3

I have an InnoDB database table with more than 2 million rows. I am running efficienty indexed queries to reduce server load, but site becomes slower day by day.

I ran Mysqltuner.pl to identify any problems with server configuration. I don't have any prior experience with MySQL tweaking. Please suggest me the correct configuration on the basis of below info.

Mysqltuner.pl result

root@site:~# perl mysqltuner.pl
 >>  MySQLTuner 1.6.0 - Major Hayden 
 >>  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 5.5.41-0ubuntu0.14.04.1
[OK] Operating on 64-bit architecture

-------- Storage Engine Statistics -------------------------------------------
[--] Status: +ARCHIVE +BLACKHOLE +CSV -FEDERATED +InnoDB +MRG_MYISAM
[--] Data in InnoDB tables: 872M (Tables: 386)
[--] Data in MyISAM tables: 790K (Tables: 60)
[!!] Total fragmented tables: 386

-------- Security Recommendations  -------------------------------------------
[OK] There is no anonymous account in all database users
[OK] All database users have passwords assigned
[--] There is 605 basic passwords in the list.

-------- Performance Metrics -------------------------------------------------
[--] Up for: 2d 8h 23m 55s (6M q [32.888 qps], 1M conn, TX: 936M, RX: 425M)
[--] Reads / Writes: 61% / 39%
[--] Binary logging is disabled
[--] Total buffers: 192.0M global + 2.7M per thread (151 max threads)
[OK] Maximum reached memory usage: 600.5M (0.93% of installed RAM)
[OK] Maximum possible memory usage: 597.8M (0.93% of installed RAM)
[OK] Slow queries: 0% (8/6M)
[!!] Highest connection usage: 100%  (152/151)
[OK] Aborted connections: 1.99%  (26343/1321702)
[OK] Query cache efficiency: 34.9% (635K cached / 1M selects)
[!!] Query cache prunes per day: 15154
[OK] Sorts requiring temporary tables: 0% (0 temp sorts / 281K sorts)
[!!] Joins performed without indexes: 686
[!!] Temporary tables created on disk: 79% (24K on disk / 30K total)
[OK] Thread cache hit rate: 99% (8K created / 1M connections)
[!!] Table cache hit rate: 6% (400 open / 5K opened)
[OK] Open file limit used: 7% (78/1K)
[OK] Table locks acquired immediately: 99% (1M immediate / 1M locks)

-------- MyISAM Metrics -----------------------------------------------------
[!!] Key buffer used: 18.3% (3M used / 16M cache)
[OK] Key buffer size / total MyISAM indexes: 16.0M/641.0K
[!!] Read Key buffer hit rate: 91.7% (743 cached / 62 reads)
[OK] Write Key buffer hit rate: 100.0% (152 cached / 0 writes)

-------- InnoDB Metrics -----------------------------------------------------
[--] InnoDB is enabled.
[!!] InnoDB buffer pool / data size: 128.0M/873.0M
[OK] InnoDB buffer pool instances: 1
[OK] InnoDB Used buffer: 100.00% (8191 used/ 8191 total)
[OK] InnoDB Read buffer efficiency: 99.83% (534148120 hits/ 535061164 total)
[!!] InnoDB Write buffer efficiency: 0.00% (0 hits/ 1 total)
[OK] InnoDB log waits: 0.00% (0 waits / 745272 writes)

-------- AriaDB Metrics -----------------------------------------------------
[--] AriaDB is disabled.

-------- Replication Metrics -------------------------------------------------
[--] No replication slave(s) for this server.
[--] This is a standalone server..

-------- Recommendations -----------------------------------------------------
General recommendations:
    Run OPTIMIZE TABLE to defragment tables for better performance
    Enable the slow query log to troubleshoot bad queries
    Reduce or eliminate persistent connections to reduce connection usage
    Adjust your join queries to always utilize indexes
    When making adjustments, make tmp_table_size/max_heap_table_size equal
    Reduce your SELECT DISTINCT queries which have no LIMIT clause
    Increase table_open_cache gradually to avoid file descriptor limits
    Read this before increasing table_open_cache over 64: http://bit.ly/1mi7c4C
    Beware that open_files_limit (1024) variable
    should be greater than table_open_cache ( 400)
Variables to adjust:
    max_connections (> 151)
    wait_timeout ( 16M)
    join_buffer_size (> 128.0K, or always use indexes with joins)
    tmp_table_size (> 16M)
    max_heap_table_size (> 16M)
    table_open_cache (> 400)
    innodb_buffer_pool_size (>= 872M) if possible.
root@site:~#

my.cnf

#
# The MySQL database server configuration file.
#
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
# 
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
[client]
port        = 3306
socket      = /var/run/mysqld/mysqld.sock

# Here is entries for some specific programs
# The following values assume you have at least 32M ram

# This was formally known as [safe_mysqld]. Both versions are currently parsed.
[mysqld_safe]
socket      = /var/run/mysqld/mysqld.sock
nice        = 0

[mysqld]
local-infile=0
#
# * Basic Settings
#
user        = mysql
pid-file    = /var/run/mysqld/mysqld.pid
socket      = /var/run/mysqld/mysqld.sock
port        = 3306
basedir     = /usr
datadir     = /var/lib/mysql
tmpdir      = /tmp
lc-messages-dir = /usr/share/mysql
skip-external-locking
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
# bind-address      = 127.0.0.1
#
# * Fine Tuning
#
key_buffer      = 16M
max_allowed_packet  = 16M
thread_stack        = 192K
thread_cache_size       = 8



max_connections=500

# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover         = BACKUP
#max_connections        = 100
#table_cache            = 64
#thread_concurrency     = 10
#
# * Query Cache Configuration
#
query_cache_limit   = 1M
query_cache_size        = 16M
#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1
#
# Error log - should be very few entries.
#
log_error = /var/log/mysql/error.log
#
# Here you can see queries with especially long duration
#log_slow_queries   = /var/log/mysql/mysql-slow.log
#long_query_time = 2
#log-queries-not-using-indexes
#
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
#       other settings you may need to change.
#server-id      = 1
#log_bin            = /var/log/mysql/mysql-bin.log
expire_logs_days    = 10
max_binlog_size         = 100M
#binlog_do_db       = include_database_name
#binlog_ignore_db   = include_database_name
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
#
# * Security Features
#
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
#
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
#
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem



[mysqldump]
quick
quote-names
max_allowed_packet  = 16M

[mysql]
#no-auto-rehash # faster start of mysql but no tab completition

[isamchk]
key_buffer      = 16M

#
# * IMPORTANT: Additional settings that can override those from this file!
#   The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/

MySQL running on a server with 64GB RAM, 2TB HDD.

Update

Global Variables

auto_increment_increment    1
auto_increment_offset   1
autocommit  ON
automatic_sp_privileges ON
back_log    50
basedir /usr
big_tables  OFF
binlog_cache_size   32768
binlog_direct_non_transactional_updates OFF
binlog_format   STATEMENT
binlog_stmt_cache_size  32768
bulk_insert_buffer_size 8388608
character_set_client    latin1
character_set_connection    latin1
character_set_database  latin1
character_set_filesystem    binary
character_set_results   latin1
character_set_server    latin1
character_set_system    utf8
character_sets_dir  /usr/share/mysql/charsets/
collation_connection    latin1_swedish_ci
collation_database  latin1_swedish_ci
collation_server    latin1_swedish_ci
completion_type NO_CHAIN
concurrent_insert   AUTO
connect_timeout 10
datadir /var/lib/mysql/
date_format %Y-%m-%d
datetime_format %Y-%m-%d %H:%i:%s
default_storage_engine  InnoDB
default_week_format 0
delay_key_write ON
delayed_insert_limit    100
delayed_insert_timeout  300
delayed_queue_size  1000
div_precision_increment 4
engine_condition_pushdown   ON
event_scheduler OFF
expire_logs_days    10
flush   OFF
flush_time  0
foreign_key_checks  ON
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/lib/mysql/site.log
group_concat_max_len    1024
have_compress   YES
have_crypt  YES
have_csv    YES
have_dynamic_loading    YES
have_geometry   YES
have_innodb YES
have_ndbcluster NO
have_openssl    DISABLED
have_partitioning   YES
have_profiling  YES
have_query_cache    YES
have_rtree_keys YES
have_ssl    DISABLED
have_symlink    YES
hostname    site.com
ignore_builtin_innodb   OFF
init_connect    
init_file   
init_slave  
innodb_adaptive_flushing    ON
innodb_adaptive_hash_index  ON
innodb_additional_mem_pool_size 8388608
innodb_autoextend_increment 8
innodb_autoinc_lock_mode    1
innodb_buffer_pool_instances    1
innodb_buffer_pool_size 134217728
innodb_change_buffering all
innodb_checksums    ON
innodb_commit_concurrency   0
innodb_concurrency_tickets  500
innodb_data_file_path   ibdata1:10M:autoextend
innodb_data_home_dir    
innodb_doublewrite  ON
innodb_fast_shutdown    1
innodb_file_format  Antelope
innodb_file_format_check    ON
innodb_file_format_max  Antelope
innodb_file_per_table   OFF
innodb_flush_log_at_trx_commit  1
innodb_flush_method 
innodb_force_load_corrupted OFF
innodb_force_recovery   0
innodb_io_capacity  200
innodb_large_prefix OFF
innodb_lock_wait_timeout    50
innodb_locks_unsafe_for_binlog  OFF
innodb_log_buffer_size  8388608
innodb_log_file_size    5242880
innodb_log_files_in_group   2
innodb_log_group_home_dir   ./
Variable_name   Value
innodb_max_dirty_pages_pct  75
innodb_max_purge_lag    0
innodb_mirrored_log_groups  1
innodb_old_blocks_pct   37
innodb_old_blocks_time  0
innodb_open_files   300
innodb_print_all_deadlocks  OFF
innodb_purge_batch_size 20
innodb_purge_threads    0
innodb_random_read_ahead    OFF
innodb_read_ahead_threshold 56
innodb_read_io_threads  4
innodb_replication_delay    0
innodb_rollback_on_timeout  OFF
innodb_rollback_segments    128
innodb_spin_wait_delay  6
innodb_stats_method nulls_equal
innodb_stats_on_metadata    ON
innodb_stats_sample_pages   8
innodb_strict_mode  OFF
innodb_support_xa   ON
innodb_sync_spin_loops  30
innodb_table_locks  ON
innodb_thread_concurrency   0
innodb_thread_sleep_delay   10000
innodb_use_native_aio   ON
innodb_use_sys_malloc   ON
innodb_version  5.5.41
innodb_write_io_threads 4
interactive_timeout 28800
join_buffer_size    131072
keep_files_on_create    OFF
key_buffer_size 16777216
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
lc_messages en_US
lc_messages_dir /usr/share/mysql/
lc_time_names   en_US
license GPL
local_infile    OFF
lock_wait_timeout   31536000
locked_in_memory    OFF
log OFF
log_bin OFF
log_bin_trust_function_creators OFF
log_error   /var/log/mysql/error.log
log_output  FILE
log_queries_not_using_indexes   OFF
log_slave_updates   OFF
log_slow_queries    OFF
log_warnings    1
long_query_time 10.000000
low_priority_updates    OFF
lower_case_file_system  OFF
lower_case_table_names  0
max_allowed_packet  16777216
max_binlog_cache_size   18446744073709547520
max_binlog_size 104857600
max_binlog_stmt_cache_size  18446744073709547520
max_connect_errors  10
max_connections 151
max_delayed_threads 20
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_long_data_size  16777216
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
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  BACKUP
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   OFF
open_files_limit    1024
Variable_name   Value
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
performance_schema  OFF
performance_schema_events_waits_history_long_size   10000
performance_schema_events_waits_history_size    10
performance_schema_max_cond_classes 80
performance_schema_max_cond_instances   1000
performance_schema_max_file_classes 50
performance_schema_max_file_handles 32768
performance_schema_max_file_instances   10000
performance_schema_max_mutex_classes    200
performance_schema_max_mutex_instances  1000000
performance_schema_max_rwlock_classes   30
performance_schema_max_rwlock_instances 1000000
performance_schema_max_table_handles    100000
performance_schema_max_table_instances  50000
performance_schema_max_thread_classes   50
performance_schema_max_thread_instances 1000
pid_file    /var/run/mysqld/mysqld.pid
plugin_dir  /usr/lib/mysql/plugin/
port    3306
preload_buffer_size 32768
profiling   OFF
profiling_history_size  15
protocol_version    10
query_alloc_block_size  8192
query_cache_limit   1048576
query_cache_min_res_unit    4096
query_cache_size    16777216
query_cache_type    ON
query_cache_wlock_invalidate    OFF
query_prealloc_size 8192
range_alloc_block_size  4096
read_buffer_size    131072
read_only   OFF
read_rnd_buffer_size    262144
relay_log   
relay_log_index 
relay_log_info_file relay-log.info
relay_log_purge ON
relay_log_recovery  OFF
relay_log_space_limit   0
report_host 
report_password 
report_port 3306
report_user 
rpl_recovery_rank   0
secure_auth OFF
secure_file_priv    
server_id   0
skip_external_locking   ON
skip_name_resolve   OFF
skip_networking OFF
skip_show_database  OFF
slave_compressed_protocol   OFF
slave_exec_mode STRICT
slave_load_tmpdir   /tmp
slave_max_allowed_packet    1073741824
slave_net_timeout   3600
slave_skip_errors   OFF
slave_transaction_retries   10
slave_type_conversions  
slow_launch_time    2
slow_query_log  OFF
slow_query_log_file /var/lib/mysql/site-slow.log
socket  /var/run/mysqld/mysqld.sock
sort_buffer_size    2097152
sql_auto_is_null    OFF
sql_big_selects ON
sql_big_tables  OFF
sql_buffer_result   OFF
sql_log_bin ON
sql_log_off OFF
sql_low_priority_updates    OFF
sql_max_join_size   18446744073709551615
sql_mode    
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_key 
storage_engine  InnoDB
stored_program_cache    256
sync_binlog 0
sync_frm    ON
sync_master_info    0
sync_relay_log  0
sync_relay_log_info 0
system_time_zone    CEST
table_definition_cache  400
table_open_cache    400
thread_cache_size   8
thread_concurrency  10
Variable_name   Value
thread_handling one-thread-per-connection
thread_stack    196608
time_format %H:%i:%s
time_zone   SYSTEM
timed_mutexes   OFF
tmp_table_size  16777216
tmpdir  /tmp
transaction_alloc_block_size    8192
transaction_prealloc_size   4096
tx_isolation    REPEATABLE-READ
unique_checks   ON
updatable_views_with_limit  YES
version 5.5.41-0ubuntu0.14.04.1
version_comment (Ubuntu)
version_compile_machine x86_64
version_compile_os  debian-linux-gnu
wait_timeout    28800

Global Status

Aborted_clients 115
Aborted_connects    30024
Binlog_cache_disk_use   0
Binlog_cache_use    0
Binlog_stmt_cache_disk_use  0
Binlog_stmt_cache_use   0
Bytes_received  756398641
Bytes_sent  1626522859
Com_admin_commands  607
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 0
Com_alter_tablespace    0
Com_analyze 0
Com_begin   0
Com_binlog  0
Com_call_procedure  0
Com_change_db   8198
Com_change_master   0
Com_check   0
Com_checksum    0
Com_commit  0
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  321
Com_delete_multi    0
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   0
Com_drop_view   0
Com_empty_query 0
Com_execute_sql 0
Com_flush   2
Com_grant   0
Com_ha_close    0
Com_ha_open 0
Com_ha_read 0
Com_help    0
Com_insert  360542
Com_insert_select   3
Com_install_plugin  0
Com_kill    0
Com_load    0
Com_lock_tables 6
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 2
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  2518409
Com_set_option  2226490
Com_signal  0
Com_show_authors    0
Com_show_binlog_events  0
Com_show_binlogs    0
Com_show_charsets   0
Com_show_collations 0
Com_show_contributors   0
Com_show_create_db  6
Com_show_create_event   0
Com_show_create_func    0
Com_show_create_proc    0
Com_show_create_table   693
Com_show_create_trigger 0
Com_show_databases  18
Variable_name   Value
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 2327
Com_show_function_status    0
Com_show_grants 2
Com_show_keys   77
Com_show_master_status  8
Com_show_open_tables    0
Com_show_plugins    0
Com_show_privileges 0
Com_show_procedure_status   0
Com_show_processlist    0
Com_show_profile    0
Com_show_profiles   0
Com_show_relaylog_events    0
Com_show_slave_hosts    0
Com_show_slave_status   8
Com_show_status 4
Com_show_storage_engines    0
Com_show_table_status   693
Com_show_tables 74
Com_show_triggers   686
Com_show_variables  25
Com_show_warnings   0
Com_slave_start 0
Com_slave_stop  0
Com_stmt_close  259289
Com_stmt_execute    259368
Com_stmt_fetch  0
Com_stmt_prepare    259368
Com_stmt_reprepare  0
Com_stmt_reset  0
Com_stmt_send_long_data 0
Com_truncate    0
Com_uninstall_plugin    0
Com_unlock_tables   6
Com_update  423377
Com_update_multi    0
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
Connections 2305560
Created_tmp_disk_tables 3090
Created_tmp_files   8
Created_tmp_tables  4930
Delayed_errors  0
Delayed_insert_threads  0
Delayed_writes  0
Flush_commands  1
Handler_commit  3295801
Handler_delete  108324
Handler_discover    0
Handler_prepare 0
Handler_read_first  454203
Handler_read_key    3702631
Handler_read_last   2528
Handler_read_next   43371729
Handler_read_prev   960844
Handler_read_rnd    731609
Handler_read_rnd_next   22229713335
Handler_rollback    5378
Handler_savepoint   0
Handler_savepoint_rollback  0
Handler_update  423166
Handler_write   389137
Innodb_buffer_pool_pages_data   7956
Innodb_buffer_pool_bytes_data   130351104
Innodb_buffer_pool_pages_dirty  121
Innodb_buffer_pool_bytes_dirty  1982464
Innodb_buffer_pool_pages_flushed    2068247
Innodb_buffer_pool_pages_free   1
Innodb_buffer_pool_pages_misc   234
Innodb_buffer_pool_pages_total  8191
Innodb_buffer_pool_read_ahead_rnd   0
Innodb_buffer_pool_read_ahead   3924
Innodb_buffer_pool_read_ahead_evicted   489
Innodb_buffer_pool_read_requests    2984617530
Innodb_buffer_pool_reads    789039
Innodb_buffer_pool_wait_free    0
Innodb_buffer_pool_write_requests   5340758
Innodb_data_fsyncs  913759
Innodb_data_pending_fsyncs  0
Innodb_data_pending_reads   0
Innodb_data_pending_writes  0
Innodb_data_read    13800804352
Innodb_data_reads   842209
Innodb_data_writes  2949500
Innodb_data_written 68415039488
Innodb_dblwr_pages_written  2068247
Innodb_dblwr_writes 48481
Innodb_have_atomic_builtins ON
Innodb_log_waits    0
Innodb_log_write_requests   455394
Variable_name   Value
Innodb_log_writes   791872
Innodb_os_log_fsyncs    816965
Innodb_os_log_pending_fsyncs    0
Innodb_os_log_pending_writes    0
Innodb_os_log_written   629937664
Innodb_page_size    16384
Innodb_pages_created    10373
Innodb_pages_read   842200
Innodb_pages_written    2068247
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   2
Innodb_rows_deleted 108324
Innodb_rows_inserted    355176
Innodb_rows_read    22146370939
Innodb_rows_updated 422711
Innodb_truncated_status_writes  0
Key_blocks_not_flushed  0
Key_blocks_unused   13389
Key_blocks_used 19
Key_read_requests   938
Key_reads   48
Key_write_requests  228
Key_writes  0
Last_query_cost 0.000000
Max_used_connections    66
Not_flushed_delayed_rows    0
Open_files  20
Open_streams    0
Open_table_definitions  400
Open_tables 400
Opened_files    14328
Opened_table_definitions    1603
Opened_tables   3281
Performance_schema_cond_classes_lost    0
Performance_schema_cond_instances_lost  0
Performance_schema_file_classes_lost    0
Performance_schema_file_handles_lost    0
Performance_schema_file_instances_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_table_handles_lost   0
Performance_schema_table_instances_lost 0
Performance_schema_thread_classes_lost  0
Performance_schema_thread_instances_lost    0
Prepared_stmt_count 2
Qcache_free_blocks  899
Qcache_free_memory  14960424
Qcache_hits 1765289
Qcache_inserts  2509742
Qcache_lowmem_prunes    56303
Qcache_not_cached   7290
Qcache_queries_in_cache 1477
Qcache_total_blocks 4089
Queries 10101950
Questions   9582685
Rpl_status  AUTH_MASTER
Select_full_join    957
Select_full_range_join  10
Select_range    7045
Select_range_check  0
Select_scan 459980
Slave_heartbeat_period  0.000
Slave_open_temp_tables  0
Slave_received_heartbeats   0
Slave_retried_transactions  0
Slave_running   OFF
Slow_launch_threads 0
Slow_queries    1161
Sort_merge_passes   1
Sort_range  625185
Sort_rows   1139800
Sort_scan   425
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_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
Variable_name   Value
Ssl_version 
Table_locks_immediate   3313726
Table_locks_waited  0
Tc_log_max_pages_used   0
Tc_log_page_size    0
Tc_log_page_waits   0
Threads_cached  1
Threads_connected   18
Threads_created 7950
Threads_running 1
Uptime  272444
Uptime_since_flush_status   272444
  • Instead of the my.cnf you should probably add results of show global variables; and show global status;. From a quick look your innodb_buffer_pool_size seems to be default but it you have enough RAM available, so make it bigger than sum of your InnoDB tables (say 1GB for start or even bigger if your data grow fast). – jkavalik Sep 22 '15 at 10:08
  • show global variables & show global status results added. – codygate Sep 22 '15 at 10:45
2

Observations:

Version: 5.5.41-0ubuntu0.14.04.1
64 GB of RAM
Uptime = 3d 03:40:44
You are not running on Windows.
Running 64-bit version
You appear to be running entirely (or mostly) InnoDB.

The More Important Issues

Increase innodb_buffer_pool_size to at least 1G (not more than 45G). Sounds like most of your 64GB is unused? Or do you expect a huge growth in data?

Turn off the Query Cache; it does not seem to be useful:

query_cache_size = 0
query_cache_type = OFF

Set long_query_time = 2 and turn on the slowlog. After a day, run pt-query-digest to find the worst queries. Then work on optimizing them. (Composite indexes, reformulating queries, etc. Ask for help if needed.)

Supporting details and other suggestions

( innodb_buffer_pool_size / _ram ) = 128M / 65536M = 0.20% -- % of RAM used for InnoDB buffer_pool ( (key_buffer_size / 0.20 + innodb_buffer_pool_size / 0.70) / _ram ) = (16M / 0.20 + 128M / 0.70) / 65536M = 0.40% -- Most of available ram should be made available for caching. -- http://mysql.rjweb.org/doc.php/memory

[!!] InnoDB buffer pool / data size: 128.0M/873.0M
So innodb_buffer_pool_size should be at least 1G.

[!!] InnoDB Write buffer efficiency: 0.00% (0 hits/ 1 total)
0 out of 1 -- bogus to mark it "!!"

( Innodb_pages_written / Innodb_buffer_pool_write_requests ) = 2,068,247 / 5340758 = 38.7% -- Write requests that had to hit disk -- Check innodb_buffer_pool_size

( innodb_file_per_table ) = OFF -- Put each file in its own tablespace -- (Mildly recommended, especially for large tables)

( Qcache_hits / Qcache_inserts ) = 1,765,289 / 2,509,742 = 0.703 -- Hit to insert ratio -- high is good -- Consider turning off the query cache.

( (query_cache_size - Qcache_free_memory) / Qcache_queries_in_cache / query_alloc_block_size ) = (16M - 14960424) / 1477 / 8192 = 0.15 -- query_alloc_block_size vs formula -- Adjust query_alloc_block_size

[!!] Query cache prunes per day: 15154

( Created_tmp_disk_tables / (Created_tmp_disk_tables + Created_tmp_tables) ) = 3,090 / (3090 + 4930) = 38.5% -- Percent of temp tables that spilled to disk -- maybe increase tmp_table_size and max_heap_table_size; avoid blobs, etc.

( Select_scan ) = 459,980 / 272444 = 1.7 /sec -- full table scans -- Add indexes / optimize queries (unless they are tiny tables)

( Select_scan / Com_select ) = 459,980 / 2518409 = 18.3% -- % of selects doing full table scan. (May be fooled by Stored Routines.) -- Add indexes / optimize queries

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

( log_slow_queries ) = OFF -- Whether to log slow queries. (Before 5.1.29, 5.6.1)

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

( long_query_time ) = 10.000000 = 10 -- Cutoff (Seconds) for defining a "slow" query. -- Suggest 2

( Connections ) = 2,305,560 / 272,444 = 8.5 /sec -- Connections -- Increase wait_timeout; use pooling?

( Max_used_connections ) = 66 -- How many simultaneous connections you had (highwater mark).
[!!] Highest connection usage: 100% (152/151)
Those disagree; perhaps you restarted?

( open_files_limit ) = 1,024 -- ulimit -n -- To allow more files, change ulimit or /etc/security/limits.conf or in sysctl.conf (kern.maxfiles & kern.maxfilesperproc) or something else (OS dependent) -- If you get more tables, raising this will be important.

( Opened_tables ) = 43/hour
[!!] Table cache hit rate: 6% (400 open / 5K opened)
These disagree; perhaps there is no problem here.

[!!] Key buffer used: 18.3% (3M used / 16M cache)
[!!] Read Key buffer hit rate: 91.7% (743 cached / 62 reads)
Not a problem since there is virtually no MyISAM usage and key_buffer_size is only a tiny percentage of RAM.

19 issues flagged, out of 133 computed Variables/Status/Expressions

My take on Tuner's recommendations:

Run OPTIMIZE TABLE to defragment tables for better performance -- waste of time!
Enable the slow query log to troubleshoot bad queries -- yes
Reduce or eliminate persistent connections to reduce connection usage -- ok
Adjust your join queries to always utilize indexes -- yes (use slowlog to find them)
When making adjustments, make tmp_table_size/max_heap_table_size equal -- ok
Reduce your SELECT DISTINCT queries which have no LIMIT clause -- yawn
Increase table_open_cache gradually to avoid file descriptor limits --
    ok, but may not be critical
Read this before increasing table_open_cache over 64: http://bit.ly/1mi7c4C
Beware that open_files_limit (1024) variable -- noted
should be greater than table_open_cache ( 400) -- it is

max_connections (> 151) -- No; figure out why there are so many connections
wait_timeout ( 16M) -- probably not important
join_buffer_size (> 128.0K, or always use indexes with joins) -- might help, might not
tmp_table_size (> 16M) -- first look for other ways to improve queries
max_heap_table_size (> 16M)
table_open_cache (> 400)
innodb_buffer_pool_size (>= 872M) if possible. -- yes

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