title: MySQL server has gone away - in exactly 60 seconds
body: <p>I recently discovered that a sql query that was running fine earlier is now timing out after 60 seconds and throwing an error. The query is slow but runs as part of a nightly job so that's not a problem in itself (so please don't suggest I optimize it). </p>
  
  <p>I'm able to reproduce the error consistently by running "select SLEEP(120);" from PHP as shown below. However, running the same statement from a MySQL client is successful (returns 0). I've tried adjusting wait_timeout (set to 28800), but have had no luck. I've also rebooted both the db server and machine itself.</p>
  
  <p>The fact that it always times out at exactly 60 seconds suggests to me that it is likely to be a setting and not a limited resources issue.</p>
  
  <p>I'm running:<br>
  Windows Server 2003<br>
  MySql 5.1.36-community<br>
  PHP 5.3</p>
  
  <p>Below are my test code, the output and the results from SHOW VARIABLES</p>
  
  <p>Thanks!</p>
  
  <p>CODE:</p>
  
  <pre><code>set_error_handler("sqlErrorHandler");
  set_time_limit(12000);
  
  
  $link = mysql_connect("$MYSQL_Host","$MYSQL_User","$MYSQL_Pass");
  mysql_select_db($MYSQL_db, $link);
  
  echo "mysql_ping = " . (mysql_ping($link) ? "LIVE" : "DEAD") . "&lt;br /&gt;&lt;br /&gt;"; 
  
  $sql = "SELECT SLEEP(120);";
  
  $start = microtime(true);
  mysql_query($sql, $link);
  
  echo "**query done**&lt;br /&gt;";
  allDone();
  
  function allDone(){
   global $start, $sql;
  
   $end = microtime(true);
   echo "sql : $sql&lt;br /&gt;";
   echo "elapsed : " . ($end - $start) . "&lt;br /&gt;";
   echo "&lt;br /&gt;";
  }
  
  function sqlErrorHandler($errno, $errstr, $errfile, $errline){
   global $link;
   echo "Error : $errno&lt;br /&gt;$errstr&lt;br /&gt;";
   echo "mysql_ping : " . (mysql_ping($link) ? "LIVE" : "DEAD") . "&lt;br /&gt;"; 
   echo "&lt;br /&gt;";
  
   allDone();
  }
  </code></pre>
  
  <p>OUTPUT :</p>
  
  <pre><code>mysql_ping = LIVE
  
  Error : 2
  mysql_query() [function.mysql-query]: MySQL server has gone away
  mysql_ping : DEAD
  
  sql : SELECT SLEEP(120);
  elapsed : 60.051116943359
  
  Error : 2
  mysql_query() [function.mysql-query]: Error reading result set's header
  mysql_ping : DEAD
  
  sql : SELECT SLEEP(120);
  elapsed : 60.0511469841
  
  **query done**
  sql : SELECT SLEEP(120);
  elapsed : 60.051155090332
  </code></pre>
  
  <p>SHOW VARIABLES:</p>
  
  <pre><code>Variable_name=Value
  auto_increment_increment=1
  auto_increment_offset=1
  autocommit=ON
  automatic_sp_privileges=ON
  back_log=50
  basedir=C:\\Program Files\\MySQL\\MySQL Server 5.1\\
  big_tables=OFF
  binlog_cache_size=32768
  binlog_format=STATEMENT
  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 5.1\\share\\charsets\\
  collation_connection=utf8_general_ci
  collation_database=latin1_swedish_ci
  collation_server=latin1_swedish_ci
  completion_type=0
  concurrent_insert=1
  connect_timeout=10
  datadir=C:\\Documents and Settings\\All Users\\Application Data\\MySQL\\MySQL Server 5.1\\Data\\
  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=300
  delayed_queue_size=1000
  div_precision_increment=4
  engine_condition_pushdown=ON
  error_count=0
  event_scheduler=OFF
  expire_logs_days=0
  flush=OFF
  flush_time=1800
  foreign_key_checks=ON
  ft_boolean_syntax=+ -&gt;&lt;()~*:""&amp;|
  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=C:\\Documents and Settings\\All Users\\Application Data\\MySQL\\MySQL Server 5.1\\Data\\p1.log
  group_concat_max_len=1024
  have_community_features=YES
  have_compress=YES
  have_crypt=NO
  have_csv=YES
  have_dynamic_loading=YES
  have_geometry=YES
  have_innodb=YES
  have_ndbcluster=NO
  have_openssl=DISABLED
  have_partitioning=YES
  have_query_cache=YES
  have_rtree_keys=YES
  have_ssl=DISABLED
  have_symlink=YES
  identity=0
  ignore_builtin_innodb=OFF
  init_connect=
  init_file=
  init_slave=
  innodb_adaptive_hash_index=ON
  innodb_additional_mem_pool_size=2097152
  innodb_autoextend_increment=8
  innodb_autoinc_lock_mode=1
  innodb_buffer_pool_size=96468992
  innodb_checksums=ON
  innodb_commit_concurrency=0
  innodb_concurrency_tickets=500
  innodb_data_file_path=ibdata1:10M:autoextend
  innodb_data_home_dir=D:\\MySQL Datafiles\\
  innodb_doublewrite=ON
  innodb_fast_shutdown=1
  innodb_file_io_threads=4
  innodb_file_per_table=OFF
  innodb_flush_log_at_trx_commit=1
  innodb_flush_method=
  innodb_force_recovery=0
  innodb_lock_wait_timeout=50
  innodb_locks_unsafe_for_binlog=OFF
  innodb_log_buffer_size=1048576
  innodb_log_file_size=19922944
  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=300
  innodb_rollback_on_timeout=OFF
  innodb_stats_on_metadata=ON
  innodb_support_xa=ON
  innodb_sync_spin_loops=20
  innodb_table_locks=ON
  innodb_thread_concurrency=8
  innodb_thread_sleep_delay=10000
  innodb_use_legacy_cardinality_algorithm=ON
  insert_id=0
  interactive_timeout=28800
  join_buffer_size=131072
  keep_files_on_create=OFF
  key_buffer_size=50331648
  key_cache_age_threshold=300
  key_cache_block_size=1024
  key_cache_division_limit=100
  language=C:\\Program Files\\MySQL\\MySQL Server 5.1\\share\\english\\
  large_files_support=ON
  large_page_size=0
  large_pages=OFF
  last_insert_id=0
  lc_time_names=en_US
  license=GPL
  local_infile=ON
  log=OFF
  log_bin=OFF
  log_bin_trust_function_creators=OFF
  log_bin_trust_routine_creators=OFF
  log_error=C:\\Documents and Settings\\All Users\\Application Data\\MySQL\\MySQL Server 5.1\\Data\\p1.err
  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=ON
  lower_case_table_names=1
  max_allowed_packet=1048576
  max_binlog_cache_size=4294963200
  max_binlog_size=1073741824
  max_connect_errors=10
  max_connections=800
  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
  min_examined_row_limit=0
  multi_range_count=256
  myisam_data_pointer_size=6
  myisam_max_sort_file_size=107374182400
  myisam_recover_options=OFF
  myisam_repair_threads=1
  myisam_sort_buffer_size=12582912
  myisam_stats_method=nulls_unequal
  myisam_use_mmap=OFF
  named_pipe=OFF
  net_buffer_length=16384
  net_read_timeout=30
  net_retry_count=10
  net_write_timeout=80
  new=OFF
  old=OFF
  old_alter_table=OFF
  old_passwords=OFF
  open_files_limit=2048
  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
  pid_file=C:\\Documents and Settings\\All Users\\Application Data\\MySQL\\MySQL Server 5.1\\Data\\p1.pid
  plugin_dir=C:\\Program Files\\MySQL\\MySQL Server 5.1\\lib/plugin
  port=3306
  preload_buffer_size=32768
  profiling=OFF
  profiling_history_size=15
  protocol_version=10
  pseudo_thread_id=3230
  query_alloc_block_size=8192
  query_cache_limit=1048576
  query_cache_min_res_unit=4096
  query_cache_size=33554432
  query_cache_type=ON
  query_cache_wlock_invalidate=OFF
  query_prealloc_size=8192
  rand_seed1=
  rand_seed2=
  range_alloc_block_size=4096
  read_buffer_size=65536
  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_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
  shared_memory=OFF
  shared_memory_base_name=MYSQL
  skip_external_locking=ON
  skip_networking=OFF
  skip_show_database=OFF
  slave_compressed_protocol=OFF
  slave_exec_mode=STRICT
  slave_load_tmpdir=C:\\WINDOWS\\TEMP
  slave_net_timeout=3600
  slave_skip_errors=OFF
  slave_transaction_retries=10
  slow_launch_time=2
  slow_query_log=OFF
  slow_query_log_file=C:\\Documents and Settings\\All Users\\Application Data\\MySQL\\MySQL Server 5.1\\Data\\p1-slow.log
  sort_buffer_size=262144
  sql_auto_is_null=ON
  sql_big_selects=ON
  sql_big_tables=OFF
  sql_buffer_result=OFF
  sql_log_bin=ON
  sql_log_off=OFF
  sql_log_update=ON
  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=
  sql_warnings=OFF
  ssl_ca=
  ssl_capath=
  ssl_cert=
  ssl_cipher=
  ssl_key=
  storage_engine=InnoDB
  sync_binlog=0
  sync_frm=ON
  system_time_zone=Eastern Daylight Time
  table_definition_cache=256
  table_lock_wait_timeout=50
  table_open_cache=619
  table_type=InnoDB
  thread_cache_size=38
  thread_handling=one-thread-per-connection
  thread_stack=196608
  time_format=%H:%i:%s
  time_zone=SYSTEM
  timed_mutexes=OFF
  timestamp=1256827484
  tmp_table_size=16777216
  tmpdir=C:\\WINDOWS\\TEMP
  transaction_alloc_block_size=8192
  transaction_prealloc_size=4096
  tx_isolation=REPEATABLE-READ
  unique_checks=ON
  updatable_views_with_limit=YES
  version=5.1.36-community
  version_comment=MySQL Community Server (GPL)
  version_compile_machine=ia32
  version_compile_os=Win32
  wait_timeout=28800
  warning_count=0
  </code></pre>