Magento 2 Allowed Memory Size Exhausted – AWS S3 Module Issue

It looks to me based on what you state at the start (run reindex all) that you are currently using the command line shell/index.php to do your reindexing.

In the default configuration of servers, PHP runs two ini files one which deals with command line, and one which deals with your web server. So the .htaccess information would not actually be used.

Depending on your server configuration, there are a few places that the file may exist so if you have a look in

/etc/php

/etc/php5

You will hopefully find a sub directory structure which reveals a cli folder perhaps under conf.d and within that you will have the php.ini file which is used to configure the CLI tool you are using. This file needs to have the value for memory_limit increased.

If you run a phpinfo() from the CLI you may find it will tell you in the output the actual ini file loaded (and of course the information to do with the current values.

Hope that helps.

You can add the following in index.php - make sure the log file path is correct

function shutdownCapture() {
    global $lastQueryString;
    $error = error_get_last();
    if ($error !== null && strpos($error['message'], 'Allowed memory size') !== false) {
      file_put_contents(MAGENTO_ROOT.'/var/log/oom.log', print_r(array($lastQueryString, $_REQUEST, $_SERVER, $error), true), FILE_APPEND);
      mail('info@examplecom', 'Server Memory Error', print_r(array($lastQueryString, $_REQUEST, $_SERVER, $error), true), 'Cc: mycolleague@example.com');
    }
}
register_shutdown_function('shutdownCapture');

and set these variables in the last reported function where the error occurs

+       global $lastQueryString;
+       $lastQueryString = $this->_stmt->queryString;

This excellent description comes from Sonassi

https://www.sonassi.com/blog/capturing-memory-exhaustion-in-magento