Score:0

Mysql constantly writing to binlog, rapidly using up disk space

in flag
jla

My Ubuntu server started running a high amount of IO operations. The server has a few WordPress websites on it, but they get at most a few dozen views per day. In a couple of days 30GB of disk space was used.

Checking iotop

Running iotop showed that mysql was constantly writing to disk. A typical output was like this:

Total DISK READ:         0.00 B/s | Total DISK WRITE:       390.38 K/s
Current DISK READ:       0.00 B/s | Current DISK WRITE:     664.80 K/s
    TID  PRIO  USER     DISK READ  DISK WRITE  SWAPIN     IO>    COMMAND                                                                        
    298 be/3 root        0.00 B/s    0.00 B/s  0.00 %    4.79 %  [jbd2/vda1-8]
    981 be/4 mysql       0.00 B/s    0.00 B/s  0.00 %    0.55 %  mysqld [ib_log_flush]
    960 be/4 mysql       0.00 B/s    0.00 B/s  0.00 %    0.42 %  mysqld [ib_io_wr-1]
  63310 be/4 mysql       0.00 B/s   30.92 K/s  0.00 %    0.17 %  mysqld [connection]
  62908 be/4 mysql       0.00 B/s   34.79 K/s  0.00 %    0.09 %  mysqld [connection]
  64165 be/4 mysql       0.00 B/s   34.79 K/s  0.00 %    0.07 %  mysqld [connection]
    964 be/4 mysql       0.00 B/s  185.52 K/s  0.00 %    0.05 %  mysqld [ib_pg_flush_co]
    983 be/4 mysql       0.00 B/s  100.49 K/s  0.00 %    0.00 %  mysqld [ib_log_writer]
  71067 be/4 www-data    0.00 B/s    3.87 K/s  0.00 %    0.00 %  apache2 -k start

Indeed, checking in the /var/lib/mysql directory showed hundreds of binlog files, totaling a size of about 30GB. The timestamps indicated that mysql was writing to binlogs at a rate close to 1GB per hour, with no sign of slowing.

Checking mysql processes

Running mysql -p -e "show processlist" to view mysql processes showed nothing.

+--------+------+-----------+------+---------+------+-------+------------------+
| Id     | User | Host      | db   | Command | Time | State | Info             |
+--------+------+-----------+------+---------+------+-------+------------------+
| 627525 | root | localhost | NULL | Query   |    0 | init  | show processlist |
+--------+------+-----------+------+---------+------+-------+------------------+

Checking the binlog files

Using mysqlbinlog to view the binlog files showed they were full of some sort of hash. A typical file looked like:

# The proper term is pseudo_replica_mode, but we use this compatibility alias
# to make the statement usable on server versions 8.0.24 and older.
/*!50530 SET @@SESSION.PSEUDO_SLAVE_MODE=1*/;
/*!50003 SET @OLD_COMPLETION_TYPE=@@COMPLETION_TYPE,COMPLETION_TYPE=0*/;
DELIMITER /*!*/;
# at 4
#220515  4:09:54 server id 1  end_log_pos 126 CRC32 0x070b8f09  Start: binlog v 4, server v 8.0.29-0ubuntu0.20.04.3 created 220515  4:09:54
BINLOG '
En2AYg8BAAAAegAAAH4AAAAAAAQAOC4wLjI5LTB1YnVudHUwLjIwLjA0LjMAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAEwANAAgAAAAABAAEAAAAYgAEGggAAAAICAgCAAAACgoKKioAEjQA
CigAAQmPCwc=
'/*!*/;
# at 126
#220515  4:09:54 server id 1  end_log_pos 157 CRC32 0x433aa4c9  Previous-GTIDs
# [empty]
# at 157
#220515  4:09:54 server id 1  end_log_pos 236 CRC32 0x671d08bc  Anonymous_GTID  last_committed=0        sequence_number=1       rbr_only=yes    original_committed_timestamp=1652587794635604   immediate_commit_timestamp=1652587794635604     transaction_length=14092
/*!50718 SET TRANSACTION ISOLATION LEVEL READ COMMITTED*//*!*/;
# original_commit_timestamp=1652587794635604 (2022-05-15 04:09:54.635604 UTC)
# immediate_commit_timestamp=1652587794635604 (2022-05-15 04:09:54.635604 UTC)
/*!80001 SET @@session.original_commit_timestamp=1652587794635604*//*!*/;
/*!80014 SET @@session.original_server_version=80029*//*!*/;
/*!80014 SET @@session.immediate_server_version=80029*//*!*/;
SET @@SESSION.GTID_NEXT= 'ANONYMOUS'/*!*/;
# at 236
#220515  4:09:54 server id 1  end_log_pos 334 CRC32 0x71a6c06f  Query   thread_id=614826        exec_time=0     error_code=0
SET TIMESTAMP=1652587794/*!*/;
SET @@session.pseudo_thread_id=614826/*!*/;
SET @@session.foreign_key_checks=1, @@session.sql_auto_is_null=0, @@session.unique_checks=1, @@session.autocommit=1/*!*/;
SET @@session.sql_mode=1149239296/*!*/;
SET @@session.auto_increment_increment=1, @@session.auto_increment_offset=1/*!*/;
/*!\C utf8mb4 *//*!*/;
SET @@session.character_set_client=246,@@session.collation_connection=246,@@session.collation_server=255/*!*/;
SET @@session.lc_time_names=0/*!*/;
SET @@session.collation_database=DEFAULT/*!*/;
/*!80011 SET @@session.default_collation_for_utf8mb4=255*//*!*/;
BEGIN
/*!*/;
# at 334
#220515  4:09:54 server id 1  end_log_pos 415 CRC32 0x6976a620  Table_map: `wordpress-jessjohn`.`wp_options` mapped to number 81
# at 415
#220515  4:09:54 server id 1  end_log_pos 14218 CRC32 0x8cd2158b        Update_rows: table id 81 flags: STMT_END_F

BINLOG '
En2AYhMBAAAAUQAAAJ8BAAAAAFEAAAAAAAEAEndvcmRwcmVzcy1qZXNzam9obgAKd3Bfb3B0aW9u
cwAECA/8DwX8AgRQAAABAYACAfYgpnZp
En2AYh8BAAAA6zUAAIo3AAAAAFEAAAAAAAEAAgAE//8AHQAAAAAAAAANAHJld3JpdGVfcnVsZXMA
AAAAA3llcwAdAAAAAAAAAA0AcmV3cml0ZV9ydWxlc4c1AABhOjE0MDp7czoxMToiXndwLWpzb24v
PyQiO3M6MjI6ImluZGV4LnBocD9yZXN0X3JvdXRlPS8iO3M6MTQ6Il53cC1qc29uLyguKik/Ijtz
OjMzOiJpbmRleC5waHA/cmVzdF9yb3V0ZT0vJG1hdGNoZXNbMV0iO3M6MjE6Il5pbmRleC5waHAv
d3AtanNvbi8/JCI7czoyMjoiaW5kZXgucGhwP3Jlc3Rfcm91dGU9LyI7czoyNDoiXmluZGV4LnBo
cC93cC1qc29uLyguKik/IjtzOjMzOiJpbmRleC5waHA/cmVzdF9yb3V0ZT0vJG1hdGNoZXNbMV0i
O3M6MTc6Il53cC1zaXRlbWFwXC54bWwkIjtzOjIzOiJpbmRleC5waHA/c2l0ZW1hcD1pbmRleCI7

... 245 lines of this ...

dD0kbWF0Y2hlc1sxXSZjcGFnZT0kbWF0Y2hlc1syXSI7czoyMjoiW14vXSsvKFteL10rKS9lbWJl
ZC8/JCI7czo0MzoiaW5kZXgucGhwP2F0dGFjaG1lbnQ9JG1hdGNoZXNbMV0mZW1iZWQ9dHJ1ZSI7
fQN5ZXOLFdKM
'/*!*/;
# at 14218
#220515  4:09:54 server id 1  end_log_pos 14249 CRC32 0x322d3658        Xid = 18716628
COMMIT/*!*/;
# at 14249
#220515  4:09:54 server id 1  end_log_pos 14329 CRC32 0xc4b6c15a        Anonymous_GTID  last_committed=1        sequence_number=2       rbr_only=yes    original_committed_timestamp=1652587794702570   immediate_commit_timestamp=1652587794702570     transaction_length=100144
/*!50718 SET TRANSACTION ISOLATION LEVEL READ COMMITTED*//*!*/;
# original_commit_timestamp=1652587794702570 (2022-05-15 04:09:54.702570 UTC)
# immediate_commit_timestamp=1652587794702570 (2022-05-15 04:09:54.702570 UTC)
/*!80001 SET @@session.original_commit_timestamp=1652587794702570*//*!*/;
/*!80014 SET @@session.original_server_version=80029*//*!*/;
/*!80014 SET @@session.immediate_server_version=80029*//*!*/;
SET @@SESSION.GTID_NEXT= 'ANONYMOUS'/*!*/;
# at 14329
#220515  4:09:54 server id 1  end_log_pos 14427 CRC32 0x1328bf8c        Query   thread_id=614825        exec_time=0     error_code=0
SET TIMESTAMP=1652587794/*!*/;
BEGIN
/*!*/;
# at 14427
#220515  4:09:54 server id 1  end_log_pos 14507 CRC32 0x64436ee3        Table_map: `wordpress-jessjohn`.`wp_usermeta` mapped to number 95
# at 14507
#220515  4:09:54 server id 1  end_log_pos 114362 CRC32 0xec16092b       Update_rows: table id 95 flags: STMT_END_F

BINLOG '
En2AYhMBAAAAUAAAAKs4AAAAAF8AAAAAAAEAEndvcmRwcmVzcy1qZXNzam9obgALd3BfdXNlcm1l
dGEABAgID/wD/AMEDAEBwAIB9uNuQ2Q=
En2AYh8BAAAAD4YBALq+AQAAAF8AAAAAAAEAAgAE//8ANwAAAAAAAAABAAAAAAAAAA4Ac2Vzc2lv

... and so on for another >200 lines

What is causing all this logging?

I'm not very familiar with mysql logging so not sure where to go from here. I suppose a quick fix would be to just turn logging off. I don't understand what the binlog files are saying, or what might be causing so much to be logged.

Wilson Hauck avatar
jp flag
Additional information request, please. RAM size, # cores, any SSD or NVME devices on MySQL Host server? Post on pastebin.com and share the links. From your SSH login root, Text results of: A) SELECT COUNT(*) FROM information_schema.tables; B) SHOW GLOBAL STATUS; after minimum 24 hours UPTIME C) SHOW GLOBAL VARIABLES; D) SHOW FULL PROCESSLIST; AND very helpful OS information, includes - htop OR top for most active apps, ulimit -a for list of limits, iostat -xm 5 3 for IOPS by device & core/cpu count, for server binlog tuning analysis to provide suggestions.
ua flag
Do you have a replica? What is its "server_id"?
Score:1
in flag

Binlogs in MySQL are used for replication between master and slave(s). If you do not use such architecture you can disable it by executing this:

SET sql_log_bin = 0;

If you have such structure you can strip old (already replicated) records by using command like:

PURGE BINARY LOGS BEFORE '2019-04-02 22:46:26';

or

PURGE BINARY LOGS TO 'mysql-bin.010';

For more information you can use this answer.

mangohost

Post an answer

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