-server/5.5.23-25.3/Percona-Server/sql/mysqld: Normal shutdown 120922 14:22:10 [Note] Event Scheduler: Purging the queue. 0 events 120922 14:22:10 InnoDB: Starting shutdown... 120922 14:22:12 InnoDB: Shutdown completed; log sequence number 12603534 120922 14:22:12 [Note] /work/sources/percona-server/5.5.23-25.3/Percona-Server/sql/mysqld: Shutdown complete