i upgrade my WHM server / Cent-OS 7 from MySQL 5.6 to 5.7. after that upgrade every few hours my server memory full by MySQL which after hours of MySQL restart it exceed 80% of whole memory. i increase my server ram from 13GB to 17.5GB and still get same problem also i create swap for 3GB and still same problem. i change in MySQL configuration without any luck. so if anyone can help with that.
i try also mysqltuner but the problem that MySQL restarting every few hours and they said that MySQL must be running more than 24 hour at lease for recommendation to be accurate.
this is the configuration of the etc/my.cnf file:
[mysqld]
default-storage-engine=INNODB
innodb_file_per_table=1
max_allowed_packet=268435456
open_files_limit=80000
collation_server=utf8_unicode_ci
character_set_server=utf8
slow_query_log=1
long_query_time=3
max_connections = 200
sort_buffer_size=16M
join_buffer_size=1M
innodb_sort_buffer_size=16M
read_buffer_size=1M
read_rnd_buffer_size=2M
max_heap_table_size=64M
tmp_table_size=64M
key_buffer_size=128M
#event_scheduler=on
innodb_log_file_size=384M
query_cache_type=0
query_cache_size=0
table_open_cache=78000
table_definition_cache=39400
innodb_buffer_pool_instances=3
innodb_buffer_pool_size=3G
and the result of mysql tuner i don't know if it can help as MySQL not running from a long time:
>> MySQLTuner 1.7.19 - Major Hayden <major@mhtx.net>
>> 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] Currently running supported MySQL version 5.7.31-log
[OK] Operating on 64-bit architecture
-------- Log file Recommendations ------------------------------------------------------------------
[OK] Log file /var/lib/mysql/bilal.hosting.err exists
[--] Log file: /var/lib/mysql/bilal.hosting.err(10K)
[OK] Log file /var/lib/mysql/bilal.hosting.err is readable.
[OK] Log file /var/lib/mysql/bilal.hosting.err is not empty
[OK] Log file /var/lib/mysql/bilal.hosting.err is smaller than 32 Mb
[!!] /var/lib/mysql/bilal.hosting.err contains 16 warning(s).
[!!] /var/lib/mysql/bilal.hosting.err contains 2 error(s).
[--] 2 start(s) detected in /var/lib/mysql/bilal.hosting.err
[--] 1) 2020-09-12T11:38:30.571913Z 0 [Note] /usr/sbin/mysqld: ready for connections.
[--] 2) 2020-09-12T05:40:13.253650Z 0 [Note] /usr/sbin/mysqld: ready for connections.
[--] 0 shutdown(s) detected in /var/lib/mysql/bilal.hosting.err
-------- Storage Engine Statistics -----------------------------------------------------------------
[--] Status: +ARCHIVE +BLACKHOLE +CSV -FEDERATED +InnoDB +MEMORY +MRG_MYISAM +MyISAM +PERFORMANCE_SCHEMA
[--] Data in MyISAM tables: 10.0M (Tables: 51)
[--] Data in InnoDB tables: 5.4G (Tables: 30538)
[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: 1h 20m 30s (407K q [84.438 qps], 8K conn, TX: 248M, RX: 48M)
[--] Reads / Writes: 98% / 2%
[--] Binary logging is disabled
[--] Physical Memory : 17.0G
[--] Max MySQL memory : 57.2G
[--] Other process memory: 0B
[--] Total buffers: 3.2G global + 276.2M per thread (200 max threads)
[--] P_S Max memory usage: 72B
[--] Galera GCache Max memory usage: 0B
[OK] Maximum reached memory usage: 5.1G (29.97% of installed RAM)
[!!] Maximum possible memory usage: 57.2G (336.45% of installed RAM)
[!!] Overall possible memory usage with other process exceeded memory
[OK] Slow queries: 0% (21/407K)
[OK] Highest usage of available connections: 3% (7/200)
[OK] Aborted connections: 0.01% (1/8243)
[!!] 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: 3% (872 temp sorts / 25K sorts)
[!!] Joins performed without indexes: 2920
[OK] Temporary tables created on disk: 1% (4K on disk / 414K total)
[OK] Thread cache hit rate: 99% (7 created / 8K connections)
[!!] Table cache hit rate: 4% (39K open / 851K opened)
[!!] table_definition_cache(39400) is lower than number of tables(44053)
[OK] Open file limit used: 0% (312/80K)
[OK] Table locks acquired immediately: 99% (1K immediate / 1K locks)
-------- Performance schema ------------------------------------------------------------------------
[--] Memory used by P_S: 72B
[--] Sys schema is installed.
-------- ThreadPool Metrics ------------------------------------------------------------------------
[--] ThreadPool stat is disabled.
-------- MyISAM Metrics ----------------------------------------------------------------------------
[!!] Key buffer used: 18.3% (24M used / 134M cache)
[OK] Key buffer size / total MyISAM indexes: 128.0M/1.1M
[OK] Read Key buffer hit rate: 98.8% (4K cached / 55 reads)
[!!] Write Key buffer hit rate: 92.5% (40 cached / 37 writes)
-------- InnoDB Metrics ----------------------------------------------------------------------------
[--] InnoDB is enabled.
[--] InnoDB Thread Concurrency: 0
[OK] InnoDB File per table is activated
[!!] InnoDB buffer pool / data size: 3.0G/5.4G
[OK] Ratio InnoDB log file size / InnoDB Buffer pool size: 384.0M * 2/3.0G should be equal to 25%
[OK] InnoDB buffer pool instances: 3
[--] Number of InnoDB Buffer Pool Chunk : 24 for 3 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: 99.95% (216374723 hits/ 216488054 total)
[!!] InnoDB Write Log efficiency: 86.23% (10420 hits/ 12084 total)
[OK] InnoDB log waits: 0.00% (0 waits / 1664 writes)
-------- AriaDB Metrics ----------------------------------------------------------------------------
[--] AriaDB is disabled.
-------- 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:
Control warning line(s) into /var/lib/mysql/bilal.hosting.err file
Control error line(s) into /var/lib/mysql/bilal.hosting.err file
MySQL was started within the last 24 hours - recommendations may be inaccurate
Reduce your overall MySQL memory footprint for system stability
Dedicate this server to your database for highest performance.
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).
Increase table_open_cache gradually to avoid file descriptor limits
Read this before increasing table_open_cache over 64: https://bit.ly/2Fulv7r
Read this before increasing for MariaDB https://mariadb.com/kb/en/library/optimizing-table_open_cache/
This is MyISAM only table_cache scalability problem, InnoDB not affected.
See more details here: https://bugs.mysql.com/bug.php?id=49177
This bug already fixed in MySQL 5.7.9 and newer MySQL versions.
Beware that open_files_limit (80000) variable
should be greater than table_open_cache (39895)
Variables to adjust:
*** MySQL's maximum memory usage is dangerously high ***
*** Add RAM before increasing MySQL buffer variables ***
join_buffer_size (> 1.0M, or always use indexes with JOINs)
table_open_cache (> 39895)
table_definition_cache(39400) > 44053 or -1 (autosizing if supported)
innodb_buffer_pool_size (>= 5.4G) if possible.
note i try to put innodb_buffer_pool_size to 6G as recommended but still the same memory load.
in mysql tuner result they gave result that Maximum possible memory usage: 57.2G (336.45% of installed RAM) is that a problem and how to fix this issue!
also no load on the server or mysql. and on top just the mysql is taking the memory above 70% of it
and this the output of free:
total used free shared buff/cache available
Mem: 16G 13G 323M 14M 3.6G 3.6G
Swap: 3.0G 2.1G 933M
Total: 19G 15G 1.2G
OOM Log Example:
# grep -i "out of memory" /var/log/messages*
/var/log/messages:Sep 7 03:00:23 hosting kernel: Out of memory: Kill process 1969 (mysqld) score 695 or sacrifice child
/var/log/messages:Sep 7 11:41:09 hosting kernel: Out of memory: Kill process 1787 (mysqld) score 756 or sacrifice child
/var/log/messages:Sep 7 13:25:46 hosting kernel: Out of memory: Kill process 8455 (mysqld) score 723 or sacrifice child
/var/log/messages:Sep 7 15:29:27 hosting kernel: Out of memory: Kill process 28063 (mysqld) score 734 or sacrifice child
/var/log/messages:Sep 7 20:56:49 hosting kernel: Out of memory: Kill process 23450 (mysqld) score 727 or sacrifice child
/var/log/messages:Sep 7 20:56:50 hosting kernel: Out of memory: Kill process 2043 (clamd) score 80 or sacrifice child
/var/log/messages:Sep 8 03:05:20 hosting kernel: Out of memory: Kill process 26713 (mysqld) score 681 or sacrifice child
/var/log/messages:Sep 8 05:28:19 hosting kernel: Out of memory: Kill process 3038 (mysqld) score 681 or sacrifice child
/var/log/messages:Sep 8 11:14:35 hosting kernel: Out of memory: Kill process 30391 (mysqld) score 742 or sacrifice child
/var/log/messages:Sep 8 15:02:51 hosting kernel: Out of memory: Kill process 3984 (mysqld) score 742 or sacrifice child
/var/log/messages:Sep 9 12:21:44 hosting kernel: Out of memory: Kill process 1743 (mysqld) score 763 or sacrifice child
/var/log/messages:Sep 9 14:31:21 hosting kernel: Out of memory: Kill process 16796 (mysqld) score 774 or sacrifice child
/var/log/messages:Sep 10 13:01:14 hosting kernel: Out of memory: Kill process 4654 (mysqld) score 788 or sacrifice child
/var/log/messages:Sep 10 13:01:14 hosting kernel: Out of memory: Kill process 2002 (clamd) score 61 or sacrifice child
/var/log/messages:Sep 10 16:31:45 hosting kernel: Out of memory: Kill process 12720 (mysqld) score 816 or sacrifice child
Update:: 15/08/2020
this is the result of show global status:
Variable_name Value
Aborted_clients 0
Aborted_connects 6
Binlog_cache_disk_use 0
Binlog_cache_use 0
Binlog_stmt_cache_disk_use 0
Binlog_stmt_cache_use 0
Bytes_received 187149967
Bytes_sent 539231478
Com_admin_commands 3192
Com_assign_to_keycache 0
Com_alter_db 0
Com_alter_db_upgrade 0
Com_alter_event 0
Com_alter_function 0
Com_alter_instance 0
Com_alter_procedure 0
Com_alter_server 0
Com_alter_table 0
Com_alter_tablespace 0
Com_alter_user 0
Com_analyze 0
Com_begin 707
Com_binlog 0
Com_call_procedure 10
Com_change_db 3467
Com_change_master 0
Com_change_repl_filter 0
Com_check 0
Com_checksum 0
Com_commit 752
Com_create_db 0
Com_create_event 0
Com_create_function 0
Com_create_index 0
Com_create_procedure 0
Com_create_server 0
Com_create_table 0
Com_create_trigger 0
Com_create_udf 0
Com_create_user 0
Com_create_view 0
Com_dealloc_sql 0
Com_delete 790
Com_delete_multi 39
Com_do 0
Com_drop_db 0
Com_drop_event 0
Com_drop_function 0
Com_drop_index 0
Com_drop_procedure 0
Com_drop_server 0
Com_drop_table 0
Com_drop_trigger 0
Com_drop_user 1
Com_drop_view 0
Com_empty_query 0
Com_execute_sql 0
Com_explain_other 0
Com_flush 0
Com_get_diagnostics 0
Com_grant 0
Com_ha_close 0
Com_ha_open 0
Com_ha_read 0
Com_help 0
Com_insert 9398
Com_insert_select 0
Com_install_plugin 0
Com_kill 0
Com_load 0
Com_lock_tables 0
Com_optimize 0
Com_preload_keys 0
Com_prepare_sql 0
Com_purge 0
Com_purge_before_date 0
Com_release_savepoint 0
Com_rename_table 0
Com_rename_user 0
Com_repair 0
Com_replace 0
Com_replace_select 0
Com_reset 0
Com_resignal 0
Com_revoke 0
Com_revoke_all 0
Com_rollback 1
Com_rollback_to_savepoint 0
Com_savepoint 0
Com_select 1080660
Com_set_option 47077
Com_signal 0
Com_show_binlog_events 0
Com_show_binlogs 0
Com_show_charsets 0
Com_show_collations 0
Com_show_create_db 0
Com_show_create_event 0
Com_show_create_func 0
Com_show_create_proc 0
Variable_name Value
Com_show_create_table 35
Com_show_create_trigger 0
Com_show_databases 0
Com_show_engine_logs 0
Com_show_engine_mutex 0
Com_show_engine_status 0
Com_show_events 0
Com_show_errors 0
Com_show_fields 116
Com_show_function_code 0
Com_show_function_status 0
Com_show_grants 0
Com_show_keys 41
Com_show_master_status 1
Com_show_open_tables 0
Com_show_plugins 1
Com_show_privileges 0
Com_show_procedure_code 0
Com_show_procedure_status 0
Com_show_processlist 151
Com_show_profile 0
Com_show_profiles 0
Com_show_relaylog_events 0
Com_show_slave_hosts 0
Com_show_slave_status 1
Com_show_status 103
Com_show_storage_engines 0
Com_show_table_status 0
Com_show_tables 226
Com_show_triggers 1
Com_show_variables 42
Com_show_warnings 23
Com_show_create_user 0
Com_shutdown 0
Com_slave_start 0
Com_slave_stop 0
Com_group_replication_start 0
Com_group_replication_stop 0
Com_stmt_execute 99
Com_stmt_close 99
Com_stmt_fetch 0
Com_stmt_prepare 99
Com_stmt_reset 0
Com_stmt_send_long_data 0
Com_truncate 0
Com_uninstall_plugin 0
Com_unlock_tables 0
Com_update 2619
Com_update_multi 29
Com_xa_commit 0
Com_xa_end 0
Com_xa_prepare 0
Com_xa_recover 0
Com_xa_rollback 0
Com_xa_start 0
Com_stmt_reprepare 0
Connection_errors_accept 0
Connection_errors_internal 0
Connection_errors_max_connections 0
Connection_errors_peer_address 0
Connection_errors_select 0
Connection_errors_tcpwrap 0
Connections 21796
Created_tmp_disk_tables 7006
Created_tmp_files 5594
Created_tmp_tables 465690
Delayed_errors 0
Delayed_insert_threads 0
Delayed_writes 0
Flush_commands 1
Handler_commit 1092598
Handler_delete 3527
Handler_discover 0
Handler_external_lock 2692797
Handler_mrr_init 0
Handler_prepare 0
Handler_read_first 3291451
Handler_read_key 94909022
Handler_read_last 597
Handler_read_next 584655958
Handler_read_prev 2289457
Handler_read_rnd 22585333
Handler_read_rnd_next 1039026278
Handler_rollback 9
Handler_savepoint 0
Handler_savepoint_rollback 0
Handler_update 3001107
Handler_write 13348212
Innodb_buffer_pool_dump_status Dumping of buffer pool not started
Innodb_buffer_pool_load_status Buffer pool(s) load completed at 200915 14:25:20
Innodb_buffer_pool_resize_status
Innodb_buffer_pool_pages_data 120170
Innodb_buffer_pool_bytes_data 1968865280
Innodb_buffer_pool_pages_dirty 6
Innodb_buffer_pool_bytes_dirty 98304
Innodb_buffer_pool_pages_flushed 190308
Innodb_buffer_pool_pages_free 2047
Innodb_buffer_pool_pages_misc 8839
Innodb_buffer_pool_pages_total 131056
Innodb_buffer_pool_read_ahead_rnd 0
Variable_name Value
Innodb_buffer_pool_read_ahead 35380
Innodb_buffer_pool_read_ahead_evicted 842
Innodb_buffer_pool_read_requests 1230004513
Innodb_buffer_pool_reads 156026
Innodb_buffer_pool_wait_free 0
Innodb_buffer_pool_write_requests 9391121
Innodb_data_fsyncs 13083
Innodb_data_pending_fsyncs 0
Innodb_data_pending_reads 0
Innodb_data_pending_writes 0
Innodb_data_read 3170914816
Innodb_data_reads 223898
Innodb_data_writes 197504
Innodb_data_written 3536651776
Innodb_dblwr_pages_written 24887
Innodb_dblwr_writes 2505
Innodb_log_waits 0
Innodb_log_write_requests 14091
Innodb_log_writes 3345
Innodb_os_log_fsyncs 4539
Innodb_os_log_pending_fsyncs 0
Innodb_os_log_pending_writes 0
Innodb_os_log_written 10433536
Innodb_page_size 16384
Innodb_pages_created 1257
Innodb_pages_read 193533
Innodb_pages_written 190308
Innodb_row_lock_current_waits 0
Innodb_row_lock_time 0
Innodb_row_lock_time_avg 0
Innodb_row_lock_time_max 0
Innodb_row_lock_waits 0
Innodb_rows_deleted 3519
Innodb_rows_inserted 20139923
Innodb_rows_read 1686296409
Innodb_rows_updated 4347
Innodb_num_open_files 30356
Innodb_truncated_status_writes 0
Innodb_available_undo_logs 128
Key_blocks_not_flushed 0
Key_blocks_unused 107124
Key_blocks_used 47
Key_read_requests 4732
Key_reads 47
Key_write_requests 20
Key_writes 17
Locked_connects 0
Max_execution_time_exceeded 0
Max_execution_time_set 0
Max_execution_time_set_failed 0
Max_used_connections 12
Max_used_connections_time 2020-09-15 16:00:04
Not_flushed_delayed_rows 0
Ongoing_anonymous_transaction_count 0
Open_files 328
Open_streams 0
Open_table_definitions 17900
Open_tables 31428
Opened_files 2817777
Opened_table_definitions 2090652
Opened_tables 880851
Performance_schema_accounts_lost 0
Performance_schema_cond_classes_lost 0
Performance_schema_cond_instances_lost 0
Performance_schema_digest_lost 0
Performance_schema_file_classes_lost 0
Performance_schema_file_handles_lost 0
Performance_schema_file_instances_lost 0
Performance_schema_hosts_lost 0
Performance_schema_index_stat_lost 0
Performance_schema_locker_lost 0
Performance_schema_memory_classes_lost 0
Performance_schema_metadata_lock_lost 0
Performance_schema_mutex_classes_lost 0
Performance_schema_mutex_instances_lost 0
Performance_schema_nested_statement_lost 0
Performance_schema_prepared_statements_lost 0
Performance_schema_program_lost 0
Performance_schema_rwlock_classes_lost 0
Performance_schema_rwlock_instances_lost 0
Performance_schema_session_connect_attrs_lost 0
Performance_schema_socket_classes_lost 0
Performance_schema_socket_instances_lost 0
Performance_schema_stage_classes_lost 0
Performance_schema_statement_classes_lost 0
Performance_schema_table_handles_lost 0
Performance_schema_table_instances_lost 0
Performance_schema_table_lock_stat_lost 0
Performance_schema_thread_classes_lost 0
Performance_schema_thread_instances_lost 0
Performance_schema_users_lost 0
Prepared_stmt_count 0
Qcache_free_blocks 0
Qcache_free_memory 0
Qcache_hits 0
Qcache_inserts 0
Qcache_lowmem_prunes 0
Qcache_not_cached 0
Qcache_queries_in_cache 0
Qcache_total_blocks 0
Variable_name Value
Queries 1668933
Questions 1166498
Rsa_public_key -----BEGIN PUBLIC KEY-----
MIIBIjANBgkqhkiG9w0BAQE...
Select_full_join 8768
Select_full_range_join 91
Select_range 41874
Select_range_check 0
Select_scan 67251
Slave_open_temp_tables 0
Slow_launch_threads 0
Slow_queries 10
Sort_merge_passes 9043
Sort_range 86052
Sort_rows 15315042
Sort_scan 51047
Ssl_accept_renegotiates 0
Ssl_accepts 0
Ssl_callback_cache_hits 0
Ssl_cipher
Ssl_cipher_list
Ssl_client_connects 0
Ssl_connect_renegotiates 0
Ssl_ctx_verify_depth 18446744073709551615
Ssl_ctx_verify_mode 5
Ssl_default_timeout 0
Ssl_finished_accepts 0
Ssl_finished_connects 0
Ssl_server_not_after Sep 4 04:04:27 2030 GMT
Ssl_server_not_before Sep 6 04:04:27 2020 GMT
Ssl_session_cache_hits 0
Ssl_session_cache_misses 0
Ssl_session_cache_mode SERVER
Ssl_session_cache_overflows 0
Ssl_session_cache_size 128
Ssl_session_cache_timeouts 0
Ssl_sessions_reused 0
Ssl_used_session_cache_entries 0
Ssl_verify_depth 0
Ssl_verify_mode 0
Ssl_version
Table_locks_immediate 590
Table_locks_waited 0
Table_open_cache_hits 2872174
Table_open_cache_misses 880851
Table_open_cache_overflows 849416
Tc_log_max_pages_used 0
Tc_log_page_size 0
Tc_log_page_waits 0
Threads_cached 3
Threads_connected 7
Threads_created 12
Threads_running 4
Uptime 7541
Uptime_since_flush_status 7541
below is the link for the output of: SHOW GLOBAL VARIABLES
linux limits: ulimit -a output:
output of iostat -xm 5 3:
for htop process:
https://pasteboard.co/JriBpd2.png
Thanks,
Best Answer
Rate Per Second = RPS Suggestions to consider for your my.cnf [mysqld] section
Observations: Keep innodb_buffer_pool_instances at 2 until you have more RAM and CPU/cores
You should find these changes will REDUCE CPU busy significantly.
For additional assistance, please view my profile, Network profile for free downloadable Utility Scripts to assist with performance tuning.