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I need to track Jitter and Packet Loss over a MPLS line. What's the most accurate way to capture this information without interfering with the data being sent back and forth?

Is SmokePing the best tool for the job or is there something better?

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Depending how much detail you want a frequently measured MOS score may well fulfill your requirement MOS

The link given above will suggest some tools but if you have any devices that manage VoIP (intelligent switches, routers or a VoIP PBX) then that could also measure the MOS score for you

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I've found the VOIP space to be well versed in what causes poor voice quality. MOS is interesting. The neatest tool is telchemy.com/vqmonep.html given their use of a Markov Model with the various inputs. –  Noah Campbell Jun 9 '09 at 21:53
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Hmmm... hadn't heard of Smokeping. I use something pretty similar to it (almost identical), though looks like MTR has more field categories for Packet delivery and Jitter statistics.

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MTR is a great tool, for sure. –  Noah Campbell Jun 8 '09 at 23:14
    
Looks like The Matrix –  Mark Henderson Jan 14 '10 at 1:28
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Smokeping isn't bad, it is great to have running 24/7.

For running more detailed tests you can run iperf in udp mode with a low rate limit, that gives great stats for jitter and packet loss.

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