Regular slowdown of the server - how to diagnose the problem?

Question

PHP

We have a grocery server on hetzner EX60 Debian-76-wheezy-64

Intel® Core™ i7-920 Quadcore
with Hyper-Threading Technology
48GB DDR3 RAM 2 x 2TB SATA 3Gb/s 7200RPM Hard Drives
(Software-RAID 1)

It runs php-fpm, nginx, mongodb, rabbitmq, redis
The server is under load of about 3k requests per minute.
I paid attention to complaints - for a long time answers come periodically.
Munin does not report anything that may seem strange.
I started profiling, I found that subvisons happen on requests either to Monga or on reading an AMQPLib socket (Monga grabs WriteLock on an insert because of this, other requests get in the queue, RabbitMQ is not clear)
Moreover, this behavior is not constant, but occurs with sufficient
frequency happens for about 30 seconds every 5 -7 minutes.
I have a suspicion that Monga and Rabbit hang not through their own fault, but for some external reason.
Help diagnose and fix the problem.

Answer 1

Throw it out. Fuck. EX60.
This is hellish junk with dead braked SATA-2 class disks.

Answer 2

to begin with, is there something in the crown that runs with such a frequency?

Answer 3

Tuned the core? Maybe a problem with the limit of sockets, open files, connections or ports.