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    Running 1000 bytes through the serial port will take quite some time: the bytes are sent one after the other. Your Arduino should just process each byte as it receives it. Commented Jun 15, 2016 at 14:34
  • Do you have any code yet? Commented Jun 15, 2016 at 16:22
  • @EdgarBonet The bytes are commands to be executed by the machine. So processing might take long Commented Jun 16, 2016 at 8:08
  • @DaveX Do you mean the code for serial communication? Commented Jun 16, 2016 at 8:08
  • @dark32 I mean have you got any semi-working code to show what issue you are having. From the Q, it seems you can process about 40 bytes per few minutes, and you seek to buffer 2-25 commands worth of data within the Arduino. There's code in 3D printers that processes megabytes worth of serial commands on-the-fly at command-execution speed by using buffering and handshaking on the sending end. They rely on a state machine to assemble a command and its parameters from a serial stream, and don't pull data out of the the buffer until they are ready for it. Commented Jun 16, 2016 at 15:40