I created a basic TCP server that reads incoming binary data in protocol buffer format, and writes a binary msg as response. I would like to benchmark the the roundtrip time
You can always stick a shell loop around a program like iperf. Also, assuming iperf can read from a file (thus stdin) or programs like ttcp, could allow a shell loop catting a file N times into iperf/ttcp.
If you want a program which sends a file, waits for your binary response, and then sends another copy of the file, you probably are going to need to code that yourself.