Why is my MySQL connection timing out after 60 seconds from PHP, but not from the MySQL client?

MySQL server outage - exactly 60 seconds later

Problem description:

I recently found a SQL that was working fine before The query now times out after 60 seconds and throws an error. The query is slower, but it's run as part of a nightly job, so that's not a problem per se (so please don't suggest I optimize it).

I can consistently reproduce the error by running "select SLEEP(120);" from PHP as shown below. However, running the same statement from the MySQL client succeeds (returns 0). I tried adjusting wait_timeout (set to 28800) with no success. I also restarted the database server and the machine itself.

The fact that it always times out at 60 seconds makes me think this is probably a setup issue rather than a resource constraint issue.

My running environment is as follows:

• Windows Server 2003
• MySql 5.1.36-community
• PHP 5.3

The following is my test code, output and SHOW Result of VARIABLES:

Test 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") . "<br /><br />";

$sql = "SELECT SLEEP(120);";

$start = microtime(true);
mysql_query($sql, $link);

echo "**query done**<br />";
allDone();

function allDone(){
 global $start, $sql;

 $end = microtime(true);
 echo "sql : $sql<br />";
 echo "elapsed : " . ($end - $start) . "<br />";
 echo "<br />";
}

function sqlErrorHandler($errno, $errstr, $errfile, $errline){
 global $link;
 echo "Error : $errno<br />$errstr<br />";
 echo "mysql_ping : " . (mysql_ping($link) ? "LIVE" : "DEAD") . "<br />";
 echo "<br />";

 allDone();
}

Output:

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

SHOW VARIABLES :

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=+ -><()~*:""&|
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

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