Startup troubles, Unresponsive PuTTY during pump priming, no stir bar motion

[Braden Crowe]

Hello! We've loaded firmware onto our recently assembled Main and OD boards and are running into a few issues. We're hoping to first test the OD measurement cell to see how the signal responds over our anticipated density levels, so don't have a pump or solenoid valves connected at this point.

The first sign of trouble comes during the pump priming step (we don't have a pump attached, but looking to make sure we can send successful signals to/from the main board). After hitting "open" in PuTTY to open a connection to the serial port, we do not see any output (picture below) when we are hoping for a stream of numbers. 

Ignoring this and launching servostat.py (after modifying the configuration file to match the appropriate COM port), we receive the output attached. None of the .dat log files are created, although it looks like the program might be hanging up due to multiple orphaned threads (i.e., "num threads: 5"). We were expecting to see more output at this point.

When connecting the OD and main boards via the ethernet cable, the lasers turn on, but stir motors do not (we've adjusted board output to 400 ma by setting Vref to 0.22 V, as per the stir bar motor instructions). Perhaps the motors turn on after an initialization step we haven't quite reached, although looking through the .py's it seems they should power on once powered.

It's nice to see some signs of life, although it looks like there are a few issues to resolve. We're excited to test the system, hopefully it works as well on algal systems as it has with bacteria. Pictures of the OD and main board are below for reference. Main board is V2.1, OD board V3.4.

Thank you for your help! We're available by phone if it's any easier.

Braden

[anmo...@colorado.edu]

Chris probably will be able to help you with your Putty issues better than I can, but the reason for the stir bars not spinning is likely due to an issue with the firmware on the OD board. Seems like we all had this issue when first starting our turbidostat. You can see how to resolve this problem in the one of the previous threads on this group titled "stir bars not spinning"

-Andrew

[Braden Crowe]

Andrew - Thanks for the suggestion. It looks like Chris may have uploaded the ODboardv32.hex to github, as that's what I loaded onto the ODboard. Just to be sure, I tried updating the firmware using the message board posted .hex file, although still a no go. I notice that whenever I load firmware via Atmel Studio 7, the ISP clock returns to 125 kHz, instead of the target 16.1 kHz, even though the CKDIV8 fuse selection and .hex file map remain as they were previously programmed.

Both main and OD boards are programmed via the AVR pin on the Atmel ICE, correct?

I'm not entirely confident in my main board soldering job, although I would think I'd get stirring in the chamber even if something was wrong with the main board, given that the laser is showing power.

Braden

[Chris Takahashi]

The OD boards should start spinning when powered.  make sure the 5v_12v jumper is set to 12v on the mainboard though (it's covered up by the serial cable on the photo).  missing that jumper will prevent stirring.

If all else is good it could be the crystal isn't soldered all the way.  Without it nothing will happen.  To troubleshoot that you have to set the internal oscillator back on in the fuse bits (8mhz) and try a baud rate of 9600 (half of 19200).  

[Braden Crowe]

I definitely missed that jumper wire. Connecting gets the stir bars going. Great!

I tried turning the internal oscillator back on, then changing the baud rate to 9600. Putty is still unresponsive (no numbers appear), so something is still amiss. No obvious issues when inspecting the AVR chip with a 10x magnification loop. I'll try resoldering the crystal.

[Braden Crowe]

I desoldered the crystal. It was fairly well connected at all three contacts. Putty is still unresponsive with a resoldered unit. Any other troubleshooting tips? Sorry for the hassle. I may try putting together a new main board.

Braden

[Braden Crowe]

Resoldering a new main board solved it. Thanks!

[krch...@tamu.edu]

Hello!

I get the same output as Braden's when I run servostat.py but I don't have issues connecting to the serial port. Any suggestions on how to troubleshoot this issue?

 I'm using raspberry pi 3B to connect and I see a stream of numbers as output on minicom, so I don't think its an issue with the main board.

Also, how do I set 12 v on 5v_12v jumper?

Thanks,

Karthik

[Chris Takahashi]

The jumper should probably be set to 12v unless you've got some very old chamber PCBs.
running servostat.py should print the same thing as the screenshot above then start dumping numbers to the screen.  if that's not what you see but you are seeing numbers in minicom then make sure the config.ini has the right serial port in it.

[krch...@tamu.edu]

Thanks Chris,

I don't see numbers being dumped on to the screen after running servostat.py (see below). I do have the right serial port in config.ini. I mostly see a series of 0s and 5 in minicom. 

pi@raspberrypi:~/Desktop/Flexostat $ python servostat.py

Reading config file from config.ini

pump init

Closing all valves;

num threads: 5

Welcome to minicom 2.7

OPTIONS: I18n

Compiled on May 7 2017, 05:18:49.

Port /dev/ttyUSB1, 21:47:47

Press CTRL-A Z for help on special keys

0 5 0 5

0 0 0 0 0 5 0 5 0 5 0 5 0 5 0 5

0 0 59 0 0 5 0 5 0 5 0 5 0 5 0 5

0 0 59 0 0 5 0 5 0 5 0 5 0 5 0 5

0 0 59 0 0 5 0 5 0 5 0 5 0 5 0 5

0 0 59 0 0 5 0 5 0 5 0 5 0 5 0 5

0 0 59 0 0 5 0 5 0 5 0 5 0 5 0 5

0 0 59 0 0 5 0 5 0 5 0 5 59 0 0 5

0 5 0 0 0 5 0 5 0 5 0 5 0 5 0 0

0 0 59 0 0 5 0 5 0 5 0 5 0 5 0 0

0 0 59 0 0 5 0 5 0 5 0 5 0 5 0 5

0 0 59 0 0 5 0 5 0 5 0 5 0 5 0 0

0 0 59 0 0 5 0 5 0 5 0 5 0 5 0 5

0 0 59 0 0 5 0 5 0 5 0 5 0 5 0 5

0 0 0 0 0 5 0 5 0 5 0 5 0 5 0 0

0 0 59 0 0 5 0 5 0 5 0 5 0 5 0 5

0 0 59 0 0 5 0 5 0 5 0 5 0 5 0 5

0 5 0 0 0 5 0 5 0 5 0 5 0 5 0 5

0 5 0 0 0 5 0 5 0 5 0 5 0 5 0 5

0 5 0 0 0 5 0 5 0 5 0 5 0 5 0 5

0 5 0 0 0 5 0 5 0 5 0 5 0 5 0 5

0 5 0 0 0 5 0 5 0 5 0 5 0 5 0 5  

[Chris Takahashi]

Is minicom open at the same time as when you run servostat.py? You can't have them both open at once or the behavior is undefined.  You may also have to reboot after that condition.  the 0 5 numbers are what you get when no chamber is plugged in.  Because the inputs are floating sometimes they'll also show up as random numbers too.

Chris

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[krch...@tamu.edu]

Yes, minicom was also open. It is working now! Thanks Chris!

However, I still don’t see the stir bars spinning. I seem to have the same issue as Braden….

“the ISP clock returns to 125 kHz, instead of the target 16.1 kHz, even though the CKDIV8 fuse selection and .hex file map remain as they were previously programmed”.

Or is it the jumper wire? If so, how do I connect the jumper wire? 

 

Thanks

Karthik

[Chris Takahashi]

It looks like you need to connect the 12v motor supply on the mainboard (see photo):