insert - Mysql commit sometimes takes minutes to finish -

ive been having problem on 1 week now. ive allready gone though similar problems other people had here on stackoverflow. im running mysql 5.6.10.

1. "query end" step long @ random times
2. update statements in "query end state"
3. lots of "query end" states in mysql, connections used in matter of minutes

it happends randomly. every 5 minutes or so, commit takes very long time. , size of transation insert around 1-2000 rows.

ive been changing settings much, ive kind of lost decided create questions here.

my inserts/updates sqlfiles have been generated program. have windows service runs every 1,5 minutes processing files. build string of many sql files in transaction mode. works 4 out of 5 time smooth, 1 out of 5 jams.

it happends on same table, , of times regarding inserts happends on updates. doubt has structure of tables never know until solved :)

this table structure

create table `int_links_root_1` (   `intlinksrootid` bigint(20) not null auto_increment,   `urlid` int(11) not null,   `link` varchar(2000) not null,   `anchortext` varchar(500) default null,   `title` varchar(2000) default null,   `pagetext` varchar(8000) default null,   `added` datetime default null,   `lastmodifieddatetime` datetime default null,   primary key (`intlinksrootid`),   key `int_links_urlid_idx_1` (`urlid`),   fulltext key `fulltext` (`anchortext`,`title`,`pagetext`),   constraint `int_links_urlid_idx_1` foreign key (`urlid`) references `urls` (`urlid`) on delete cascade on update no action ) engine=innodb auto_increment=1708708 default charset=utf8$$ 

these 'show variables'

auto_increment_increment    1 auto_increment_offset   1 autocommit  on automatic_sp_privileges on back_log    90 basedir c:/program files/mysql/mysql server 5.6/ big_tables  off bind_address    * binlog_cache_size   32768 binlog_checksum crc32 binlog_direct_non_transactional_updates off binlog_format   statement 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 character_set_client    utf8 character_set_connection    utf8 character_set_database  latin1 character_set_filesystem    binary character_set_results   utf8 character_set_server    latin1 character_set_system    utf8 character_sets_dir  c:\program files\mysql\mysql server 5.6\share\charsets\ collation_connection    utf8_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 d:\mysql6\ 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    0 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 3 ft_query_expansion_limit    20 ft_stopword_file    (built-in) general_log on general_log_file    d:\mysql6\win-0pccfi7ppin.log group_concat_max_len    1024 gtid_executed    gtid_mode   off gtid_next   automatic gtid_owned   gtid_purged  have_compress   yes have_crypt  no 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 328 hostname    win-0pccfi7ppin 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    8 innodb_buffer_pool_load_abort   off innodb_buffer_pool_load_at_startup  off innodb_buffer_pool_load_now off innodb_buffer_pool_size 524288000 innodb_change_buffer_max_size   25 innodb_change_buffering 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   ibdata1:10m:autoextend innodb_data_home_dir    d:\mysql6 innodb_disable_sort_file_cache  off 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   on innodb_flush_log_at_timeout 1 innodb_flush_log_at_trx_commit  0 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_server_stopword_table  innodb_ft_sort_pll_degree   2 innodb_ft_user_stopword_table    innodb_io_capacity  200 innodb_io_capacity_max  2000 innodb_large_prefix off innodb_lock_wait_timeout    30 innodb_locks_unsafe_for_binlog  off innodb_log_buffer_size  2097152 innodb_log_file_size    262144000 innodb_log_files_in_group   2 innodb_log_group_home_dir   .\ innodb_lru_scan_depth   1024 innodb_max_dirty_pages_pct  0 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   2000 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_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  off innodb_support_xa   off innodb_sync_array_size  1 innodb_sync_spin_loops  30 innodb_table_locks  on innodb_thread_concurrency   10 innodb_thread_sleep_delay   0 innodb_undo_directory   . innodb_undo_logs    128 innodb_undo_tablespaces 0 innodb_use_native_aio   on innodb_use_sys_malloc   on innodb_version  1.2.10 innodb_write_io_threads 20 insert_id   0 interactive_timeout 28800 join_buffer_size    262144 keep_files_on_create    off key_buffer_size 67108864 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 c:\program files\mysql\mysql server 5.6\share\ lc_time_names   en_us license gpl local_infile    on lock_wait_timeout   31536000 log_bin off log_bin_basename     log_bin_index    log_bin_trust_function_creators off log_bin_use_v1_row_events   off log_error   d:\mysql6\error_log.txt log_output  table log_queries_not_using_indexes   off log_slave_updates   off log_throttle_queries_not_using_indexes  0 log_warnings    1 long_query_time 3.000000 low_priority_updates    off lower_case_file_system  on lower_case_table_names  1 master_info_repository  file master_verify_checksum  off max_allowed_packet  4194304 max_binlog_cache_size   18446744073709547520 max_binlog_size 1073741824 max_binlog_stmt_cache_size  18446744073709547520 max_connect_errors  100 max_connections 200 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_prepared_stmt_count 16382 max_relay_log_size  0 max_seeks_for_key   4294967295 max_sort_length 1024 max_sp_recursion_depth  0 max_tmp_tables  32 max_user_connections    0 max_write_lock_count    4294967295 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   107374182400 myisam_mmap_size    18446744073709551615 myisam_recover_options  off myisam_repair_threads   1 myisam_sort_buffer_size 209715200 myisam_stats_method nulls_unequal myisam_use_mmap off named_pipe  on 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    7048 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,loosesc... 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 5000 performance_schema_events_stages_history_long_size  1000 performance_schema_events_stages_history_size   10 performance_schema_events_statements_history_long_size  1000 performance_schema_events_statements_history_size   10 performance_schema_events_waits_history_long_size   1000 performance_schema_events_waits_history_size    10 performance_schema_hosts_size   100 performance_schema_max_cond_classes 80 performance_schema_max_cond_instances   1215 performance_schema_max_file_classes 50 performance_schema_max_file_handles 32768 performance_schema_max_file_instances   1750 performance_schema_max_mutex_classes    200 performance_schema_max_mutex_instances  4429 performance_schema_max_rwlock_classes   30 performance_schema_max_rwlock_instances 2286 performance_schema_max_socket_classes   10 performance_schema_max_socket_instances 300 performance_schema_max_stage_classes    150 performance_schema_max_statement_classes    167 performance_schema_max_table_handles    2858 performance_schema_max_table_instances  556 performance_schema_max_thread_classes   50 performance_schema_max_thread_instances 358 performance_schema_session_connect_attrs_size   512 performance_schema_setup_actors_size    100 performance_schema_setup_objects_size   100 performance_schema_users_size   100 port    3330 preload_buffer_size 32768 profiling   off profiling_history_size  15 protocol_version    10 proxy_user   pseudo_slave_mode   off pseudo_thread_id    1520 query_alloc_block_size  8192 query_cache_limit   1048576 query_cache_min_res_unit    4096 query_cache_size    0 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    65536 read_only   off read_rnd_buffer_size    262144 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_user  secure_auth on secure_file_priv     server_id   0 server_id_bits  32 server_uuid 48f32a6c-9836-11e2-9e13-984be17fa006 shared_memory   off shared_memory_base_name mysql 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   d:\mysql6\temp 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_file d:\mysql6\win-0pccfi7ppin-slow.log socket  mysqlpipe6 sort_buffer_size    524288 sql_auto_is_null    off sql_big_selects on sql_buffer_result   off sql_log_bin on sql_log_off off sql_mode    strict_trans_tables,no_auto_create_user,no_engine_substitution sql_notes   on sql_quote_show_create   on sql_safe_updates    on 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    w. europe daylight time table_definition_cache  1400 table_open_cache    2000 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   system timed_mutexes   off timestamp   1368530016.924189 tmp_table_size  211812352 tmpdir  d:/mysql6/temp 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 5.6.10-log version_comment mysql community server (gpl) version_compile_machine x86_64 version_compile_os  win64 wait_timeout    28800 warning_count   0 

this show status

aborted_clients 26 aborted_connects    1 binlog_cache_disk_use   0 binlog_cache_use    0 binlog_stmt_cache_disk_use  0 binlog_stmt_cache_use   0 bytes_received  1203 bytes_sent  1936957 com_admin_commands  17 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_alter_user  0 com_analyze 0 com_begin   0 com_binlog  0 com_call_procedure  0 com_change_db   1 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  0 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   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  0 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    0 com_rollback_to_savepoint   0 com_savepoint   0 com_select  5 com_set_option  6 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 com_show_create_table   0 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 0 com_show_function_code  0 com_show_function_status    0 com_show_grants 0 com_show_keys   0 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    0 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 3 com_show_storage_engines    0 com_show_table_status   0 com_show_tables 0 com_show_triggers   0 com_show_variables  9 com_show_warnings   0 com_slave_start 0 com_slave_stop  0 com_stmt_close  0 com_stmt_execute    0 com_stmt_fetch  0 com_stmt_prepare    0 com_stmt_reprepare  0 com_stmt_reset  0 com_stmt_send_long_data 0 com_truncate    0 com_uninstall_plugin    0 com_unlock_tables   0 com_update  0 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 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 152 created_tmp_disk_tables 0 created_tmp_files   5 created_tmp_tables  9 delayed_errors  0 delayed_insert_threads  0 delayed_writes  0 flush_commands  1 handler_commit  0 handler_delete  0 handler_discover    0 handler_external_lock   8 handler_mrr_init    0 handler_prepare 0 handler_read_first  0 handler_read_key    0 handler_read_last   0 handler_read_next   0 handler_read_prev   0 handler_read_rnd    1122 handler_read_rnd_next   2463 handler_rollback    0 handler_savepoint   0 handler_savepoint_rollback  0 handler_update  0 handler_write   1333 innodb_buffer_pool_dump_status  not started innodb_buffer_pool_load_status  not started innodb_buffer_pool_pages_data   259 innodb_buffer_pool_bytes_data   4243456 innodb_buffer_pool_pages_dirty  170 innodb_buffer_pool_bytes_dirty  2785280 innodb_buffer_pool_pages_flushed    122362 innodb_buffer_pool_pages_free   380 innodb_buffer_pool_pages_misc   1 innodb_buffer_pool_pages_total  640 innodb_buffer_pool_read_ahead_rnd   0 innodb_buffer_pool_read_ahead   14036 innodb_buffer_pool_read_ahead_evicted   370 innodb_buffer_pool_read_requests    15129702 innodb_buffer_pool_reads    196618 innodb_buffer_pool_wait_free    152 innodb_buffer_pool_write_requests   727352 innodb_data_fsyncs  18008 innodb_data_pending_fsyncs  1 innodb_data_pending_reads   0 innodb_data_pending_writes  0 innodb_data_read    3462483968 innodb_data_reads   211501 innodb_data_writes  155812 innodb_data_written 4099368960 innodb_dblwr_pages_written  122602 innodb_dblwr_writes 2140 innodb_have_atomic_builtins on innodb_log_waits    0 innodb_log_write_requests   157303 innodb_log_writes   29814 innodb_os_log_fsyncs    4332 innodb_os_log_pending_fsyncs    0 innodb_os_log_pending_writes    1 innodb_os_log_written   83195392 innodb_page_size    16384 innodb_pages_created    3118 innodb_pages_read   211072 innodb_pages_written    122514 innodb_row_lock_current_waits   0 innodb_row_lock_time    261518 innodb_row_lock_time_avg    411 innodb_row_lock_time_max    30420 innodb_row_lock_waits   635 innodb_rows_deleted 0 innodb_rows_inserted    103754 innodb_rows_read    3291528 innodb_rows_updated 86170 innodb_num_open_files   52 innodb_truncated_status_writes  0 innodb_available_undo_logs  128 key_blocks_not_flushed  0 key_blocks_unused   53581 key_blocks_used 4 key_read_requests   248 key_reads   4 key_write_requests  0 key_writes  0 last_query_cost 10.499000 last_query_partial_plans    1 max_used_connections    8 not_flushed_delayed_rows    0 open_files  22 open_streams    0 open_table_definitions  86 open_tables 96 opened_files    207 opened_table_definitions    0 opened_tables   0 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  10468392 qcache_hits 0 qcache_inserts  0 qcache_lowmem_prunes    0 qcache_not_cached   107 qcache_queries_in_cache 0 qcache_total_blocks 1 queries 56190 questions   25 select_full_join    0 select_full_range_join  0 select_range    0 select_range_check  0 select_scan 10 slave_heartbeat_period   slave_last_heartbeat     slave_open_temp_tables  0 slave_received_heartbeats    slave_retried_transactions   slave_running   off slow_launch_threads 0 slow_queries    2 sort_merge_passes   0 sort_range  0 sort_rows   1122 sort_scan   2 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   50440 table_locks_waited  0 table_open_cache_hits   4 table_open_cache_misses 0 table_open_cache_overflows  0 tc_log_max_pages_used   0 tc_log_page_size    0 tc_log_page_waits   0 threads_cached  3 threads_connected   5 threads_created 8 threads_running 3 uptime  3329 uptime_since_flush_status   3329 

i have tried different innodb_flush_log_at_trx_commit settings. im queries optimal run fast occasionaly, im has flushing. ive tried disabling autocommit still happends. query cache disabled. ideas more welcome. maybe disks slow?

the system not in production can restart , test suggestions.

please let me know if can provide more details.

are sure previous commits finished ? not faniliar inner structure of mysql couldnt rebuild indexing, slow large tables. or can run multiple queries @ time fifth 1 out of rhreads count , in queue waiting rest finish.