Nginx – FastCGI sent in stderr: “Primary script unknown” while reading response header from upstream

The error message “primary script unknown” is almost always related to a wrongly set SCRIPT_FILENAME in the nginx fastcgi_param directive (or incorrect permissions, see other answers).

You’re using an if in the configuration you posted first. Well it should be well known by now that if is evil and often produces problems.

Setting the root directive within a location block is bad practice, of course it works.

You could try something like the following:

server {
    location / {
        location ~* \.php$ {
            include fastcgi_params;
            fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
            fastcgi_pass 127.0.0.1:9000;
            try_files $uri @yii =404;
        }
    }
    location @yii {
        fastcgi_param SCRIPT_FILENAME $document_root$yii_bootstrap;
    }
}

Please note that the above configuration is untested. You should execute nginx -t before applying it to check for problems that nginx can detect right away.

Using try_files $uri =404; first!

location ~ \.php$ {
        try_files  $uri =404;
        fastcgi_split_path_info ^(.+\.php)(/.+)$;
        fastcgi_pass unix:/var/run/php5-fpm.sock;
        fastcgi_index index.php;
        include fastcgi_params;
}

Thanks to http://nginxlibrary.com/resolving-no-input-file-specified-error/