The command file you provided is perfectly valid. As you are reading from terminal, the read speed is only 10Bps, meaning reading just 5B will take 0.5 usecs which is 500 000 usecs! I am assuming you are running the verbose output of the sample solution, which causes it to give up at around 100 000usecs. Run the non-verbose version and you will get the correct measurement of 500283 0.