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I have a third party app and I would like to see how it communicates with the server. Why kind of software/server I am supposed to run to log all possible connections attempts to all possible ports? (let's assume, that it could be https connections, telnet, socket opening etc.)

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Wireshark, tshark, simple tcpdump,smokeping, iPerf. If you need a graphical representation use Cacti and RRDtool together.

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