Hacking MySQL 5!

I had the same thing happen -- only on a PRODUCTION database! When I went back to try to use the original in another location, my original was bad, as well!

I suspect that INNODB tables know their location in the file system, and won't work if moved or copied. I've crawled all over the website looking for clues, and found none. If this is true, you'd think it would be documented somewhere!
 

In InnoDB if you don't run it on separate file using 'innodb_file_per_table' in your my.ini/.conf, you'd end up having your database/tables stored in a huge file that is in data/. That is clearly explained in the manual.

Plus I've noticed that file_per_table generates huge files! I had a table which occupied 9M on InnoDB, I converted it to MyISAM and it reduced to only 550KB.

How did you get things in order? mysqldump and reload?
 

You can't copy the InnoDB tables from directory to directory or installation to installation as you can with MyISAM. Not even with InnoDB's file per table option:

"Note: You cannot freely move .ibd files between database directories as you can with MyISAM table files. This is because the table definition is stored in the InnoDB shared tablespace, and because InnoDB must preserve the consistency of transaction IDs and log sequence numbers." http://dev.mysql.com/doc/refman/5.0/en/multiple-tablespaces.html

The error log probably had an error message which directed you to the manual page on troubleshooting InnoDB data dictionary operations. If it didn't and you're using one of the latest builds, please file a bug report about the faulty error message. Page is at http://dev.mysql.com/doc/refman/5.0/en/innodb-troubleshooting-datadict.html .

Innodb_file_per_table isn't really responsible for huge file sizes. InnoDB itself has them, though it's improved quite a bit in 5.0 with the compact row format. Chances are that the table either has lots of NULLs or lots of rows with small column sizes. Either of those multiplies the overhead effect. Heikki wrote a bit about this at http://forums.mysql.com/read.php?22,58946,58946#msg-58946 . There should be substantial improvement if the compressed format ends up in 5.1 - gzip compression at page level.

James Day, Support Engineer, MySQL AB.
 

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