[NbConvertApp] Converting notebook TimePix-b/t3pa_2cls_tokamak.ipynb to html [NbConvertApp] Executing notebook with kernel: python3 [NbConvertApp] ERROR | Timeout waiting for execute reply (20s). Traceback (most recent call last): File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 609, in _async_poll_for_reply msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout)) File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/util.py", line 85, in ensure_async result = await obj File "/opt/anaconda3/lib/python3.8/site-packages/jupyter_client/asynchronous/channels.py", line 48, in get_msg raise Empty _queue.Empty During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/opt/anaconda3/bin/jupyter-nbconvert", line 11, in sys.exit(main()) File "/opt/anaconda3/lib/python3.8/site-packages/jupyter_core/application.py", line 270, in launch_instance return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs) File "/opt/anaconda3/lib/python3.8/site-packages/traitlets/config/application.py", line 845, in launch_instance app.start() File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 350, in start self.convert_notebooks() File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 524, in convert_notebooks self.convert_single_notebook(notebook_filename) File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 489, in convert_single_notebook output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer) File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 418, in export_single_notebook output, resources = self.exporter.from_filename(notebook_filename, resources=resources) File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 181, in from_filename return self.from_file(f, resources=resources, **kw) File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 199, in from_file return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw) File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/exporters/html.py", line 119, in from_notebook_node return super().from_notebook_node(nb, resources, **kw) File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/exporters/templateexporter.py", line 369, in from_notebook_node nb_copy, resources = super().from_notebook_node(nb, resources, **kw) File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 143, in from_notebook_node nb_copy, resources = self._preprocess(nb_copy, resources) File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 318, in _preprocess nbc, resc = preprocessor(nbc, resc) File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/preprocessors/base.py", line 47, in __call__ return self.preprocess(nb, resources) File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 79, in preprocess self.execute() File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/util.py", line 74, in wrapped return just_run(coro(*args, **kwargs)) File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/util.py", line 53, in just_run return loop.run_until_complete(coro) File "/opt/anaconda3/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete return future.result() File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 540, in async_execute await self.async_execute_cell( File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 123, in async_execute_cell cell, resources = self.preprocess_cell(cell, self.resources, cell_index) File "/opt/anaconda3/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 146, in preprocess_cell cell = run_sync(NotebookClient.async_execute_cell)(self, cell, index, store_history=self.store_history) File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/util.py", line 74, in wrapped return just_run(coro(*args, **kwargs)) File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/util.py", line 53, in just_run return loop.run_until_complete(coro) File "/opt/anaconda3/lib/python3.8/site-packages/nest_asyncio.py", line 96, in run_until_complete return f.result() File "/opt/anaconda3/lib/python3.8/asyncio/futures.py", line 178, in result raise self._exception File "/opt/anaconda3/lib/python3.8/asyncio/tasks.py", line 282, in __step result = coro.throw(exc) File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 816, in async_execute_cell exec_reply = await self.task_poll_for_reply File "/opt/anaconda3/lib/python3.8/asyncio/futures.py", line 260, in __await__ yield self # This tells Task to wait for completion. File "/opt/anaconda3/lib/python3.8/asyncio/tasks.py", line 349, in __wakeup future.result() File "/opt/anaconda3/lib/python3.8/asyncio/futures.py", line 178, in result raise self._exception File "/opt/anaconda3/lib/python3.8/asyncio/tasks.py", line 280, in __step result = coro.send(None) File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 633, in _async_poll_for_reply await self._async_handle_timeout(timeout, cell) File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 683, in _async_handle_timeout raise CellTimeoutError.error_from_timeout_and_cell( nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 20 seconds. The message was: Cell execution timed out. Here is a preview of the cell contents: ------------------- ['# -*- coding: utf-8 -*-', '"""', 'Created on Mon Apr 26 23:41:04 2021', '', '@author: Stepan'] ... ['T_cl, E_cl, index_cl, matrix_index_cl, ToA_cl, ToT_cl, FToA_cl, RowNo_cl, ClmNo_cl, overflow_cl,pocet_cl, Tfirst, Tlast, Etot, dT = clustering(T_tcl, E_tcl, index_tcl, matrix_index_tcl,ToA_tcl, ToT_tcl, FToA_tcl, RowNo_tcl, ClmNo_tcl, overflow_tcl, pocet)', '', 'file_t3pa_cls(t3pa_cls,T_cl, E_cl, index_cl, matrix_index_cl, ToA_cl, ToT_cl, FToA_cl, RowNo_cl, ClmNo_cl, overflow_cl,pocet_cl, Tfirst, Tlast, Etot, dT)', '', 'energy_spectrum(Tfirst, Etot)'] ------------------- [NbConvertApp] Converting notebook TimePix-e/t3pa_2cls_tokamak.ipynb to html [NbConvertApp] Executing notebook with kernel: python3 [NbConvertApp] Writing 722715 bytes to TimePix-e/analysis.html