Undefined index error upon $em->clear() in Symfony2

Symfony logs all SQL queries in dev environment, so first you need to disable it

// disable logger$em->getConnection()->getConfiguration()->setSQLLogger(null);

You may use event listeners on entities, it may also increase memory usage. You can disable them like so

// remove all listenersforeach ($em->getEventManager()->getListeners() as $event => $listeners) {    foreach ($listeners as $listener) {        $em->getEventManager()->removeEventListener($event, $listener);    }}

Remove unset from your code, there is no need for them, as you clear entity manager every step of your loop.

// save and clear$em->flush();$em->getUnitOfWork()->clear();

Remember that doctrine can optimize your queries, and improve perfomance if you group queries into one flush. So the best practice would be to execute flush once over some parts of your data. For example:

// collect 100 entities and then save themif (($i % 100) == 0) {    $em->flush();    $em->getUnitOfWork()->clear();}

Try to reset the entity manager with:

$this->getContainer()->get('doctrine')->resetEntityManager();

and then:

$em = $this->getContainer()->get('doctrine')->getEntityManager();