mariaDB bulk update very slow - symfony

Question

I need to update 290 000 lines from a csv file in my database.
I created a loop on each line to do an update, the quesry looks like this :
UPDATE lines_table
INNER JOIN account ON lines_table.account_id = account.id
SET account.is_updated = 1
WHERE account.is_updated = 1
AND lines_table.user_id=XXXXX
AND lines_table.code = 'YY';
AND account.compte 'ZZZZZZZ';
the php loop looks like this :
$conn = $this->em->getConnection();
while (([$key, $account, $user] = fgetcsv($handle, 1000, ';')) !== false) {
$stmt = $conn->prepare($sql);
$stmt->execute();
}
On my computer (wamp + symfony3 + SSD + mariaDB), it updates 85 lines per second.
When i execute this loop in my test environment (linux + symfony3 + 48 HDD 10k rpm, mariaDB), it updates only 4 lines per second.
Is there a config that could be different and make this loop slower ?