First off, I made some changes to your system, I increased the
APC.shm.size to 128 This will allow more data to be cached by apc, in
theory itâll store more data.
I also made some changes to the vhost.conf file for the shop site,
historically disabling open_basedir allows magento to work slightly better.
I also made some changes to your mysql database server.
I increased the table cache and enabled the slow query log, this will
allow us to nail down if the problem is database related or something
else. I also decreased query_cache_size & key_buffer_size as mysql was
using over 95% of the systemâs memory, this is causing httpd and other
processes to use a lot of swap space, not good.
Mysql is logging all queries that run over 2 seconds to
Check this out every now and then, its pretty awesome for knocking out
database related performance issues.
I also noticed that your iowait was pretty high, hovering around 5-10%
This is very bad as your system is having to wait on the disk before it
can serve data. This will slow down website and drive up load times.
This was probably due to your mysql misconfiguration.
After those changes were made to my managed server, Magento started to
perform great with response times of 0.8-2 seconds.