Mysql innoDB write operations are extremely slow

I’m having serious performance problems with MySQL and the InnoDB engine. Even the simplest table makes writing operations (creating the table, inserting, updating and deleting) horribly slow, as you can see in the following snippet.

mysql> CREATE TABLE `test` (`id` int(11) not null auto_increment,
   -> PRIMARY KEY(`id`)) ENGINE=InnoDB;
Query OK, 0 rows affected (4.61 sec)

mysql> insert into test values ();
Query OK, 1 row affected (1.92 sec)

mysql> insert into test values ();
Query OK, 1 row affected (0.88 sec)

mysql> insert into test values ();
Query OK, 1 row affected (1.10 sec)

mysql> insert into test values ();
Query OK, 1 row affected (6.27 sec)

mysql> select * from test;
+----+
| id |
+----+
|  1 |
|  2 |
|  3 |
|  4 |
+----+
4 rows in set (0.00 sec)

mysql> delete from test where id = 2;
Query OK, 1 row affected (0.28 sec)

mysql> delete from test where id = 3;
Query OK, 1 row affected (6.37 sec)

I have been looking at htop and the long waiting times are not because of abnormal CPU load. It’s almost zero, and memory usage is also normal. If I create the same table using the MyISAM engine, then it works normally. My my.cnf file contains this (if I remember right I haven’t changed anything from the default Debian configuration):

[client]
port        = 3306
socket      = /var/run/mysqld/mysqld.sock
[mysqld_safe]
socket      = /var/run/mysqld/mysqld.sock
nice        = 0

[mysqld]
user        = mysql
pid-file    = /var/run/mysqld/mysqld.pid
socket      = /var/run/mysqld/mysqld.sock
port        = 3306
basedir     = /usr
datadir     = /var/lib/mysql
tmpdir      = /tmp
language    = /usr/share/mysql/english
skip-external-locking
bind-address        = 127.0.0.1
key_buffer      = 40M
max_allowed_packet  = 16M
thread_stack        = 128K
thread_cache_size       = 8
myisam-recover         = BACKUP
max_connections        = 100
table_cache            = 64
thread_concurrency     = 10
query_cache_limit   = 1M
query_cache_size        = 40M
log_slow_queries    = /var/log/mysql/mysql-slow.log
long_query_time = 2
log-queries-not-using-indexes
expire_logs_days    = 10
max_binlog_size         = 100M

[mysqldump]
quick
quote-names
max_allowed_packet  = 16M

[isamchk]
key_buffer      = 16M
!includedir /etc/mysql/conf.d/

I have also tried to restart the server, but it doesn’t solve anything.

The slow queries log doesn’t give any extra information.

• innodb_flush_log_at_trx_commit = 2 for better speed (=1 for better safety)

• sync_binlog = 0 if you are not using the binlog.

• “Batch” INSERTs — many rows in a single INSERT statement. (If you have lots, do 100 at a time.) LOAD DATA is also excellent for loading.

• innodb_buffer_pool_size = 70% of available RAM.

• auto_commit = 1, or use BEGIN ... COMMIT

• thread_stack = 256K I’m surprised it did not crash with your small value.

Still, the times (1s-6s) are grossly unreasonable. Even with everything set “wrong”, 0.1s for a simple INSERT should be expected.

Is this running in a “cloud”? Is something else going on?

Kindly ensure you have innodb_buffer_pool_size to 80% of your VM’s memory. And make other changes for InnoDB that best suite for your application. Below are the few recommendations. First try buffer_pool and let me know how inserts are going for you.

default-storage-engine         
innodb_file_per_table          
innodb_additional_mem_pool_size    
innodb_buffer_pool_size            
innodb_thread_concurrency          
innodb_flush_log_at_trx_commit     
innodb_log_buffer_size             
innodb_log_file_size               
innodb_log_files_in_group          
innodb_max_dirty_pages_pct         
innodb_lock_wait_timeout           

If your database is already slow, running batch inserts may decrease your performance further. Especially in InnoDB where each write operation is recorded in transaction logs.

Suggest that you first tune your system and/or upgrade hardware before taking the benefit of batch insertions in InnoDB.