Zabbix calculates data from empty items

If you define a graph (as opposed to just clicking on an item and seeing the adhoc graph) you can specify that an item should be shown as its MAX value for the period represented by each pixel.

But if you are storing deltas (count per second) for things like traffic counters, printer page counters, etc., then you can also just use AVG and then do the following:

1. When you want to know the total for a period of time, graph the item over that period using an adhoc graph
   • Look at the average over the period (printed on the graph), and then multiply by the number of seconds in the period

I think that the bottleneck is the disc. Here are my reasons for this:

You have a pretty busy web server. Zabbix is slow, I suspect to be reads from the disk (can be from the network too).

Run again the strace, and find the file descriptor in Zabbix

Then find if the file descriptor is a file or a socket:

ls -l /prod/<PID_of_straced_process>/fd/<FD_from_strace>

EDIT1:
You should not change the TIME_WAIT timeouts. The problem with small HTTP keep-alive, or with no HTTP keep-alive is that you increase the latency and bandwidth. Instead you should increase a little bit the HTTP keep-alive and install/enable SPDY.

EDIT2: Use dstat -ta 10 and compare the first line with the rest. The first line is the average since boot. Next lines are 10 seconds average (the last parameter).

EDIT3: Check if you do not have packets lost, use something like smokeping to monitor the server and the website from outside your network. You have a significant number of connections in CLOSING, FIN_WAIT1, FIN_WAIT2, SYN_RECV, LAST_ACK. I think your network is congested or you have a lot of short lived connections (confirmed by the high TIME_WAIT/ESTABILISHED ratio). See: http://en.wikipedia.org/wiki/Transmission_Control_Protocol#Protocol_operation