error loading shared libraries: libaltera_s5_ref_mmd.so: cannot open shared obj

The missing library file is exactly in the path that you have commented out in your environmental variables (/eda/intel/16.1/hld/board/s5_ref/linux64/lib). Remove the# sign and close your terminal and open a new one to load the new settings. Also make sure the path is correct; some of your paths are pointing to "/altera/quartus_16.1_standard", while others are pointing to "/intel/16.1".

Also your AOCL_BOARD_PACKAGE_ROOT is pointing to the Terasic BSP, while your LD_LIBRARY_PATH is pointing to Altera's reference S5 board. This is not correct; both should point to the same board. You should probably also add --board=XXXX to your aoc command line to make sure you are targeting the correct board for emulation.