The way to tune InnoDB is centered around

• InnoDB Buffer Pool : It caches data pages and index pages. The amount of data and index you can cache is not a function of disk space constraints but a function of available memory and diskspace currently used by InnoDB.
• InnoDB MetaData : By default, the file ibdata1 normally houses anything and everything InnoDB. That would include data pages, index pages, table metadata, MVCC data.

Here is a formula I have used for the past 5 years to compute the InnoDB Buffer Pool based on diskspace used by InnoDB data and index pages:

SELECT CONCAT(ROUND(KBS/POWER(1024,IF(Power1024<0,0,
IF(Power1024>3,0,Power1024)))+0.49999),SUBSTR(' KMG',IF(Power1024<0,0,
IF(Power1024>3,0,Power1024))+1,1)) recommended_innodb_buffer_pool_size
FROM (SELECT SUM(data_length+index_length) KBS FROM information_schema.tables
WHERE engine='InnoDB') A,(SELECT 2 Power1024) B;

• Use (SELECT 0 Power1024) for Bytes
• Use (SELECT 1 Power1024) for KB
• Use (SELECT 2 Power1024) for MB
• Use (SELECT 3 Power1024) for GB
• Use (SELECT 4 Power1024) for TB (Email Me if you have TerraBytes of RAM)

Of course, I said a function of available memory and diskspace currently used by InnoDB. From here, just use common sense. The recommended number from the above query SHOULD NOT EXCEED 75% OF INSTALLED RAM !!! That's the simplest rule-of-thumb for sizing the InnoDB Buffer Pool.

You should also set innodb_flush_method to O_DIRECT since it will provided stable synchronous writes of InnoDB. I have also written a post on how to optimize Disk Storage for InnoDB.

With regard to the message Table does not support optimize, doing recreate + analyze instead, the reason why you get that error message is the fact that the storage engine is InnoDB. Mechanically, OPTIMIZE TABLE just copies the table to a temp table and performs ANALYZE TABLE.

In reality, ANALYZE TABLE against InnoDB is completely useless. Even if you ran ANALYZE TABLE on an InnoDB table, the InnoDB storage engine performs dives into the index for cardinality approximations over and over again, thus trashing the statistics you just compiled. In fact, Percona performed some tests on ANALYZE TABLE and came to that same conclusion as well.

Here are other posts I have made over the year about InnoDB Tuning

• https://stackoverflow.com/questions/3927690/howto-clean-a-mysql-innodb-storage-engine/4056261#4056261
• https://stackoverflow.com/questions/5248420/at-what-point-does-mysql-innodb-fine-tuning-become-a-requirement/5250306#5250306
• https://serverfault.com/questions/155455/how-do-myisam-and-innodb-utilize-hd-space/246111#246111
• https://serverfault.com/questions/230551/mysql-innodb-innodb-file-per-table-cons/231400#231400
• https://serverfault.com/questions/253059/mysql-innodb-optimisation/253233#253233
• How do you tune MySQL for a heavy InnoDB workload?

I have very bad news for you.

You should not have deleted the ibdata1 file. Here is why:

ibdata1 contains four type of information:

• table metadata
• MVCC data
• data pages (with innodb_file_per_table enabled)
• index pages (with innodb_file_per_table enabled)

Each InnoDB table created has a numercial id assigned to it via some auto increment metadata feature to each ibd file. That internal tablespace id (ITSID) is embedded in the .ibd file. That number is checked against the list of ITSIDs maintained, guess where, ... ibdata1.

I also have very good news for you along with some bad news.

It is possible to reconstruct ibdata1 to have the correct ITSIDs but it takes work to do it. While I personally have not done procedure alone, I assisted a client at my employer's web hosting to do this. We figured this out together but since the client hosed ibdata1, I let him do most of the work (30 InnoDB tables).

Anyway, here a past post I made in the DBA StackExchange. I answered another question whose root cause was the mixing up of ITSIDs.

To cut right to the chase, here is the article explaining what to do with reference to ITSID and how to massage ibdata1 into acknowledging the presence of the ITSID contained within the .ibd file.

I am sorry there is no quick-and-dirty method for recovering the .ibd file other than playing games with ITSIDs.

UPDATE 2011-10-17 06:19 EDT

Here is your original innodb configuration from your question:

innodb_file_per_table=1
innodb_flush_method=O_DIRECT
innodb_log_file_size=1G
innodb_buffer_pool_size=4G
innodb_data_file_path=ibdata1:10M:autoextend
innodb_buffer_pool_size = 384M
innodb_log_file_size=5M
innodb_lock_wait_timeout = 18000 

Please notice that innodb_log_file_size is there twice. Look carefully...

innodb_file_per_table=1
innodb_flush_method=O_DIRECT
innodb_log_file_size=1G <----
innodb_buffer_pool_size=4G
innodb_data_file_path=ibdata1:10M:autoextend
innodb_buffer_pool_size = 384M
innodb_log_file_size=5M <----
innodb_lock_wait_timeout = 18000 

The last setting of innodb_log_file_size takes precedence. MySQL expected to start up with the log files being 5M. Your ib_logfile0 and ib_logfile1 were 1G when you tried to start up mysqld. It saw a size conflict and took the path of least resistance, which was to disable InnoDB. That's why InnoDB was missing from show engines;. Mystery solved !!!

UPDATE 2011-10-17 11:07 EDT

The error message was deceptive because innodb_log_file_size was smaller than the log files (ib_logfile0 and ib_logfile1), which were 1G at the time. What's interesting is this: Corruption was reported because the file was expected to be 5M and the files were bigger. If the situation were reversed and the innodb log files were smaller than the declared size in my.cnf you should get something like this in the error log:

110216 9:48:41 InnoDB: Initializing buffer pool, size = 128.0M
110216 9:48:41 InnoDB: Completed initialization of buffer pool
InnoDB: Error: log file ./ib_logfile0 is of different size 0 5242880 bytes
InnoDB: than specified in the .cnf file 0 33554432 bytes!
110216 9:48:41 [ERROR] Plugin 'InnoDB' init function returned error.
110216 9:48:41 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.

In this example, the log files were already existing as 5M and the setting for innodb_log_file_size was bigger (in this case, 32M).

For this particular question, I blame MySQL (eh Oracle [still hate saying it]) for the inconsistent error message protocol.