Python Script (Labs) Error: "An exception occured while running the Python kernel. See log for details"

Nancyjay · October 1, 2022, 1:33pm

Hello,

I’m unable to use Python Script (Labs) node. When I open the node’s config dialog an error says:
“An exception occured while running the Python kernel. See log for details”

I thought there was a conflict with some libraries in my conda env. I’ve even started from scratch; uninstalling/reinstalling miniconda and creating fresh environments for Python3, Python2, and a separate Python3 env for labs.

I created the current env for Python Script (Labs) via the “New environment” option within KNIME preferences, but I still get the same error.

My version are:
KNIME 4.6.1
conda 22.9.0
python 3.9.13

What is strange is that if I connect a fresh Table Creator node with no data to the Python Script (Labs) node and open it, it successfully loads input data and I can even print to the console. When I try to connect anything with data to the input of the Python Script (Labs) node, I get the above error again.
The following are the logs from when I print “Hello” (with no data connected to input), then connect a node with data to the input of Python Script (Labs):

INFO Python Script (Labs) 5:3616 DEBUG Python Script (Labs) 5:3616 DEBUG Python Script (Labs) 5:3616 DEBUG Python Script (Labs) 5:3616 DEBUG Python Script (Labs) 5:3616 DEBUG Python Script (Labs) 5:3616 DEBUG WorkflowEditor DEBUG NodeContainerEditPart DEBUG NodeContainerEditPart DEBUG CreateConnectionCommand DEBUG Python Script (Labs) 5:3616 DEBUG Python Script (Labs) 5:3616 DEBUG NodeContainer DEBUG Python Script (Labs) 5:3616 DEBUG NodeContainer DEBUG WorkflowManager DEBUG WorkflowEditor DEBUG WorkflowEditor DEBUG ConnectionContainerEditPart DEBUG ConnectionContainerEditPart DEBUG ConnectionContainerEditPart DEBUG ConnectionContainerEditPart DEBUG NodeContainerEditPart DEBUG NodeContainerEditPart DEBUG Buffer DEBUG Python Script (Labs) 5:3616 DEBUG Python Script (Labs) 5:3616 DEBUG DefaultPythonGateway HELLO
reset
clean output ports.
Python Script (Labs) 5:3616 has new state: IDLE
Configure succeeded. (Python Script (Labs))
Python Script (Labs) 5:3616 has new state: CONFIGURED
Workflow event triggered: WorkflowEvent [type=NODE_SETTINGS_CHANGED;node=5:3616;old=null;new=null;timestamp=1 Oct 2022, 14:23:06]
Python Script (Labs) 5:3616 (CONFIGURED)
Cross Joiner 5:3112 (EXECUTED)
adding connection from 5:3112 1 to 5:3616 1
reset
clean output ports.
Python Script (Labs) 5:3616 has new state: IDLE
Configure succeeded. (Python Script (Labs))
Python Script (Labs) 5:3616 has new state: CONFIGURED
Added new connection from node 5:3112(1) to node 5:3616(1)
Workflow event triggered: WorkflowEvent [type=CONNECTION_REMOVED;node=null;old=STD[5:3617(1) → 5:3616( 1)];new=null;timestamp=1 Oct 2022, 14:23:09]
Workflow event triggered: WorkflowEvent [type=CONNECTION_ADDED;node=null;old=null;new=STD[5:3112(1) → 5:3616( 1)];timestamp=1 Oct 2022, 14:23:09]
refreshing visuals for: STD[5:3112(1) → 5:3616( 1)]
modelling info: bendpoints:
refreshing visuals for: STD[5:3112(1) → 5:3616( 1)]
modelling info: bendpoints:
Cross Joiner 5:3112 (EXECUTED)
Python Script (Labs) 5:3616 (CONFIGURED)
Closing input stream on “/private/var/folders/l_/999cl7p931q_x93c3ptlrtxm0000gn/T/knime_container_20221001_14625678616656096097.tmp”, 0 remaining
Closing input stream on “/private/var/folders/l_/999cl7p931q_x93c3ptlrtxm0000gn/T/knime_container_20221001_14625678616656096097.tmp”, 0 remaining
Closing file /private/var/folders/l_/999cl7p931q_x93c3ptlrtxm0000gn/T/knime_3C_10_R10_Lazad38548/knime_container_20221001_7903022919326639153.knable (4 KB)
Connected to Python process with PID: 24067 after ms: 309

Thanks in advance

Kyle_Watkins · October 5, 2022, 9:48pm

Hi Nancyjay,

Sorry to hear about this issue!
Can you send a screenshot of the KNIME > Preferences > Python window and also the KNIME > Preferences > Python (Labs) window?

Also are there error messages when running the regular (non-Labs) Python Script node?

Thanks,
Kyle

Nancyjay · October 10, 2022, 11:31am

Hi Kyle,

thanks for your response. No I don’t get an error with the regular Python Script node.

Here are the two Python pref windows:

Below are screenshots of the Python debug console logged when I drag & drop and connect an upstream node containing data to:

a new Python Script node:

Screenshot 2022-10-10 at 12.27.021920×380 71.5 KB
a new Python Script (Labs) node:

Screenshot 2022-10-10 at 12.27.251920×522 83.1 KB

Thanks,
Nancy

mlauber71 · October 10, 2022, 11:47am

@Nancyjay could you check the following

try to use a Cache – KNIME Hub node just before you use the Python node.
store your Python environment with a Conda Environment propagation so we could see what your Python is like (https://www.knime.com/blog/how-to-manage-python-environments-conda-and-knime) and provide a minimal example
provide us with a detailed log on DEBUG level (Files Corrupted During File Transfer - #8 by mlauber71)
test what happens when you use the (new) Columnar Storage format (KNIME Columnar Table Backend Boosts Performance | KNIME)
see if you have columns other than String and numbers that might require special attention (as of now) in the Python Labs node (Error with pandas in the Labs Python Integration - #9 by mlauber71)

Daniel_Weikert · October 10, 2022, 5:36pm

Have you tried the “older” python nodes? If so do you get the same error?
br

system · January 8, 2023, 5:37pm

This topic was automatically closed 90 days after the last reply. New replies are no longer allowed.