Timeout waiting for output from cgi script error

Hello, I’m getting 504 Gateway Error when I’m loading some pages in my website. It doesn’t occur every time I load a page. I looked through the server error log and I found the error:
“Timeout waiting for output from CGI script”
The file content is:
define(‘WP_USE_THEMES’, true);
require( dirname( __FILE__ ) . ‘/wp-blog-header.php’ );
What can I do to prevent this error?

Additional information:
it’s on multisite, there are lots of plugins but the client wants them all, I increased the PHP memory but the error keeps showing.