Открываем /etc/my.cnf
Добавляем
[mysqld]
# InnoDB settings
innodb_data_home_dir =
innodb_data_file_path = ibdata1:100M:autoextend
set-variable = innodb_buffer_pool_size=100M
set-variable = innodb_additional_mem_pool_size=10M
innodb_flush_log_at_trx_commit=1
Убираем skip-innodb.
Перезагружаем — пользуемся.