The impact of enabling MySQL sync_binlog – really high disk IO

If you enable this feature in your MySQL you could

increase your disk IO time and write by 8-10x times.

Generally this feature could save your replication scheme if a power failure occurs or OS crash and it could guarantee that no transaction is lost from the binary log. When enabled the binary log is synchronized on disk before transactions are committed. You can check the manual here: https://dev.mysql.com/doc/refman/5.7/en/replication-options-binary-log.html#sysvar_sync_binlog and it also says there could be a great impact on disk writes but how many?
So here are two setups:

SETUP 1) 2 x 3T hard drives TOSHIBA DT01ACA300 in software RAID1

The impact of setting the sync_binlog=1 is 8-10 times the IO time and IO writes. Here is images of several hours of sync_binlog=1 and then we disabled it online:

SCREENSHOT 1) Enable the binary log synchronization with sync_binlog=1.

As you can see the increase in the disk IO time and disk write IOPS are significant – somewhere between 5 and 6 times more! The load is not increased more than 1.5x as normal, but it should be noted the server is off-peak and it has plenty of RAM 32G. Still mush load when some other IO appears.

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Set MySQL sync_binlog=1 in a software raid of two hard drives

SCREENSHOT 2) Disabling the binary log synchronization with sync_binlog=0.

The decrease of the disk IO time and disk write IOPS are significant – somewhere between 5 and 6 times more! Everything back to normal.

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Set MySQL sync_binlog=0 in a software raid of two hard drives.

SCREENSHOT 3) Enable the binary log synchronization with sync_binlog=1.

As you can see the increase in the disk IO time and disk write IOPS are significant – somewhere between 8 and 10 times more! The load is not increased, but it should be noted the server is off-peak and it has plenty of RAM 192G. Still mush load when some other IO appears.

SET GLOBAL sync_binlog=0;

SETUP 2) 2 x 960G SSD SAMSUNG SM863 in software RAID1

The impact of setting the sync_binlog=1 is also 8-10 times the IO time and IO writes. Here is images of several hours of sync_binlog=1 and then we disabled it online:

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Set MySQL sync_binlog=1 in a software raid of two enterprise SSDs

SCREENSHOT 4) Disabling the binary log synchronization with sync_binlog=0.

The decrease of the disk IO time and disk write IOPS are significant – somewhere between 8 and 10 times more and even more! Everything back to normal.

main menu
Set MySQL sync_binlog=0 in a software raid of two enterprise SSDs

SCREENSHOT 5) Enable the binary log synchronization with sync_binlog=1.

Just the period of the graphs are bigger. As you can see the increase in the disk IO time and disk write IOPS are significant – somewhere between 8 and 10 times more! The load is not increased, but it should be noted the server is off-peak and it has plenty of RAM 192G. Still mush load when some other IO appears.

main menu
Set MySQL sync_binlog=1 in a software raid of two enterprise SSDs (big period)

SCREENSHOT 6) Disabling the binary log synchronization with sync_binlog=0.

Just the period of the graphs are bigger. The decrease of the disk IO time and disk write IOPS are significant – somewhere between 8 and 10 times more and even more! Everything back to normal.

main menu
Set MySQL sync_binlog=0 in a software raid of two enterprise SSDs (big period)

BONUS – MySQL changed the default value from 0 (disabled) to 1 (enabled) from 5.7 (in fact MySQL >= 5.7.7).

SO BE CAREFUL now when upgrading from older versions like MySQL 5.1, 5.5, 5.6 – you would probably need to disable it in the MySQL configuration file my.cnf.

mysql – Error ‘Column count of mysql.user is wrong. Expected 45, found 43. The table is probably corrupted’ on query.

If you

upgraded your MySQL server (from 5.6 to 5.7 or above)

or

imported a MySQL dump SQL file from older version

than your current server you may encounter when granting permissions to a user:

Error 'Column count of mysql.user is wrong. Expected 45, found 43. The table is probably corrupted' on query. Default database: ''. Query: 'GRANT REPLICATION SLAVE ON *.* TO 'replusr'@'144.76.156.182''

Do not panic probably it is not corrupted just continue reading.

There is the simple fix, just

execute mysql_upgrade

It will automatically detect what to upgrade and it will upgrade it:

[myuser@mysql1 ~]# screen -R upgrade
[myuser@mysql1 ~]# mysql_upgrade 
Checking if update is needed.
Checking server version.
Running queries to upgrade MySQL server.
Checking system database.
mysql.columns_priv                                 OK
mysql.db                                           OK
mysql.engine_cost                                  OK
mysql.event                                        OK
mysql.func                                         OK
mysql.general_log                                  OK
mysql.gtid_executed                                OK
mysql.help_category                                OK
mysql.help_keyword                                 OK
mysql.help_relation                                OK
mysql.help_topic                                   OK
mysql.host                                         OK
mysql.innodb_index_stats                           OK
mysql.innodb_table_stats                           OK
mysql.ndb_binlog_index                             OK
mysql.plugin                                       OK
mysql.proc                                         OK
mysql.procs_priv                                   OK
mysql.proxies_priv                                 OK
mysql.server_cost                                  OK
mysql.servers                                      OK
mysql.slave_master_info                            OK
mysql.slave_relay_log_info                         OK
mysql.slave_worker_info                            OK
mysql.slow_log                                     OK
mysql.tables_priv                                  OK
mysql.time_zone                                    OK
mysql.time_zone_leap_second                        OK
mysql.time_zone_name                               OK
mysql.time_zone_transition                         OK
mysql.time_zone_transition_type                    OK
mysql.user                                         OK
The sys schema is already up to date (version 1.5.1).
Found 0 sys functions, but expected 22. Re-installing the sys schema.
Upgrading the sys schema.
Checking databases.
phpmyadmin.pma__bookmark                           OK
phpmyadmin.pma__central_columns                    OK
phpmyadmin.pma__column_info                        OK
phpmyadmin.pma__designer_settings                  OK
phpmyadmin.pma__export_templates                   OK
phpmyadmin.pma__favorite                           OK
phpmyadmin.pma__history                            OK
phpmyadmin.pma__navigationhiding                   OK
phpmyadmin.pma__pdf_pages                          OK
phpmyadmin.pma__recent                             OK
phpmyadmin.pma__relation                           OK
phpmyadmin.pma__savedsearches                      OK
phpmyadmin.pma__table_coords                       OK
phpmyadmin.pma__table_info                         OK
phpmyadmin.pma__table_uiprefs                      OK
phpmyadmin.pma__tracking                           OK
phpmyadmin.pma__userconfig                         OK
phpmyadmin.pma__usergroups                         OK
phpmyadmin.pma__users                              OK
sys.sys_config                                     OK
db1.access                                         OK
db1.users                                          OK
db1.objects                                        OK
db1.isp                                            OK
db1.desc                                           OK
Upgrade process completed successfully.
Checking if update is needed.

It works when the server is up and running and it is a good idea to execute the command in a screen.
It does not need to be logged as root, but mysql_upgrade does need to have the root MySQL password. In the example above it did not asked for password, because we have it in ~/.my.cnf file.

Just to note you might upgraded a long before this error to appear!

If you do not use a certain functionality you could live up happily with the old mysql.user scheme (and all old mysql.* tables). In our case we upgraded one of our slaves and several days after when a grant command on the master was issued the replication just stopped with this error! Of course, if someone were used the command in our slave the error would have appeared there sooner.
We also had case where old MySQL SQL dump file (5.6) was imported in a newer MySQL server 5.7 and there had been no issues for weeks till the GRANT command.

perror

Th error code is 1805.

[myuser@mysql1 ~]# perror 1805
MySQL error code 1805 (ER_COL_COUNT_DOESNT_MATCH_CORRUPTED_V2): Column count of %s.%s is wrong. Expected %d, found %d. The table is probably corrupted