InnoDB takes over an hour to import 600MB file, MyISAM in a few minutes

Solution 1:

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.

Solution 2:

Have you tried starting a transaction at the outset and committing it at the end? From the question you linked: "Modify the Insert Data step to start a transaction at the start and to commit it at the end. You will get an improvement, I guarantee it."

Remember that InnoDB is transactional, MyISAM is not. Transactional engines treat every statement as an individual transaction if you don't explicitly control the transaction. This can be costly.

Solution 3:

I found the hard drive to be the bottleneck - old-fashioned disks are hopeless, SSD is okay-ish but still far from perfect. Importing to tmpfs and copying out the data is way faster, details: https://dba.stackexchange.com/a/89367/56667

Solution 4:

I had issues doing a lot of bulk importing and recommend the accepted answer. I found you can also speed things up significantly by:

1. Dropping all indexes (other than primary key), loading the data then re-adding indexes
2. Checking your innodb_log_file_size * innodb_log_files_in_group is sufficient to avoid writing to disk in sub-second frequency

Regarding #2 the defaults of 5M * 2 will not be enough on a modern system. For details see innodb_log_file_size and innodb_log_files_in_group