Fix and tests for bug #49511 . mysqlnd and the MySQL Client Library (libmysql) use different networking APIs. mysqlnd does use PHP streams whereas libmysql uses its own wrapper of the operating level network calls. PHP sets by default a read timeout of 60s for streams - php.ini, default_socket_timeout. This default applies to all streams that set no other timeout value. mysqlnd has not set any other value and therefore it connections of long running queries can have been cut off after default_socket_timeout seconds resulting in a 2006 - MySQL Server has gone away error message. The MySQL Client Library sets a default timeout of 365 * 24 * 3600 seconds (1year) and waits for other timeouts to happen, e.g. TCP/IP timeouts. mysqlnd now uses the same very long timeout. The value is configurable through a new php.ini setting: mysqlnd.net_read_timeout. mysqlnd.net_read_timeout gets used by any extension (ext/mysql, ext/mysqli, PDO_MySQL) that uses mysqlnd. mysqlnd tells PHP Streams to use mysqlnd.net_read_timeout. Please note that there may be subtle differences between MYSQL_OPT_READ_TIMEOUT from the MySQL Client Library and PHP Streams. E.g. MYSQL_OPT_READ_TIMEOUT is documented to work only for TCP/IP connections and, prior to MySQL 5.1.2, only for Windows. PHP streams may not have this limitation. Please check the streams documentation, if in doubt.

ext/mysql/tests/mysql_mysqlnd_read_timeout_long.phpt

@@ -0,0 +1,37 @@
+--TEST--
+mysqlnd.net_read_timeout > default_socket_timeout
+--SKIPIF--
+<?php
+require_once('skipif.inc');
+require_once('skipifconnectfailure.inc');
+require_once('connect.inc');
+?>
+--INI--
+default_socket_timeout=1
+mysqlnd.net_read_timeout=12
+max_execution_time=12
+--FILE--
+<?php
+	set_time_limit(12);
+	include ("connect.inc");
+
+	if (!$link = my_mysql_connect($host, $user, $passwd, $db, $port, $socket)) {
+		printf("[001] Connect failed, [%d] %s\n", mysql_errno(), mysqlerror());
+	}
+
+	if (!$res = mysql_query("SELECT SLEEP(6)", $link))
+		printf("[002] [%d] %s\n",  mysql_errno($link), mysql_error($link));
+
+	var_dump(mysql_fetch_assoc($res));
+
+	mysql_free_result($res);
+	mysql_close($link);
+
+	print "done!";
+?>
+--EXPECTF--
+array(1) {
+  [%u|b%"SLEEP(6)"]=>
+  %unicode|string%(1) "0"
+}
+done!

ext/mysqli/tests/mysqli_mysqlnd_read_timeout.phpt

@@ -0,0 +1,36 @@
+--TEST--
+mysqlnd.net_read_timeout limit check
+--SKIPIF--
+<?php
+require_once('skipif.inc');
+require_once('skipifconnectfailure.inc');
+require_once('connect.inc');
+if (!$IS_MYSQLND)
+	/* The libmysql read_timeout limit default is 365 * 24 * 3600 seconds. It cannot be altered through PHP API calls */
+	die("skip mysqlnd only test");
+?>
+--INI--
+default_socket_timeout=60
+max_execution_time=60
+mysqlnd.net_read_timeout=1
+--FILE--
+<?php
+	include ("connect.inc");
+
+	if (!$link = mysqli_connect($host, $user, $passwd, $db, $port, $socket)) {
+		printf("[001] Connect failed, [%d] %s\n", mysqli_connect_errno(), mysqli_connect_error());
+	}
+
+	if (!$res = mysqli_query($link, "SELECT SLEEP(5)"))
+		printf("[002] [%d] %s\n",  mysqli_errno($link), mysqli_error($link));
+
+	mysqli_close($link);
+
+	print "done!";
+?>
+--EXPECTF--
+Warning: mysqli_query(): MySQL server has gone away in %s on line %d
+
+Warning: mysqli_query(): Error reading result set's header in %s on line %d
+[002] [%d] %s
+done!

ext/mysqli/tests/mysqli_mysqlnd_read_timeout_long.phpt

@@ -0,0 +1,37 @@
+--TEST--
+mysqlnd.net_read_timeout > default_socket_timeout
+--SKIPIF--
+<?php
+require_once('skipif.inc');
+require_once('skipifconnectfailure.inc');
+require_once('connect.inc');
+?>
+--INI--
+default_socket_timeout=1
+mysqlnd.net_read_timeout=12
+max_execution_time=12
+--FILE--
+<?php
+	set_time_limit(12);
+	include ("connect.inc");
+
+	if (!$link = mysqli_connect($host, $user, $passwd, $db, $port, $socket)) {
+		printf("[001] Connect failed, [%d] %s\n", mysqli_connect_errno(), mysqli_connect_error());
+	}
+
+	if (!$res = mysqli_query($link, "SELECT SLEEP(6)"))
+		printf("[002] [%d] %s\n",  mysqli_errno($link), mysqli_error($link));
+
+	var_dump($res->fetch_assoc());
+
+	mysqli_free_result($res);
+	mysqli_close($link);
+
+	print "done!";
+?>
+--EXPECTF--
+array(1) {
+  [%u|b%"SLEEP(6)"]=>
+  %unicode|string%(1) "0"
+}
+done!

ext/mysqli/tests/mysqli_mysqlnd_read_timeout_zero.phpt

@@ -0,0 +1,36 @@
+--TEST--
+mysqlnd.net_read_timeout = 0
+--SKIPIF--
+<?php
+require_once('skipif.inc');
+require_once('skipifconnectfailure.inc');
+require_once('connect.inc');
+?>
+--INI--
+default_socket_timeout=10
+max_execution_time=10
+mysqlnd.net_read_timeout=0
+--FILE--
+<?php
+	include ("connect.inc");
+
+	if (!$link = mysqli_connect($host, $user, $passwd, $db, $port, $socket)) {
+		printf("[001] Connect failed, [%d] %s\n", mysqli_connect_errno(), mysqli_connect_error());
+	}
+
+	if (!$res = mysqli_query($link, "SELECT SLEEP(2)"))
+		printf("[002] [%d] %s\n",  mysqli_errno($link), mysqli_error($link));
+
+	var_dump($res->fetch_assoc());
+
+	mysqli_free_result($res);
+	mysqli_close($link);
+
+	print "done!";
+?>
+--EXPECTF--
+array(1) {
+  [%u|b%"SLEEP(2)"]=>
+  %unicode|string%(1) "0"
+}
+done!

ext/mysqlnd/mysqlnd.c

@@ -627,6 +627,10 @@ PHPAPI MYSQLND *mysqlnd_connect(MYSQLND *conn,
 		mnd_efree(hashed_details);
 	}
 
+	if (!conn->options.timeout_read) {
+		/* should always happen because read_timeout cannot be set via API */
+		conn->options.timeout_read = (unsigned int) MYSQLND_G(net_read_timeout);
+	}
 	if (conn->options.timeout_read)
 	{
 		tv.tv_sec = conn->options.timeout_read;

ext/mysqlnd/mysqlnd.h

@@ -374,6 +374,7 @@ ZEND_BEGIN_MODULE_GLOBALS(mysqlnd)
 #ifdef MYSQLND_THREADED
 	THREAD_T		thread_id;
 #endif
+	long			net_read_timeout;
 ZEND_END_MODULE_GLOBALS(mysqlnd)
 
 ZEND_EXTERN_MODULE_GLOBALS(mysqlnd);

ext/mysqlnd/php_mysqlnd.c

@@ -136,6 +136,7 @@ static PHP_GINIT_FUNCTION(mysqlnd)
 	mysqlnd_globals->dbg = NULL;	/* The DBG object*/
 	mysqlnd_globals->net_cmd_buffer_size = 2048;
 	mysqlnd_globals->net_read_buffer_size = 32768;
+	mysqlnd_globals->net_read_timeout = 31536000;
 	mysqlnd_globals->log_mask = 0;
 }
 /* }}} */
@@ -149,6 +150,7 @@ PHP_INI_BEGIN()
 	STD_PHP_INI_ENTRY("mysqlnd.debug",					NULL, 	PHP_INI_SYSTEM, OnUpdateString,	debug, zend_mysqlnd_globals, mysqlnd_globals)
 	STD_PHP_INI_ENTRY("mysqlnd.net_cmd_buffer_size",	"2048",	PHP_INI_ALL,	OnUpdateLong,	net_cmd_buffer_size,	zend_mysqlnd_globals,		mysqlnd_globals)
 	STD_PHP_INI_ENTRY("mysqlnd.net_read_buffer_size",	"32768",PHP_INI_ALL,	OnUpdateLong,	net_read_buffer_size,	zend_mysqlnd_globals,		mysqlnd_globals)
+	STD_PHP_INI_ENTRY("mysqlnd.net_read_timeout",		"31536000", PHP_INI_SYSTEM, OnUpdateLong, net_read_timeout, zend_mysqlnd_globals, mysqlnd_globals)
 	STD_PHP_INI_ENTRY("mysqlnd.log_mask",				"0", 	PHP_INI_ALL,	OnUpdateLong,	log_mask, zend_mysqlnd_globals, mysqlnd_globals)
 PHP_INI_END()
 /* }}} */