It looks like an application specific issue and my server(Linode) is using an excessive amount of I/O.
(config: Ubuntu 12.0.4+Nginx+MariaDB+PHP-FPM+APC+iONCube+igBinary)
I'm trying to figure out where is right direction but it can be a very complex issue to debug. However my I/O will certainly cause a problem for your system.
Total DISK READ: 0.00 B/s | Total DISK WRITE: 132.51 M/s
TID PRIO USER DISK READ DISK WRITE SWAPIN IO> COMMAND
26474 be/4 www-data 0.00 B/s 91.29 M/s 0.00 % 0.31 % php-fpm: pool www
26255 be/4 www-data 0.00 B/s 72.49 M/s 0.00 % 0.82 % php-fpm: pool www
The problem seems to be specifically with PHP based on your error logs:
: 66.249.76.233, server: myprestashop.com, request: "POST /module/mailalerts/actions?process=check HTTP/1.1", upstream: "fastcgi://unix:/tmp/php5-fpm.sock:", host: "myprestashop.com", referrer: "https://myprestashop.com/farmacia-y-medicinas/15038-garamicina-frasco-ampula-5-80mg-antibiotico-7501050610537.html"
2014/05/03 04:27:32 [crit] 13627#0: *25936 connect() to unix:/tmp/php5-fpm.sock failed (2: No such file or directory) while connecting to upstream, client: 66.249.76.233, server: myprestashop.com, request: "GET /sistema-nervioso/11634-rapix-capsulas-10-10mg-7501314703821.html HTTP/1.1", upstream: "fastcgi://unix:/tmp/php5-fpm.sock:", host: "myprestashop.com"
I restarted PHP:
root@luna:/etc/nginx/sites-enabled# killall php5-fpm root@luna:/etc/nginx/sites-enabled# /etc/init.d/php5-fpm start
However after that I get new messages in the error log:
2014/05/03 04:31:43 [error] 13627#0: *26155 FastCGI sent in stderr: "PHP message: PHP Warning: array_shift() expects parameter 1 to be array, boolean given in /sites/myprestashop.com/public/modules/productcomments/ProductComment.php on line 140
PHP message: PHP Warning: array_shift() expects parameter 1 to be array, boolean given in /sites/myprestashop.com/public/modules/productcomments/ProductComment.php on line 140" while reading response header from upstream, client: 65.55.55.231, server: myprestashop.com, request: "GET /higiene-personal/4519-koleston-cast-osc-viol-int-366-7501007455174.html HTTP/1.1", upstream: "fastcgi://unix:/tmp/php5-fpm.sock:", host: "myprestashop.com"
2014/05/03 04:32:06 [error] 13626#0: *26195 FastCGI sent in stderr: "PHP message: PHP Notice: Undefined index: product_mode in /sites/myprestashop.com/public/cache/smarty/compile/b0/9a/32/b09a3295da69c6626cf2789ed62cd44f2fbed7f6.file.product-list.tpl.php on line 36
PHP message: PHP Notice: Undefined index: product_mode in /sites/myprestashop.com/public/cache/smarty/compile/b0/9a/32/b09a3295da69c6626cf2789ed62cd44f2fbed7f6.file.product-list.tpl.php on line 146
PHP message: PHP Notice: Undefined index: product_mode in /sites/myprestashop.com/public/cache/smarty/compile/b0/9a/32/b09a3295da69c6626cf2789ed62cd44f2fbed7f6.file.product-list.tpl.php on line 146" while reading response header from upstream, client: 66.249.76.233, server: myprestashop.com, request: "GET /26-cuidado-del-cabello?amp%252525252525253Bselected_filters=%3Fcontroller%3D404&p=14 HTTP/1.1", upstream: "fastcgi://unix:/tmp/php5-fpm.sock:", host: "myprestashop.com"
It looks like the code itself has issues that will need to be resolved.
EDIT
there are 2 APC instance, one in modes-available and the other one in conf.d
also php-fpm log
[03-May-2014 11:38:11] ERROR: An another FPM instance seems to already listen on /tmp/php5-fpm.sock
[03-May-2014 11:38:11] ERROR: FPM initialization failed
may be the solution here is to remove php+igbinary+ioncube