We're running a social networking site that logs every member's action (including visiting other member's pages); this involves a lot of writes to the db. These actions are stored in a MyISAM table and since something is starting to tax the CPU, my first thought was that it's the table locking of MyISAM that is causing this stress on the CPU.
Notwithstanding any benefits / drawbacks of its use, which are discussed in other threads ( MyISAM versus InnoDB ), migration is a nontrivial process.
Consider
You will doubtless need to change things in a large software platform; this is ok, but seeing as you (hopefully) have a lot of auto-test coverage, change should be acceptable.
PS: If "Something is starting to tax the CPU", then you should a) Find out what, in a non-production environment, b) Try various options to reduce it, in a non-production environment. You should not blindly start doing major things like changing database engines when you haven't fully analysed the problem.
All performance testing should be done in a non-production environment, with production-like data and on production-grade hardware. Otherwise it is difficult to interpret results correctly.
With regards to other potential migration problems:
1) Space - InnoDB tables often require more disk space, though the Barracuda file format for new versions of InnoDB have narrowed the difference. You can get a sense for this by converting a recent backup of the tables and comparing the size. Use "show table status" to compare the data length.
2) Full text search - only on MyISAM
3) GIS/Spatial datatypes - only on MyISAM
On performance, as the other answers and the referenced answer indicate, it depends on your workload. MyISAM is much faster for full table scans. InnoDB tends to be much faster for highly concurrent access. InnoDB can also be much faster if your lookups are based on the primary key.
Another performance issue is that MyISAM can always keep a row count, since it only does table level locking. So, if you're frequently trying to get the row count for a very large table, it may be much slower with InnoDB. Search the Internet if you need a workaround for this, as I've seen several proposed.
Depending on the size of the table(s), you may also need to update your MySQL config file. At the very least, you may want to shift bytes from key_buffer to innodb_buffer_pool_size. You won't get a fair comparison if you leave the database as being optimized for MyISAM. Read up on all the innodb_* configuration properties.
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