Convert InnoDB tables to use a separate idb files instead of the shared, giant ibdata1.

convert_innodb_to_per_table_idb.rb

#!/usr/bin/env ruby

# Converts an InnoDB database that uses a shared InnoDB tablespace file (e.g. ibdata1) to use
# a separate file per table.
#
# - First change your my.cnf file to use separate files by adding "innodb_file_per_table" to 
#   the [mysqld] section. (This is safe: MySQL will revert to the giant file if it cannot find
#   the per table file.)
# - Restart the MySQL server
# - cd to the directory of your database (cd /opt/mysql/data/mydb)
# - Run this script from that directory
#
# This script will run ALTER TABLE name ENGINE=InnoDB for all your tables that are not yet converted.
# This will move the data of that table to a separate idb file and this can take quite some time. 
# You can interrupt this script at any time; restarting it will resume the operation. The database
# will remain functional (albeit slow) at all times)
#
# After you have converted *ALL* databases into using separate ibd files, you can remove the
# ibdata1 files (and ibdata2, ibdata3, ...)

require 'rubygems'
require 'mysql2'
require 'benchmark'

frm_files = Dir['./*.frm'].map { |file| File.basename(file, '.frm') }
idb_files = Dir['./*.ibd'].map { |file| File.basename(file, '.ibd') }

current_database = File.basename(Dir.pwd)
unconverted_tables = frm_files - idb_files

if unconverted_tables.size > 0
  client = Mysql2::Client.new(:host => 'localhost', :username => 'root', :database => current_database)

  if idb_files.empty?
    puts "Starting conversion of #{current_database} database."
  else
    puts "Resuming conversion of #{current_database} database."
  end
  
  puts " Tables to convert: "
  puts "- " + unconverted_tables.join("\n- ")
  puts

  unconverted_tables.each do |table|
    print "Converting table #{table}..."
    $stdout.flush
    duration = Benchmark.realtime { client.query("ALTER TABLE #{table} ENGINE=InnoDB") }
    puts ' Done in %0.2fs!' % duration
  end

  puts "Finished conversion!"
else
  puts "#{current_database} database already completely converted."
end

Hello! Found this and wanted to run after installing a few dependencies on my Ubuntu 12.04.5 chrooted. I run into an error then:

Converting table time_zone_name.../var/lib/gems/1.8/gems/mysql2-0.4.5/lib/mysql2/client.rb:125:in _query': Storage engine 'InnoDB' does not support system tables. [mysql.time_zone_name] (Mysql2::Error) from /var/lib/gems/1.8/gems/mysql2-0.4.5/lib/mysql2/client.rb:125:in \query'
from ./convert_innodb_to_per_table_ibd.rb:47
from /usr/lib/ruby/1.8/benchmark.rb:308:in `realtime'
from ./convert_innodb_to_per_table_ibd.rb:47
from ./convert_innodb_to_per_table_ibd.rb:44:in `each'
from ./convert_innodb_to_per_table_ibd.rb:44

On mysql5.5, if you run this, the tables convert, but when you rm ibdata1 and ib_logfile0, etc, then do a mysql restart, your DB will become corrupted. The meta data saved in ibdata1 is now lost. Isn't this also the case on higher versions of MySQL, up to 5.7?