PHP PDO SQL - update inner join query freezes during execution - php

Question

I need to run a daily PHP script that downloads a data file and executes a bunch of SQL Queries in sequence to import and optimize the data.
I'm having a problem executing one of my queries within PHP which appears to freeze the mysqld process on my server. Oddly, running the same query does not case a similar problem when run from the Sequel Pro Database client program (Mac).
The query is running an update on a large table with over a million rows. Here is the stored procedure I'm using:
DELIMITER ;;
CREATE PROCEDURE spSetTripIdInStopTimes()
BEGIN
-- SET META_TRIP_ID IN IMPORT_STOP_TIMES
UPDATE import_stop_times
INNER JOIN ref_trips ON
(
import_stop_times.trip_id = ref_trips.trip_id
AND import_stop_times.meta_agency_id =ref_trips.meta_agency_id
)
SET import_stop_times.meta_trip_id = ref_trips.meta_trip_id;
END;;
DELIMITER ;
When the procedure is called with
CALL spSetTripIdInStopTimes;
inside Sequel Pro, the result is 1241483 rows affected and the time taken is around 90 seconds.
With PHP PDO I run the same command with
$result = $database->runExecQuery("CALL spSetTripIdInStopTimes");
However, it gets stuck on this query for over 24 hrs and still has not completed. When I cancel the PHP script I can see that the mysqld process is still taking %99.5 CPU. At this point I restart SQL with 'sudo service mysql restart'.
I also tried using PHP's mysqli, but the freezing also occurs with this method.
$mysqli->query("CALL spSetTripIdInStopTimes")
Would anyone be able to reason why this is happening or suggest another method?
Thank you in advance.
Note: I also tried using the older mysql on PHP, but the version I'm using (5.5.9-1ubuntu4.14) tells me the command is deprecated and stops the script.
[UPDATE]
I've also tried running the stored procedure directly on the command line:
mysql --user=[username] --password=[password] --execute="call spSetTripIdInStopTimes()" [tablename]
which worked.
So I tried running the same command with PHP's exec() function:
exec("mysql --user=[username] --password=[password] --execute=\"call spSetTripIdInStopTimes()\" [table name]");
Unfortunately, it stills hangs. I'm starting to wonder if this is due to the limitation or overhead of PHP.
[UPDATE 2]
Here is the array of PHP PDO connection options I use:
array(
PDO::ATTR_ERRMODE => PDO::ERRMODE_EXCEPTION,
// Allow file reading, need following settings to import data from txt files
PDO::MYSQL_ATTR_LOCAL_INFILE => true,
PDO::MYSQL_ATTR_USE_BUFFERED_QUERY => true,
PDO::ATTR_EMULATE_PREPARES => true)
[UPDATE 3]
I'm using a custom database object, so I'll show the function for $database->runExecQuery() for clarification:
function runExecQuery($queryString)
{
$db = $this-> getConnection(); // Connect to database
try{
return array(
"success"=> true,
"data"=>$db->exec($queryString)
);
}
catch (PDOException $ex)
{
return array(
"success"=> false,
"errMessage"=> "ERROR[{$ex->getCode()}]".($this-> Debug ? "{$ex}" : "")
);
}
}
The variable $db is the connection variable that is initialized as follows:
// Create address string
$db_address =
"mysql:host={$settings['db_hostname']};".
"dbname={$settings['db_name']};".
"charset={$settings['db_charset']}";
// Create connection to database
$db = new PDO($db_address, $settings['db_user'], $settings['db_pw'], $options);
where $options is the array from [Update 2].
[Update 4]
Mihai's suggestion of changing PDO::MYSQL_ATTR_USE_BUFFERED_QUERY => false had some promising results as query appeared to finish. However, after more testing I found that the PHP script will sometimes still hang on the Query about 50% of the time it is run. This is true even with the same set of data in the SQL tables.