Category: General

Monitoring MySql and Optimization

Next part in monitoring and optimization of LAMP stack is, Monitoring MySql and optimization.

As we are aware that MySQL is RDBMS, so, here, I will detail out the Mysql server monitoring and configuration to Database level optimization.

Monitoring MySql

your MySQL server may contain more than one Databases, which will be connected to different applications.

There are various tools available, command line to Graphical to connect with MySQL server, some of the most utilized tools are


[Command line]

  • mysqladmin [mysqladmin -u <user> -p status] [default installed with MySQL command-line utilities]
Uptime: 783136  Threads: 1  Questions: 46141  Slow queries: 0  Opens: 73993  Flush tables: 1  Open tables: 2000  Queries per second avg: 0.058
MySQL on localhost (5.7.27)                                                                                                                               load 2.64 2.93 2.86 1/1457 17872 up 9+01:35:50 [13:06:43]
  Queries: 45.0k    qps:    0 Slow:     0.0         Se/In/Up/De(%):    78/08/02/00 
 Key Efficiency: 87.7%  Bps in/out:  18.3/ 86.6   
    Id      User         Host/IP         DB       Time    Cmd    State Query                                                                                                                                        --      ----         -------         --       ----    ---    ----- ----------                                                                                                                                  828      root       localhost                     0  Query starting show full processlist                                                                                                                    

All these tools will help you figure out the current processlist , processed, running queries, server configuration and stats about the past data.

As these are just an interface to visualize information, let’s start with most utilized tool, PHPMyAdmin

If you login PHPMyAdmin as an admin, you will get an status tab, which will show,

There are also more details available. let’s figure out the meaning of these stats, which is processes, showing current executing processes. This can also be gathered by executing query

show processlist;

Most Important variables those are adjusted

  • max_conenctions
SHOW VARIABLES LIKE "max_connections";
  • innodb_buffer_pool_size
  • innodb_io_capacity
  • query_cache_size

Tuning / Optimization MySql as server

Once you get the status, and now, you want to lookup for what can be optimized. Although PHPMyAdmin also has an advisor which is suggesting tuning the server variables,

apart from that, there is a Perl script that can also look up the database logs and provide your recommendations.

You can download this script and run it on server, like


output of this command will be

        MySQLTuner 1.8.5 - Major Hayden [email protected]
      Bug reports, feature requests, and downloads at
      Run with '--help' for additional options and output filtering    
 [--] Skipped version check for MySQLTuner script
 [!!] Successfully authenticated with no password - SECURITY RISK!
 [OK] Currently running supported MySQL version 5.7.27-0ubuntu0.18.04.1
 [OK] Operating on 64-bit architecture
 -------- Log file Recommendations ------------------------------------------------------------------
 [!!] Log file /var/log/mysql/error.log doesn't exist
 -------- Storage Engine Statistics -----------------------------------------------------------------
 [--] Data in MyISAM tables: 6.0M (Tables: 36)
 [--] Data in InnoDB tables: 8.4G (Tables: 13843)
 [OK] Total fragmented tables: 0
 -------- Analysis Performance Metrics --------------------------------------------------------------
 [--] innodb_stats_on_metadata: OFF
 [OK] No stat updates during querying INFORMATION_SCHEMA.
 -------- Security Recommendations ------------------------------------------------------------------
 [OK] There are no anonymous accounts for any database users
 [OK] All database users have passwords assigned
 [!!] User 'root'@'%' has user name as password.
 [!!] User 'root'@% does not specify hostname restrictions.
 [!!] There is no basic password file list!
 -------- CVE Security Recommendations --------------------------------------------------------------
 [--] Skipped due to --cvefile option undefined
 -------- Performance Metrics -----------------------------------------------------------------------
 [--] Up for: 9d 0h 26m 43s (43K q [0.056 qps], 683 conn, TX: 60M, RX: 13M)
 [--] Reads / Writes: 88% / 12%
 [--] Binary logging is disabled
 [--] Physical Memory     : 11.4G
 [--] Max MySQL memory    : 2.7G
 [--] Other process memory: 0B
 [--] Total buffers: 192.0M global + 17.1M per thread (151 max threads)
 [--] P_S Max memory usage: 72B
 [--] Galera GCache Max memory usage: 0B
 [OK] Maximum reached memory usage: 277.3M (2.37% of installed RAM)
 [OK] Maximum possible memory usage: 2.7G (23.63% of installed RAM)
 [OK] Overall possible memory usage with other process is compatible with memory available
 [OK] Slow queries: 0% (0/43K)
 [OK] Highest usage of available connections: 3% (5/151)
 [OK] Aborted connections: 0.00%  (0/683)
 [!!] name resolution is active : a reverse name resolution is made for each new connection and can reduce performance
 [OK] Query cache is disabled by default due to mutex contention on multiprocessor machines.
 [OK] Sorts requiring temporary tables: 0% (0 temp sorts / 9K sorts)
 [!!] Joins performed without indexes: 3515
 [!!] Temporary tables created on disk: 51% (5K on disk / 10K total)
 [OK] Thread cache hit rate: 99% (5 created / 683 connections)
 [OK] Table cache hit rate: 94% (46K hits / 49K requests)
 [!!] table_definition_cache(1400) is lower than number of tables(14158) 
 [OK] Open file limit used: 0% (7/5K)
 [OK] Table locks acquired immediately: 100% (886 immediate / 886 locks)
 -------- Performance schema ------------------------------------------------------------------------
 [--] Memory used by P_S: 72B
 [--] Sys schema is installed.
 -------- ThreadPool Metrics ------------------------------------------------------------------------
 [--] ThreadPool stat is disabled.
 -------- MyISAM Metrics ----------------------------------------------------------------------------
 [!!] Key buffer used: 18.2% (2.9M used / 16.0M cache)
 [OK] Key buffer size / total MyISAM indexes: 16.0M/330.0K
 [!!] Read Key buffer hit rate: 37.5% (8 cached / 5 reads)
 -------- InnoDB Metrics ----------------------------------------------------------------------------
 [--] InnoDB is enabled.
 [--] InnoDB Thread Concurrency: 0
 [OK] InnoDB File per table is activated
 [!!] InnoDB buffer pool / data size: 128.0M/8.4G
 [!!] Ratio InnoDB log file size / InnoDB Buffer pool size (75 %): 48.0M * 2/128.0M should be equal to 25%
 [OK] InnoDB buffer pool instances: 1
 [--] Number of InnoDB Buffer Pool Chunk : 1 for 1 Buffer Pool Instance(s)
 [OK] Innodb_buffer_pool_size aligned with Innodb_buffer_pool_chunk_size & Innodb_buffer_pool_instances
 [OK] InnoDB Read buffer efficiency: 99.75% (1225155 hits/ 1228218 total)
 [!!] InnoDB Write Log efficiency: 77.65% (8621 hits/ 11103 total)
 [OK] InnoDB log waits: 0.00% (0 waits / 2482 writes)
 -------- Aria Metrics ------------------------------------------------------------------------------
 [--] Aria Storage Engine not available.
 -------- TokuDB Metrics ----------------------------------------------------------------------------
 [--] TokuDB is disabled.
 -------- XtraDB Metrics ----------------------------------------------------------------------------
 [--] XtraDB is disabled.
 -------- Galera Metrics ----------------------------------------------------------------------------
 [--] Galera is disabled.
 -------- Replication Metrics -----------------------------------------------------------------------
 [--] Galera Synchronous replication: NO
 [--] No replication slave(s) for this server.
 [--] Binlog format: ROW
 [--] XA support enabled: ON
 [--] Semi synchronous replication Master: Not Activated
 [--] Semi synchronous replication Slave: Not Activated
 [--] This is a standalone server
 -------- Recommendations ---------------------------------------------------------------------------
 General recommendations:
     Set up a Secure Password for 'root'@'%' user: SET PASSWORD FOR 'root'@'%' = PASSWORD('secure_password');
     Restrict Host for 'root'@'%' to 'root'@LimitedIPRangeOrLocalhost
     RENAME USER 'root'@'%' TO 'root'@LimitedIPRangeOrLocalhost;
     Configure your accounts with ip or subnets only, then update your configuration with skip-name-resolve=1
     We will suggest raising the 'join_buffer_size' until JOINs not using indexes are found.
              (specially the conclusions at the bottom of the page).
     When making adjustments, make tmp_table_size/max_heap_table_size equal
     Reduce your SELECT DISTINCT queries which have no LIMIT clause
     Before changing innodb_log_file_size and/or innodb_log_files_in_group read this:
 Variables to adjust:
     join_buffer_size (> 256.0K, or always use indexes with JOINs)
     tmp_table_size (> 16M)
     max_heap_table_size (> 16M)
     table_definition_cache(1400) > 14158 or -1 (autosizing if supported)
     innodb_buffer_pool_size (>= 8.4G) if possible.
     innodb_log_file_size should be (=16M) if possible, so InnoDB total log files size equals to 25% of buffer pool size.

MySql server becomes slow if the queries running over the server takes much time to execute, by this, upcoming connections queries will be waiting for locks.

All about Slow Query and Slow Query Logs.

There is a variable at the server, called “slow_query_log”, which will setup mysql to log all queries with some statistics which are taking more than defined time to execute.

This configuration can be defined either at configuration file or by setting up globally by using MySQL query

set global slow_query_log = 'ON';
set global log_queries_not_using_indexes = 'ON';
set global slow_query_log_file ='/var/log/mysql/slow-query.log';
set global long_query_time = 2; // 2 second

by setting from MySQL query prompt or in configuration file [.cnf] like

slow_query_log = ON
log_queries_not_using_indexes = ON
slow_query_log_file = /var/log/mysql/slow-query.log
long_query_time = 2

How to read slow query log file ?

These log files can be parsed into a more analyzed format through various utilities. One of the most used utility is pt-query-digest

pt-query-digest <path to slow query log>

This will output like

# 4.3s user time, 200ms system time, 39.12M rss, 4.12G vsz
# Current date: Thu Nov 29 10:02:45 2018
# Hostname: JJG.local
# Files: slowquery.log
# Overall: 4.51k total, 36 unique, 1.27 QPS, 15.65x concurrency __________
# Time range: 2018-11-27 21:00:23 to 21:59:38
# Attribute          total     min     max     avg     95%  stddev  median
# ============     ======= ======= ======= ======= ======= ======= =======
# Exec time         55640s      5s    118s     12s     16s      4s     13s
# Lock time        18446744073714s    34us 18446744073710s 4085657602s   260us 271453769812s   194us
# Rows sent          2.95M       0 103.99k  684.27       0   8.14k       0
# Rows examine     293.63M       0  18.67M  66.59k    0.99 583.21k    0.99
# Query size        44.63M      79   1.22M  10.12k   2.16k  97.85k   2.06k

# Profile
# Rank Query ID                      Response time    Calls R/Call  V/M  
# ==== ============================= ================ ===== ======= =====
#    1 0x5AE6E128A4790517E5CFFD03… 52666.0213 94.7%  4363 12.0711  0.86 UPDATE some_table
#    2 0x222A6FC43B63B119D2C46918…   618.3909  1.1%    29 21.3238  1.91 UPDATE some_table
#    3 0xD217B90797E8F34704CF55AF…   463.7665  0.8%    29 15.9919  0.07 SELECT some_other_table some_other_other_table

You can also log the slow query in a mysql table rather than file.

--log_output=TABLE  // by default it is file.

By setting up this variable, logs can be written to MySQL table as well.

that table is present under the default MySQL database.

SHOW CREATE TABLE mysql.slow_log;

That table has the following structure.

start_timetimestamp(6)NOCURRENT_TIMESTAMP(6)Time the query began.
user_hostmediumtextNONULLUser and host combination.
query_timetime(6)NONULLTotal time the query took to execute.
lock_timetime(6)NONULLTotal time the query was locked.
rows_sentint(11)NONULLNumber of rows sent.
rows_examinedint(11)NONULLNumber of rows examined.
dbvarchar(512)NONULLDefault database.
insert_idint(11)NONULLInsert id.
server_idint(10) unsignedNONULLThe server’s id.
sql_textmediumtextNONULLFull query.
thread_idbigint(21) unsignedNONULLThread id.
rows_affectedint(11)NONULLNumber of rows affected by an UPDATE or DELETE (from MariaDB 10.1.2)

As soon as you are aware of the slow queries, next thing is to detail out each query and its execution plan.

How to know the query execution plan ?

By using EXPLAIN keyword at start of the SQL, you will get the query execution plan

EXPLAIN select * from user left join company_users on company_users.userid =

this will provide you the result like this

1SIMPLEcompany_usersNULLALLcompuser_usedep_uixNULLNULLNULL9100.00Using where; Using join buffer (Block Nested Loop)

To learn more about explain

Now, you can start optimizing your tables, queries basis on recommendations.

Read Next

Monitoring PHP and Performance Tuning

The next part of the series is, Monitoring PHP and Performance Tuning

PHP is a scripting language, which is interpreted by PHP interpreter.

You may be running a PHP file either directly using PHP Interpreter [Command line]

Or By A mediator, who is telling PHP Interpreter to execute the code. This means in the case of apahce HTTP server,

  • running PHP as module
  • running PHP as cgi/fastcgi
  • running PHP as fpm

You can only run one version of PHP as a module. If you are running multiple version of PHP, then you can achieve that by running PHP as FPM [Fast process manager]

Monitoring PHP running as FPM

  • FPM is a process manager, which runs PHP process in the background.
  • Same as the apache process and threads, it also manages threads whose numbers can be configured.
  • all configuration related values are defined in www.conf file, generally located in /etc/php-fpm.d/www.conf

How to get the status ?

to get the status you need to modify www.conf

pm.status_path = /status

and add the code in one of the virtual host or apache conf file

<LocationMatch "/status">
    SetHandler "proxy:unix:/run/php-fpm/www.sock|fcgi://localhost/status"

try to access it from a public URL or command line through curl

WARNING:These must NOT be publicly accessible as this is a security risk.


You will get the information like this.

pidthe PID of the process
statethe state of the process (Idle, Running, …)
start timethe date and time the process has started
start sincethe number of seconds since the process has started
requeststhe number of requests the process has served
request durationthe duration in µs [micro seconds] of the requests
request methodthe request method (GET, POST, …)
request URIthe request URI with the query string
content lengththe content length of the request (only with POST)
userthe user (PHP_AUTH_USER) (or ‘-‘ if not set)
scriptthe main script called (or ‘-‘ if not set)
last request cputhe %cpu the last request consumed. it’s always 0 if the process is not in Idle state because CPU calculation is done when the request processing has terminated
last request memorythe max amount of memory the last request consumed. it’s always 0 if the process is not in Idle state because memory calculation is done when the request processing has terminated

How to enable slow logs ?

You can also enable access logs and slow logs. [slow logs mean script taking more than the desired time to execute]. This value can also be set

access.log = log/$pool.access.log
access.format = "%R - %u %t \"%m %r%Q%q\" %s %f %{mili}d %{kilo}M %C%%"
slowlog = /var/log/php-fpm/www-slow.log
request_slowlog_timeout = 20s ; script taking more than 20 seconds

As you can monitor this, now we come to the part where we can do the optimization.


1- Setting up configuration

pm.max_children = 80
pm.start_servers = 8
pm.min_spare_servers = 5
pm.max_spare_servers = 35
pm.max_requests = 500

The above value defines the number of processes running PHP scripts. This can be modified on basis of your hardware resources availbility.

REMEMBER : PHP page is handled by FPM , apart from that, any static and HTML page, or the files does not have .PHP [defined extension to handle] can be directly server by webserver.

So setting Apache conifguration is differnet compare to PHP-FPM configuration

for more php-fpm conifguration

Apart from this,

2:- Caching Compiled Byte Code

PHP performance can be improved by storing precompiled script bytecode in shared memory, thereby removing the need for PHP to load and parse scripts on each request.

you can monitor the cache usage by a GUI

The following article provides a detailed description among different available PHP accelerator

Read Next