Is it possible that your InnoDB settings are way too small ?

The default innodb_buffer_pool_size is 8M. Could you increase it ?

The default innodb_log_file_size is 5M. Could you increase it ?

You should resize them as follows:

Goto this link to compute the proper size for the innodb_buffer_pool_size based on the amount of InnoDB you have or 75% of installed RAM, whichever is smaller.

Once you have this number, set innodb_log_file_size to 25% of the computed innodb_buffer_pool_size. In order to resize them, you will have to shutdown mysql, delete the innodb log files, and start mysql.

Give it a Try !!!

CAVEAT

IMHO The reason for this conjecture is that lots of MVCC activity + default InnoDB configs spells a lot of internal InnoDB maintenance we may never know is going on.

Here are other possibilities :

• Could the .ibd file be corrupt ?
• Is the .ibd on a degraded array ?
• Is there an insufficient number for the innodb_open_files option ?
• Is tmpdir folder too full (tmp tables log jamming in the tmp folder) ???
• Are the my.cnf files of the two instances identical (less server_id) ???

ASPECT #1

What catches my eye here is innodb_flush_method. You do not have it set. What does this imply? That you are letting the OS do some of InnoDB's dirty work.

If you set innodb_flush_method to O_DIRECT (which uses fsync()), then mysqld will shoulder the responsibility of flushing data and metadata changes to disk. This may make disk I/O increase slightly but it should remain constant and will provide better data consistency.

Without setting innodb_flush_method, the default value is really O_DSYNC using fdatasync(). This gives you asynchronous writes to disk. It appears faster at first, but when the OS has to do some syncing of the data from its viewpoint, it hits this massive wall of activity that is simply unavoidable.

[mysqld]
innodb_flush_method=O_DIRECT

I have a post about this from Mar 04, 2011: Clarification on MySQL innodb_flush_method variable

ASPECT #2 (Optional)

I also noticed that you have ibdata1 and ibdata2 split up in innodb_data_file_path. You also have innodb_file_per_table configured. This means no data and no indexes are in the ibdata files. In light of this, what other classes of information live in ibdata1 and ibdata2?

• MVCC (Multiversioning Concurrency Control) Data
  • Rollback Segments
  • Undo Space
• Table Metadata (Data Dictionary)
• Double Write Buffer (background writing to prevent reliance on OS caching)
• Insert Buffer (managing changes to non-unique secondary indexes)
• See the Pictorial Representation of ibdata1

You can collapse this to one ibdata1 file. Otherwise, you could find yourself with situation like:

• UNDO logs split across the files that are needed for the same transaction
• UNDO logs and Rollback Segments split across the files that are needed for the same transaction
• InnoDB Buffer Pool using different tablespace files for double write buffering and index updates.

These may not be as I/O impacting as flushing to disk but would could present fragmentation challenges to InnoDB during normal operation.

If you choose to collapse InnoDB Infrastructure to a single tablespace file, please see my StackOverflow post on how : Howto: Clean a mysql InnoDB storage engine?

ASPECT #3

Without knowing your hardware, I would just the same look over your storage.

• Using InnoDB on RAID10? you need to check out
  • Every Disk in the Arrays for I/O issues
  • RAID Controller for Latest Firmware updates
  • RAID Controller Battery-Backed Cache : https://dba.stackexchange.com/questions/33431/consequences-of-using-innodb-flush-method-o-direct-without-having-a-battery/33434#33434
• Using InnoDB on SATA? Please move to a SAN
• Using InnoDB on RAID5? You need a good psychiatrist : Is raid 5 suitable for a mysql installation?