How to solve intermittent MySQL performance issues on simple queries?

Question

We are currently experiencing an intermittent issue with UPDATE/DELETE/INSERT performance.

Simple queries like the following take a long time:

DELETE FROM ip_filter WHERE filter_id = '348';

Queries like these sometimes take 2 seconds or even longer.

An index is established on the filter_id field, and an explain yields the following results:

id, select_type, table, type, possible_keys, key, key_len, ref, rows, Extra

'1', 'SIMPLE', 'ip_filter', 'ref', 'ip_and_filter_id', 'ip_and_filter_id', '4', 'const', '8', 'Using index'

One of the problems is that these issues happen sporadically, and generally after one of these slow queries happens, the next similar query will be fast.

A thing of note is that these tables will get a lot of SELECT activity, as they are queried often, even though the tables themself are pretty small.

We have experimented with reducing our query cache size from 512MB to 256MB to see if this would alleviate the problem. It currently seems that the issue is not as prevalent anymore as it previously was, but it still does occur.

Are there any other steps we could take to debug this issue?

EDIT as requested, the table structure:

CREATE TABLE `ip_filter` (
 `id` int(10) unsigned NOT NULL AUTO_INCREMENT,
 `filter_id` int(10) unsigned NOT NULL,
 `ip_from` int(10) unsigned zerofill DEFAULT NULL,
 `ip_to` int(10) unsigned zerofill DEFAULT NULL,
 PRIMARY KEY (`id`),
 KEY `ip_and_filter_id` (`filter_id`,`ip_from`,`ip_to`),
 KEY `ip_range` (`ip_from`,`ip_to`,`filter_id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8

EDIT2: as requested, SHOW GLOBAL STATUS and SHOW GLOBAL VARIABLES (apologies for any possible formatting errors, and in addition some entries were omitted to stay in the character limit for this post):

mysql> SHOW GLOBAL STATUS;
+-----------------------------------------------+--------------------------------------------------+
| Variable_name | Value |
+-----------------------------------------------+--------------------------------------------------+
| Aborted_clients | 1002|
| Aborted_connects| 13620 |
| Binlog_cache_disk_use| 18304 |
| Binlog_cache_use| 50907641 |
| Binlog_stmt_cache_disk_use| 21583 |
| Binlog_stmt_cache_use| 693818 |
| Bytes_received | 373853485296 |
| Bytes_sent | 2307802779423 |
| Compression| OFF |
| Connections| 560733528|
| Created_tmp_disk_tables | 479926 |
| Created_tmp_files | 244099 |
| Created_tmp_tables | 4792534 |
| Delayed_errors | 64869 |
| Delayed_insert_threads | 1 |
| Delayed_writes | 79287 |
| Flush_commands | 1 |
| Handler_commit | 405017753|
| Handler_delete | 960022 |
| Handler_discover| 0 |
| Handler_external_lock| 2007319506 |
| Handler_mrr_init| 0 |
| Handler_prepare | 100974274|
| Handler_read_first | 10746649 |
| Handler_read_key| 18232267091 |
| Handler_read_last | 19 |
| Handler_read_next | 56428606901 |
| Handler_read_prev | 245978 |
| Handler_read_rnd| 4498710625 |
| Handler_read_rnd_next| 45742264916 |
| Handler_rollback| 6178|
| Handler_savepoint | 0 |
| Handler_savepoint_rollback| 0 |
| Handler_update | 8254153588 |
| Handler_write | 11890926042 |
| Innodb_buffer_pool_dump_status | not started |
| Innodb_buffer_pool_load_status | Buffer pool(s) load completed at 141128 8:04:25 |
| Innodb_background_log_sync| 3798209 |
| Innodb_buffer_pool_pages_data | 483817 |
| Innodb_buffer_pool_bytes_data | 7926857728 |
| Innodb_buffer_pool_pages_dirty | 699 |
| Innodb_buffer_pool_bytes_dirty | 11452416 |
| Innodb_buffer_pool_pages_flushed | 192945519|
| Innodb_buffer_pool_pages_LRU_flushed| 0 |
| Innodb_buffer_pool_pages_free | 8192|
| Innodb_buffer_pool_pages_made_not_young | 1838366113 |
| Innodb_buffer_pool_pages_made_young | 10981231 |
| Innodb_buffer_pool_pages_misc | 32271 |
| Innodb_buffer_pool_pages_old | 178434 |
| Innodb_buffer_pool_pages_total | 524280 |
| Innodb_buffer_pool_read_ahead_rnd | 0 |
| Innodb_buffer_pool_read_ahead | 3381468 |
| Innodb_buffer_pool_read_ahead_evicted | 0 |
| Innodb_buffer_pool_read_requests | 240688389755 |
| Innodb_buffer_pool_reads | 49368230 |
| Innodb_buffer_pool_wait_free | 0 |
| Innodb_buffer_pool_write_requests | 24744355863 |
| Innodb_checkpoint_age| 3081858 |
| Innodb_checkpoint_max_age | 80826164 |
| Innodb_data_fsyncs | 74420033 |
| Innodb_data_pending_fsyncs| 0 |
| Innodb_data_pending_reads | 0 |
| Innodb_data_pending_writes| 0 |
| Innodb_data_read| 880507834368 |
| Innodb_data_reads | 50348628 |
| Innodb_data_writes | 116817456|
| Innodb_data_written | 8742201090048 |
| Innodb_dblwr_pages_written| 192945519|
| Innodb_dblwr_writes | 5548104 |
| Innodb_deadlocks| 0 |
| Innodb_have_atomic_builtins | ON |
| Innodb_history_list_length| 2465|
| Innodb_ibuf_discarded_delete_marks | 0 |
| Innodb_ibuf_discarded_deletes | 0 |
| Innodb_ibuf_discarded_inserts | 0 |
| Innodb_ibuf_free_list| 2216|
| Innodb_ibuf_merged_delete_marks| 112003 |
| Innodb_ibuf_merged_deletes| 74608 |
| Innodb_ibuf_merged_inserts| 4805145 |
| Innodb_ibuf_merges | 1033719 |
| Innodb_ibuf_segment_size | 2218|
| Innodb_ibuf_size| 1 |
| Innodb_log_waits| 4812|
| Innodb_log_write_requests | 5014978044 |
| Innodb_log_writes | 56207419 |
| Innodb_lsn_current | 21913335542724|
| Innodb_lsn_flushed | 21913335542724|
| Innodb_lsn_last_checkpoint| 21913332460866|
| Innodb_master_thread_active_loops | 3798046 |
| Innodb_master_thread_idle_loops| 163 |
| Innodb_max_trx_id | 3124981165 |
| Innodb_mem_adaptive_hash | 680116592|
| Innodb_mem_dictionary| 41727522 |
| Innodb_mem_total| 8791261184 |
| Innodb_mutex_os_waits| 9260778 |
| Innodb_mutex_spin_rounds | 459072900|
| Innodb_mutex_spin_waits | 230355306|
| Innodb_oldest_view_low_limit_trx_id | 0 |
| Innodb_os_log_fsyncs | 56456392 |
| Innodb_os_log_pending_fsyncs | 0 |
| Innodb_os_log_pending_writes | 0 |
| Innodb_os_log_written| 2419507923968 |
| Innodb_page_size| 16384 |
| Innodb_pages_created | 32015116 |
| Innodb_pages_read | 53741803 |
| Innodb_pages_written | 192945519|
| Innodb_purge_trx_id | 3124980536 |
| Innodb_purge_undo_no | 0 |
| Innodb_row_lock_current_waits | 0 |
| Innodb_current_row_locks | 0 |
| Innodb_row_lock_time | 555071 |
| Innodb_row_lock_time_avg | 113 |
| Innodb_row_lock_time_max | 10579 |
| Innodb_row_lock_waits| 4881|
| Innodb_rows_deleted | 960706 |
| Innodb_rows_inserted | 1781038652 |
| Innodb_rows_read| 106500471157 |
| Innodb_rows_updated | 4216691817 |
| Innodb_num_open_files| 276 |
| Innodb_read_views_memory | 608 |
| Innodb_descriptors_memory | 8000|
| Innodb_s_lock_os_waits | 1518546 |
| Innodb_s_lock_spin_rounds | 88671245 |
| Innodb_s_lock_spin_waits | 32303938 |
| Innodb_truncated_status_writes | 0 |
| Innodb_available_undo_logs| 128 |
| Innodb_x_lock_os_waits | 3751147 |
| Innodb_x_lock_spin_rounds | 274895733|
| Innodb_x_lock_spin_waits | 12452149 |
| Key_blocks_not_flushed | 0 |
| Key_blocks_unused | 639319 |
| Key_blocks_used | 730098 |
| Key_read_requests | 98022049796 |
| Key_reads | 597390 |
| Key_write_requests | 4123062130 |
| Key_writes | 2076944 |
| Last_query_cost | 0.000000 |
| Last_query_partial_plans | 0 |
| Max_statement_time_exceeded | 0 |
| Max_statement_time_set | 0 |
| Max_statement_time_set_failed | 0 |
| Max_used_connections | 486 |
| Not_flushed_delayed_rows | 0 |
| Open_files | 307 |
| Open_streams | 0 |
| Open_table_definitions | 244 |
| Open_tables| 1966|
| Opened_files | 2315351 |
| Opened_table_definitions | 15832 |
| Opened_tables | 21898 |
| Qcache_free_blocks | 27443 |
| Qcache_free_memory | 44816704 |
| Qcache_hits| 244230270|
| Qcache_inserts | 388578154|
| Qcache_lowmem_prunes | 264072283|
| Qcache_not_cached | 9221053 |
| Qcache_queries_in_cache | 119845 |
| Qcache_total_blocks | 268253 |
| Queries | 7122289356 |
| Questions | 1818979018 |
| Select_full_join| 74006 |
| Select_full_range_join | 603 |
| Select_range | 134013323|
| Select_range_check | 44 |
| Select_scan| 2861498 |
| 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 | 1510|
| Sort_merge_passes | 255576 |
| Sort_range | 999591 |
| Sort_rows | 2156328903 |
| Sort_scan | 4467016 |
| Table_locks_immediate| 999835187|
| Table_locks_waited | 3484|
| Table_open_cache_hits| 936160886|
| Table_open_cache_misses | 6442|
| Table_open_cache_overflows| 461 |
| Tc_log_max_pages_used| 0 |
| Tc_log_page_size| 0 |
| Tc_log_page_waits | 0 |
| Threadpool_idle_threads | 0 |
| Threadpool_threads | 0 |
| Threads_cached | 6 |
| Threads_connected | 16 |
| Threads_created | 1430444 |
| Threads_running | 3 |
+-----------------------------------------------+--------------------------------------------------+
397 rows in set (0.00 sec)
mysql> SHOW GLOBAL VARIABLES;
+----------------------------------------------------------------------------------------------------------+
| Variable_name | Value |
+--------------------------------------------------------+---------------------------------------+
| auto_increment_increment | 1|
| auto_increment_offset | 1|
| autocommit| ON |
| automatic_sp_privileges | ON |
| back_log | 250 |
| basedir | /usr/local |
| big_tables| OFF |
| bind_address | *|
| binlog_cache_size | 32768 |
| binlog_checksum| CRC32 |
| binlog_direct_non_transactional_updates | OFF |
| binlog_format | MIXED |
| 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 |
| bulk_insert_buffer_size | 8388608 |
| completion_type| NO_CHAIN |
| concurrent_insert | AUTO |
| connect_timeout| 10 |
| core_file | OFF |
| datadir | /home/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 |
| enforce_storage_engine | |
| eq_range_index_dive_limit| 10 |
| event_scheduler| OFF |
| expand_fast_index_creation | OFF |
| expire_logs_days | 2|
| explicit_defaults_for_timestamp | OFF |
| extra_max_connections | 1|
| extra_port| 0|
| 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 | /home/mysql/sql01.log|
| group_concat_max_len| 1024 |
| gtid_executed | |
| gtid_mode | OFF |
| 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_statement_timeout | YES |
| have_symlink | YES |
| host_cache_size| 653 |
| hostname | sql01.<STRIPPED>.com |
| 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_hash_index_partitions | 1|
| 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| ON |
| innodb_buffer_pool_dump_now | OFF |
| innodb_buffer_pool_filename | ib_buffer_pool |
| innodb_buffer_pool_instances | 8|
| innodb_buffer_pool_load_abort | OFF |
| innodb_buffer_pool_load_at_startup | ON |
| innodb_buffer_pool_load_now | OFF |
| innodb_buffer_pool_populate | OFF |
| innodb_buffer_pool_size | 8589934592 |
| innodb_change_buffer_max_size | 25 |
| innodb_change_buffering | all |
| innodb_checksum_algorithm| innodb|
| innodb_checksums | ON |
| innodb_cleaner_lsn_age_factor | high_checkpoint |
| 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_corrupt_table_action | assert|
| innodb_data_file_path | ibdata1:12M:autoextend |
| innodb_data_home_dir| /home/mysql/ |
| innodb_disable_sort_file_cache| OFF |
| innodb_doublewrite | ON |
| innodb_empty_free_list_algorithm | backoff |
| innodb_fake_changes | 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| 1|
| innodb_flush_method | |
| innodb_flush_neighbors | 1|
| innodb_flushing_avg_loops| 30 |
| innodb_force_load_corrupted | OFF |
| innodb_force_recovery | 0|
| innodb_foreground_preflush | exponential_backoff |
| 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_kill_idle_transaction | 0|
| innodb_large_prefix | OFF |
| innodb_lock_wait_timeout | 50 |
| innodb_locking_fake_changes | ON |
| innodb_locks_unsafe_for_binlog| OFF |
| innodb_log_arch_dir | /home/mysql/ |
| innodb_log_arch_expire_sec | 0|
| innodb_log_archive | OFF |
| innodb_log_block_size | 512 |
| innodb_log_buffer_size | 8388608 |
| innodb_log_checksum_algorithm | innodb|
| innodb_log_compressed_pages | ON |
| innodb_log_file_size| 50331648 |
| innodb_log_files_in_group| 2|
| innodb_log_group_home_dir| /home/mysql/ |
| innodb_lru_scan_depth | 1024 |
| innodb_max_bitmap_file_size | 104857600 |
| innodb_max_changed_pages | 1000000 |
| 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 | 2048 |
| 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_show_locks_held | 10 |
| innodb_show_verbose_locks| 0|
| innodb_sort_buffer_size | 1048576 |
| innodb_spin_wait_delay | 6|
| innodb_stats_auto_recalc | ON |
| 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_strict_mode | ON |
| 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_track_changed_pages | OFF |
| innodb_undo_directory | .|
| innodb_undo_logs | 128 |
| innodb_undo_tablespaces | 0|
| innodb_use_atomic_writes | OFF |
| innodb_use_global_flush_log_at_trx_commit | ON |
| innodb_use_native_aio | OFF |
| innodb_use_sys_malloc | ON |
| innodb_version | 5.6.15-63.0|
| innodb_write_io_threads | 4|
| interactive_timeout | 14400 |
| join_buffer_size | 262144|
| keep_files_on_create| OFF |
| key_buffer_size| 1073741824 |
| 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/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 | /home/mysql/mysql-bin|
| log_bin_index | /home/mysql/mysql-bin.index |
| log_bin_trust_function_creators | OFF |
| log_bin_use_v1_row_events| OFF |
| log_error | /home/mysql/mysql-error.log |
| log_output| FILE |
| log_queries_not_using_indexes | OFF |
| log_slave_updates | ON |
| log_slow_admin_statements| OFF |
| log_slow_filter| |
| log_slow_rate_limit | 1|
| log_slow_rate_type | session |
| log_slow_slave_statements| OFF |
| log_slow_sp_statements | ON |
| log_slow_verbosity | |
| log_throttle_queries_not_using_indexes | 0|
| log_warnings | 1|
| log_warnings_suppress | |
| 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 | 16777216 |
| max_binlog_cache_size | 18446744073709547520 |
| max_binlog_files | 0|
| max_binlog_size| 1073741824 |
| max_binlog_stmt_cache_size | 18446744073709547520 |
| max_connect_errors | 1000 |
| max_connections| 1000 |
| max_delayed_threads | 20 |
| max_error_count| 64 |
| max_heap_table_size | 33554432 |
| 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_statement_time | 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 | BACKUP,FORCE |
| myisam_repair_threads | 1|
| myisam_sort_buffer_size | 67108864 |
| 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 | 22190 |
| 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 | 6948 |
| performance_schema_max_file_classes| 50 |
| performance_schema_max_file_handles| 32768 |
| performance_schema_max_file_instances | 7856 |
| performance_schema_max_mutex_classes | 200 |
| performance_schema_max_mutex_instances | 21240 |
| performance_schema_max_rwlock_classes | 40 |
| performance_schema_max_rwlock_instances | 10944 |
| performance_schema_max_socket_classes | 10 |
| performance_schema_max_socket_instances | 2020 |
| performance_schema_max_stage_classes | 150 |
| performance_schema_max_statement_classes| 176 |
| performance_schema_max_table_handles | 4096 |
| performance_schema_max_table_instances | 12500 |
| performance_schema_max_thread_classes | 50 |
| performance_schema_max_thread_instances | 2100 |
| 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 | /home/mysql/sql01.<STRIPPED>.com.pid |
| plugin_dir| /usr/local/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 | 2048 |
| query_cache_size | 268435456 |
| query_cache_strip_comments | ON |
| query_cache_type | ON |
| query_cache_wlock_invalidate | OFF |
| query_prealloc_size | 8192 |
| range_alloc_block_size | 4096 |
| read_buffer_size | 1048576 |
| read_only | OFF |
| read_rnd_buffer_size| 4194304 |
| relay_log | /home/mysql/mysql-relay-bin |
| relay_log_basename | /home/mysql/mysql-relay-bin |
| relay_log_index| /home/mysql/mysql-relay-bin.index |
| relay_log_info_file | relay-log.info |
| relay_log_info_repository| TABLE |
| relay_log_purge| ON |
| relay_log_recovery | ON |
| 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 | |
| server_id | 72 |
| server_id_bits | 32 |
| server_uuid | <SNIP>|
| 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 | /home/mysql/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 | OFF |
| slave_sql_verify_checksum| ON |
| slave_transaction_retries| 10 |
| slave_type_conversions | |
| slow_launch_time | 2|
| slow_query_log | ON |
| slow_query_log_always_write_time | 10.000000 |
| slow_query_log_file | /home/mysql/mysql-slow.log|
| slow_query_log_timestamp_always | OFF |
| slow_query_log_timestamp_precision | second|
| slow_query_log_use_global_control | |
| socket | /tmp/mysql.sock |
| sort_buffer_size | 1048576 |
| 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 | CET |
| table_definition_cache | 1424 |
| table_open_cache | 2048 |
| table_open_cache_instances | 1|
| thread_cache_size | 16 |
| thread_concurrency | 16 |
| thread_handling| one-thread-per-connection |
| thread_pool_high_prio_mode | transactions |
| thread_pool_high_prio_tickets | 4294967295 |
| thread_pool_idle_timeout | 60 |
| thread_pool_max_threads | 100000|
| thread_pool_oversubscribe| 3|
| thread_pool_size | 16 |
| thread_pool_stall_limit | 500 |
| thread_stack | 262144|
| thread_statistics | OFF |
| time_format | %H:%i:%s |
| time_zone | SYSTEM|
| timed_mutexes | OFF |
| tmp_table_size | 33554432 |
| tmpdir | /home/mysql/tmp/|
| transaction_alloc_block_size | 8192 |
| transaction_prealloc_size| 4096 |
| tx_isolation | REPEATABLE-READ |
| tx_read_only | OFF |
| unique_checks | ON |
| updatable_views_with_limit | YES |
| userstat | OFF |
| version | 5.6.15-log |
| version_comment| Source distribution |
| version_compile_machine | amd64 |
| version_compile_os | FreeBSD8.3 |
| wait_timeout | 300 |
474 rows in set (0.00 sec)

• sumeetgautam: could you share the table structure?

Answer 1

Your indexes involve all of 4 fields in the table. i.e. PK implicitly exists in all other secondary indexes. After each insert/update/delete, the indexes will be re-organizes, and from time to time will be optimized, which lead to slow queries some times. One way to improve that is to optimize the indexes, and that is highly dependent on the queries you run.

For example, for your delete query, you need an index on filter only.

Optimizing indexes helps in doing less memory paging, and higher hit ration for cached data.

Answer 2

Because reducing query_cache_size to 256MB helped, please consider reducing again by 50%. Some advisors suggest limiting query_cache_size to 50MB to reduce query_cache overhead.

If you could share SHOW GLOBAL STATUS and SHOW GLOBAL VARIABLES, we would have opportunity to look at other likely contributing factors.

Thanks for your details.