If you modify the innodb_log_file_size, MySQL will fail to restart and InnoDB will complain about the size of the changed log file.
The proper way to increase the innodb_log_file_size:
1. shutdown mysql server
2. make backup of data and log files
3. remove InnoDB log files
4. set new value for innodb_log_file_size in my.cnf
5. start mysqld
6. check error logs to ensure everything went fine.
Also see:
Choosing proper innodb_log_file_size
from MySQL DBA blog