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Gazebo is built against the version of protoc released to the ubuntu repos. On 16.04 that version is 2.6.1.

There is no guarantee it will work using the newer protobuf version, but you can try building gazebo from source following this tutorial:

The cartographer instructions install protobuf system wide using the script here: . If building gazebo from source doesn't work then I recommend opening an issue on the cartographer repo asking how to build and run it without installing proto3 system wide.