I'm searching for 3 days already and can't find out, why my MySQL server uses so much CPU. For example, when I run a query to SELECT like 100 rows from one of the tables, the CPU goes from 0 to 50%, or when I take a value from one of the tables and INSERT a row in another table, the CPU goes from 0 to 10-30%. Currently, it uses 170MB, I've tried with a clean one and the CPU was under 1% all the time. Queries are not slow, they finish the job in under 0.05 seconds, but still use ~30% CPU. If I have over 30 people on the website and they all do that the website slows down really bad. That didn't happen until some time ago so maybe I made something wrong somewhere while working on the project.

Here is MySQLTuner's result:

 >>  MySQLTuner 1.7.0 - Major Hayden <[email protected]>
 >>  Bug reports, feature requests, and downloads at http://mysqltuner.com/
 >>  Run with '--help' for additional options and output filtering

[--] Skipped version check for MySQLTuner script
[OK] Logged in using credentials from debian maintenance account.
[OK] Currently running supported MySQL version 5.5.52-0+deb7u1
[OK] Operating on 64-bit architecture

-------- Storage Engine Statistics ---------------------------------------------                            --------------------
[--] Data in MyISAM tables: 23K (Tables: 10)
[--] Data in InnoDB tables: 218M (Tables: 18)
[OK] Total fragmented tables: 0

-------- Security Recommendations ----------------------------------------------                            --------------------
[OK] There are no anonymous accounts for any database users
[OK] All database users have passwords assigned
[--] There are 612 basic passwords in the list.

-------- CVE Security Recommendations ------------------------------------------                            --------------------
[!!] CVE-2016-6662(<= 5.5.52) : "Oracle MySQL through 5.5.52
[--] False positive CVE(s) for MySQL and MariaDB 5.5.x can be found.
[--] Check careful each CVE for those particular versions
[!!] 1 CVE(s) found for your MySQL release.

-------- Performance Metrics -----------------------------------------------------------------------
[--] Up for: 13m 39s (2K q [2.452 qps], 434 conn, TX: 925K, RX: 146K)
[--] Reads / Writes: 70% / 30%
[--] Binary logging is disabled
[--] Physical Memory     : 3.8G
[--] Max MySQL memory    : 597.8M
[--] Other process memory: 63.7M
[--] Total buffers: 192.0M global + 2.7M per thread (151 max threads)
[--] P_S Max memory usage: 0B
[--] Galera GCache Max memory usage: 0B
[OK] Maximum reached memory usage: 232.3M (6.00% of installed RAM)
[OK] Maximum possible memory usage: 597.8M (15.44% of installed RAM)
[OK] Overall possible memory usage with other process is compatible with memory available
[OK] Slow queries: 0% (0/2K)
[OK] Highest usage of available connections: 9% (15/151)
[OK] Aborted connections: 0.00%  (0/434)
[!!] name resolution is active : a reverse name resolution is made for each new connection and can reduce performance
[!!] Query cache may be disabled by default due to mutex contention.
[OK] Sorts requiring temporary tables: 0% (0 temp sorts / 5 sorts)
[OK] No joins without indexes
[OK] Temporary tables created on disk: 25% (69 on disk / 273 total)
[OK] Thread cache hit rate: 96% (15 created / 434 connections)
[OK] Table cache hit rate: 91% (72 open / 79 opened)
[OK] Open file limit used: 6% (68/1K)
[OK] Table locks acquired immediately: 100% (224 immediate / 224 locks)

-------- Performance schema ------------------------------------------------------------------------
[--] Performance schema is disabled.

-------- ThreadPool Metrics ------------------------------------------------------------------------
[--] ThreadPool stat is disabled.

-------- MyISAM Metrics ----------------------------------------------------------------------------
[!!] Key buffer used: 18.2% (3M used / 16M cache)
[OK] Key buffer size / total MyISAM indexes: 16.0M/124.0K

-------- InnoDB Metrics ----------------------------------------------------------------------------
[--] InnoDB is enabled.
[--] InnoDB Thread Cucurrency: 0
[!!] InnoDB File per table is not activated
[!!] InnoDB buffer pool / data size: 128.0M/218.7M
[!!] Ratio InnoDB log file size / InnoDB Buffer pool size (3.90625 %): 5.0M/128.0M should be equal 25%
[OK] InnoDB buffer pool instances: 1
[--] InnoDB Buffer Pool Chunk Size not used or defined in your version
[OK] InnoDB Read buffer efficiency: 99.98% (4252997 hits/ 4253965 total)
[!!] InnoDB Write Log efficiency: 17.98% (16 hits/ 89 total)
[OK] InnoDB log waits: 0.00% (0 waits / 73 writes)

-------- AriaDB Metrics ----------------------------------------------------------------------------
[--] AriaDB is disabled.

-------- TokuDB Metrics ----------------------------------------------------------------------------
[--] TokuDB is disabled.

-------- XtraDB Metrics ----------------------------------------------------------------------------
[--] XtraDB is disabled.

-------- RocksDB Metrics ---------------------------------------------------------------------------
[--] RocksDB is disabled.

-------- Spider Metrics ----------------------------------------------------------------------------
[--] Spider is disabled.

-------- Connect Metrics ---------------------------------------------------------------------------
[--] Connect is disabled.

-------- Galera Metrics ----------------------------------------------------------------------------
[--] Galera is disabled.

-------- Replication Metrics -----------------------------------------------------------------------
[--] Galera Synchronous replication: NO
[--] No replication slave(s) for this server.
[--] This is a standalone server.

-------- Recommendations ---------------------------------------------------------------------------
General recommendations:
    1 CVE(s) found for your MySQL release. Consider upgrading your version !
    MySQL started within last 24 hours - recommendations may be inaccurate
    Enable the slow query log to troubleshoot bad queries
    Configure your accounts with ip or subnets only, then update your configuration with skip-name-resolve=1
Variables to adjust:
    query_cache_type (=0)
    innodb_buffer_pool_size (>= 218M) if possible.
    innodb_log_file_size should be equals to 1/4 of buffer pool size (=32M) if possible.

And here is my.cnf:

# * Basic Settings
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
lc-messages-dir = /usr/share/mysql
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address        =
# * Fine Tuning
key_buffer      = 16M
max_allowed_packet  = 16M
thread_stack        = 192K
thread_cache_size       = 8
wait_timeout = 1800
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover         = BACKUP
#max_connections        = 100
#table_cache            = 64
#thread_concurrency     = 10
# * Query Cache Configuration
query_cache_limit   = 1M
query_cache_size        = 16M
# * Logging and Replication
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1
# Error logging goes to syslog due to /etc/mysql/conf.d/mysqld_safe_syslog.cnf.
# Here you can see queries with especially long duration
#log_slow_queries   = /var/log/mysql/mysql-slow.log
#long_query_time = 2
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
#       other settings you may need to change.
#server-id      = 1
#log_bin            = /var/log/mysql/mysql-bin.log
expire_logs_days    = 10
max_binlog_size         = 100M
#binlog_do_db       = include_database_name
#binlog_ignore_db   = include_database_name
# * InnoDB
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
# * Security Features
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem

max_allowed_packet  = 16M

#no-auto-rehash # faster start of mysql but no tab completition

key_buffer      = 16M

# * IMPORTANT: Additional settings that can override those from this file!
#   The files must end with '.cnf', otherwise they'll be ignored.
!includedir /etc/mysql/conf.d/

I've also checked the slow queries log, but nothing was slow enough to go there. I only use one index on one column in the users-table. That speeds up some queries but just that, MySQL's CPU usage is the same with and without it.

I have 3 tables with almost 1.000.000 rows but I'm only using one index in the users table. Here is the explain of one of my queries:

EXPLAIN SELECT * FROM bets WHERE user = 76561198156588991

(Here is the result: gyazo.com/201c91cc5fd903667e30a26067001d0e and it was executed in 0.02 sec but CPU went from 0 to 15% just with this query).

2 Answers 2


There are many reasons for the problem but first from what You need to start

InnoDB buffer pool / data size: 128.0M

Give for MySQL at least half of server memory

Second - high cpu show bad index work and/or a lot of sort operations in queries

it is not possible to make conclusion without server check - monitoring and profile all top queries

The speed - it only one side of medal, query could be fast (because data is very small), but if not use indexes or make group by / order by for big data sets - this is give high cpu usage now and will be bottle neck when loading will increase.

Try to use some of available tools for collect real queries statistics:

  • MONyog
  • JetProfiler
  • Neor Profiler

Thank analyse top 20% of queries by:

  • top by server time
  • top by number of execution

based on result - add indexes, change queries when necessary

in 99.99% cases after this - problem will gone

  • Thank you for your amazing answer, I'll try when I come back from school. Commented Nov 11, 2016 at 10:28

Please provide SHOW CREATE bets. I suspect it will say that user is a VARCHAR. In comparing a VARCHAR to a number, a table scan is required; this is slow. Put quotes around 76561198156588991.

Also, make sure bets has some kind of index starting with user.

You probably have other queries that are running slower than necessary; let's see them.

Increase innodb_buffer_pool_size to 300M.

  • yes, sure. on attached query plan picture - query do full scan, so - or no index on this column or it archer and mysql convert all rows for compare
    – a_vlad
    Commented Nov 14, 2016 at 0:35

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