Software error

[mpatterson]

Hi,

Last night a Chi.Bio run I started stopped with an error I have never seen before. We have an ethernet connection, if this is helpful. Here is what the PuTTY terminal said:

ogin as: root
Pre-authentication banner message from server:
| Debian GNU/Linux 10
|
| BeagleBoard.org Debian Buster IoT Image 2020-08-25
|
| Support: https://bbb.io/debian
|
| default username:password is [debian:temppwd]
|
End of banner message from server
root@192.168.7.2’s password:

The programs included with the Debian GNU/Linux system are free software;
the exact distribution terms for each program are described in the
individual files in /usr/share/doc/*/copyright.

Debian GNU/Linux comes with ABSOLUTELY NO WARRANTY, to the extent
permitted by applicable law.
Last login: Sun Sep 18 12:38:09 2022 from 192.168.7.1
root@beaglebone:~# cd chibio/
root@beaglebone:~/chibio# bash cb.sh
[2022-09-19 09:07:04 +0000] [2154] [INFO] Starting gunicorn 20.1.0
[2022-09-19 09:07:04 +0000] [2154] [INFO] Listening at: http://192.168.7.2:5000 (2154)
[2022-09-19 09:07:04 +0000] [2154] [INFO] Using worker: sync
[2022-09-19 09:07:04 +0000] [2157] [INFO] Booting worker with pid: 2157
2022-09-19 09:07:11.497619 Starting watchdog
2022-09-19 09:07:13.981907 Initialising devices
2022-09-19 09:07:14.214711 Initialised M0, Device ID: 38921214501243657614
2022-09-19 09:07:14.920611 Initialised M1, Device ID: 17422214321243657614
2022-09-19 09:07:15.612081 Initialised M2, Device ID: 40980108961243657614
2022-09-19 09:07:16.303531 Initialised M3, Device ID: 22538214021243657614
2022-09-19 09:07:16.994009 Initialised M4, Device ID: 35846214461243657614
2022-09-19 09:07:17.688432 Initialised M5, Device ID: 46094628061728357670
2022-09-19 09:07:18.381632 Initialised M6, Device ID: 50190214001243657614
2022-09-19 09:07:19.077057 Initialised M7, Device ID: 36881626021728357670
2022-09-19 09:07:19.683443 Start Up Complete
2022-09-19 09:08:05.270217 Set item: OD to value 0.7 on M0
2022-09-19 09:08:11.694383Calibrated OD
2022-09-19 09:08:14.830650 Set item: Volume to value 20.0 on M0
2022-09-19 09:08:19.902254 Set item: Thermostat to value 18.0 on M0
2022-09-19 09:08:22.776415 Set item: OD to value 0.7 on M1
2022-09-19 09:08:27.833143Calibrated OD
2022-09-19 09:08:28.376124 Set item: Volume to value 20.0 on M1
2022-09-19 09:08:29.255281 Set item: Thermostat to value 18.0 on M1
2022-09-19 09:08:31.583020 Set item: OD to value 0.7 on M2
2022-09-19 09:08:36.423446Calibrated OD
2022-09-19 09:08:36.871878 Set item: Volume to value 20.0 on M2
2022-09-19 09:08:38.311542 Set item: Thermostat to value 18.0 on M2
2022-09-19 09:08:40.591614 Set item: OD to value 0.7 on M3
2022-09-19 09:08:45.647558Calibrated OD
2022-09-19 09:08:46.312037 Set item: Volume to value 20.0 on M3
2022-09-19 09:08:47.288072 Set item: Thermostat to value 18.0 on M3
2022-09-19 09:08:49.264113 Set item: OD to value 0.7 on M4
2022-09-19 09:08:52.488308Calibrated OD
2022-09-19 09:08:52.936374 Set item: Volume to value 20.0 on M4
2022-09-19 09:08:53.912464 Set item: Thermostat to value 18.0 on M4
2022-09-19 09:08:56.296440 Set item: OD to value 0.7 on M5
2022-09-19 09:09:00.024728Calibrated OD
2022-09-19 09:09:00.625565 Set item: Volume to value 20.0 on M5
2022-09-19 09:09:01.832750 Set item: Thermostat to value 18.0 on M5
2022-09-19 09:09:04.192962 Set item: OD to value 0.7 on M6
2022-09-19 09:09:09.578282Calibrated OD
2022-09-19 09:09:09.912548 Set item: Volume to value 20.0 on M6
2022-09-19 09:09:10.353738 Set item: Volume to value 20.0 on M6
2022-09-19 09:09:11.600701 Set item: Thermostat to value 18.0 on M6
2022-09-19 09:09:13.657917 Set item: OD to value 0.7 on M7
2022-09-19 09:09:18.274523Calibrated OD
2022-09-19 09:09:18.649917 Set item: Volume to value 20.0 on M7
2022-09-19 09:09:19.057709 Set item: Volume to value 20.0 on M7
2022-09-19 09:09:20.354624 Set item: Thermostat to value 18.0 on M7
2022-09-19 09:12:35.528622 Failed Pumps comms 1 times on device M1
2022-09-19 09:12:35.551245 Failed Pumps comms 2 times on device M1
2022-09-19 09:12:35.581002 Failed Pumps comms 1 times on device M1
2022-09-19 09:13:35.609492 Failed Pumps comms 1 times on device M1
2022-09-19 11:40:46.640482 Failed Pumps comms 1 times on device M1
2022-09-19 11:40:46.663005 Failed Pumps comms 2 times on device M1
2022-09-19 11:40:46.769610 Failed Multiplexer Comms 1 times
2022-09-19 11:40:46.877625 Failed Multiplexer Comms 2 times
Exception in thread Thread-51847:
Traceback (most recent call last):
File “/usr/lib/python3.7/threading.py”, line 917, in _bootstrap_inner
self.run()
File “/usr/lib/python3.7/threading.py”, line 865, in run
self._target(*self._args, **self._kwargs)
File “/root/chibio/app.py”, line 2110, in runExperiment
MeasureTemp(M,’Internal’) #Measuring all temperatures
File “/root/chibio/app.py”, line 1664, in MeasureTemp
temperature=float(int(tempData,2))/16.0
ValueError: invalid literal for int() with base 2: ”

2022-09-19 11:41:47.927114 Trying to communicate with absent device – bug in software!. Disabling hardware and software!
[2022-09-19 11:41:47 +0000] [2154] [INFO] Shutting down: Master
[2022-09-19 11:41:47 +0000] [2154] [INFO] Reason: App failed to load.

I was able to restart this morning with no issues.

[harrison]

It looks as if the digital communication on the device may have falled mid-way through it trying to read data from the thermometer. Not sure that there is a particularly convenient fix or reason for this; was there any liquid on the top of the reactor afterward?

[mpatterson]

Yes, actually, it looks like there is a liquid stain on top of M1. We are using the three-port caps, one for the media, one for waste, and I have a little foil cap on the third port but it had fallen off. That probably indicates some liquid came out with significant force. I’m not sure why that happened, there’s nothing blocking any of the lines as far as I can tell.

[harrison]

Potentially outlet pump may not be working effectively, i.e. if the tubing is not settled in the pump rotor well, or if it is very old tubing and has been ground down over time and hence makes a poor seal. I’d try pulling the tube through the pump head (so there is a fresh bit inside the pump) and see how it performs.

[mpatterson]

Okay I will try that- it has been awhile since I’ve replaced the tubing. Thank you!

[Author]

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