There are several ways in which you can set the timeout for php-fpm. In /etc/php5/fpm/pool.d/www.conf I added this line:

request_terminate_timeout = 180

Also, in /etc/nginx/sites-available/default I added the following line to the location block of the server in question:

fastcgi_read_timeout 180;

The entire location block looks like this:

location ~ \.php$ {
    fastcgi_pass unix:/var/run/php5-fpm.sock;
    fastcgi_index index.php;
    fastcgi_param   SCRIPT_FILENAME $document_root$fastcgi_script_name;
    fastcgi_read_timeout 180;
    include fastcgi_params;
} 

Now just restart php-fpm and nginx and there should be no more timeouts for requests taking less than 180 seconds.

Script will not stop executing until they reach php timeout itself.

The 504 error are generated on the gateway / proxy itself, it's not coming from the php process.

It's because this, if you have an Apache with Apache-mod-php you will never receive this error, because there's not a proxy.

Extending the explanation, think as follows:

You have a PHP process. The PHP process can be a PHP-FPM, PHP-CGI, or Apache-MOD-PHP. On this process, you have a timeout (configured on php.ini or with a ini_set).

The PHP proxy gives a response in the allowed time (aka: if you have a set_time_limit(600), your PHP process can be running up to 10 minutes).

Without relation on this sentence, you can have another process waiting for these response: That's the case of a apache (configured to contact to php by cgi or fpm), a nginx, a lighthttpd, and others. That's not the case of a apache configured by apache-mod-php. This second process, have a new timeout (proxy_timeout), configured on the vhost / general server app config. That's the time the program will wait for a response from PHP processing engine.

The last sentence, can be repeated on each proxy / gateway.

Think on this scenario:

haproxy (Timeout 1) --> Nginx (Frontend / cache) (Timeout 2) --> Apache (Timeout 3) -> PHP-FPM (PHP Timeout / set_time_limit).

And a very simple scenario:

Apache (with apache-mod-php) (PHP Timeout / set_time_limit).

Each timeout appearance (except the PHP Timeout itself) is a probable origin of a 504 HTTP gateway timeout error.

You can increase maximum execution time in php.

ini_set('max_execution_time', 300); //300 seconds = 5 minutes

Increasing the max_execution_time limit in php.ini

max_execution_time=600

Increase the default timeout value in the httpd.conf

Timeout 600

At the beginning of the script, start displaying information, for example

print " ";

continue to send data periodically to maintain the connection

I encountered the same problem and I used ini_set('default_socket_timeout', 6000); to fix it. http://php.net/manual/en/filesystem.configuration.php#ini.default-socket-timeout