I have 8 different system with Arduino Uno boards controlling serial devices though open source software (Micro-manager) and these have been working perfectly for years. I bought a new computer (Mac Mini) running El Capitan this winter and set it up the same as all the other systems. It generally works, but has a problem we can't solve. The software runs LED illuminators for a microscope. The LED's are turned off and on at intervals over many hours by the Arduino. If you run the software in time lapse mode, it fails with an "Arduino Shutter error" each time. When that happens is not reproducible. Sometimes it is after a few minutes and sometimes after many hours, but always the same error, and the error code seems to be a serial port error where the software does not get an answer from the Arduino. I read about the serial port issues with El Capitan in other posts, but those seem to be about getting the Arduino recognized by the computer and that does not appear to be my problem. However, I am thinking that perhaps something else about serial communication is happening with the Arduino. Any suggestions as to how to fix this? I have tried swapping boards, cables and USB ports and none of those matter. It seems to be something with that computer and OS.
I think I fixed the problem. I re-checked everything and found that the Power-nap feature was not disengaged for the software using the Arduino. If you are not aware, if you click on the application and do a Get Info, there is a check box that Prevents Power Nap. After checking that box, I have done two long runs with no communications errors.