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Re: INSERT/UPDATE within transactions (autocommit=0)
Posted by: Alexander Golubowitsch
Date: August 05, 2010 03:18AM

Hi again,

my excuses for the late reply.

To answer a few of your questions:
The How big (GB) are all the tables combined? Perhaps your database is so small that it would all fit in the 3G you have now.
~700 tables, about 16GB.

What is key_buffer_size? Probably 500M would be plenty.
512MB.



We have made a lot of changes that pretty much solved the whole problem.
It seems that INSERT and general I/O load caused the problems.

- User Tracking:
We are using a table that stores information about each page request. INSERTs would regularly queue up at times. I have changed that to INSERT DELAYED, which helped great deal. The table is basically never read from, only written to.

mysql> SHOW VARIABLES LIKE "delayed%";
+------------------------+-------+
| Variable_name          | Value |
+------------------------+-------+
| delayed_insert_limit   | 100   |
| delayed_insert_timeout | 90    |
| delayed_queue_size     | 200   |
+------------------------+-------+

- User Sessions:
We store Session data in a database table. The implementation causes one SELECT + 1 INSERT IGNORE + one UPDATE to that table for each request. That used to be done for any visitors, also spiders. Now we only do that for the small percentage of requests that are not from the top 5 spiders.

- Query Cache:
We have updated any queries we definitely do not want to be cached to read SELECT
SQL_NO_CACHE. DEMAND is a good point, but we'll have to wait a little before we tackle that.



As was to be expected, now there's a couple of new questions coming up. I'll leave them here even though they may get a little off-topic:


- Query Cache:
You mwentioned you're not a fan, I quite like it though. What puzzles me are the following investigations: It is set to 512MB - As long as it keeps filling up, all appears to be good. Once it hits its limit and starts removing queries to free space, Qcache_free_blocks goes up to some 60k, Qcache_free_memory goes up to about half of the 512MB, Qcache_queries_in_cache (was at ~400k) goes down again. If I issue a FLUSH QUERY CACHE, Qcache_free_blocks goes back to the former value of 1, and the cache starts filling again.

What's the point - just plain memory fragmentation?
Should I FLUSH QUERY CACHE once a day, or are the numbers just tricking me?


- Sleeping Clients / Aborted Connections:
Biggest problem right nowe - we are seeing sporadic PHP PDO Exceptions with the following message - google'ing for it didn't help much, haven't checked this forum, yet, though:
SQLSTATE[HY000] [2013] Lost connection to MySQL server at 'waiting for initial communication packet', system error: 95
I see a dozen of these Exceptions thrown at visitors every hour or so. I have tried doubling max_connections to 512, but that didn't help.

max. concurrent connections  	202
Failed attempts 	1,766
Aborted 	20
Total 	2,130 k

mysql> SHOW VARIABLES LIKE "%connect%";
+--------------------------+-----------------+
| Variable_name            | Value           |
+--------------------------+-----------------+
| connect_timeout          | 30              |
| init_connect             |                 |
| max_connect_errors       | 10              |
| max_connections          | 512             |
| max_user_connections     | 0               |
+--------------------------+-----------------+

mysql> SHOW VARIABLES LIKE "%timeout%";
+----------------------------+-------+
| Variable_name              | Value |
+----------------------------+-------+
| connect_timeout            | 30    |
| delayed_insert_timeout     | 90    |
| innodb_lock_wait_timeout   | 50    |
| interactive_timeout        | 28800 |
| net_read_timeout           | 30    |
| net_write_timeout          | 60    |
| slave_net_timeout          | 3600  |
| table_lock_wait_timeout    | 50    |
| wait_timeout               | 28800 |
+----------------------------+-------+

I have no idea where the problems are coming from, but the situation is pretty drastic. Can you give any hints?





PS:

mysql> SHOW VARIABLES;
+---------------------------------+--------------------------------------+
| Variable_name                   | Value                                |
+---------------------------------+--------------------------------------+
| auto_increment_increment        | 1                                    |
| auto_increment_offset           | 1                                    |
| automatic_sp_privileges         | ON                                   |
| back_log                        | 50                                   |
| basedir                         | /usr/                                |
| binlog_cache_size               | 32768                                |
| bulk_insert_buffer_size         | 8388608                              |
| character_set_client            | utf8                                 |
| character_set_connection        | utf8                                 |
| character_set_database          | utf8                                 |
| character_set_filesystem        | binary                               |
| character_set_results           | utf8                                 |
| character_set_server            | utf8                                 |
| character_set_system            | utf8                                 |
| character_sets_dir              | /usr/share/mysql/charsets/           |
| collation_connection            | utf8_general_ci                      |
| collation_database              | utf8_general_ci                      |
| collation_server                | utf8_general_ci                      |
| completion_type                 | 0                                    |
| concurrent_insert               | 1                                    |
| connect_timeout                 | 30                                   |
| datadir                         | /var/lib/mysql/                      |
| date_format                     | %Y-%m-%d                             |
| datetime_format                 | %Y-%m-%d %H:%i:%s                    |
| default_week_format             | 0                                    |
| delay_key_write                 | ON                                   |
| delayed_insert_limit            | 100                                  |
| delayed_insert_timeout          | 90                                   |
| delayed_queue_size              | 200                                  |
| div_precision_increment         | 4                                    |
| keep_files_on_create            | OFF                                  |
| engine_condition_pushdown       | OFF                                  |
| expire_logs_days                | 0                                    |
| flush                           | OFF                                  |
| flush_time                      | 0                                    |
| ft_boolean_syntax               | + -><()~*:""&|                       |
| ft_max_word_len                 | 84                                   |
| ft_min_word_len                 | 1                                    |
| ft_query_expansion_limit        | 20                                   |
| group_concat_max_len            | 4096                                 |
| have_archive                    | NO                                   |
| have_bdb                        | NO                                   |
| have_blackhole_engine           | NO                                   |
| have_compress                   | YES                                  |
| have_crypt                      | YES                                  |
| have_csv                        | NO                                   |
| have_dynamic_loading            | YES                                  |
| have_example_engine             | NO                                   |
| have_federated_engine           | NO                                   |
| have_geometry                   | YES                                  |
| have_innodb                     | YES                                  |
| have_isam                       | NO                                   |
| have_merge_engine               | YES                                  |
| have_ndbcluster                 | NO                                   |
| have_openssl                    | DISABLED                             |
| have_ssl                        | DISABLED                             |
| have_query_cache                | YES                                  |
| have_raid                       | NO                                   |
| have_rtree_keys                 | YES                                  |
| have_symlink                    | YES                                  |
| init_connect                    |                                      |
| init_file                       |                                      |
| init_slave                      |                                      |
| innodb_additional_mem_pool_size | 25165824                             |
| innodb_autoextend_increment     | 8                                    |
| innodb_buffer_pool_awe_mem_mb   | 0                                    |
| innodb_buffer_pool_size         | 3221225472                           |
| innodb_checksums                | ON                                   |
| innodb_commit_concurrency       | 0                                    |
| innodb_concurrency_tickets      | 500                                  |
| innodb_data_file_path           | ibdata1:10M:autoextend               |
| innodb_data_home_dir            |                                      |
| innodb_adaptive_hash_index      | ON                                   |
| innodb_doublewrite              | ON                                   |
| innodb_fast_shutdown            | 1                                    |
| innodb_file_io_threads          | 4                                    |
| innodb_file_per_table           | ON                                   |
| innodb_flush_log_at_trx_commit  | 0                                    |
| innodb_flush_method             |                                      |
| innodb_force_recovery           | 0                                    |
| innodb_lock_wait_timeout        | 50                                   |
| innodb_locks_unsafe_for_binlog  | OFF                                  |
| innodb_log_arch_dir             |                                      |
| innodb_log_archive              | OFF                                  |
| innodb_log_buffer_size          | 67108864                             |
| innodb_log_file_size            | 536870912                            |
| innodb_log_files_in_group       | 2                                    |
| innodb_log_group_home_dir       | ./                                   |
| innodb_max_dirty_pages_pct      | 90                                   |
| innodb_max_purge_lag            | 0                                    |
| innodb_mirrored_log_groups      | 1                                    |
| innodb_open_files               | 5000                                 |
| innodb_rollback_on_timeout      | OFF                                  |
| innodb_support_xa               | OFF                                  |
| innodb_sync_spin_loops          | 20                                   |
| innodb_table_locks              | ON                                   |
| innodb_thread_concurrency       | 0                                    |
| innodb_thread_sleep_delay       | 10000                                |
| interactive_timeout             | 28800                                |
| join_buffer_size                | 131072                               |
| key_buffer_size                 | 536870912                            |
| 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_time_names                   | en_US                                |
| license                         | GPL                                  |
| local_infile                    | ON                                   |
| locked_in_memory                | OFF                                  |
| log                             | OFF                                  |
| log_bin                         | OFF                                  |
| log_bin_trust_function_creators | OFF                                  |
| log_queries_not_using_indexes   | OFF                                  |
| log_slave_updates               | OFF                                  |
| log_slow_queries                | ON                                   |
| log_warnings                    | 1                                    |
| long_query_time                 | 10                                   |
| low_priority_updates            | OFF                                  |
| lower_case_file_system          | OFF                                  |
| lower_case_table_names          | 0                                    |
| max_allowed_packet              | 268435456                            |
| max_binlog_cache_size           | 18446744073709547520                 |
| max_binlog_size                 | 1073741824                           |
| max_connect_errors              | 10                                   |
| max_connections                 | 512                                  |
| 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_tmp_tables                  | 32                                   |
| max_user_connections            | 0                                    |
| max_write_lock_count            | 18446744073709551615                 |
| multi_range_count               | 256                                  |
| myisam_data_pointer_size        | 6                                    |
| myisam_max_sort_file_size       | 9223372036853727232                  |
| myisam_recover_options          | OFF                                  |
| myisam_repair_threads           | 1                                    |
| myisam_sort_buffer_size         | 8388608                              |
| myisam_stats_method             | nulls_unequal                        |
| net_buffer_length               | 8192                                 |
| net_read_timeout                | 30                                   |
| net_retry_count                 | 10                                   |
| net_write_timeout               | 60                                   |
| new                             | OFF                                  |
| old_passwords                   | OFF                                  |
| open_files_limit                | 12266                                |
| optimizer_prune_level           | 1                                    |
| optimizer_search_depth          | 62                                   |
| port                            | 3306                                 |
| preload_buffer_size             | 32768                                |
| protocol_version                | 10                                   |
| query_alloc_block_size          | 8192                                 |
| query_cache_limit               | 1048576                              |
| query_cache_min_res_unit        | 4096                                 |
| query_cache_size                | 536870912                            |
| 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            | 6291456                              |
| relay_log                       |                                      |
| relay_log_index                 |                                      |
| relay_log_info_file             | relay-log.info                       |
| relay_log_purge                 | ON                                   |
| relay_log_space_limit           | 0                                    |
| rpl_recovery_rank               | 0                                    |
| secure_auth                     | OFF                                  |
| secure_file_priv                |                                      |
| server_id                       | 0                                    |
| skip_external_locking           | ON                                   |
| skip_networking                 | OFF                                  |
| skip_show_database              | OFF                                  |
| slave_compressed_protocol       | OFF                                  |
| slave_load_tmpdir               | /tmp/                                |
| slave_net_timeout               | 3600                                 |
| slave_skip_errors               | OFF                                  |
| slave_transaction_retries       | 10                                   |
| slow_launch_time                | 2                                    |
| socket                          | /var/run/mysqld/mysqld.sock          |
| sort_buffer_size                | 4194304                              |
| sql_big_selects                 | ON                                   |
| sql_mode                        |                                      |
| sql_notes                       | ON                                   |
| sql_warnings                    | OFF                                  |
| ssl_ca                          |                                      |
| ssl_capath                      |                                      |
| ssl_cert                        |                                      |
| ssl_cipher                      |                                      |
| ssl_key                         |                                      |
| storage_engine                  | MyISAM                               |
| sync_binlog                     | 0                                    |
| sync_frm                        | ON                                   |
| system_time_zone                | CEST                                 |
| table_cache                     | 6000                                 |
| table_lock_wait_timeout         | 50                                   |
| table_type                      | MyISAM                               |
| thread_cache_size               | 48                                   |
| thread_stack                    | 262144                               |
| time_format                     | %H:%i:%s                             |
| time_zone                       | SYSTEM                               |
| timed_mutexes                   | OFF                                  |
| tmp_table_size                  | 33554432                             |
| tmpdir                          | /tmp                                 |
| transaction_alloc_block_size    | 8192                                 |
| transaction_prealloc_size       | 4096                                 |
| tx_isolation                    | REPEATABLE-READ                      |
| updatable_views_with_limit      | YES                                  |
| version                         | 5.0.60-log                           |
| version_comment                 | Gentoo Linux mysql-5.0.60-r1         |
| version_compile_machine         | x86_64                               |
| version_compile_os              | pc-linux-gnu                         |
| wait_timeout                    | 28800                                |
+---------------------------------+--------------------------------------+

mysql> SHOW STATUS;
+-----------------------------------+-------------+
| Variable_name                     | Value       |
+-----------------------------------+-------------+
| Aborted_clients                   | 22          |
| Aborted_connects                  | 1781        |
| Binlog_cache_disk_use             | 0           |
| Binlog_cache_use                  | 0           |
| Bytes_received                    | 21110       |
| Bytes_sent                        | 397550      |
| Com_admin_commands                | 0           |
| Com_alter_db                      | 0           |
| Com_alter_table                   | 0           |
| Com_analyze                       | 0           |
| Com_backup_table                  | 0           |
| Com_begin                         | 0           |
| Com_call_procedure                | 0           |
| Com_change_db                     | 0           |
| Com_change_master                 | 0           |
| Com_check                         | 0           |
| Com_checksum                      | 0           |
| Com_commit                        | 0           |
| Com_create_db                     | 0           |
| Com_create_function               | 0           |
| Com_create_index                  | 0           |
| Com_create_table                  | 0           |
| Com_create_user                   | 0           |
| Com_dealloc_sql                   | 0           |
| Com_delete                        | 0           |
| Com_delete_multi                  | 0           |
| Com_do                            | 0           |
| Com_drop_db                       | 0           |
| Com_drop_function                 | 0           |
| Com_drop_index                    | 0           |
| Com_drop_table                    | 0           |
| Com_drop_user                     | 0           |
| Com_execute_sql                   | 0           |
| Com_flush                         | 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_kill                          | 0           |
| Com_load                          | 0           |
| Com_load_master_data              | 0           |
| Com_load_master_table             | 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_rename_table                  | 0           |
| Com_repair                        | 0           |
| Com_replace                       | 0           |
| Com_replace_select                | 0           |
| Com_reset                         | 0           |
| Com_restore_table                 | 0           |
| Com_revoke                        | 0           |
| Com_revoke_all                    | 0           |
| Com_rollback                      | 0           |
| Com_savepoint                     | 0           |
| Com_select                        | 1           |
| Com_set_option                    | 2           |
| Com_show_binlog_events            | 0           |
| Com_show_binlogs                  | 0           |
| Com_show_charsets                 | 0           |
| Com_show_collations               | 0           |
| Com_show_column_types             | 0           |
| Com_show_create_db                | 0           |
| Com_show_create_table             | 0           |
| Com_show_databases                | 1           |
| Com_show_errors                   | 0           |
| Com_show_fields                   | 734         |
| Com_show_grants                   | 0           |
| Com_show_innodb_status            | 0           |
| Com_show_keys                     | 0           |
| Com_show_logs                     | 0           |
| Com_show_master_status            | 0           |
| Com_show_ndb_status               | 0           |
| Com_show_new_master               | 0           |
| Com_show_open_tables              | 0           |
| Com_show_privileges               | 0           |
| Com_show_processlist              | 0           |
| Com_show_slave_hosts              | 0           |
| Com_show_slave_status             | 0           |
| Com_show_status                   | 1           |
| Com_show_storage_engines          | 0           |
| Com_show_tables                   | 1           |
| Com_show_triggers                 | 0           |
| Com_show_variables                | 6           |
| 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_reset                    | 0           |
| Com_stmt_send_long_data           | 0           |
| Com_truncate                      | 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         |
| Connections                       | 2146576     |
| Created_tmp_disk_tables           | 0           |
| Created_tmp_files                 | 117617      |
| Created_tmp_tables                | 9           |
| Delayed_errors                    | 0           |
| Delayed_insert_threads            | 1           |
| Delayed_writes                    | 1917457     |
| Flush_commands                    | 1           |
| Handler_commit                    | 0           |
| Handler_delete                    | 0           |
| Handler_discover                  | 0           |
| Handler_prepare                   | 0           |
| Handler_read_first                | 0           |
| Handler_read_key                  | 0           |
| Handler_read_next                 | 0           |
| Handler_read_prev                 | 0           |
| Handler_read_rnd                  | 0           |
| Handler_read_rnd_next             | 1005        |
| Handler_rollback                  | 0           |
| Handler_savepoint                 | 0           |
| Handler_savepoint_rollback        | 0           |
| Handler_update                    | 0           |
| Handler_write                     | 1129        |
| Innodb_buffer_pool_pages_data     | 152466      |
| Innodb_buffer_pool_pages_dirty    | 1           |
| Innodb_buffer_pool_pages_flushed  | 256219      |
| Innodb_buffer_pool_pages_free     | 1           |
| Innodb_buffer_pool_pages_latched  | 1           |
| Innodb_buffer_pool_pages_misc     | 44141       |
| Innodb_buffer_pool_pages_total    | 196608      |
| Innodb_buffer_pool_read_ahead_rnd | 8637        |
| Innodb_buffer_pool_read_ahead_seq | 10410       |
| Innodb_buffer_pool_read_requests  | 50044425340 |
| Innodb_buffer_pool_reads          | 534600      |
| Innodb_buffer_pool_wait_free      | 0           |
| Innodb_buffer_pool_write_requests | 68853199    |
| Innodb_data_fsyncs                | 316457      |
| Innodb_data_pending_fsyncs        | 1           |
| Innodb_data_pending_reads         | 0           |
| Innodb_data_pending_writes        | 0           |
| Innodb_data_read                  | 20360138752 |
| Innodb_data_reads                 | 652060      |
| Innodb_data_writes                | 378021      |
| Innodb_data_written               | 11092307456 |
| Innodb_dblwr_pages_written        | 256219      |
| Innodb_dblwr_writes               | 24098       |
| Innodb_log_waits                  | 0           |
| Innodb_log_write_requests         | 5425786     |
| Innodb_log_writes                 | 228980      |
| Innodb_os_log_fsyncs              | 243342      |
| Innodb_os_log_pending_fsyncs      | 1           |
| Innodb_os_log_pending_writes      | 0           |
| Innodb_os_log_written             | 2689167872  |
| Innodb_page_size                  | 16384       |
| Innodb_pages_created              | 118352      |
| Innodb_pages_read                 | 1242423     |
| Innodb_pages_written              | 256219      |
| Innodb_row_lock_current_waits     | 0           |
| Innodb_row_lock_time              | 20883       |
| Innodb_row_lock_time_avg          | 10441       |
| Innodb_row_lock_time_max          | 16386       |
| Innodb_row_lock_waits             | 2           |
| Innodb_rows_deleted               | 14740       |
| Innodb_rows_inserted              | 11351904    |
| Innodb_rows_read                  | 15173723255 |
| Innodb_rows_updated               | 300598      |
| Key_blocks_not_flushed            | 0           |
| Key_blocks_unused                 | 28215       |
| Key_blocks_used                   | 428684      |
| Key_read_requests                 | 1139162211  |
| Key_reads                         | 1335992     |
| Key_write_requests                | 87513238    |
| Key_writes                        | 4267065     |
| Last_query_cost                   | 10.499000   |
| Max_used_connections              | 202         |
| Not_flushed_delayed_rows          | 0           |
| Open_files                        | 262         |
| Open_streams                      | 0           |
| Open_tables                       | 3635        |
| Opened_tables                     | 0           |
| Prepared_stmt_count               | 0           |
| Qcache_free_blocks                | 60381       |
| Qcache_free_memory                | 198429408   |
| Qcache_hits                       | 124848796   |
| Qcache_inserts                    | 74927607    |
| Qcache_lowmem_prunes              | 72480227    |
| Qcache_not_cached                 | 368353241   |
| Qcache_queries_in_cache           | 282692      |
| Qcache_total_blocks               | 626813      |
| Questions                         | 584661739   |
| Rpl_status                        | NULL        |
| Select_full_join                  | 0           |
| Select_full_range_join            | 0           |
| Select_range                      | 0           |
| Select_range_check                | 0           |
| Select_scan                       | 9           |
| Slave_open_temp_tables            | 0           |
| Slave_retried_transactions        | 0           |
| Slave_running                     | OFF         |
| Slow_launch_threads               | 0           |
| Slow_queries                      | 0           |
| Sort_merge_passes                 | 0           |
| Sort_range                        | 0           |
| Sort_rows                         | 0           |
| Sort_scan                         | 0           |
| 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           |
| Ssl_version                       |             |
| Table_locks_immediate             | 441419185   |
| Table_locks_waited                | 145341      |
| Tc_log_max_pages_used             | 0           |
| Tc_log_page_size                  | 0           |
| Tc_log_page_waits                 | 0           |
| Threads_cached                    | 28          |
| Threads_connected                 | 21          |
| Threads_created                   | 1808        |
| Threads_running                   | 6           |
| Uptime                            | 653205      |
+-----------------------------------+-------------+
248 rows in set (0.04 sec)


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Re: INSERT/UPDATE within transactions (autocommit=0)
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August 05, 2010 03:18AM


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