Mysql – Changing tables from MyISAM to InnoDB make the system slow

• Setting a large innodb_buffer_pool_size (2GB or more)
• preread your old myisam data/index files using shell commands
• increase innodb_log_file_size (256 MB)
• Do the alter table in X parallel threads, where X is the qty of CPU cores on your server
• other minor tweaks for conversion only (innodb_doublewrite=0, innodb_flush_log_at_trx_commit=0)

setting innodb_buffer_pool_size as high as possible is the typical way to speed up innodb tables creation - your dataset looks like it could fit inside a 2GB innodb buffer pool, so any decent 64 bits server should allow that. alter table type=innodb is also faster than dump+reimport solution, and is easy to run in parallel.

Also make sure you have increased the innodb_log_file_size from the default of 5Mb to 128 or 256MB. Careful with that, and it needs a clean shutdown + erasing the old ib_logfile*.

If your server has something like 8GB of ram, and that you run a 64 bits version of mysql I would suggest a 2GB innodb_buffer_pool, and you can even preread the old MYD and MYI files before closing for downtime, so that they will be in the OS's page cache when the real work starts.

If you also go for the minor tweaks, please keep in mind that you need to undo them after the conversion (another small downtime) to have your data safe, I doubt they are worth it for such a small dataset though.

Good luck.

Did you try the Bulk Data Loading Tips from the InnoDB Performance Tuning Tips (especially the first one):

• When importing data into InnoDB, make sure that MySQL does not have autocommit mode enabled because that requires a log flush to disk for every insert. To disable autocommit during your import operation, surround it with SET autocommit and COMMIT statements:

  SET autocommit=0;
  ... SQL import statements ...
  COMMIT;
  

  If you use the mysqldump option --opt, you get dump files that are fast to import into an InnoDB table, even without wrapping them with the SET autocommit and COMMIT statements.

• If you have UNIQUE constraints on secondary keys, you can speed up table imports by temporarily turning off the uniqueness checks during the import session:

  SET unique_checks=0;
  ... SQL import statements ...
  SET unique_checks=1;
  

  For big tables, this saves a lot of disk I/O because InnoDB can use its insert buffer to write secondary index records in a batch. Be certain that the data contains no duplicate keys.

• If you have FOREIGN KEY constraints in your tables, you can speed up table imports by turning the foreign key checks off for the duration of the import session:

  SET foreign_key_checks=0;
  ... SQL import statements ...
  SET foreign_key_checks=1;
  

  For big tables, this can save a lot of disk I/O.

IMO, the whole chapter is worth the read.