MySQL server responds slowly to Wordpress

Question

I have a web server running Windows, IIS, PHP, which hosts a fully-repaired WordPress site. The database is located on a separate server inside the DMZ, which runs on Windows and MySQL 5.7.13.

When accessing a WordPress site, it takes from 6 to 16 seconds to return the first byte.

Completing this ridiculously unoptimized query from the MySQL Workbench (on a web server) takes only 0.858 seconds.

SELECT * FROM wp_posts INNER JOIN wp_postmeta ON wp_postmeta.post_id = wp_posts.ID INNER JOIN wp_comments ON wp_comments.comment_post_id = wp_posts.ID INNER JOIN wp_commentmeta ON wp_commentmeta.comment_id = wp_comments.comment_ID 

This is my full my.ini file:

 # Other default tuning values # MySQL Server Instance Configuration File # ---------------------------------------------------------------------- # Generated by the MySQL Server Instance Configuration Wizard # # # Installation Instructions # ---------------------------------------------------------------------- # # On Linux you can copy this file to /etc/my.cnf to set global options, # mysql-data-dir/my.cnf to set server-specific options # (@ localstatedir@ for this installation) or to # ~/.my.cnf to set user-specific options. # # On Windows you should keep this file in the installation directory # of your server (eg C:\Program Files\MySQL\MySQL Server XY). To # make sure the server reads the config file use the startup option # "--defaults-file". # # To run run the server from the command line, execute this in a # command line shell, eg # mysqld --defaults-file="C:\Program Files\MySQL\MySQL Server XY\my.ini" # # To install the server as a Windows service manually, execute this in a # command line shell, eg # mysqld --install MySQLXY --defaults-file="C:\Program Files\MySQL\MySQL Server XY\my.ini" # # And then execute this in a command line shell to start the server, eg # net start MySQLXY # # # Guildlines for editing this file # ---------------------------------------------------------------------- # # In this file, you can use all long options that the program supports. # If you want to know the options a program supports, start the program # with the "--help" option. # # More detailed information about the individual options can also be # found in the manual. # # For advice on how to change settings please see # http://dev.mysql.com/doc/refman/5.7/en/server-configuration-defaults.html # # # CLIENT SECTION # ---------------------------------------------------------------------- # # The following options will be read by MySQL client applications. # Note that only client applications shipped by MySQL are guaranteed # to read this section. If you want your own MySQL client program to # honor these values, you need to specify it as an option during the # MySQL client library initialization. # [client] no-beep= # pipe= # socket=0.0 port=3306 [mysql] default-character-set=utf8 # SERVER SECTION # ---------------------------------------------------------------------- # # The following options will be read by the MySQL Server. Make sure that # you have installed the server correctly (see above) so it reads this # file.= # # server_type=3 [mysqld] # Skip reverse DNS lookup of clients skip-name-resolve # The next three options are mutually exclusive to SERVER_PORT below. # skip-networking= # enable-named-pipe= # shared-memory= # shared-memory-base-name=MYSQL # The Pipe the MySQL Server will use # socket=MYSQL # The TCP/IP Port the MySQL Server will listen on port=3306 # Path to installation directory. All paths are usually resolved relative to this. # basedir="C:/Program Files/MySQL/MySQL Server 5.7/" # Path to the database root # datadir=C:/ProgramData/MySQL/MySQL Server 5.7\Data datadir=D:\MySQL\Data # The default character set that will be used when a new schema or table is # created and no character set is defined character-set-server=utf8 # The default storage engine that will be used when create new tables when default-storage-engine=INNODB # Set the SQL mode to strict sql-mode="STRICT_TRANS_TABLES,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION" # Enable Windows Authentication # plugin-load=authentication_windows.dll # General and Slow logging. log-output=FILE slow-query-log=1 slow_query_log_file="PRDMYSQL-slow.log" long_query_time=10 # Binary Logging. # log-bin= # Error Logging. # Server Id. server-id=1 # Secure File Priv. secure-file-priv="C:/ProgramData/MySQL/MySQL Server 5.7/Uploads" # The maximum amount of concurrent sessions the MySQL server will # allow. One of these connections will be reserved for a user with # SUPER privileges to allow the administrator to login even if the # connection limit has been reached. max_connections=151 # Query cache is used to cache SELECT results and later return them # without actual executing the same query once again. Having the query # cache enabled may result in significant speed improvements, if your # have a lot of identical queries and rarely changing tables. See the # "Qcache_lowmem_prunes" status variable to check if the current value # is high enough for your load. # Note: In case your tables change very often or if your queries are # textually different every time, the query cache may result in a # slowdown instead of a performance improvement. query_cache_size=16M # The number of open tables for all threads. Increasing this value # increases the number of file descriptors that mysqld requires. # Therefore you have to make sure to set the amount of open files # allowed to at least 4096 in the variable "open-files-limit" in # section [mysqld_safe] table_open_cache=2000 # Maximum size for internal (in-memory) temporary tables. If a table # grows larger than this value, it is automatically converted to disk # based table This limitation is for a single table. There can be many # of them. tmp_table_size=60M # How many threads we should keep in a cache for reuse. When a client # disconnects, the client threads are put in the cache if there aren't # more than thread_cache_size threads from before. This greatly reduces # the amount of thread creations needed if you have a lot of new # connections. (Normally this doesn't give a notable performance # improvement if you have a good thread implementation.) thread_cache_size=10 # *** MyISAM Specific options # The maximum size of the temporary file MySQL is allowed to use while # recreating the index (during REPAIR, ALTER TABLE or LOAD DATA INFILE. # If the file-size would be bigger than this, the index will be created # through the key cache (which is slower). myisam_max_sort_file_size=100G # If the temporary file used for fast index creation would be bigger # than using the key cache by the amount specified here, then prefer the # key cache method. This is mainly used to force long character keys in # large tables to use the slower key cache method to create the index. myisam_sort_buffer_size=111M # Size of the Key Buffer, used to cache index blocks for MyISAM tables. # Do not set it larger than 30% of your available memory, as some memory # is also required by the OS to cache rows. Even if you're not using # MyISAM tables, you should still set it to 8-64M as it will also be # used for internal temporary disk tables. key_buffer_size=16M # Size of the buffer used for doing full table scans of MyISAM tables. # Allocated per thread, if a full scan is needed. read_buffer_size=64K read_rnd_buffer_size=256K # *** INNODB Specific options *** # innodb_data_home_dir=0.0 # Use this option if you have a MySQL server with InnoDB support enabled # but you do not plan to use it. This will save memory and disk space # and speed up some things. # skip-innodb= # If set to 1, InnoDB will flush (fsync) the transaction logs to the # disk at each commit, which offers full ACID behavior. If you are # willing to compromise this safety, and you are running small # transactions, you may set this to 0 or 2 to reduce disk I/O to the # logs. Value 0 means that the log is only written to the log file and # the log file flushed to disk approximately once per second. Value 2 # means the log is written to the log file at each commit, but the log # file is only flushed to disk approximately once per second. innodb_flush_log_at_trx_commit=1 # The size of the buffer InnoDB uses for buffering log data. As soon as # it is full, InnoDB will have to flush it to disk. As it is flushed # once per second anyway, it does not make sense to have it very large # (even with long transactions). innodb_log_buffer_size=1M # InnoDB, unlike MyISAM, uses a buffer pool to cache both indexes and # row data. The bigger you set this the less disk I/O is needed to # access data in tables. On a dedicated database server you may set this # parameter up to 80% of the machine physical memory size. Do not set it # too large, though, because competition of the physical memory may # cause paging in the operating system. Note that on 32bit systems you # might be limited to 2-3.5G of user level memory per process, so do not # set it too high. innodb_buffer_pool_size=2048M # Size of each log file in a log group. You should set the combined size # of log files to about 25%-100% of your buffer pool size to avoid # unneeded buffer pool flush activity on log file overwrite. However, # note that a larger logfile size will increase the time needed for the # recovery process. innodb_log_file_size=48M # Number of threads allowed inside the InnoDB kernel. The optimal value # depends highly on the application, hardware as well as the OS # scheduler properties. A too high value may lead to thread thrashing. innodb_thread_concurrency=8 # The increment size (in MB) for extending the size of an auto-extend InnoDB system tablespace file when it becomes full. innodb_autoextend_increment=64 # The number of regions that the InnoDB buffer pool is divided into. # For systems with buffer pools in the multi-gigabyte range, dividing the buffer pool into separate instances can improve concurrency, # by reducing contention as different threads read and write to cached pages. innodb_buffer_pool_instances=8 # Determines the number of threads that can enter InnoDB concurrently. innodb_concurrency_tickets=5000 # Specifies how long in milliseconds (ms) a block inserted into the old sublist must stay there after its first access before # it can be moved to the new sublist. innodb_old_blocks_time=1000 # It specifies the maximum number of .ibd files that MySQL can keep open at one time. The minimum value is 10. innodb_open_files=300 # When this variable is enabled, InnoDB updates statistics during metadata statements. innodb_stats_on_metadata=0 # When innodb_file_per_table is enabled (the default in 5.6.6 and higher), InnoDB stores the data and indexes for each newly created table # in a separate .ibd file, rather than in the system tablespace. innodb_file_per_table=1 # Use the following list of values: 0 for crc32, 1 for strict_crc32, 2 for innodb, 3 for strict_innodb, 4 for none, 5 for strict_none. innodb_checksum_algorithm=0 # The number of outstanding connection requests MySQL can have. # This option is useful when the main MySQL thread gets many connection requests in a very short time. # It then takes some time (although very little) for the main thread to check the connection and start a new thread. # The back_log value indicates how many requests can be stacked during this short time before MySQL momentarily # stops answering new requests. # You need to increase this only if you expect a large number of connections in a short period of time. back_log=80 # If this is set to a nonzero value, all tables are closed every flush_time seconds to free up resources and # synchronize unflushed data to disk. # This option is best used only on systems with minimal resources. flush_time=0 # The minimum size of the buffer that is used for plain index scans, range index scans, and joins that do not use # indexes and thus perform full table scans. join_buffer_size=256K # The maximum size of one packet or any generated or intermediate string, or any parameter sent by the # mysql_stmt_send_long_data() C API function. max_allowed_packet=4M # If more than this many successive connection requests from a host are interrupted without a successful connection, # the server blocks that host from performing further connections. max_connect_errors=100 # Changes the number of file descriptors available to mysqld. # You should try increasing the value of this option if mysqld gives you the error "Too many open files". open_files_limit=4161 # Set the query cache type. 0 for OFF, 1 for ON and 2 for DEMAND. query_cache_type=1 # If you see many sort_merge_passes per second in SHOW GLOBAL STATUS output, you can consider increasing the # sort_buffer_size value to speed up ORDER BY or GROUP BY operations that cannot be improved with query optimization # or improved indexing. sort_buffer_size=256K # The number of table definitions (from .frm files) that can be stored in the definition cache. # If you use a large number of tables, you can create a large table definition cache to speed up opening of tables. # The table definition cache takes less space and does not use file descriptors, unlike the normal table cache. # The minimum and default values are both 400. table_definition_cache=1400 # Specify the maximum size of a row-based binary log event, in bytes. # Rows are grouped into events smaller than this size if possible. The value should be a multiple of 256. binlog_row_event_max_size=8K # If the value of this variable is greater than 0, a replication slave synchronizes its master.info file to disk. # (using fdatasync()) after every sync_master_info events. sync_master_info=10000 # If the value of this variable is greater than 0, the MySQL server synchronizes its relay log to disk. # (using fdatasync()) after every sync_relay_log writes to the relay log. sync_relay_log=10000 # If the value of this variable is greater than 0, a replication slave synchronizes its relay-log.info file to disk. # (using fdatasync()) after every sync_relay_log_info transactions. sync_relay_log_info=10000 # Load mysql plugins at start."plugin_x ; plugin_y". plugin_load="mysqlx" # MySQL server plugin configuration. loose_mysqlx_port=33060 log-error = "D:/MySQL/Data/PRDMYSQL.err" expire_logs_days = 3 log-tc-size = 10240 

Answer 1

Using the WordPress Query Monitor plugin, I found that something was doing 8000 !! additional requests per page.

I found that the plugin we used for several months received an update introducing this behavior. I did not understand that one of the site content editors applied the update.

Disabling this plugin returned the site back to normal load time.

Answer 2

Turn on MySQL Common Log. Run briefly (until the problem arises), then turn it off.

Then use pt-query-digest to find out which queries were running and who started them. From this, you can determine what causes it.