I have set up a local testing VM with Ubuntu Server 12.04 LTS and the LEMP stack. It's kind of an unconventional setup because instead of having all my PHP scripts on the local machine, I've mounted an NTFS share as the document root because I do my development on Windows. I had everything working perfectly up until this morning, now I keep getting a dreaded 'File not found.' error.

I am almost certain this must be somehow permission related, because if I copy my site over to /var/www, nginx and php-fpm have no problems serving my PHP scripts. What I can't figure out is why all of a sudden (after a reboot of the server), no PHP files will be served but instead just the 'File not found.' error. Static files work fine, so I think it's PHP that is causing the headache.

Both nginx and php-fpm are configured to run as the user www-data:

root@ubuntu-server:~# ps aux | grep 'nginx\|php-fpm'
root      1095  0.0  0.0   5816   792 ?        Ss   11:11   0:00 nginx: master process /opt/nginx/sbin/nginx -c /etc/nginx/nginx.conf
www-data  1096  0.0  0.1   6016  1172 ?        S    11:11   0:00 nginx: worker process
www-data  1098  0.0  0.1   6016  1172 ?        S    11:11   0:00 nginx: worker process
root      1130  0.0  0.4 175560  4212 ?        Ss   11:11   0:00 php-fpm: master process (/etc/php5/php-fpm.conf)
www-data  1131  0.0  0.3 175560  3216 ?        S    11:11   0:00 php-fpm: pool www
www-data  1132  0.0  0.3 175560  3216 ?        S    11:11   0:00 php-fpm: pool www
www-data  1133  0.0  0.3 175560  3216 ?        S    11:11   0:00 php-fpm: pool www
root      1686  0.0  0.0   4368   816 pts/1    S+   11:11   0:00 grep --color=auto nginx\|php-fpm

I have mounted the NTFS share at /mnt/webfiles by editing /etc/fstab and adding the following line:

//192.168.0.199/c$/Websites/ /mnt/webfiles cifs username=Jordan,password=mypasswordhere,gid=33,uid=33 0 0

Where gid 33 is the www-data group and uid 33 is the user www-data. If I list the contents of one of my sites you can in fact see that they belong to the user www-data:

root@ubuntu-server:~# ls -l /mnt/webfiles/nTv5-2.0
total 8
drwxr-xr-x 0 www-data www-data    0 Jun  6 19:12 app
drwxr-xr-x 0 www-data www-data    0 Aug 22 19:00 assets
-rwxr-xr-x 0 www-data www-data 1150 Jan  4  2012 favicon.ico
-rwxr-xr-x 0 www-data www-data 1412 Dec 28  2011 index.php
drwxr-xr-x 0 www-data www-data    0 Jun  3 16:44 lib
drwxr-xr-x 0 www-data www-data    0 Jan  3  2012 plugins
drwxr-xr-x 0 www-data www-data    0 Jun  3 16:45 vendors

If I switch to the www-data user, I have no problem creating a new file on the share:

root@ubuntu-server:~# su www-data
$ > /mnt/webfiles/test.txt
$ ls -l /mnt/webfiles | grep test\.txt
-rwxr-xr-x 0 www-data www-data 0 Sep  8 11:19 test.txt

There should be no problem reading or writing to the share with php-fpm running as the user www-data.

When I examine the error log of nginx, it's filled with a bunch of lines that look like the following:

2012/09/08 11:22:36 [error] 1096#0: *1 FastCGI sent in stderr: "Primary script unknown" while reading response header from upstream, client: 192.168.0.199, server: , request: "GET / HTTP/1.1", upstream: "fastcgi://unix:/var/run/php5-fpm.sock:", host: "192.168.0.123"
2012/09/08 11:22:39 [error] 1096#0: *1 FastCGI sent in stderr: "Primary script unknown" while reading response header from upstream, client: 192.168.0.199, server: , request: "GET /apc.php HTTP/1.1", upstream: "fastcgi://unix:/var/run/php5-fpm.sock:", host: "192.168.0.123"

It's bizarre that this was working previously and now all of sudden PHP is complaining that it can't "find" the scripts on the share. Does anybody know why this is happening?

EDIT

I tried editing php-fpm.conf and changing chdir to the following:

chdir = /mnt/webfiles

When I try and restart the php-fpm service, I get the error:

Starting php-fpm [08-Sep-2012 14:20:55] ERROR: [pool www] the chdir path '/mnt/webfiles' does not exist or is not a directory

This is a total load of bullshit because this directory DOES exist and is mounted! Any ls commands to list that directory work perfectly. Why the hell can't PHP-FPM see this directory?!

Here are my configuration files for reference:

nginx.conf

user www-data;
worker_processes     2;
error_log  /var/log/nginx/nginx.log info;
pid        /var/run/nginx.pid;

events {
  worker_connections  1024;
  multi_accept on;
}

http {
  include           fastcgi.conf;
  include           mime.types;
  default_type      application/octet-stream;
  set_real_ip_from  127.0.0.1;
  real_ip_header    X-Forwarded-For;

  ## Proxy
  proxy_redirect          off;
  proxy_set_header        Host  $host;
  proxy_set_header        X-Real-IP $remote_addr;
  proxy_set_header        X-Forwarded-For $proxy_add_x_forwarded_for;
  client_max_body_size    32m;
  client_body_buffer_size 128k;
  proxy_connect_timeout   90;
  proxy_send_timeout      90;
  proxy_read_timeout      90;
  proxy_buffers           32 4k;

  ## Compression
  gzip             on;
  gzip_types       text/plain text/css application/x-javascript text/xml application/xml application/xml+rss text/javascript;
  gzip_disable     "MSIE [1-6]\.(?!.*SV1)";

  ### TCP options
  tcp_nodelay         on;
  tcp_nopush          on;
  keepalive_timeout   65;
  sendfile            on;

  include /etc/nginx/sites-enabled/*;

}

my site config

server {

  listen 80;

  access_log  /var/log/nginx/$host.access.log;
  error_log   /var/log/nginx/error.log;

  root    /mnt/webfiles/nTv5-2.0/app/webroot;
  index   index.php;

  ## Block bad bots
  if ($http_user_agent ~* (HTTrack|HTMLParser|libcurl|discobot|Exabot|Casper|kmccrew|plaNETWORK|RPT-HTTPClient)) {
    return 444;
  }

  ## Block certain Referers (case insensitive)
  if ($http_referer ~* (sex|vigra|viagra) ) {
    return 444;
  }

  ## Deny dot files:
  location ~ /\. {
    deny all;
  }

  ## Favicon Not Found
  location = /favicon.ico {
    access_log off;
    log_not_found off;
  }

  ## Robots.txt Not Found
  location = /robots.txt {
    access_log off;
    log_not_found off;
  }

  if (-f $document_root/maintenance.html) {
    rewrite ^(.*)$ /maintenance.html last;
  }

  location ~* \.(?:ico|css|js|gif|jpe?g|png)$ {
    # Some basic cache-control for static files to be sent to the browser
    expires max;
    add_header Pragma public;
    add_header Cache-Control "max-age=2678400, public, must-revalidate";
  }

  location / {
    try_files $uri $uri/ index.php;
    if (-f $request_filename) {
      break;
    }
    rewrite ^(.+)$ /index.php?url=$1 last;
  }

  location ~ \.php$ {
    include /etc/nginx/fastcgi.conf;
    fastcgi_pass unix:/var/run/php5-fpm.sock;
  }

}

php-fpm.conf

;;;;;;;;;;;;;;;;;;;;;
; FPM Configuration ;
;;;;;;;;;;;;;;;;;;;;;

; All relative paths in this configuration file are relative to PHP's install
; prefix (/opt/php5). This prefix can be dynamicaly changed by using the
; '-p' argument from the command line.

; Include one or more files. If glob(3) exists, it is used to include a bunch of
; files from a glob(3) pattern. This directive can be used everywhere in the
; file.
; Relative path can also be used. They will be prefixed by:
;  - the global prefix if it's been set (-p arguement)
;  - /opt/php5 otherwise
;include=etc/fpm.d/*.conf

;;;;;;;;;;;;;;;;;;
; Global Options ;
;;;;;;;;;;;;;;;;;;

[global]
; Pid file
; Note: the default prefix is /opt/php5/var
; Default Value: none
pid = /var/run/php-fpm.pid

; Error log file
; Note: the default prefix is /opt/php5/var
; Default Value: log/php-fpm.log
error_log = /var/log/php5-fpm/php-fpm.log

; Log level
; Possible Values: alert, error, warning, notice, debug
; Default Value: notice
;log_level = notice

; If this number of child processes exit with SIGSEGV or SIGBUS within the time
; interval set by emergency_restart_interval then FPM will restart. A value
; of '0' means 'Off'.
; Default Value: 0
;emergency_restart_threshold = 0

; Interval of time used by emergency_restart_interval to determine when 
; a graceful restart will be initiated.  This can be useful to work around
; accidental corruptions in an accelerator's shared memory.
; Available Units: s(econds), m(inutes), h(ours), or d(ays)
; Default Unit: seconds
; Default Value: 0
;emergency_restart_interval = 0

; Time limit for child processes to wait for a reaction on signals from master.
; Available units: s(econds), m(inutes), h(ours), or d(ays)
; Default Unit: seconds
; Default Value: 0
;process_control_timeout = 0

; Send FPM to background. Set to 'no' to keep FPM in foreground for debugging.
; Default Value: yes
;daemonize = yes

;;;;;;;;;;;;;;;;;;;;
; Pool Definitions ; 
;;;;;;;;;;;;;;;;;;;;

; Multiple pools of child processes may be started with different listening
; ports and different management options.  The name of the pool will be
; used in logs and stats. There is no limitation on the number of pools which
; FPM can handle. Your system will tell you anyway :)

; 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]

; Per pool prefix
; It only applies on the following directives:
; - 'slowlog'
; - 'listen' (unixsocket)
; - 'chroot'
; - 'chdir'
; - 'php_values'
; - 'php_admin_values'
; When not set, the global prefix (or /opt/php5) applies instead.
; Note: This directive can also be relative to the global prefix.
; Default Value: none
;prefix = /path/to/pools/$pool

; 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 = 127.0.0.1:9000
listen = /var/run/php5-fpm.sock

; Set listen(2) backlog. A value of '-1' means unlimited.
; Default Value: 128 (-1 on FreeBSD and OpenBSD)
;listen.backlog = -1

; List of ipv4 addresses of FastCGI clients which are allowed to connect.
; Equivalent to the FCGI_WEB_SERVER_ADDRS environment variable in the original
; PHP FCGI (5.2.2+). Makes sense only with a tcp listening socket. Each address
; must be separated by a comma. If this value is left blank, connections will be
; accepted from any ip address.
; Default Value: any
;listen.allowed_clients = 127.0.0.1

; 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 0666
;listen.owner = www-data
;listen.group = www-data
;listen.mode = 0666

; 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

; Choose how the process manager will control the number of child processes.
; Possible Values:
;   static  - a fixed number (pm.max_children) of child processes;
;   dynamic - the number of child processes are set dynamically based on the
;             following directives:
;             pm.max_children      - the maximum number of children that can
;                                    be alive at the same time.
;             pm.start_servers     - the number of children created on startup.
;             pm.min_spare_servers - the minimum number of children in 'idle'
;                                    state (waiting to process). If the number
;                                    of 'idle' processes is less than this
;                                    number then some children will be created.
;             pm.max_spare_servers - the maximum number of children in 'idle'
;                                    state (waiting to process). If the number
;                                    of 'idle' processes is greater than this
;                                    number then some children will be killed.
; Note: This value is mandatory.
pm = dynamic

; The number of child processes to be created when pm is set to 'static' and the
; maximum number of child processes to be created when pm is set to 'dynamic'.
; This value sets the limit on the number of simultaneous requests that will be
; served. Equivalent to the ApacheMaxClients directive with mpm_prefork.
; Equivalent to the PHP_FCGI_CHILDREN environment variable in the original PHP
; CGI.
; Note: Used when pm is set to either 'static' or 'dynamic'
; Note: This value is mandatory.
pm.max_children = 50

; The number of child processes created on startup.
; Note: Used only when pm is set to 'dynamic'
; Default Value: min_spare_servers + (max_spare_servers - min_spare_servers) / 2
pm.start_servers = 20

; The desired minimum number of idle server processes.
; Note: Used only when pm is set to 'dynamic'
; Note: Mandatory when pm is set to 'dynamic'
pm.min_spare_servers = 5

; The desired maximum number of idle server processes.
; Note: Used only when pm is set to 'dynamic'
; Note: Mandatory when pm is set to 'dynamic'
pm.max_spare_servers = 35

; The number of requests each child process should execute before respawning.
; This can be useful to work around memory leaks in 3rd party libraries. For
; endless request processing specify '0'. Equivalent to PHP_FCGI_MAX_REQUESTS.
; Default Value: 0
pm.max_requests = 500

; The URI to view the FPM status page. If this value is not set, no URI will be
; recognized as a status page. By default, the status page shows the following
; information:
;   accepted conn        - the number of request accepted by the pool;
;   pool                 - the name of the pool;
;   process manager      - static or dynamic;
;   idle processes       - the number of idle processes;
;   active processes     - the number of active processes;
;   total processes      - the number of idle + active processes.
;   max children reached - number of times, the process limit has been reached,
;                          when pm tries to start more children (works only for
;                          pm 'dynamic')
; The values of 'idle processes', 'active processes' and 'total processes' are
; updated each second. The value of 'accepted conn' is updated in real time.
; Example output:
;   accepted conn:        12073
;   pool:                 www
;   process manager:      static
;   idle processes:       35
;   active processes:     65
;   total processes:      100
;   max children reached: 1
; By default the status page output is formatted as text/plain. Passing either
; 'html' or 'json' as a query string will return the corresponding output
; syntax. Example:
;   http://www.foo.bar/status
;   http://www.foo.bar/status?json
;   http://www.foo.bar/status?html
; Note: The value must start with a leading slash (/). The value can be
;       anything, but it may not be a good idea to use the .php extension or it
;       may conflict with a real PHP file.
; Default Value: not set 
pm.status_path = /status

; The ping URI to call the monitoring page of FPM. If this value is not set, no
; URI will be recognized as a ping page. This could be used to test from outside
; that FPM is alive and responding, or to
; - create a graph of FPM availability (rrd or such);
; - remove a server from a group if it is not responding (load balancing);
; - trigger alerts for the operating team (24/7).
; Note: The value must start with a leading slash (/). The value can be
;       anything, but it may not be a good idea to use the .php extension or it
;       may conflict with a real PHP file.
; Default Value: not set
ping.path = /ping

; This directive may be used to customize the response of a ping request. The
; response is formatted as text/plain with a 200 response code.
; Default Value: pong
ping.response = pong

; The timeout for serving a single request after which the worker process will
; be killed. This option should be used when the 'max_execution_time' ini option
; does not stop script execution for some reason. A value of '0' means 'off'.
; Available units: s(econds)(default), m(inutes), h(ours), or d(ays)
; Default Value: 0
;request_terminate_timeout = 0

; The timeout for serving a single request after which a PHP backtrace will be
; dumped to the 'slowlog' file. A value of '0s' means 'off'.
; Available units: s(econds)(default), m(inutes), h(ours), or d(ays)
; Default Value: 0
;request_slowlog_timeout = 0

; The log file for slow requests
; Default Value: not set
; Note: slowlog is mandatory if request_slowlog_timeout is set
;slowlog = log/$pool.log.slow

; Set open file descriptor rlimit.
; Default Value: system defined value
;rlimit_files = 1024

; Set max core size rlimit.
; Possible Values: 'unlimited' or an integer greater or equal to 0
; Default Value: system defined value
;rlimit_core = 0

; Chroot to this directory at the start. This value must be defined as an
; absolute path. When this value is not set, chroot is not used.
; Note: you can prefix with '$prefix' to chroot to the pool prefix or one
; of its subdirectories. If the pool prefix is not set, the global prefix
; will be used instead.
; Note: chrooting is a great security feature and should be used whenever 
;       possible. However, all PHP paths will be relative to the chroot
;       (error_log, sessions.save_path, ...).
; Default Value: not set
;chroot = 

; Chdir to this directory at the start.
; Note: relative path can be used.
; Default Value: current directory or / when chroot
;chdir = /var/www

; Redirect worker stdout and stderr into main error log. If not set, stdout and
; stderr will be redirected to /dev/null according to FastCGI specs.
; Note: on highloaded environement, this can cause some delay in the page
; process time (several ms).
; Default Value: no
;catch_workers_output = yes

; Pass environment variables like LD_LIBRARY_PATH. All $VARIABLEs are taken from
; the current environment.
; Default Value: clean env
;env[HOSTNAME] = $HOSTNAME
;env[PATH] = /usr/local/bin:/usr/bin:/bin
;env[TMP] = /tmp
;env[TMPDIR] = /tmp
;env[TEMP] = /tmp

; Additional php.ini defines, specific to this pool of workers. These settings
; overwrite the values previously defined in the php.ini. The directives are the
; same as the PHP SAPI:
;   php_value/php_flag             - you can set classic ini defines which can
;                                    be overwritten from PHP call 'ini_set'. 
;   php_admin_value/php_admin_flag - these directives won't be overwritten by
;                                     PHP call 'ini_set'
; For php_*flag, valid values are on, off, 1, 0, true, false, yes or no.

; Defining 'extension' will load the corresponding shared extension from
; extension_dir. Defining 'disable_functions' or 'disable_classes' will not
; overwrite previously defined php.ini values, but will append the new value
; instead.

; Note: path INI options can be relative and will be expanded with the prefix
; (pool, global or /opt/php5)

; Default Value: nothing is defined by default except the values in php.ini and
;                specified at startup with the -d argument
;php_admin_value[sendmail_path] = /usr/sbin/sendmail -t -i -f [email protected]
;php_flag[display_errors] = off
;php_admin_value[error_log] = /var/log/fpm-php.www.log
;php_admin_flag[log_errors] = on
;php_admin_value[memory_limit] = 32M

php_admin_value[sendmail_path] = /usr/sbin/sendmail -t -i