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Is it possible to use MTR over TCP? If not is there an alternative? I have done some research and I am not finding any way to do such a thing, so I'm wondering if anyone has had any experience with doing such a thing. If there really is no such thing what is the best way to do an extended test with very rapid ICMP requests to a MySQL server from a network perspective so we can troubleshoot a very quick packet loss issue through the network.

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MTR can be quite effective for this kind of trouble shooting. Try leaving it running with an interval of 15 seconds or 60 seconds. The statistics will give you information on which routers or segments may be causing problems. With the recent trend to use of level 2 routers, these will be invisible to MTR (and other tools).

Many TCP stacks have counters available which can be used to identify problems. Retransmitted and out of order packets may be indications of problems, especially if the percentage is out of normal.

If you are sending large blocks of data, then TCP windowing can cause problems. Check to see if you may be experiencing Bufferbloat issues.

There are tools like tcptraceroute which can do similar tracing to that provided by MTR over TCP, This can work around restrictions on ICMP echo packets.

Tools like Munin, Nagios, or Icinga can be used to monitor your network and database server on an ongoing basis. They can also send alerts if problems are identified.

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+1 for Munin, looks good. –  Matthew Salsamendi Aug 25 '13 at 1:15

Have you considered using nping? You should be able to generate and send packets quite rapidly. If you're trying to identify periodic packet loss or latency you could try a tool like smokeping. I've had excellent results using smokeping for trying to correlate network events over time - especially for wireless point-to-point links. There's no MySQL probe but smokeping is modular so you could write your own if you so desired.

These tools, along with Wireshark, have been very useful in eliminating Layer-3/4 issues from the equation when troubleshooting.

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