nginx/1.4.6 (Ubuntu) server throwing 404 on all sites except just after reboot

@EpicCDN cheers but the issue had been resolved now (see solution below), thank you so much for your help!

Sorry I just read your reply, but www.conf is incomplete, please paste that complete as is the most important part here.

Sure, here is my /etc/php5/fpm/pool.d/www.conf:

; Start a new pool named 'www'.
; the variable $pool can we used in any directive and will be replaced by the
; pool name ('www' here)
[www]

; Unix user/group of processes
; Note: The user is mandatory. If the group is not set, the default user's group
;       will be used.
user = www-data
group = www-data

; The address on which to accept FastCGI requests.
; Valid syntaxes are:
;   'ip.add.re.ss:port'    - to listen on a TCP socket to a specific address on
;                            a specific port;
;   'port'                 - to listen on a TCP socket to all addresses on a
;                            specific port;
;   '/path/to/unix/socket' - to listen on a unix socket.
; Note: This value is mandatory.
listen = /var/run/php5-fpm.sock

; Set listen(2) backlog.
; Default Value: 65535 (-1 on FreeBSD and OpenBSD)
;listen.backlog = 65535

; Set permissions for unix socket, if one is used. In Linux, read/write
; permissions must be set in order to allow connections from a web server. Many
; BSD-derived systems allow connections regardless of permissions.
; Default Values: user and group are set as the running user
;                 mode is set to 0660
listen.owner = www-data
listen.group = www-data
listen.mode = 0660
[...]

Here is a site:

server {
    # URL: Correct way to redirect URL's
    server_name www.simmalugnt.se;
    rewrite ^/(.*)$ http://simmalugnt.se/$1 permanent;
}
server {
    server_name simmalugnt.se new.simmalugnt.se;
    root /var/www/simmalugnt;
    access_log /var/log/nginx/www.simmalugnt.se.access.log;
    error_log /var/log/nginx/www.simmalugnt.se.error.log;
    include global/common.conf;
    include global/wordpress.conf;
}

Here are the included configfiles:

# Global configuration file.
# ESSENTIAL : Configure Nginx Listening Port
listen 80;
# ESSENTIAL : Default file to serve. If the first file isn't found,
index index.php index.html index.htm;
# ESSENTIAL : no favicon logs
location = /favicon.ico {
    log_not_found off;
    access_log off;
}
# ESSENTIAL : robots.txt
location = /robots.txt {
    allow all;
    log_not_found off;
    access_log off;
}
# ESSENTIAL : Configure 404 Pages
error_page 404 /404.html;
# ESSENTIAL : Configure 50x Pages
error_page 500 502 503 504 /50x.html;
    location = /50x.html {
        root /usr/share/nginx/www;
    }
# SECURITY : Deny all attempts to access hidden files .abcde
location ~ /\. {
    deny all;
}
# PERFORMANCE : Set expires headers for static files and turn off logging.
location ~* ^.+\.(js|css|swf|xml|txt|ogg|ogv|svg|svgz|eot|otf|woff|mp4|ttf|rss|atom|jpg|jpeg|gif|png|ico|zip|tgz|gz|rar|bz2|doc|xls|exe|ppt|tar|mid|midi|wav|bmp|rtf)$ {
    access_log off; log_not_found off; expires 30d;
}

# WORDPRESS : Rewrite rules, sends everything through index.php and keeps the appended query string intact
location / {
    try_files $uri $uri/ /index.php?q=$uri&$args;
}

# SECURITY : Deny all attempts to access PHP Files in the uploads directory
location ~* /(?:uploads|files)/.*\.php$ {
    deny all;
}
# REQUIREMENTS : Enable PHP Support
location ~ \.php$ {
    # SECURITY : Zero day Exploit Protection
    try_files $uri =404;
    # ENABLE : Enable PHP, listen fpm sock
    fastcgi_split_path_info ^(.+\.php)(/.+)$;
    fastcgi_pass unix:/var/run/php5-fpm.sock;
    fastcgi_index index.php;
    include fastcgi_params;
}
# PLUGINS : Enable Rewrite Rules for Yoast SEO SiteMap
rewrite ^/sitemap_index\.xml$ /index.php?sitemap=1 last;
rewrite ^/([^/]+?)-sitemap([0-9]+)?\.xml$ /index.php?sitemap=$1&sitemap_n=$2 last;

#Yeah! you did it.

I’m a bit of a novice at this but I think I’m using just one pool for all sites, but htop shows no big server load…

Yeah, your php-fpm is failing so you need to find out why, ie is the php running out of memory? or there is some other issue, probably the first one.

can you copy/paste your nginx (one of the sites or two of them should be better) and your php-fpm www.conf?

Also do you have a single pool (php-fpm) for all your sites or use multiple pools one for each site?

Hi @EpicCDN thanks for your reply, php5-fpm is running and I’m running cloudflare on all sites.

I’m getting these errors in /var/log/nginx:

2015/07/28 19:53:35 [error] 984#0: *858 connect() to unix:/var/run/php5-fpm.sock failed (11: Resource temporarily unavailable) while connecting to upstream, client: 173.245.56.221, server: simmalugnt.se, request: "POST /wp-login.php HTTP/1.1", upstream: "fastcgi://unix:/var/run/php5-fpm.sock:", host: "simmalugnt.se"
2015/07/28 19:53:35 [error] 984#0: *858 open() "/usr/share/nginx/www/50x.html" failed (2: No such file or directory), client: 173.245.56.221, server: simmalugnt.se, request: "POST /wp-login.php HTTP/1.1", upstream: "fastcgi://unix:/var/run/php5-fpm.sock", host: "simmalugnt.se"

and

2015/07/28 20:05:01 [crit] 9630#0: *101 connect() to unix:/var/run/php5-fpm.sock failed (2: No such file or directory) while connecting to upstream, client: 141.101.99.233, server: simmalugnt.se, request: "GET /favicon.ico HTTP/1.1", upstream: "fastcgi://unix:/var/run/php5-fpm.sock:", host: "simmalugnt.se", referrer: "http://simmalugnt.se/"

Is your php-fpm runnig? check service php-fpm status for it.

Sounds like your php is not handling well all the requests. Also try looking into a caching solution like Varnish + Cloudflare