[mattkratz]

Well seems like the image didn’t render properly (at least on my end). Here’s the drive link:

https://photos.google.com/share/AF1QipObQ9rygGEcdp9TLO_wQu3L5Ofwlju49mNnXEjqefEyTTXD-iU_MfNTvPeJe7bSsQ?key=SUl5b2JkSUI2ajVwSXdQY0xhSmhRaFJIZUZQSTlB

[mattkratz]

Hey Harrison,

thanks for the prompt response

1. Without the control board, there are still no lights when connected via micro-usb. It seems like one way or another it got shorted so not much we can do at this point.

2. Yes the old board has been flashed with the new OS. I assumed the chi bio boards were green based off the serial numbers printed on the side (same info/serial from EEPROM). Specifically, all the chi bio boards have BBBG in their serial, which from a quick internet search (when i first posted) was associated with the green beagleboard, although I just had a look at this a found one BBB black rev C listing that pictured a board with a BBBG serial so I’m probably wrong on this. Here are the serials:

OLD BOARD: 2315BBBK0187, CHI BIO BOARD: 000C1936BBBG0103

Here’s a pic of the chi bio BB (removed control PCB):

[mattkratz]

Hey Harrison,

With regards to the first problem, the error with the kernel panic occurred when running the initialization script. Additionally, we are using the V1.1 of the control board, out of curiosity, what are the major changes between the two versions? With regards to the reactor LED that is permanently on, it does seem to be on at very high power, although I haven’t probed it in the API as I’m afraid it may end up melting the source piece if I leave it on too long (occurred with a previous reactor). I’ll get into contact with labmaker looking for replacements.

[mattkratz]

Hey Harrison, here’s the terminal output of the debug run. Experiment starts at 17:17 in the 2nd panel, previous stuff is just process starting up.

[mattkratz]

Hey Harrison, false alarm, I’m still getting the same error (tandem pump comm failures, separated by 2s) albeit at a much lower frequency, once every 1-2 hours instead of once every 5 minutes. I’m running the same app.py with your debug line right now and will update you ASAP.

[mattkratz]

Hey Harrison, finally got around to testing your new app.py (got my 2nd vaccine dose and had to take a couple days off). Seems to be working properly, with constant turning on and off of pumps not producing any errors. I also did a quick run where it automatically manipulates the pumps and it still seems to be running well. I’m gonna let it run over night to test it a bit more.

[mattkratz]

Hey Harrison, I tried replacing the old app.py with the new app.py. I also deleted the associated pyc of the old app.py. We’re still getting the same error messages unfortunately… Is there anything else I ought to do beyond adding the new py file? I also tried completely replacing the root directory with the git hub repo and still the same results. I also had a closer look and confirmed that the specific Debian version is indeed 10.1.

[mattkratz]

FYI, also did this on another control board (has same warning messages and behavior) we have and outputs are the same

[mattkratz]

Hey harrison, sorry its taken so long to get back.

lsb_release -a (debian OS version) output is:

root@beaglebone:~/chibio# lsb_release -a
No LSB modules are available.
Distributor ID: Debian
Description: Debian GNU/Linux 10 (buster)
Release: 10
Codename: buster

pip3 list output is:

root@beaglebone:~/chibio# pip3 list
Package Version
————- ——-
Adafruit-BBIO 1.1.1
Click 7.0
colorama 0.3.7
decorator 4.3.0
distro 1.3.0
Flask 1.0.2
itsdangerous 0.24
Jinja2 2.10
MarkupSafe 1.1.0
numpy 1.16.2
pip 18.1
pyctrl 0.4.3
rcpy 0.5.1
scipy 1.1.0
setuptools 40.8.0
Werkzeug 0.14.1

[mattkratz]

We wanted to check on the forums if it was potentially a fixable non-hardware issue. Now that it seems it’s very likely that it is a hardware issue we’ll probably contact lab maker to see if we can the pump boards replaced. Thanks for the advice and feedback, I’ll keep you updated on how things evolve!

[mattkratz]

Woops meant to send my previous post as a reply to you

[mattkratz]

Hey Harrison,

I’m a lab mate of Sam who’s also been working quite heavily with the Chi bios. Couple of comments, that specific console output Sam posted was from a run with an empty chi bio i.e. no tube, with the motors just pumping ethanol in a closed loop in a separate container. Furthermore, in the experiments where we grow stuff, we’re using the 3D printed sealed cap you guys made, so unless we very sloppily screw on the cap/tubes, it seems like liquid droplets exiting due to air pumping is unlikely.

Additionally, that specific console output that Sam posted may have been the result of using a power supply that was 12 V 1A and not 12V 3A. Nonetheless, when we run with a proper power supply, we still get several pump comm errors popping up. In several previous runs, this pump comm error will eventually occur 11 times consecutively and then shutdown the device (console output below *). We always see this pump comm error intermittently (1 to 2 failures in series every 10 minutes or so), but I’ve only seen the hard shutdown on 16 hr + runs.

I also wanted to elaborate on some specific configurations we’ve looked at:
– We’ve used brand new reactors with the same pump board(s) and control board. We still get intermittent pump comm errors.
– We’ve used a brand-new control and pump board with both old and new reactors. The old V1.2 reactor (the one Sam references) initializes and has the pump comm errors. New reactors have the same pump comm errors at similar frequencies to the old V1.2 reactor.
– We’ve also tried two different brands of micro-usb cables, still same pump comm errors.

All the above were performed with an empty chi bio or with a chi bio with a flask of media (no air pumping). To further add, I’ve just ran three chi bios simultaneously (empty cultures) using a new control pump board and we got the following errors overnight (same console output as below, now with three devices :P). We didn’t get the serial error that leads to device shutdown, and I’m going to let them run another evening to see if we can get this serial error to occur.

*
2021-03-03 03:21:26.078056 Failed Pumps comms 1 times on device M2
2021-03-03 03:21:28.126103 Failed Pumps comms 2 times on device M2
2021-03-03 03:21:28.234715 Failed Pumps comms 1 times on device M2
2021-03-03 03:23:05.194113 Failed Pumps comms 1 times on device M2
2021-03-03 03:23:07.262103 Failed Pumps comms 2 times on device M2
2021-03-03 03:23:47.646114 Failed Pumps comms 1 times on device M2
2021-03-03 03:23:49.694203 Failed Pumps comms 2 times on device M2
2021-03-03 03:28:51.269245 Failed Pumps comms 1 times on device M2
2021-03-03 03:33:05.086061 Failed Pumps comms 1 times on device M2
2021-03-03 03:33:07.134103 Failed Pumps comms 2 times on device M2
2021-03-03 03:35:43.226033 Failed Pumps comms 1 times on device M2
2021-03-03 03:35:45.278092 Failed Pumps comms 2 times on device M2
2021-03-03 03:36:17.950060 Failed Pumps comms 1 times on device M2
2021-03-03 03:36:19.998105 Failed Pumps comms 2 times on device M2
2021-03-03 03:36:52.990063 Failed Pumps comms 1 times on device M2
2021-03-03 03:36:55.038106 Failed Pumps comms 2 times on device M2
2021-03-03 03:37:24.318060 Failed Pumps comms 1 times on device M2
2021-03-03 03:37:26.367069 Failed Pumps comms 2 times on device M2
2021-03-03 03:37:43.362097 Failed Pumps comms 1 times on device M2
2021-03-03 03:37:45.438092 Failed Pumps comms 2 times on device M2
2021-03-03 03:40:05.542024 Failed Pumps comms 1 times on device M2
2021-03-03 03:40:07.614096 Failed Pumps comms 2 times on device M2
2021-03-03 03:42:12.094059 Failed Pumps comms 1 times on device M2
2021-03-03 03:42:14.142102 Failed Pumps comms 2 times on device M2
2021-03-03 03:52:12.778016 Failed Pumps comms 1 times on device M2
2021-03-03 03:52:14.846093 Failed Pumps comms 2 times on device M2
2021-03-03 03:55:25.725839 Failed Pumps comms 1 times on device M2
2021-03-03 03:55:27.774103 Failed Pumps comms 2 times on device M2
2021-03-03 03:58:45.046032 Failed Pumps comms 1 times on device M2
2021-03-03 03:58:47.102145 Failed Pumps comms 2 times on device M2
2021-03-03 04:06:01.406067 Failed Pumps comms 1 times on device M2
2021-03-03 04:06:03.454103 Failed Pumps comms 2 times on device M2
2021-03-03 04:13:26.974064 Failed Pumps comms 1 times on device M2
2021-03-03 04:13:29.022103 Failed Pumps comms 2 times on device M2
2021-03-03 04:14:46.238016 Failed Pumps comms 1 times on device M2
2021-03-03 04:14:48.286090 Failed Pumps comms 2 times on device M2
2021-03-03 04:19:18.462058 Failed Pumps comms 1 times on device M2
2021-03-03 04:19:20.510101 Failed Pumps comms 2 times on device M2
2021-03-03 04:29:47.486029 Failed Pumps comms 1 times on device M2
2021-03-03 04:29:49.534096 Failed Pumps comms 2 times on device M2
2021-03-03 04:31:25.214155 Failed Pumps comms 1 times on device M2
2021-03-03 04:31:27.262107 Failed Pumps comms 2 times on device M2
2021-03-03 04:33:34.878150 Failed Pumps comms 1 times on device M2
2021-03-03 04:33:36.926103 Failed Pumps comms 2 times on device M2
2021-03-03 04:44:10.270116 Failed Pumps comms 1 times on device M2
2021-03-03 04:44:12.318107 Failed Pumps comms 2 times on device M2
2021-03-03 04:44:51.494197 Failed Pumps comms 1 times on device M2
2021-03-03 04:44:53.566090 Failed Pumps comms 2 times on device M2
2021-03-03 04:45:17.614121 Failed Pumps comms 1 times on device M2
2021-03-03 04:45:19.678200 Failed Pumps comms 2 times on device M2
2021-03-03 04:54:20.255675 Failed Pumps comms 1 times on device M2
2021-03-03 04:54:20.303669 Failed Pumps comms 2 times on device M2
2021-03-03 04:54:20.326110 Failed Pumps comms 3 times on device M2
2021-03-03 04:54:20.348655 Failed Pumps comms 4 times on device M2
2021-03-03 04:54:20.371241 Failed Pumps comms 5 times on device M2
2021-03-03 04:54:20.393793 Failed Pumps comms 6 times on device M2
2021-03-03 04:54:20.416273 Failed Pumps comms 7 times on device M2
2021-03-03 04:54:20.438787 Failed Pumps comms 8 times on device M2
2021-03-03 04:54:20.461300 Failed Pumps comms 9 times on device M2
2021-03-03 04:54:20.483801 Failed Pumps comms 10 times on device M2
2021-03-03 04:54:20.506252 Failed Pumps comms 11 times on device M2
Failed to communicate to a device 10 times. Disabling hardware and software!
[2021-03-03 04:54:20 +0000] [32547] [INFO] Shutting down: Master
[2021-03-03 04:54:20 +0000] [32547] [INFO] Reason: App failed to load.

occasionally also get failed PWM comms and failed transmission tests on Pumps

**

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