Could you please post a "strange error about std c++ 2011" you obtained on ubuntu 16.04 ?
For example do
./build-unix 2>&1 |tee build_it.log
and send me build_it.log file ?
On Windows simutron currently uses \\\\.\\CNCA0 ..
\\\\.\\CNCB0 virtual port pair.
com0com installer should create it by default. Try look com0com documentation for how to set and use those ports.
When you open 3-axes_CNC_machine.simu example file, it already contains serial connection component.
Dragging avr serial connection on to the atmega128 would create another extra one.
Near to the atmega128 you should see a box with "uart0" inside - it's it. The label on top of it should show the virtual com device name, where your host program should connect. Try double click "uart0" box - this should start simple terminal program supplied.
On Linux I'd advise to download and build latest trunk sources .
For example do:
svn checkout https://svn.code.sf.net/p/simutron/code/trunk
Note: it requires Qt5 now.
Look updated README.txt in the simutron-code dir for build instructions.
Build tested on latest Fedora Linux 25 release, x86_64