I got a Python kernel memory error when I tried to execute a “Python Script 1 => 1” node. The script just runs some basic data profiling on the input data (from an “Excel Reader” node), and works fine when I execute it in the “Configure…” window. The input data saves as a 200 MB CSV file, so should not be too much for my 20 GB machine.
What should I try?
Hi allen_n,
Could you please upload your knime.log file here? You can find it here: <KNIME-workspace>/.metadata/knime/knime.log or via View > Open KNIME log.
Thanks!
Marcel
Hi Marcel,
I simplified the workflow to just two nodes (“Excel Reader (XLS)” and “Python Script (1 => 1)”), and now I’m getting a different issue:
ERROR PythonKernel LookupError: No serializer extension having the id or processing python type "pandas.core.series.Series" could be found. Column: "NA", column type: "<class 'pandas.core.series.Series'>". ERROR Python Script (1⇒1) 0:15 Execute failed: An exception occured while running the Python kernel. See log for details.
The script still executes okay from the Configuration popup.
Not sure how far to go back in the log; I think this starts when I reloaded KNIME with the simplified workflow:
`2018-10-16 14:48:49,038 : DEBUG : python-message-distribute-loop-0 : ThreadUtils : : : Unnecessary call to runnableWithContext, because no context is available
org.knime.core.util.ThreadUtils$UnnecessaryCallException
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:381)
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:357)
at org.knime.core.util.ThreadUtils$ExecutorServiceWithContext.submit(ThreadUtils.java:94)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.run(DefaultTaskFactory.java:184)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.handle(DefaultTaskFactory.java:217)
at org.knime.python2.kernel.messaging.DefaultTaskFactory.handle(DefaultTaskFactory.java:103)
at org.knime.python2.kernel.messaging.MessageDistributorLoop.loop(MessageDistributorLoop.java:86)
at org.knime.python2.kernel.messaging.AbstractMessageLoop.doLoop(AbstractMessageLoop.java:175)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
2018-10-16 14:49:22,886 : DEBUG : KNIME-Worker-3 : Buffer : Python Script (1⇒1) : 0:15 : Closing input stream on “C:\Users\allen.nugent\AppData\Local\Temp\knime_KNIME_project1a65570\knime_container_20181016_1397557997931084858.tmp”, 0 remaining
2018-10-16 14:49:29,399 : DEBUG : python-message-distribute-loop-0 : ThreadUtils : : : Unnecessary call to runnableWithContext, because no context is available
org.knime.core.util.ThreadUtils$UnnecessaryCallException
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:381)
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:357)
at org.knime.core.util.ThreadUtils$ExecutorServiceWithContext.submit(ThreadUtils.java:94)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.run(DefaultTaskFactory.java:184)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.handle(DefaultTaskFactory.java:217)
at org.knime.python2.kernel.messaging.DefaultTaskFactory.handle(DefaultTaskFactory.java:103)
at org.knime.python2.kernel.messaging.MessageDistributorLoop.loop(MessageDistributorLoop.java:86)
at org.knime.python2.kernel.messaging.AbstractMessageLoop.doLoop(AbstractMessageLoop.java:175)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
2018-10-16 14:49:29,464 : INFO : Thread-12 : PythonKernel : : : Traceback (most recent call last):
2018-10-16 14:49:29,464 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\PythonKernelLauncher.py”, line 84, in
2018-10-16 14:49:29,464 : INFO : Thread-12 : PythonKernel : : : kernel.start()
2018-10-16 14:49:29,464 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 93, in start
2018-10-16 14:49:29,464 : INFO : Thread-12 : PythonKernel : : : self._monitor.wait_for_close()
2018-10-16 14:49:29,464 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 172, in wait_for_close
2018-10-16 14:49:29,464 : INFO : Thread-12 : PythonKernel : : : self.check_exception()
2018-10-16 14:49:29,464 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 168, in check_exception
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : raise self._exception
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : File “C:\Users\allen.nugent\AppData\Local\Programs\Python\Python37-32\lib\concurrent\futures\thread.py”, line 57, in run
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : result = self.fn(*self.args, **self.kwargs)
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 235, in _monitored_fn
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : raise ex
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 232, in _monitored_fn
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : return fn(*args, **kwargs)
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\messaging\Task.py”, line 185, in run
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : raise ex
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\messaging\Task.py”, line 180, in run
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : self._runnable()
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\messaging\Task.py”, line 145, in _run_internal
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : received, self._message_handlers, self._message_id_supplier, self._set_result, self._workspace)
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\messaging\AbstractTaskHandler.py”, line 76, in handle
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : if self._handle_custom_message(message, message_id_supplier, message_to_send, result_consumer, workspace):
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\messaging\RequestHandlers.py”, line 91, in _handle_custom_message
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : response = self._respond(message, response_message_id_supplier(), workspace)
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\messaging\RequestHandlers.py”, line 196, in _respond
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : data_bytes = workspace.serializer.data_frame_to_bytes(data_frame_chunk, start)
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\Serializer.py”, line 197, in data_frame_to_bytes
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : table = FromPandasTable(data_frame, self, start_row_number)
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\DataTables.py”, line 79, in init
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : column_type, serializer_id = serializer.simpletype_for_column(self._data_frame, column)
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\Serializer.py”, line 356, in simpletype_for_column
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : raise e
2018-10-16 14:49:29,465 : INFO : Thread-12 : PythonKernel : : : LookupError: No serializer extension having the id or processing python type “pandas.core.series.Series” could be found. Column: “NA”, column type: “<class ‘pandas.core.series.Series’>”.
2018-10-16 14:49:29,467 : DEBUG : Thread-13 : PythonKernel : : : Python error with stacktrace:
2018-10-16 14:49:29,467 : DEBUG : Thread-13 : PythonKernel : : : Traceback (most recent call last):
2018-10-16 14:49:29,468 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\PythonKernelLauncher.py”, line 88, in
2018-10-16 14:49:29,469 : DEBUG : Thread-13 : PythonKernel : : : raise ex
2018-10-16 14:49:29,469 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\PythonKernelLauncher.py”, line 84, in
2018-10-16 14:49:29,470 : DEBUG : Thread-13 : PythonKernel : : : kernel.start()
2018-10-16 14:49:29,470 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 93, in start
2018-10-16 14:49:29,471 : DEBUG : Thread-13 : PythonKernel : : : self._monitor.wait_for_close()
2018-10-16 14:49:29,471 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 172, in wait_for_close
2018-10-16 14:49:29,472 : DEBUG : Thread-13 : PythonKernel : : : self.check_exception()
2018-10-16 14:49:29,473 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 168, in check_exception
2018-10-16 14:49:29,474 : DEBUG : Thread-13 : PythonKernel : : : raise self._exception
2018-10-16 14:49:29,474 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Users\allen.nugent\AppData\Local\Programs\Python\Python37-32\lib\concurrent\futures\thread.py”, line 57, in run
2018-10-16 14:49:29,475 : DEBUG : Thread-13 : PythonKernel : : : result = self.fn(*self.args, **self.kwargs)
2018-10-16 14:49:29,475 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 235, in _monitored_fn
2018-10-16 14:49:29,476 : DEBUG : Thread-13 : PythonKernel : : : raise ex
2018-10-16 14:49:29,476 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 232, in _monitored_fn
2018-10-16 14:49:29,478 : DEBUG : Thread-13 : PythonKernel : : : return fn(*args, **kwargs)
2018-10-16 14:49:29,478 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\messaging\Task.py”, line 185, in run
2018-10-16 14:49:29,479 : DEBUG : Thread-13 : PythonKernel : : : raise ex
2018-10-16 14:49:29,479 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\messaging\Task.py”, line 180, in run
2018-10-16 14:49:29,481 : DEBUG : Thread-13 : PythonKernel : : : self._runnable()
2018-10-16 14:49:29,481 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\messaging\Task.py”, line 145, in _run_internal
2018-10-16 14:49:29,482 : DEBUG : Thread-13 : PythonKernel : : : received, self._message_handlers, self._message_id_supplier, self._set_result, self._workspace)
2018-10-16 14:49:29,482 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\messaging\AbstractTaskHandler.py”, line 76, in handle
2018-10-16 14:49:29,483 : DEBUG : Thread-13 : PythonKernel : : : if self._handle_custom_message(message, message_id_supplier, message_to_send, result_consumer, workspace):
2018-10-16 14:49:29,483 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\messaging\RequestHandlers.py”, line 91, in _handle_custom_message
2018-10-16 14:49:29,484 : DEBUG : Thread-13 : PythonKernel : : : response = self._respond(message, response_message_id_supplier(), workspace)
2018-10-16 14:49:29,484 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\messaging\RequestHandlers.py”, line 196, in _respond
2018-10-16 14:49:29,486 : DEBUG : Thread-13 : PythonKernel : : : data_bytes = workspace.serializer.data_frame_to_bytes(data_frame_chunk, start)
2018-10-16 14:49:29,486 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\Serializer.py”, line 197, in data_frame_to_bytes
2018-10-16 14:49:29,487 : DEBUG : Thread-13 : PythonKernel : : : table = FromPandasTable(data_frame, self, start_row_number)
2018-10-16 14:49:29,487 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\DataTables.py”, line 79, in init
2018-10-16 14:49:29,489 : DEBUG : Thread-13 : PythonKernel : : : column_type, serializer_id = serializer.simpletype_for_column(self._data_frame, column)
2018-10-16 14:49:29,489 : DEBUG : Thread-13 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\Serializer.py”, line 356, in simpletype_for_column
2018-10-16 14:49:29,490 : DEBUG : Thread-13 : PythonKernel : : : raise e
2018-10-16 14:49:29,490 : ERROR : Thread-13 : PythonKernel : : : LookupError: No serializer extension having the id or processing python type “pandas.core.series.Series” could be found. Column: “NA”, column type: “<class ‘pandas.core.series.Series’>”.
2018-10-16 14:49:31,482 : DEBUG : KNIME-Worker-3 : Node : Python Script (1⇒1) : 0:15 : reset
2018-10-16 14:49:31,482 : ERROR : KNIME-Worker-3 : Node : Python Script (1⇒1) : 0:15 : Execute failed: An exception occured while running the Python kernel. See log for details.
2018-10-16 14:49:31,485 : DEBUG : KNIME-Worker-3 : Node : Python Script (1⇒1) : 0:15 : Execute failed: An exception occured while running the Python kernel. See log for details.
org.knime.python2.kernel.PythonIOException: An exception occured while running the Python kernel. See log for details.
at org.knime.python2.kernel.PythonKernel.getMostSpecificPythonKernelException(PythonKernel.java:1526)
at org.knime.python2.kernel.PythonKernel.getDataTable(PythonKernel.java:868)
at org.knime.python2.nodes.script.PythonScriptNodeModel.execute(PythonScriptNodeModel.java:96)
at org.knime.core.node.NodeModel.execute(NodeModel.java:733)
at org.knime.core.node.NodeModel.executeModel(NodeModel.java:567)
at org.knime.core.node.Node.invokeFullyNodeModelExecute(Node.java:1177)
at org.knime.core.node.Node.execute(Node.java:964)
at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:561)
at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:95)
at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:179)
at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:110)
at org.knime.core.util.ThreadUtils$RunnableWithContextImpl.runWithContext(ThreadUtils.java:328)
at org.knime.core.util.ThreadUtils$RunnableWithContext.run(ThreadUtils.java:204)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246)
Caused by: java.util.concurrent.ExecutionException: java.lang.Exception: Failed to receive message from Python or forward received message.
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.get(DefaultTaskFactory.java:196)
at org.knime.python2.kernel.PythonKernel.getDataTable(PythonKernel.java:853)
… 15 more
Caused by: java.lang.Exception: Failed to receive message from Python or forward received message.
at org.knime.python2.kernel.messaging.AbstractMessageLoop.throwExceptionInLoop(AbstractMessageLoop.java:76)
at org.knime.python2.kernel.messaging.DefaultMessageReceiverLoop.loop(DefaultMessageReceiverLoop.java:98)
at org.knime.python2.kernel.messaging.AbstractMessageLoop.doLoop(AbstractMessageLoop.java:175)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Suppressed: java.lang.Exception: Failed to distribute message from Python. Cause: Message receiver loop terminated.
at org.knime.python2.kernel.messaging.AbstractMessageLoop.throwExceptionInLoop(AbstractMessageLoop.java:76)
at org.knime.python2.kernel.messaging.MessageDistributorLoop.loop(MessageDistributorLoop.java:93)
… 4 more
Caused by: java.io.IOException: Message receiver loop terminated.
at org.knime.python2.kernel.messaging.DefaultMessageReceiverLoop.receive(DefaultMessageReceiverLoop.java:82)
at org.knime.python2.kernel.messaging.MessageDistributorLoop.loop(MessageDistributorLoop.java:82)
… 4 more
Caused by: java.io.EOFException
at java.io.DataInputStream.readFully(DataInputStream.java:197)
at java.io.DataInputStream.readFully(DataInputStream.java:169)
at org.knime.python2.kernel.messaging.PythonMessagingUtils.readInt(PythonMessagingUtils.java:91)
at org.knime.python2.kernel.messaging.DefaultMessageReceiver.receive(DefaultMessageReceiver.java:80)
at org.knime.python2.kernel.messaging.DefaultMessageReceiverLoop.loop(DefaultMessageReceiverLoop.java:92)
… 4 more
2018-10-16 14:49:31,497 : DEBUG : KNIME-Worker-3 : WorkflowManager : Python Script (1⇒1) : 0:15 : Python Script (1⇒1) 0:15 doBeforePostExecution
2018-10-16 14:49:31,499 : DEBUG : KNIME-Worker-3 : NodeContainer : Python Script (1⇒1) : 0:15 : Python Script (1⇒1) 0:15 has new state: POSTEXECUTE
2018-10-16 14:49:31,501 : DEBUG : KNIME-Worker-3 : WorkflowManager : Python Script (1⇒1) : 0:15 : Python Script (1⇒1) 0:15 doAfterExecute - failure
2018-10-16 14:49:31,502 : DEBUG : KNIME-Worker-3 : Node : Python Script (1⇒1) : 0:15 : reset
2018-10-16 14:49:31,502 : DEBUG : KNIME-Worker-3 : Node : Python Script (1⇒1) : 0:15 : clean output ports.
2018-10-16 14:49:31,502 : DEBUG : KNIME-Worker-3 : WorkflowFileStoreHandlerRepository : Python Script (1⇒1) : 0:15 : Removing handler c9b8b96f-dfac-4100-87db-d3a51ad48923 (Python Script (1⇒1) 0:15: ) - 0 remaining
2018-10-16 14:49:31,503 : DEBUG : KNIME-Worker-3 : NodeContainer : Python Script (1⇒1) : 0:15 : Python Script (1⇒1) 0:15 has new state: IDLE
2018-10-16 14:49:31,525 : DEBUG : KNIME-Worker-3 : Node : Python Script (1⇒1) : 0:15 : Configure succeeded. (Python Script (1⇒1))
2018-10-16 14:49:31,525 : DEBUG : KNIME-Worker-3 : NodeContainer : Python Script (1⇒1) : 0:15 : Python Script (1⇒1) 0:15 has new state: CONFIGURED
2018-10-16 14:49:31,526 : DEBUG : KNIME-Worker-3 : NodeContainer : Python Script (1⇒1) : 0:15 : KNIME_project1a 0 has new state: CONFIGURED
2018-10-16 14:49:31,529 : DEBUG : KNIME-WFM-Parent-Notifier : NodeContainer : : : ROOT has new state: IDLE
2018-10-16 14:49:31,668 : DEBUG : KNIME-Node-Usage-Writer : NodeTimer$GlobalNodeStats : : : Successfully wrote node usage stats to file: C:\Users\allen.nugent\knime-workspace.metadata\knime\nodeusage_3.0.json
2018-10-16 14:55:24,583 : DEBUG : Thread-18 : PythonKernel : : : Using serialization library: Flatbuffers Column Serialization.
2018-10-16 14:55:26,450 : DEBUG : Thread-18 : ThreadUtils : : : Unnecessary call to runnableWithContext, because no context is available
org.knime.core.util.ThreadUtils$UnnecessaryCallException
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:381)
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:357)
at org.knime.core.util.ThreadUtils$ExecutorServiceWithContext.submit(ThreadUtils.java:94)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.run(DefaultTaskFactory.java:184)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.get(DefaultTaskFactory.java:195)
at org.knime.python2.kernel.PythonKernel.(PythonKernel.java:302)
at org.knime.python2.kernel.PythonKernelManager.(PythonKernelManager.java:94)
at org.knime.python2.config.PythonSourceCodePanel$3.run(PythonSourceCodePanel.java:221)
at java.lang.Thread.run(Thread.java:748)
2018-10-16 14:55:26,504 : DEBUG : Thread-18 : PythonKernel : : : Python PID: 1016
2018-10-16 14:55:26,504 : DEBUG : Thread-18 : ThreadUtils : : : Unnecessary call to runnableWithContext, because no context is available
org.knime.core.util.ThreadUtils$UnnecessaryCallException
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:381)
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:357)
at org.knime.core.util.ThreadUtils$ExecutorServiceWithContext.submit(ThreadUtils.java:94)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.run(DefaultTaskFactory.java:184)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.get(DefaultTaskFactory.java:195)
at org.knime.python2.kernel.PythonKernel.checkHasAutoComplete(PythonKernel.java:506)
at org.knime.python2.kernel.PythonKernel.(PythonKernel.java:305)
at org.knime.python2.kernel.PythonKernelManager.(PythonKernelManager.java:94)
at org.knime.python2.config.PythonSourceCodePanel$3.run(PythonSourceCodePanel.java:221)
at java.lang.Thread.run(Thread.java:748)
2018-10-16 14:55:26,506 : DEBUG : Thread-18 : ThreadUtils : : : Unnecessary call to runnableWithContext, because no context is available
org.knime.core.util.ThreadUtils$UnnecessaryCallException
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:381)
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:357)
at org.knime.core.util.ThreadUtils$ExecutorServiceWithContext.submit(ThreadUtils.java:94)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.run(DefaultTaskFactory.java:184)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.get(DefaultTaskFactory.java:195)
at org.knime.python2.kernel.PythonKernel.setupCustomModules(PythonKernel.java:517)
at org.knime.python2.kernel.PythonKernel.(PythonKernel.java:308)
at org.knime.python2.kernel.PythonKernelManager.(PythonKernelManager.java:94)
at org.knime.python2.config.PythonSourceCodePanel$3.run(PythonSourceCodePanel.java:221)
at java.lang.Thread.run(Thread.java:748)
2018-10-16 14:55:26,508 : DEBUG : Thread-18 : ThreadUtils : : : Unnecessary call to runnableWithContext, because no context is available
org.knime.core.util.ThreadUtils$UnnecessaryCallException
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:381)
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:357)
at org.knime.core.util.ThreadUtils$ExecutorServiceWithContext.submit(ThreadUtils.java:94)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.run(DefaultTaskFactory.java:184)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.get(DefaultTaskFactory.java:195)
at org.knime.python2.kernel.PythonKernel.setupSentinelConstants(PythonKernel.java:525)
at org.knime.python2.kernel.PythonKernel.(PythonKernel.java:310)
at org.knime.python2.kernel.PythonKernelManager.(PythonKernelManager.java:94)
at org.knime.python2.config.PythonSourceCodePanel$3.run(PythonSourceCodePanel.java:221)
at java.lang.Thread.run(Thread.java:748)
2018-10-16 14:55:26,515 : DEBUG : KNIME-Worker-4 : ThreadUtils : : : Unnecessary call to runnableWithContext, because no context is available
org.knime.core.util.ThreadUtils$UnnecessaryCallException
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:381)
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:357)
at org.knime.core.util.ThreadUtils$ExecutorServiceWithContext.submit(ThreadUtils.java:94)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.run(DefaultTaskFactory.java:184)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.get(DefaultTaskFactory.java:195)
at org.knime.python2.kernel.PythonKernel.putFlowVariables(PythonKernel.java:591)
at org.knime.python2.kernel.PythonKernelManager$5.run(PythonKernelManager.java:236)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246)
2018-10-16 14:55:26,532 : DEBUG : KNIME-Worker-4 : Buffer : : : Opening input stream on file “C:\Users\allen.nugent\AppData\Local\Temp\knime_KNIME_project1a65570\knime_container_20181016_1397557997931084858.tmp”, 0 open streams
2018-10-16 14:55:26,710 : DEBUG : KNIME-Worker-4 : ThreadUtils : : : Unnecessary call to runnableWithContext, because no context is available
org.knime.core.util.ThreadUtils$UnnecessaryCallException
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:381)
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:357)
at org.knime.core.util.ThreadUtils$ExecutorServiceWithContext.submit(ThreadUtils.java:94)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.run(DefaultTaskFactory.java:184)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.get(DefaultTaskFactory.java:195)
at org.knime.python2.kernel.PythonKernel.putDataTable(PythonKernel.java:764)
at org.knime.python2.kernel.PythonKernelManager$5.run(PythonKernelManager.java:241)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246)
2018-10-16 14:55:29,232 : DEBUG : python-message-distribute-loop-0 : ThreadUtils : : : Unnecessary call to runnableWithContext, because no context is available
org.knime.core.util.ThreadUtils$UnnecessaryCallException
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:381)
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:357)
at org.knime.core.util.ThreadUtils$ExecutorServiceWithContext.submit(ThreadUtils.java:94)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.run(DefaultTaskFactory.java:184)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.handle(DefaultTaskFactory.java:217)
at org.knime.python2.kernel.messaging.DefaultTaskFactory.handle(DefaultTaskFactory.java:103)
at org.knime.python2.kernel.messaging.MessageDistributorLoop.loop(MessageDistributorLoop.java:86)
at org.knime.python2.kernel.messaging.AbstractMessageLoop.doLoop(AbstractMessageLoop.java:175)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
2018-10-16 14:55:29,413 : DEBUG : KNIME-Worker-4 : Buffer : : : Closing input stream on “C:\Users\allen.nugent\AppData\Local\Temp\knime_KNIME_project1a65570\knime_container_20181016_1397557997931084858.tmp”, 0 remaining
2018-10-16 14:55:29,415 : DEBUG : KNIME-Worker-5 : ThreadUtils : : : Unnecessary call to runnableWithContext, because no context is available
org.knime.core.util.ThreadUtils$UnnecessaryCallException
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:381)
at org.knime.core.util.ThreadUtils.runnableWithContext(ThreadUtils.java:357)
at org.knime.core.util.ThreadUtils$ExecutorServiceWithContext.submit(ThreadUtils.java:94)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.run(DefaultTaskFactory.java:184)
at org.knime.python2.kernel.messaging.DefaultTaskFactory$DefaultTask.get(DefaultTaskFactory.java:195)
at org.knime.python2.kernel.PythonKernel.listVariables(PythonKernel.java:1113)
at org.knime.python2.kernel.PythonKernelManager$7.run(PythonKernelManager.java:299)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246)
2018-10-16 14:55:57,931 : DEBUG : Thread-19 : PythonKernel : : : Traceback (most recent call last):
2018-10-16 14:55:57,931 : DEBUG : Thread-20 : PythonKernel : : : Traceback (most recent call last):
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\PythonKernelLauncher.py”, line 84, in
2018-10-16 14:55:57,932 : DEBUG : Thread-20 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\PythonKernelLauncher.py”, line 88, in
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : kernel.start()
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 93, in start
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : self._monitor.wait_for_close()
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 172, in wait_for_close
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : self.check_exception()
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 168, in check_exception
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : raise self._exception
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : File “C:\Users\allen.nugent\AppData\Local\Programs\Python\Python37-32\lib\concurrent\futures\thread.py”, line 57, in run
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : result = self.fn(*self.args, **self.kwargs)
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\messaging\AbstractMessageLoop.py”, line 126, in _do_loop
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : raise ex
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\messaging\AbstractMessageLoop.py”, line 123, in _do_loop
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : self._loop()
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\messaging\MessageDistributorLoop.py”, line 97, in _loop
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : raise ex
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\messaging\MessageDistributorLoop.py”, line 92, in _loop
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : message = self._receiver.receive()
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\messaging\MessageReceiverLoop.py”, line 65, in receive
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : raise RuntimeError(“Message receive loop terminated.”)
2018-10-16 14:55:57,932 : DEBUG : Thread-19 : PythonKernel : : : RuntimeError: Message receive loop terminated.
2018-10-16 14:55:57,933 : DEBUG : Thread-20 : PythonKernel : : : raise ex
2018-10-16 14:55:57,933 : DEBUG : Thread-20 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\PythonKernelLauncher.py”, line 84, in
2018-10-16 14:55:57,934 : DEBUG : Thread-20 : PythonKernel : : : kernel.start()
2018-10-16 14:55:57,934 : DEBUG : Thread-20 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 93, in start
2018-10-16 14:55:57,936 : DEBUG : Thread-20 : PythonKernel : : : self._monitor.wait_for_close()
2018-10-16 14:55:57,936 : DEBUG : Thread-20 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 172, in wait_for_close
2018-10-16 14:55:57,937 : DEBUG : Thread-20 : PythonKernel : : : self.check_exception()
2018-10-16 14:55:57,937 : DEBUG : Thread-20 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\PythonKernel.py”, line 168, in check_exception
2018-10-16 14:55:57,939 : DEBUG : Thread-20 : PythonKernel : : : raise self._exception
2018-10-16 14:55:57,939 : DEBUG : Thread-20 : PythonKernel : : : File “C:\Users\allen.nugent\AppData\Local\Programs\Python\Python37-32\lib\concurrent\futures\thread.py”, line 57, in run
2018-10-16 14:55:57,940 : DEBUG : Thread-20 : PythonKernel : : : result = self.fn(*self.args, **self.kwargs)
2018-10-16 14:55:57,940 : DEBUG : Thread-20 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\messaging\AbstractMessageLoop.py”, line 126, in _do_loop
2018-10-16 14:55:57,941 : DEBUG : Thread-20 : PythonKernel : : : raise ex
2018-10-16 14:55:57,941 : DEBUG : Thread-20 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\messaging\AbstractMessageLoop.py”, line 123, in _do_loop
2018-10-16 14:55:57,942 : DEBUG : Thread-20 : PythonKernel : : : self._loop()
2018-10-16 14:55:57,942 : DEBUG : Thread-20 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\messaging\MessageDistributorLoop.py”, line 97, in _loop
2018-10-16 14:55:57,943 : DEBUG : Thread-20 : PythonKernel : : : raise ex
2018-10-16 14:55:57,943 : DEBUG : Thread-20 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\messaging\MessageDistributorLoop.py”, line 92, in _loop
2018-10-16 14:55:57,944 : DEBUG : Thread-20 : PythonKernel : : : message = self._receiver.receive()
2018-10-16 14:55:57,944 : DEBUG : Thread-20 : PythonKernel : : : File “C:\Program Files\KNIME\plugins\org.knime.python2_3.6.1.v201808311614\py\python3\messaging\MessageReceiverLoop.py”, line 65, in receive
2018-10-16 14:55:57,945 : DEBUG : Thread-20 : PythonKernel : : : raise RuntimeError(“Message receive loop terminated.”)
2018-10-16 14:55:57,945 : DEBUG : Thread-20 : PythonKernel : : : RuntimeError: Message receive loop terminated.
2018-10-16 14:55:59,865 : DEBUG : Thread-22 : PythonMessaging : : : Python messaging system could not be shut down gracefully. Process will be killed.`
The error you now get suggests that you’re trying to transfer a nested pandas DataFrame to KNIME, i.e., a DataFrame where each cell again contains a table (or pandas Series in this case). This does not work because KNIME largely only supports “flat” data tables (+ collection cells). Can you double-check the structure of your output DataFrame?
Also, we actually try to catch such cases and print a more expressive error message than the cryptic one you got. So I’d consider this a bug, thanks for reporting! 
Marcel
Thanks, Marcel.
You nailed it, mate! A bug in my code was producing a 2D series in one of the DataFrame columns. All good, now.
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