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My dedicated server is a XEON E3 1240 V3 8GB DDR3 1TB HDD SATA (4 cores @ 3.4 GHz), which I've had for a couple of days only and just finished migrating about 20 wordpress sites to it (each database around 50MB to 150MB in size). The server has consistently had 500%+ CPU usage from mysqld, which has caused the httpd service to crash and websites unable to load.

I have not yet changed the default my.cnf file, which is as follows:

# # This group is read both both by the client and the server # use it for options that affect everything # [client-server] # # include all files from the config directory # !includedir /etc/my.cnf.d [mysqld] log-error=/var/lib/mysql/server1.nc-ph-0741-26.web-hosting.com.err performance-schema=0 default-storage-engine=MyISAM innodb_file_per_table=1 max_allowed_packet=268435456 open_files_limit=10000

I have downloaded MySQLTuner - running perl mysqltuner.pl --host 127.0.0.1 returns the following:

[--] Skipped version check for MySQLTuner script [--] Performing tests on 127.0.0.1:3306 [OK] Currently running supported MySQL version 10.3.18-MariaDB [OK] Operating on 64-bit architecture -------- Log file Recommendations ------------------------------------------------------------------ [OK] Log file /var/lib/mysql/server1.nc-ph-0741-26.web-hosting.com.err exists [--] Log file: /var/lib/mysql/server1.nc-ph-0741-26.web-hosting.com.err(32K) [OK] Log file /var/lib/mysql/server1.nc-ph-0741-26.web-hosting.com.err is readable. [OK] Log file /var/lib/mysql/server1.nc-ph-0741-26.web-hosting.com.err is not empty [OK] Log file /var/lib/mysql/server1.nc-ph-0741-26.web-hosting.com.err is smaller than 32 Mb [!!] /var/lib/mysql/server1.nc-ph-0741-26.web-hosting.com.err contains 57 warning(s). [!!] /var/lib/mysql/server1.nc-ph-0741-26.web-hosting.com.err contains 12 error(s). [--] 6 start(s) detected in /var/lib/mysql/server1.nc-ph-0741-26.web-hosting.com.err [--] 1) 2019-10-11 1:13:04 0 [Note] /usr/sbin/mysqld: ready for connections. [--] 2) 2019-10-09 6:41:42 0 [Note] /usr/sbin/mysqld: ready for connections. [--] 3) 2019-10-09 6:41:39 0 [Note] /usr/sbin/mysqld: ready for connections. [--] 4) 2019-10-09 6:41:34 0 [Note] /usr/sbin/mysqld: ready for connections. [--] 5) 2019-10-09 6:40:48 140404223039680 [Note] /usr/sbin/mysqld: ready for connections. [--] 6) 2019-10-09 6:40:39 140607405234368 [Note] /usr/sbin/mysqld: ready for connections. [--] 5 shutdown(s) detected in /var/lib/mysql/server1.nc-ph-0741-26.web-hosting.com.err [--] 1) 2019-10-11 1:09:43 0 [Note] /usr/sbin/mysqld: Shutdown complete [--] 2) 2019-10-09 6:41:41 0 [Note] /usr/sbin/mysqld: Shutdown complete [--] 3) 2019-10-09 6:41:39 0 [Note] /usr/sbin/mysqld: Shutdown complete [--] 4) 2019-10-09 6:40:59 140404100704000 [Note] /usr/sbin/mysqld: Shutdown complete [--] 5) 2019-10-09 6:40:48 140607307523840 [Note] /usr/sbin/mysqld: Shutdown complete -------- Storage Engine Statistics ----------------------------------------------------------------- [--] Status: +Aria +CSV +InnoDB +MEMORY +MRG_MyISAM +MyISAM +PERFORMANCE_SCHEMA +SEQUENCE [--] Data in MyISAM tables: 791.8M (Tables: 738) [--] Data in InnoDB tables: 672.0K (Tables: 36) [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 [--] There are 620 basic passwords in the list. -------- CVE Security Recommendations -------------------------------------------------------------- [OK] NO SECURITY CVE FOUND FOR YOUR VERSION -------- Performance Metrics ----------------------------------------------------------------------- [--] Up for: 34m 29s (169K q [82.103 qps], 7K conn, TX: 1G, RX: 20M) [--] Reads / Writes: 99% / 1% [--] Binary logging is disabled [--] Physical Memory : 7.6G [--] Max MySQL memory : 856.4M [--] Other process memory: 0B [--] Total buffers: 417.0M global + 2.9M per thread (151 max threads) [--] P_S Max memory usage: 0B [--] Galera GCache Max memory usage: 0B [OK] Maximum reached memory usage: 472.3M (6.07% of installed RAM) [OK] Maximum possible memory usage: 856.4M (11.01% of installed RAM) [OK] Overall possible memory usage with other process is compatible with memory available [OK] Slow queries: 0% (14/169K) [OK] Highest usage of available connections: 12% (19/151) [OK] Aborted connections: 0.11% (8/7083) [!!] 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. [!!] Query cache efficiency: 0.0% (0 cached / 139K selects) [OK] Query cache prunes per day: 0 [OK] Sorts requiring temporary tables: 0% (0 temp sorts / 34K sorts) [!!] Joins performed without indexes: 4942 [!!] Temporary tables created on disk: 64% (6K on disk / 10K total) [OK] Thread cache hit rate: 99% (19 created / 7K connections) [OK] Table cache hit rate: 99% (920 open / 926 opened) [!!] table_definition_cache(400) is lower than number of tables(1039) [OK] Open file limit used: 15% (1K/10K) [OK] Table locks acquired immediately: 100% (156K immediate / 156K locks) -------- Performance schema ------------------------------------------------------------------------ [--] Performance schema is disabled. [--] Memory used by P_S: 0B [--] Sys schema is installed. -------- ThreadPool Metrics ------------------------------------------------------------------------ [--] ThreadPool stat is enabled. [--] Thread Pool Size: 8 thread(s). [--] Using default value is good enough for your version (10.3.18-MariaDB) -------- MyISAM Metrics ---------------------------------------------------------------------------- [!!] Key buffer used: 21.1% (28M used / 134M cache) [OK] Key buffer size / total MyISAM indexes: 128.0M/34.2M [OK] Read Key buffer hit rate: 100.0% (31M cached / 3K reads) [!!] Write Key buffer hit rate: 85.9% (71 cached / 61 writes) -------- InnoDB Metrics ---------------------------------------------------------------------------- [--] InnoDB is enabled. [--] InnoDB Thread Concurrency: 0 [OK] InnoDB File per table is activated [OK] InnoDB buffer pool / data size: 128.0M/672.0K [!!] 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 [!!] InnoDB Read buffer efficiency: 80.51% (2569 hits/ 3191 total) [!!] InnoDB Write Log efficiency: 0% (1 hits/ 0 total) [OK] InnoDB log waits: 0.00% (0 waits / 1 writes) -------- AriaDB Metrics ---------------------------------------------------------------------------- [--] AriaDB is enabled. [OK] Aria pagecache size / total Aria indexes: 128.0M/1B [!!] Aria pagecache hit rate: 87.1% (50K cached / 6K reads) -------- 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: MIXED [--] XA support enabled: ON [--] Semi synchronous replication Master: OFF [--] Semi synchronous replication Slave: OFF [--] This is a standalone server -------- Recommendations --------------------------------------------------------------------------- General recommendations: Control warning line(s) into /var/lib/mysql/server1.nc-ph-0741-26.web-hosting.com.err file Control error line(s) into /var/lib/mysql/server1.nc-ph-0741-26.web-hosting.com.err file MySQL was started within the last 24 hours - recommendations may be inaccurate 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. See https://dev.mysql.com/doc/internals/en/join-buffer-size.html (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 Performance schema should be activated for better diagnostics Variables to adjust: query_cache_size (=0) query_cache_type (=0) query_cache_limit (> 1M, or use smaller result sets) join_buffer_size (> 256.0K, or always use indexes with JOINs) tmp_table_size (> 16M) max_heap_table_size (> 16M) table_definition_cache(400) > 1039 or -1 (autosizing if supported) performance_schema = ON enable PFS innodb_log_file_size should be (=16M) if possible, so InnoDB total log files size equals to 25% of buffer pool size.

What can I do to fix this?

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  • Have you checked howuch swap is in use? Commented Oct 11, 2019 at 9:32

3 Answers 3

Reset to default
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Running SHOW PROCESSLIST; in phpmyadmin showed a strange query stuck on a database that had close to 1 million rows, killing that solved the issue.

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  • Move from MyISAM to InnoDB.
  • Show us that million-row query; we may be able to help improve the query so that, after converting to InnoDB, it won't cause trouble.
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Rate Per Second=RPS - Suggestions to consider for your my.cnf [mysqld] section

slow_query_log=ON # to ensure log is active query exceeds long_query_time (seconds) log_slow_verbosity=1,explain # from 0 for auto EXPLAIN in the Slow Query Log innodb_buffer_pool_size=1G # from 128M to prepare for ALL InnodDB tables + growth aria_pagecache_buffer_size=512M # from 128M to reduce aria_pagecache_reads count query_cache_size=0 # to ensure QC is not used query_cache_type=0 # to ensure QC is OFF query_cache_limit=0 # to conserve RAM when QC is OFF join_buffer_size=512K # from 256K until you can create needed indexes tmp_table_size=32M # from 16M to increase RAM capacity max_heap_table_size=32M from 16M to reduce created_tmp_disk_tables of 4,942 in 34 minutes table_definition_cache=1200 # from 400 to accomodate number of tables

Disclaimer: I am the content author of website mentioned in my profile, Network profile where you can download FREE Utility Scripts to assist with performance tuning.

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  • @user544095 Have you had an opportunity to apply these suggestions? Please comment on better/worse from your perspective. Commented Nov 11, 2019 at 19:47

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