This section describes what you can do when your
InnoDB tablespace runs out of room or when you
want to change the size of the log files.
From MySQL 3.23.50 and 4.0.2, the easiest way to increase the size
of the InnoDB tablespace is to configure it
from the beginning to be auto-extending. Specify the
autoextend attribute for the last data file in
the tablespace definition. Then InnoDB
increases the size of that file automatically in 8MB increments
when it runs out of space. Starting with MySQL 4.0.24 and 4.1.5,
the increment size can be changed by setting the value of the
innodb_autoextend_increment system variable,
which is measured in MB.
Alternatively, you can increase the size of your tablespace by
adding another data file. To do this, you have to shut down the
MySQL server, change the tablespace configuration to add a new
data file to the end of innodb_data_file_path,
and start the server again.
If your last data file was defined with the keyword
autoextend, the procedure for reconfiguring the
tablespace must take into account the size to which the last data
file has grown. Obtain the size of the data file, round it down to
the closest multiple of 1024 × 1024 bytes (= 1MB), and
specify the rounded size explicitly in
innodb_data_file_path. Then you can add another
data file. Remember that only the last data file in the
innodb_data_file_path can be specified as
auto-extending.
As an example, assume that the tablespace has just one
auto-extending data file ibdata1:
innodb_data_home_dir = innodb_data_file_path = /ibdata/ibdata1:10M:autoextend
Suppose that this data file, over time, has grown to 988MB. Here is the configuration line after modifying the original data file to not be auto-extending and adding another auto-extending data file:
innodb_data_home_dir = innodb_data_file_path = /ibdata/ibdata1:988M;/disk2/ibdata2:50M:autoextend
When you add a new file to the tablespace configuration, make sure
that it does not exist. InnoDB will create and
initialize the file when you restart the server.
Currently, you cannot remove a data file from the tablespace. To decrease the size of your tablespace, use this procedure:
Use mysqldump to dump all your
InnoDB tables.
Stop the server.
Remove all the existing tablespace files.
Configure a new tablespace.
Restart the server.
Import the dump files.
If you want to change the number or the size of your
InnoDB log files, you must stop the MySQL
server and make sure that it shuts down without errors (to ensure
that there is no information for outstanding transactions in the
logs). Then copy the old log files into a safe place just in case
something went wrong in the shutdown and you need them to recover
the tablespace. Delete the old log files from the log file
directory, edit my.cnf to change the log file
configuration, and start the MySQL server again.
mysqld sees that no log files exist at startup
and tells you that it is creating new ones.

User Comments
If you need to add/remove or change InnoDB datafiles you could change all InnoDB tables type to myisam:
ALTER TABLE table_name TYPE = myisam;
Then restart mysql server with new configuration and then change all tables type back to InnoDB:
ALTER TABLE table_name TYPE = innodb;
I'm not quite familiar with innodb storage engine, but there may some differences between innodb and myisam. InnoDB don't support FULLTEXT indexes, but in our case this is not a problem.
In the event you want to reduce the disk space allocated to the innodb you could follow the steps above. However, deviate from the instructions by setting innodb_file_per_table = 1 at some point before you re-import the tables. This will place all innodb tables into their own datafile. In the future you would be able to reclaim the excess table space on a per-table basis.
Simply run : ALTER TABLE `tbl_name` ENGINE=INNODB
I did follow the above instructions and made my time easy by making a shell script kit, see my docs at http://www.saturn.in/gpl/mysql.html
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