0

For the past few months, on a few different servers with similar FreeBSD versions and specs, I've been experiencing high swap usage with MySQL while seemingly having plenty of free RAM.

  • FreeBSD 11.2-RELEASE-p8 (Also was happening in p2)
  • mysql-server 5.6.43 (Also was happening in 5.6.40)
  • Hosted in vmware vcloud.
  • MySQL datadir is in a zvol, with vfs.zfs.arc_max="512M"
  • 4 vcpu and 8GB RAM.

It doesn't use swap immediately. It takes a couple weeks of incrementally using more swap until none remains. This particular server hasn't reached max swap yet, but it's getting there.

last pid:  7054;  load averages:  0.53,  0.44,  0.40                                         up 14+20:16:49  13:28:17
32 processes:  1 running, 31 sleeping
CPU:  0.0% user,  0.0% nice,  0.0% system,  0.0% interrupt,  100% idle
Mem: 233M Active, 1966M Inact, 1994M Laundry, 1326M Wired, 533M Buf, 412M Free
ARC: 189M Total, 47M MFU, 74M MRU, 288K Anon, 5185K Header, 62M Other
     63M Compressed, 208M Uncompressed, 3.28:1 Ratio
Swap: 6144M Total, 4684M Used, 1460M Free, 76% Inuse

  PID USERNAME    THR PRI NICE   SIZE    RES STATE   C   TIME    WCPU COMMAND
  125 root          2  20    0 22348K  5628K select  1  15:47   0.05% vmtoolsd
 7053 root          1  20    0  7920K  3600K CPU2    2   0:00   0.04% top
93525 root          1  20    0   154M   113M nanslp  1   0:36   0.02% php
 1140 mysql        30  20    0  8720M  3519M select  0 344:58   0.02% mysqld
  681 root          1  20    0 77684K 31444K select  1   5:52   0.01% snmpd
  452 root          1  20    0  9184K  1048K select  2   1:23   0.01% devd
 6958 dfairley      1  20    0 13164K  7968K select  0   0:00   0.01% sshd
93513 root          1  20    0   104M 23360K kqread  2   0:05   0.01% php-fpm
  711 root          1  20    0 12712K 12808K select  2   1:11   0.00% ntpd
  619 root          1  20    0  6416K  2004K select  0   0:36   0.00% syslogd
 1179 root          1  20    0 10456K  5204K select  1   0:20   0.00% sendmail
 6949 daemon        1  41    0   118M 63328K accept  0   0:53   0.00% php-fpm
 6954 daemon        1  31    0   116M 62008K accept  0   0:38   0.00% php-fpm
 7002 daemon        1  35    0   114M 56476K accept  2   0:21   0.00% php-fpm
 1186 root          1  20    0  6468K   800K nanslp  0   0:05   0.00% cron
 6999 daemon        1  44    0   114M 54684K accept  2   0:04   0.00% php-fpm
  401 root          1  42    0  6548K  1992K select  2   0:01   0.00% dhclient
 1182 smmsp         1  20    0 10456K  3352K pause   2   0:00   0.00% sendmail
  447 _dhcp         1  20    0  6548K  2048K select  0   0:00   0.00% dhclient
 1176 root          1  20    0 12852K  5168K select  2   0:00   0.00% sshd
  738 mysql         1  52    0  7064K     0K wait    2   0:00   0.00% <sh>
 6959 dfairley      1  20    0  7416K  3784K pause   3   0:00   0.00% csh
 6956 root          1  23    0 13164K  7920K select  0   0:00   0.00% sshd
 7052 root          1  20    0  7612K  3796K select  1   0:00   0.00% sudo
 1237 root          1  52    0  6408K  1796K ttyin   2   0:00   0.00% getty
 1238 root          1  52    0  6408K  1796K ttyin   2   0:00   0.00% getty
 1239 root          1  52    0  6408K  1796K ttyin   0   0:00   0.00% getty
 1236 root          1  52    0  6408K  1796K ttyin   3   0:00   0.00% getty
 1241 root          1  52    0  6408K  1796K ttyin   3   0:00   0.00% getty
 1242 root          1  52    0  6408K  1796K ttyin   1   0:00   0.00% getty
 1235 root          1  52    0  6408K  1796K ttyin   1   0:00   0.00% getty
 1240 root          1  52    0  6408K  1796K ttyin   3   0:00   0.00% getty

Eventually out of swap messages start hitting /var/log/messages every 10 or so minutes.

my.cnf:

[client]
port        = 3306
socket      = /tmp/mysql.sock

[mysqld]
default_time_zone=America/Vancouver
port        = 3306
socket      = /tmp/mysql.sock
key_buffer_size = 32M
expire_logs_days=30
join_buffer_size = 1M
table_definition_cache = 1500
table_open_cache = 1500
sort_buffer_size = 2M
read_buffer_size = 4M
read_rnd_buffer_size = 4M
max_allowed_packet = 128M
slave-skip-errors=1022,1050,1060,1061,1062,1169,1146
server-id   = 253051
log-bin=/data/binarylogs/mysql-bin
log-bin-index=/data/binarylogs/mysql-bin
binlog_format=mixed
innodb_log_group_home_dir=/data/mysql/logs
innodb_buffer_pool_size = 4096M
innodb_log_file_size = 512M
innodb_buffer_pool_instances = 4
skip-innodb_doublewrite
innodb_flush_log_at_trx_commit = 2
max_connections=80

[mysqldump]
quick
max_allowed_packet = 128M

[mysql]
no-auto-rehash

[mysqlhotcopy]
interactive-timeout

What can cause mysql to repeatedly allocate swap while having plenty of free memory?

Edit: Output of SHOW GLOBAL STATUS;:

Aborted_clients 0
Aborted_connects    0
Binlog_cache_disk_use   368
Binlog_cache_use    1495766
Binlog_stmt_cache_disk_use  0
Binlog_stmt_cache_use   183
Bytes_received  6673111397
Bytes_sent  16919455552
Com_admin_commands  0
Com_assign_to_keycache  0
Com_alter_db    0
Com_alter_db_upgrade    0
Com_alter_event 0
Com_alter_function  0
Com_alter_procedure 0
Com_alter_server    0
Com_alter_table 140
Com_alter_tablespace    0
Com_alter_user  0
Com_analyze 0
Com_begin   682
Com_binlog  0
Com_call_procedure  2
Com_change_db   17594185
Com_change_master   0
Com_check   1815
Com_checksum    0
Com_commit  682
Com_create_db   1
Com_create_event    0
Com_create_function 0
Com_create_index    0
Com_create_procedure    4
Com_create_server   0
Com_create_table    81
Com_create_trigger  78
Com_create_udf  0
Com_create_user 0
Com_create_view 0
Com_dealloc_sql 118
Com_delete  33434
Com_delete_multi    34
Com_do  0
Com_drop_db 1
Com_drop_event  0
Com_drop_function   0
Com_drop_index  0
Com_drop_procedure  8
Com_drop_server 0
Com_drop_table  1
Com_drop_trigger    78
Com_drop_user   0
Com_drop_view   0
Com_empty_query 0
Com_execute_sql 118
Com_flush   1
Com_get_diagnostics 0
Com_grant   0
Com_ha_close    0
Com_ha_open 0
Com_ha_read 0
Com_help    0
Com_insert  2267022
Com_insert_select   1
Com_install_plugin  0
Com_kill    0
Com_load    0
Com_lock_tables 711
Com_optimize    0
Com_preload_keys    0
Com_prepare_sql 118
Com_purge   0
Com_purge_before_date   0
Com_release_savepoint   0
Com_rename_table    0
Com_rename_user 0
Com_repair  1
Com_replace 0
Com_replace_select  0
Com_reset   0
Com_resignal    0
Com_revoke  0
Com_revoke_all  0
Com_rollback    0
Com_rollback_to_savepoint   0
Com_savepoint   0
Com_select  23827649
Com_set_option  1874466
Com_signal  0
Com_show_binlog_events  0
Com_show_binlogs    0
Com_show_charsets   0
Com_show_collations 88
Com_show_create_db  331
Com_show_create_event   0
Com_show_create_func    0
Com_show_create_proc    0
Com_show_create_table   50
Com_show_create_trigger 0
Com_show_databases  2
Com_show_engine_logs    0
Com_show_engine_mutex   0
Com_show_engine_status  1
Com_show_events 7
Com_show_errors 0
Com_show_fields 6349
Com_show_function_code  0
Com_show_function_status    0
Com_show_grants 0
Com_show_keys   2445
Com_show_master_status  0
Com_show_open_tables    0
Com_show_plugins    0
Com_show_privileges 0
Com_show_procedure_code 0
Com_show_procedure_status   0
Com_show_processlist    75
Com_show_profile    0
Com_show_profiles   0
Com_show_relaylog_events    0
Com_show_slave_hosts    0
Com_show_slave_status   0
Com_show_status 38530
Com_show_storage_engines    0
Com_show_table_status   149
Com_show_tables 1258634
Com_show_triggers   3
Com_show_variables  38882
Com_show_warnings   3
Com_slave_start 0
Com_slave_stop  0
Com_stmt_close  118
Com_stmt_execute    118
Com_stmt_fetch  0
Com_stmt_prepare    118
Com_stmt_reprepare  0
Com_stmt_reset  0
Com_stmt_send_long_data 0
Com_truncate    0
Com_uninstall_plugin    0
Com_unlock_tables   709
Com_update  488759
Com_update_multi    294
Com_xa_commit   0
Com_xa_end  0
Com_xa_prepare  0
Com_xa_recover  0
Com_xa_rollback 0
Com_xa_start    0
Compression OFF
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 586795
Created_tmp_disk_tables 303745
Created_tmp_files   269
Created_tmp_tables  3267898
Delayed_errors  0
Delayed_insert_threads  0
Delayed_writes  0
Flush_commands  1
Handler_commit  26737048
Handler_delete  206673
Handler_discover    0
Handler_external_lock   69915146
Handler_mrr_init    0
Handler_prepare 2992470
Handler_read_first  20029611
Handler_read_key    1228486328
Handler_read_last   100115
Handler_read_next   1712542996
Handler_read_prev   1412213
Handler_read_rnd    21965186
Handler_read_rnd_next   3295746264
Handler_rollback    2668
Handler_savepoint   0
Handler_savepoint_rollback  0
Handler_update  800615
Handler_write   76355829
Innodb_buffer_pool_dump_status  not started
Innodb_buffer_pool_load_status  not started
Innodb_buffer_pool_pages_data   252762
Innodb_buffer_pool_bytes_data   4141252608
Innodb_buffer_pool_pages_dirty  78
Innodb_buffer_pool_bytes_dirty  1277952
Innodb_buffer_pool_pages_flushed    4358689
Innodb_buffer_pool_pages_free   4096
Innodb_buffer_pool_pages_misc   5286
Innodb_buffer_pool_pages_total  262144
Innodb_buffer_pool_read_ahead_rnd   0
Innodb_buffer_pool_read_ahead   4428
Innodb_buffer_pool_read_ahead_evicted   20
Innodb_buffer_pool_read_requests    5898171234
Innodb_buffer_pool_reads    245395
Innodb_buffer_pool_wait_free    0
Innodb_buffer_pool_write_requests   19741903
Innodb_data_fsyncs  1553378
Innodb_data_pending_fsyncs  0
Innodb_data_pending_reads   0
Innodb_data_pending_writes  0
Innodb_data_read    6139465728
Innodb_data_reads   372118
Innodb_data_writes  5567954
Innodb_data_written 73872195072
Innodb_dblwr_pages_written  0
Innodb_dblwr_writes 0
Innodb_have_atomic_builtins ON
Innodb_log_waits    0
Innodb_log_write_requests   3607495
Innodb_log_writes   1750027
Innodb_os_log_fsyncs    316644
Innodb_os_log_pending_fsyncs    0
Innodb_os_log_pending_writes    0
Innodb_os_log_written   2416485376
Innodb_page_size    16384
Innodb_pages_created    26254
Innodb_pages_read   374718
Innodb_pages_written    4358689
Innodb_row_lock_current_waits   0
Innodb_row_lock_time    2560
Innodb_row_lock_time_avg    2
Innodb_row_lock_time_max    89
Innodb_row_lock_waits   1194
Innodb_rows_deleted 99776
Innodb_rows_inserted    2033207
Innodb_rows_read    5579212917
Innodb_rows_updated 689505
Innodb_num_open_files   1500
Innodb_truncated_status_writes  0
Innodb_available_undo_logs  128
Key_blocks_not_flushed  0
Key_blocks_unused   26756
Key_blocks_used 498
Key_read_requests   8896641
Key_reads   55
Key_write_requests  2430085
Key_writes  69
Last_query_cost 0.000000
Last_query_partial_plans    0
Max_used_connections    43
Not_flushed_delayed_rows    0
Open_files  59
Open_streams    0
Open_table_definitions  1500
Open_tables 1500
Opened_files    1225846
Opened_table_definitions    2741
Opened_tables   3734
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_locker_lost  0
Performance_schema_mutex_classes_lost   0
Performance_schema_mutex_instances_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_thread_classes_lost  0
Performance_schema_thread_instances_lost    0
Performance_schema_users_lost   0
Prepared_stmt_count 0
Qcache_free_blocks  1
Qcache_free_memory  1031432
Qcache_hits 0
Qcache_inserts  0
Qcache_lowmem_prunes    0
Qcache_not_cached   23787035
Qcache_queries_in_cache 0
Qcache_total_blocks 1
Queries 49223617
Questions   46560144
Rsa_public_key   
Select_full_join    39259
Select_full_range_join  0
Select_range    370666
Select_range_check  0
Select_scan 3833980
Slave_heartbeat_period  0.000
Slave_last_heartbeat     
Slave_open_temp_tables  0
Slave_received_heartbeats   0
Slave_retried_transactions  0
Slave_running   OFF
Slow_launch_threads 0
Slow_queries    4
Sort_merge_passes   6
Sort_range  212023
Sort_rows   34405674
Sort_scan   1616766
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    0
Ssl_ctx_verify_mode 0
Ssl_default_timeout 0
Ssl_finished_accepts    0
Ssl_finished_connects   0
Ssl_server_not_after     
Ssl_server_not_before    
Ssl_session_cache_hits  0
Ssl_session_cache_misses    0
Ssl_session_cache_mode  NONE
Ssl_session_cache_overflows 0
Ssl_session_cache_size  0
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   34856215
Table_locks_waited  1
Table_open_cache_hits   34862013
Table_open_cache_misses 3681
Table_open_cache_overflows  1819
Tc_log_max_pages_used   0
Tc_log_page_size    0
Tc_log_page_waits   0
Threads_cached  6
Threads_connected   3
Threads_created 16681
Threads_running 1
Uptime  1287299
Uptime_since_flush_status   1287299

SHOW VARIABLES;:

auto_increment_increment    1
auto_increment_offset   1
autocommit  ON
automatic_sp_privileges ON
avoid_temporal_upgrade  OFF
back_log    66
basedir /usr/local/
big_tables  OFF
bind_address    *
binlog_cache_size   32768
binlog_checksum CRC32
binlog_direct_non_transactional_updates OFF
binlog_error_action IGNORE_ERROR
binlog_format   MIXED
binlog_gtid_simple_recovery OFF
binlog_max_flush_queue_time 0
binlog_order_commits    ON
binlog_row_image    FULL
binlog_rows_query_log_events    OFF
binlog_stmt_cache_size  32768
binlogging_impossible_mode  IGNORE_ERROR
block_encryption_mode   aes-128-ecb
bulk_insert_buffer_size 8388608
character_set_client    utf8mb4
character_set_connection    utf8mb4
character_set_database  latin1
character_set_filesystem    binary
character_set_results   utf8mb4
character_set_server    latin1
character_set_system    utf8
character_sets_dir  /usr/local/share/mysql/charsets/
collation_connection    utf8mb4_general_ci
collation_database  latin1_swedish_ci
collation_server    latin1_swedish_ci
completion_type NO_CHAIN
concurrent_insert   AUTO
connect_timeout 10
core_file   OFF
datadir /var/db/mysql/
date_format %Y-%m-%d
datetime_format %Y-%m-%d %H:%i:%s
default_storage_engine  InnoDB
default_tmp_storage_engine  InnoDB
default_week_format 0
delay_key_write ON
delayed_insert_limit    100
delayed_insert_timeout  300
delayed_queue_size  1000
disconnect_on_expired_password  ON
div_precision_increment 4
end_markers_in_json OFF
enforce_gtid_consistency    OFF
eq_range_index_dive_limit   10
error_count 0
event_scheduler OFF
expire_logs_days    30
explicit_defaults_for_timestamp OFF
external_user    
flush   OFF
flush_time  0
foreign_key_checks  ON
ft_boolean_syntax   + -><()~*:""&|
ft_max_word_len 84
ft_min_word_len 4
ft_query_expansion_limit    20
ft_stopword_file    (built-in)
general_log OFF
general_log_file    /var/db/mysql/rad-bccfa.log
group_concat_max_len    1024
gtid_executed    
gtid_mode   OFF
gtid_next   AUTOMATIC
gtid_owned   
gtid_purged  
have_compress   YES
have_crypt  YES
have_dynamic_loading    YES
have_geometry   YES
have_openssl    DISABLED
have_profiling  YES
have_query_cache    YES
have_rtree_keys YES
have_ssl    DISABLED
have_symlink    YES
host_cache_size 208
hostname    rad-bccfa
identity    0
ignore_builtin_innodb   OFF
ignore_db_dirs   
init_connect     
init_file    
init_slave   
innodb_adaptive_flushing    ON
innodb_adaptive_flushing_lwm    10
innodb_adaptive_hash_index  ON
innodb_adaptive_max_sleep_delay 150000
innodb_additional_mem_pool_size 8388608
innodb_api_bk_commit_interval   5
innodb_api_disable_rowlock  OFF
innodb_api_enable_binlog    OFF
innodb_api_enable_mdl   OFF
innodb_api_trx_level    0
innodb_autoextend_increment 64
innodb_autoinc_lock_mode    1
innodb_buffer_pool_dump_at_shutdown OFF
innodb_buffer_pool_dump_now OFF
innodb_buffer_pool_filename ib_buffer_pool
innodb_buffer_pool_instances    4
innodb_buffer_pool_load_abort   OFF
innodb_buffer_pool_load_at_startup  OFF
innodb_buffer_pool_load_now OFF
innodb_buffer_pool_size 4294967296
innodb_change_buffer_max_size   25
innodb_change_buffering all
innodb_checksum_algorithm   innodb
innodb_checksums    ON
innodb_cmp_per_index_enabled    OFF
innodb_commit_concurrency   0
innodb_compression_failure_threshold_pct    5
innodb_compression_level    6
innodb_compression_pad_pct_max  50
innodb_concurrency_tickets  5000
innodb_data_file_path   ibdata1:12M:autoextend
innodb_data_home_dir     
innodb_disable_sort_file_cache  OFF
innodb_doublewrite  OFF
innodb_fast_shutdown    1
innodb_file_format  Antelope
innodb_file_format_check    ON
innodb_file_format_max  Antelope
innodb_file_per_table   ON
innodb_flush_log_at_timeout 1
innodb_flush_log_at_trx_commit  2
innodb_flush_method  
innodb_flush_neighbors  1
innodb_flushing_avg_loops   30
innodb_force_load_corrupted OFF
innodb_force_recovery   0
innodb_ft_aux_table  
innodb_ft_cache_size    8000000
innodb_ft_enable_diag_print OFF
innodb_ft_enable_stopword   ON
innodb_ft_max_token_size    84
innodb_ft_min_token_size    3
innodb_ft_num_word_optimize 2000
innodb_ft_result_cache_limit    2000000000
innodb_ft_server_stopword_table  
innodb_ft_sort_pll_degree   2
innodb_ft_total_cache_size  640000000
innodb_ft_user_stopword_table    
innodb_io_capacity  200
innodb_io_capacity_max  2000
innodb_large_prefix OFF
innodb_lock_wait_timeout    50
innodb_locks_unsafe_for_binlog  OFF
innodb_log_buffer_size  8388608
innodb_log_compressed_pages ON
innodb_log_file_size    536870912
innodb_log_files_in_group   2
innodb_log_group_home_dir   /data/mysql/logs
innodb_lru_scan_depth   1024
innodb_max_dirty_pages_pct  75
innodb_max_dirty_pages_pct_lwm  0
innodb_max_purge_lag    0
innodb_max_purge_lag_delay  0
innodb_mirrored_log_groups  1
innodb_monitor_disable   
innodb_monitor_enable    
innodb_monitor_reset     
innodb_monitor_reset_all     
innodb_old_blocks_pct   37
innodb_old_blocks_time  1000
innodb_online_alter_log_max_size    134217728
innodb_open_files   1500
innodb_optimize_fulltext_only   OFF
innodb_page_size    16384
innodb_print_all_deadlocks  OFF
innodb_purge_batch_size 300
innodb_purge_threads    1
innodb_random_read_ahead    OFF
innodb_read_ahead_threshold 56
innodb_read_io_threads  4
innodb_read_only    OFF
innodb_replication_delay    0
innodb_rollback_on_timeout  OFF
innodb_rollback_segments    128
innodb_sort_buffer_size 1048576
innodb_spin_wait_delay  6
innodb_stats_auto_recalc    ON
innodb_stats_include_delete_marked  OFF
innodb_stats_method nulls_equal
innodb_stats_on_metadata    OFF
innodb_stats_persistent ON
innodb_stats_persistent_sample_pages    20
innodb_stats_sample_pages   8
innodb_stats_transient_sample_pages 8
innodb_status_output    OFF
innodb_status_output_locks  OFF
innodb_strict_mode  OFF
innodb_support_xa   ON
innodb_sync_array_size  1
innodb_sync_spin_loops  30
innodb_table_locks  ON
innodb_thread_concurrency   0
innodb_thread_sleep_delay   10000
innodb_tmpdir    
innodb_undo_directory   .
innodb_undo_logs    128
innodb_undo_tablespaces 0
innodb_use_native_aio   OFF
innodb_use_sys_malloc   ON
innodb_version  5.6.43
innodb_write_io_threads 4
insert_id   0
interactive_timeout 28800
join_buffer_size    1048576
keep_files_on_create    OFF
key_buffer_size 33554432
key_cache_age_threshold 300
key_cache_block_size    1024
key_cache_division_limit    100
large_files_support ON
large_page_size 0
large_pages OFF
last_insert_id  0
lc_messages en_US
lc_messages_dir /usr/local/share/mysql/
lc_time_names   en_US
license GPL
local_infile    ON
lock_wait_timeout   31536000
locked_in_memory    OFF
log_bin ON
log_bin_basename    /data/binarylogs/mysql-bin
log_bin_index   /data/binarylogs/mysql-bin.index
log_bin_trust_function_creators OFF
log_bin_use_v1_row_events   OFF
log_error   ./rad-bccfa.err
log_output  FILE
log_queries_not_using_indexes   OFF
log_slave_updates   OFF
log_slow_admin_statements   OFF
log_slow_slave_statements   OFF
log_throttle_queries_not_using_indexes  0
log_warnings    1
long_query_time 10.000000
low_priority_updates    OFF
lower_case_file_system  OFF
lower_case_table_names  0
master_info_repository  FILE
master_verify_checksum  OFF
max_allowed_packet  134217728
max_binlog_cache_size   18446744073709547520
max_binlog_size 1073741824
max_binlog_stmt_cache_size  18446744073709547520
max_connect_errors  100
max_connections 80
max_delayed_threads 20
max_digest_length   1024
max_error_count 64
max_heap_table_size 16777216
max_insert_delayed_threads  20
max_join_size   18446744073709551615
max_length_for_sort_data    1024
max_prepared_stmt_count 16382
max_relay_log_size  0
max_seeks_for_key   18446744073709551615
max_sort_length 1024
max_sp_recursion_depth  0
max_tmp_tables  32
max_user_connections    0
max_write_lock_count    18446744073709551615
metadata_locks_cache_size   1024
metadata_locks_hash_instances   8
min_examined_row_limit  0
multi_range_count   256
myisam_data_pointer_size    6
myisam_max_sort_file_size   9223372036853727232
myisam_mmap_size    18446744073709551615
myisam_recover_options  OFF
myisam_repair_threads   1
myisam_sort_buffer_size 8388608
myisam_stats_method nulls_unequal
myisam_use_mmap OFF
net_buffer_length   16384
net_read_timeout    30
net_retry_count 10
net_write_timeout   60
new OFF
old OFF
old_alter_table OFF
old_passwords   0
open_files_limit    175950
optimizer_prune_level   1
optimizer_search_depth  62
optimizer_switch    index_merge=on,index_merge_union=on,index_merge_sort_union=on,index_merge_intersection=on,engine_condition_pushdown=on,index_condition_pushdown=on,mrr=on,mrr_cost_based=on,block_nested_loop=on,batched_key_access=off,materialization=on,semijoin=on,loosescan=on,firstmatch=on,subquery_materialization_cost_based=on,use_index_extensions=on
optimizer_trace enabled=off,one_line=off
optimizer_trace_features    greedy_search=on,range_optimizer=on,dynamic_range=on,repeated_subselect=on
optimizer_trace_limit   1
optimizer_trace_max_mem_size    16384
optimizer_trace_offset  -1
performance_schema  ON
performance_schema_accounts_size    100
performance_schema_digests_size 10000
performance_schema_events_stages_history_long_size  10000
performance_schema_events_stages_history_size   10
performance_schema_events_statements_history_long_size  10000
performance_schema_events_statements_history_size   10
performance_schema_events_waits_history_long_size   10000
performance_schema_events_waits_history_size    10
performance_schema_hosts_size   100
performance_schema_max_cond_classes 80
performance_schema_max_cond_instances   3420
performance_schema_max_digest_length    1024
performance_schema_max_file_classes 50
performance_schema_max_file_handles 32768
performance_schema_max_file_instances   7693
performance_schema_max_mutex_classes    200
performance_schema_max_mutex_instances  16480
performance_schema_max_rwlock_classes   40
performance_schema_max_rwlock_instances 9560
performance_schema_max_socket_classes   10
performance_schema_max_socket_instances 180
performance_schema_max_stage_classes    150
performance_schema_max_statement_classes    168
performance_schema_max_table_handles    3000
performance_schema_max_table_instances  12500
performance_schema_max_thread_classes   50
performance_schema_max_thread_instances 260
performance_schema_session_connect_attrs_size   512
performance_schema_setup_actors_size    100
performance_schema_setup_objects_size   100
performance_schema_users_size   100
pid_file    /var/db/mysql/rad-bccfa.pid
plugin_dir  /usr/local/lib/mysql/plugin/
port    3306
preload_buffer_size 32768
profiling   OFF
profiling_history_size  15
protocol_version    10
proxy_user   
pseudo_slave_mode   OFF
pseudo_thread_id    588542
query_alloc_block_size  8192
query_cache_limit   1048576
query_cache_min_res_unit    4096
query_cache_size    1048576
query_cache_type    OFF
query_cache_wlock_invalidate    OFF
query_prealloc_size 8192
rand_seed1  0
rand_seed2  0
range_alloc_block_size  4096
read_buffer_size    4194304
read_only   OFF
read_rnd_buffer_size    4194304
relay_log    
relay_log_basename   
relay_log_index  
relay_log_info_file relay-log.info
relay_log_info_repository   FILE
relay_log_purge ON
relay_log_recovery  OFF
relay_log_space_limit   0
report_host  
report_password  
report_port 3306
report_user  
rpl_stop_slave_timeout  31536000
secure_auth ON
secure_file_priv    /var/db/mysql_secure/
server_id   253051
server_id_bits  32
server_uuid 02376841-ea78-11e5-8675-00505601050e
sha256_password_private_key_path    private_key.pem
sha256_password_public_key_path public_key.pem
show_old_temporals  OFF
simplified_binlog_gtid_recovery OFF
skip_external_locking   ON
skip_name_resolve   OFF
skip_networking OFF
skip_show_database  OFF
slave_allow_batching    OFF
slave_checkpoint_group  512
slave_checkpoint_period 300
slave_compressed_protocol   OFF
slave_exec_mode STRICT
slave_load_tmpdir   /tmp/
slave_max_allowed_packet    1073741824
slave_net_timeout   3600
slave_parallel_workers  0
slave_pending_jobs_size_max 16777216
slave_rows_search_algorithms    TABLE_SCAN,INDEX_SCAN
slave_skip_errors   1022,1050,1060,1061,1062,1146,1169
slave_sql_verify_checksum   ON
slave_transaction_retries   10
slave_type_conversions   
slow_launch_time    2
slow_query_log  OFF
slow_query_log_file /var/db/mysql/rad-bccfa-slow.log
socket  /tmp/mysql.sock
sort_buffer_size    2097152
sql_auto_is_null    OFF
sql_big_selects ON
sql_buffer_result   OFF
sql_log_bin ON
sql_log_off OFF
sql_mode    NO_ENGINE_SUBSTITUTION
sql_notes   ON
sql_quote_show_create   ON
sql_safe_updates    OFF
sql_select_limit    18446744073709551615
sql_slave_skip_counter  0
sql_warnings    OFF
ssl_ca   
ssl_capath   
ssl_cert     
ssl_cipher   
ssl_crl  
ssl_crlpath  
ssl_key  
storage_engine  InnoDB
stored_program_cache    256
sync_binlog 0
sync_frm    ON
sync_master_info    10000
sync_relay_log  10000
sync_relay_log_info 10000
system_time_zone    PST
table_definition_cache  1500
table_open_cache    1500
table_open_cache_instances  1
thread_cache_size   8
thread_concurrency  10
thread_handling one-thread-per-connection
thread_stack    262144
time_format %H:%i:%s
time_zone   America/Vancouver
timed_mutexes   OFF
timestamp   1550099073.579494
tmp_table_size  16777216
tmpdir  /tmp/
transaction_alloc_block_size    8192
transaction_allow_batching  OFF
transaction_prealloc_size   4096
tx_isolation    REPEATABLE-READ
tx_read_only    OFF
unique_checks   ON
updatable_views_with_limit  YES
version 5.6.43-log
version_comment Source distribution
version_compile_machine amd64
version_compile_os  FreeBSD11.2
wait_timeout    28800
warning_count   0
  • What things can be tuned for ZFS? Do you have other processes running on the same VM (web server, php, etc)? If you provide SHOW VARIABLES; and SHOW GLOBAL STATUS; (after being up for at least a day), I may be able to discover some other issues. Meanwhile, lower innodb_buffer_pool_size to 3G in hopes that that will keep the problem from happening. (4G, even 5G, should be fine for a dedicated 8G server). – Rick James Feb 13 at 22:31
  • @RickJames Many things can be tuned for ZFS, but the swap appears to be allocated to MySQL itself, not ZFS's cache. This particular server does have php-fpm running, but the issue occurs on a different server that is 100% dedicated to MySQL. I've tried lowering the innodb buffer pool but it still swaps out. I added the output of global status. Variables are default+what's specified in the my.cnf. – Duncan Fairley Feb 13 at 22:50
  • I need the complete VARIABLES list -- the defaults change from version to version. MySQL may need swapping, but it does not allocate swap space; that is left to the OS (and ZFS driver). – Rick James Feb 13 at 23:02
  • @RickJames Thanks, I added the variables output. I just wasn't sure how long these questions should be on serverfault. – Duncan Fairley Feb 13 at 23:06
  • Your output is more compact than some; maybe that is why it fits. – Rick James Feb 13 at 23:51
0

Analysis...

Observations:

  • Version: 5.6.43-log
  • 8 GB of RAM
  • Uptime = 14d 21:34:59
  • You are not running on Windows.
  • Running 64-bit version
  • You appear to be running entirely (or mostly) InnoDB.

The More Important Issues:

Alas, nothing jumped out as the answer to your swapping problem. Anyway, here's my comments:

Set long_query_time=1 and turn on the slowlog. You have some slow queries that are likely to get worse as the tables get bigger. (16% of SELECTs are table scans.)

slave_skip_errors = 1022 1050 1060 1061 1062 1146 1169 -- That's sweeping a lot of things under the rug!

Doing USE dbname 30 times per connection (14 times per second)? What's going on?

Increase thread_cache_size to 20.

Since you don't seem to be using MyISAM, I wonder why you are doing any REPAIRs.

Is some 3rd party software doing SHOW TABLES every second? There is a bit of overhead in this.

Details and other observations:

( innodb_buffer_pool_size / _ram ) = 4096M / 8192M = 50.0% -- % of RAM used for InnoDB buffer_pool

( innodb_lru_scan_depth ) = 1,024 -- "InnoDB: page_cleaner: 1000ms intended loop took ..." may be fixed by lowering lru_scan_depth

( Innodb_pages_written / Innodb_buffer_pool_write_requests ) = 4,358,689 / 19741903 = 22.1% -- Write requests that had to hit disk -- Check innodb_buffer_pool_size

( Innodb_dblwr_pages_written/Innodb_pages_written ) = 0/4358689 = 0 -- Seems like these values should be equal?

( Innodb_os_log_written / (Uptime / 3600) / innodb_log_files_in_group / innodb_log_file_size ) = 2,416,485,376 / (1287299 / 3600) / 2 / 512M = 0.00629 -- Ratio -- (see minutes)

( Uptime / 60 * innodb_log_file_size / Innodb_os_log_written ) = 1,287,299 / 60 * 512M / 2416485376 = 4,766 -- Minutes between InnoDB log rotations Beginning with 5.6.8, this can be changed dynamically; be sure to also change my.cnf. -- (The recommendation of 60 minutes between rotations is somewhat arbitrary.) Adjust innodb_log_file_size. (Cannot change in AWS.)

( innodb_flush_method ) = innodb_flush_method = -- How InnoDB should ask the OS to write blocks. Suggest O_DIRECT or O_ALL_DIRECT (Percona) to avoid double buffering. (At least for Unix.) See chrischandler for caveat about O_ALL_DIRECT

( innodb_flush_neighbors ) = 1 -- A minor optimization when writing blocks to disk. -- Use 0 for SSD drives; 1 for HDD.

( innodb_io_capacity ) = 200 -- I/O ops per second capable on disk . 100 for slow drives; 200 for spinning drives; 1000-2000 for SSDs; multiply by RAID factor.

( sync_binlog ) = 0 -- Use 1 for added security, at some cost of I/O =1 may lead to lots of "query end"; =0 may lead to "binlog at impossible position" and lose transactions in a crash, but is faster.

( innodb_print_all_deadlocks ) = innodb_print_all_deadlocks = OFF -- Whether to log all Deadlocks. -- If you are plagued with Deadlocks, turn this on. Caution: If you have lots of deadlocks, this may write a lot to disk.

( max_connections ) = 80 -- Maximum number of connections (threads). Impacts various allocations. -- If max_connections is too high and various memory settings are high, you could run out of RAM.

( local_infile ) = local_infile = ON -- local_infile = ON is a potential security issue

( Select_scan ) = 3,833,980 / 1287299 = 3 /sec -- full table scans -- Add indexes / optimize queries (unless they are tiny tables)

( Select_scan / Com_select ) = 3,833,980 / 23827649 = 16.1% -- % of selects doing full table scan. (May be fooled by Stored Routines.) -- Add indexes / optimize queries

( binlog_error_action ) = binlog_error_action = IGNORE_ERROR -- What to do if the binlog cannot be written. -- IGNORE_ERROR is the default for backwards compatibility, but ABORT_SERVER is recommended.

( binlog_format ) = binlog_format = MIXED -- STATEMENT/ROW/MIXED. ROW is preferred; it may become the default.

( slave_skip_errors ) = slave_skip_errors = 1022 1050 1060 1061 1062 1146 1169 -- Which error cases to ignore -- It would be better to change the code than sweep problems under the rug.

( slow_query_log ) = slow_query_log = OFF -- Whether to log slow queries. (5.1.12)

( long_query_time ) = 10 -- Cutoff (Seconds) for defining a "slow" query. -- Suggest 2

( Com_change_db / Connections ) = 17,594,185 / 586795 = 30 -- Database switches per connection -- (minor) Consider using "db.table" syntax

( Com_change_db ) = 17,594,185 / 1287299 = 14 /sec -- Probably comes from USE statements. -- Consider connecting with DB, using db.tbl syntax, eliminating spurious USE statements, etc.

( Threads_created / Connections ) = 16,681 / 586795 = 2.8% -- Rapidity of process creation

You have the Query Cache half-off. You should set both query_cache_type = OFF and query_cache_size = 0 . There is (according to a rumor) a 'bug' in the QC code that leaves some code on unless you turn off both of those settings.

Abnormally large:

Com_check = 5.1 /HR
Com_create_procedure = 0.011 /HR
Com_create_trigger = 0.22 /HR
Com_drop_procedure = 0.022 /HR
Com_drop_trigger = 0.22 /HR
Com_repair = 0.0028 /HR
Com_show_tables = 0.98 /sec

Abnormal strings:

optimizer_trace = enabled=off,one_line=off
optimizer_trace_features = greedy_search=on, range_optimizer=on, dynamic_range=on, repeated_subselect=on
slave_rows_search_algorithms = TABLE_SCAN,INDEX_SCAN
version_compile_machine = amd64
  • Thanks for your analysis with this. I'll definitely be applying some of your recommendations. It's a 10 year old platform with a lot of weird stuff going on. The swap thing is new though and I'll update the post when I figure it out. – Duncan Fairley Feb 14 at 17:15
  • Has it been on FreeBSD the whole time? I don't hear of that OS much anymore. – Rick James Feb 14 at 17:22
  • Yep, the entire time. The application side of it makes use of a lot of snapshotting/clones with ZFS, before ZFS was viable on linux. – Duncan Fairley Feb 14 at 17:32
0

Rate Per Second=RPS - Suggestions to consider for your my.cnf [mysqld] section

innodb_io_capacity=1800  # from 200 to allow higher IOPS
read_rnd_buffer_size=256K  # from 4M to reduce handler_read_rnd_next RPS of 2560
query_cache_size=0  # from 1M to conserve RAM and QC is OFF already
innodb_lru_scan_depth=100  # from 1024 to conserve CPU cycles every SECOND
thread_cache_size=32  # from 8 to reduce threads_created from 16,681 in 15 days (expensive operation) 
  • This doesn't attempt to answer the question of why FreeBSD is using all swap while free ram remains. It also suggests increasing the iops that innodb expects to have, while not even knowing what kind of disks are in use. – Duncan Fairley Feb 20 at 16:33
  • @duncanfairley Then do not change anything that might help your situation. Could it be that someone is failing to terminate command line or SSHD processes and leaving tty connections when they are finished and walked away? – Wilson Hauck Feb 27 at 21:30
  • @DuncanFairley You have clues in handler_read_rnd_next that you are achieving 2560 RPS already, so allowing innodb_io_capacity above 200 would most likely be reasonable. – Wilson Hauck Mar 4 at 14:57
  • @DuncanFairley Have you tired any of the suggestions of Feb 20, 2018? We still do not know if you have any SSD or NVME or all rotating media. Please let us know if you have made any progress on expediting your delivery of query results. Thanks – Wilson Hauck Mar 16 at 0:03

Your Answer

By clicking "Post Your Answer", you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.