AttributeError: 'NoneType' object has no attribute 'thread'

[yashk2810]

After running a jupyter notebook using jupyter nbconvert --to notebook --execute <notebook_name> --ExecutePreprocessor.timeout=15000 --inplace, I get the following error:

Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "/usr/lib/python3.5/logging/__init__.py", line 1881, in shutdown
    h.flush()
  File "/home/kbuilder/.local/lib/python3.5/site-packages/absl/logging/__init__.py", line 882, in flush
    self._current_handler.flush()
  File "/home/kbuilder/.local/lib/python3.5/site-packages/absl/logging/__init__.py", line 776, in flush
    self.stream.flush()
  File "/tmpfs/src/tf_docs_env/lib/python3.5/site-packages/ipykernel/iostream.py", line 341, in flush
    if self.pub_thread.thread.is_alive():
AttributeError: 'NoneType' object has no attribute 'thread'

This is the line where it fails: https://github.com/ipython/ipykernel/blob/master/ipykernel/iostream.py#L341

What can I do to fix it?

[yashk2810]

Jupyter version: jupyter-core-4.5.0 mistune-0.8.4 nbconvert-5.5.0 nbformat-4.4.0 notebook-6.0.0

[zertrin]

Same here, executing:

jupyter nbconvert \
  --to notebook \
  --ExecutePreprocessor.kernel_name=python3 \
  --ExecutePreprocessor.timeout=600 \
  --execute ${IPYNB_OUTPUT} \
  --output ${IPYNB_OUTPUT} \
  --allow-errors

Output:

[NbConvertApp] Executing notebook with kernel: python3
 Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "/home/xxxx/anaconda3/envs/zzzz/lib/python3.7/logging/__init__.py", line 2038, in shutdown
    h.flush()
  File "/home/xxxx/anaconda3/envs/zzzz/lib/python3.7/logging/__init__.py", line 1018, in flush
    self.stream.flush()
  File "/home/xxxx/anaconda3/envs/zzzz/lib/python3.7/site-packages/ipykernel/iostream.py", line 341, in flush
    if self.pub_thread.thread.is_alive():
AttributeError: 'NoneType' object has no attribute 'thread'

Note that my notebook has been successfully converted despite the error message at the end.

Versions:

Versions:
--------------------------------
python			3.7.3
ipykernel		5.1.2
ipython			7.1.1
jupyter			1.0.0
jupyter_client		5.3.1
jupyter_console		6.0.0
jupyter_core		4.4.0
nbconvert		5.6.0
notebook		6.0.0

[ebin7joseph]

same error when running kernel on kaggle

Time
#
Log Message
1.53
1
[NbConvertApp] Converting notebook __notebook__.ipynb to notebook
3.62
2
[NbConvertApp] Executing notebook with kernel: python3
4.01
3
2019-08-23 21:02:23.719627: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcudart.so.10.0
6.54
4
2019-08-23 21:02:26.249148: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2200000000 Hz
6.54
5
2019-08-23 21:02:26.249541: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55c9e57fd190 executing computations on platform Host. Devices: 2019-08-23 21:02:26.249701: I tensorflow/compiler/xla/service/service.cc:175] StreamExecutor device (0): <undefined>, <undefined>
6.55
6
2019-08-23 21:02:26.256911: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcuda.so.1
6.67
7
2019-08-23 21:02:26.381657: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
6.68
8
2019-08-23 21:02:26.384756: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55c9e58b94e0 executing computations on platform CUDA. Devices: 2019-08-23 21:02:26.384791: I tensorflow/compiler/xla/service/service.cc:175] StreamExecutor device (0): Tesla P100-PCIE-16GB, Compute Capability 6.0 2019-08-23 21:02:26.385175: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
6.68
9
2019-08-23 21:02:26.385969: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1640] Found device 0 with properties: name: Tesla P100-PCIE-16GB major: 6 minor: 0 memoryClockRate(GHz): 1.3285 pciBusID: 0000:00:04.0 2019-08-23 21:02:26.386051: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcudart.so.10.0
6.68
10
2019-08-23 21:02:26.390300: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcublas.so.10.0
6.69
11
2019-08-23 21:02:26.392756: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcufft.so.10.0 2019-08-23 21:02:26.393349: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcurand.so.10.0
6.69
12
2019-08-23 21:02:26.396490: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcusolver.so.10.0 2019-08-23 21:02:26.398342: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcusparse.so.10.0
6.70
13
2019-08-23 21:02:26.404279: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcudnn.so.7 2019-08-23 21:02:26.404435: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
6.70
14
2019-08-23 21:02:26.405313: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero 2019-08-23 21:02:26.406100: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1763] Adding visible gpu devices: 0 2019-08-23 21:02:26.406173: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcudart.so.10.0
7.23
15
2019-08-23 21:02:26.941824: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1181] Device interconnect StreamExecutor with strength 1 edge matrix: 2019-08-23 21:02:26.941888: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1187] 0 2019-08-23 21:02:26.941901: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1200] 0: N 2019-08-23 21:02:26.942225: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
7.24
16
2019-08-23 21:02:26.943237: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero 2019-08-23 21:02:26.944098: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1326] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 9768 MB memory) -> physical GPU (device: 0, name: Tesla P100-PCIE-16GB, pci bus id: 0000:00:04.0, compute capability: 6.0)
10.06
17
Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/opt/conda/lib/python3.6/logging/__init__.py", line 1944, in shutdown h.flush() File "/opt/conda/lib/python3.6/site-packages/absl/logging/__init__.py", line 882, in flush self._current_handler.flush() File "/opt/conda/lib/python3.6/site-packages/absl/logging/__init__.py", line 776, in flush self.stream.flush() File "/opt/conda/lib/python3.6/site-packages/ipykernel/iostream.py", line 341, in flush if self.pub_thread.thread.is_alive(): AttributeError: 'NoneType' object has no attribute 'thread'
10.69
18
[NbConvertApp] Writing 24406 bytes to __notebook__.ipynb
11.56
19
[NbConvertApp] Converting notebook __notebook__.ipynb to html
11.97
20
[NbConvertApp] Writing 325062 bytes to __results__.html `

[pikachust8811]

Kaggle error ++

Logs
Time # Log Message
1.70 1 [NbConvertApp] Converting notebook __notebook__.ipynb to notebook
3.79 2 [NbConvertApp] Executing notebook with kernel: python3
4.99 3 2019-08-27 03:15:56.608591: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcudart.so.10.0
45.40 4 2019-08-27 03:16:37.022190: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2200000000 Hz
45.41 5 2019-08-27 03:16:37.025627: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55c35f313dc0 executing computations on platform Host. Devices: 2019-08-27 03:16:37.025703: I tensorflow/compiler/xla/service/service.cc:175] StreamExecutor device (0): <undefined>, <undefined> 2019-08-27 03:16:37.028552: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcuda.so.1
45.52 6 2019-08-27 03:16:37.139609: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
45.53 7 2019-08-27 03:16:37.140625: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55c35f3cfe50 executing computations on platform CUDA. Devices: 2019-08-27 03:16:37.140656: I tensorflow/compiler/xla/service/service.cc:175] StreamExecutor device (0): Tesla P100-PCIE-16GB, Compute Capability 6.0 2019-08-27 03:16:37.141051: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero 2019-08-27 03:16:37.141937: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1640] Found device 0 with properties: name: Tesla P100-PCIE-16GB major: 6 minor: 0 memoryClockRate(GHz): 1.3285 pciBusID: 0000:00:04.0 2019-08-27 03:16:37.142045: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcudart.so.10.0 2019-08-27 03:16:37.143858: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcublas.so.10.0 2019-08-27 03:16:37.145679: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcufft.so.10.0 2019-08-27 03:16:37.146132: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcurand.so.10.0 2019-08-27 03:16:37.148064: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcusolver.so.10.0
45.53 8 2019-08-27 03:16:37.149869: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcusparse.so.10.0
45.53 9 2019-08-27 03:16:37.157249: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcudnn.so.7
45.54 10 2019-08-27 03:16:37.157496: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero 2019-08-27 03:16:37.158599: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero 2019-08-27 03:16:37.159549: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1763] Adding visible gpu devices: 0 2019-08-27 03:16:37.159643: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcudart.so.10.0
46.00 11 2019-08-27 03:16:37.620453: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1181] Device interconnect StreamExecutor with strength 1 edge matrix: 2019-08-27 03:16:37.620523: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1187] 0 2019-08-27 03:16:37.620537: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1200] 0: N
46.00 12 2019-08-27 03:16:37.621046: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero 2019-08-27 03:16:37.622412: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1005] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero 2019-08-27 03:16:37.623581: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1326] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 15146 MB memory) -> physical GPU (device: 0, name: Tesla P100-PCIE-16GB, pci bus id: 0000:00:04.0, compute capability: 6.0)
49.87 13 2019-08-27 03:16:41.486388: I tensorflow/stream_executor/platform/default/dso_loader.cc:42] Successfully opened dynamic library libcublas.so.10.0
241.52 14 Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/opt/conda/lib/python3.6/logging/__init__.py", line 1944, in shutdown h.flush() File "/opt/conda/lib/python3.6/site-packages/absl/logging/__init__.py", line 882, in flush self._current_handler.flush() File "/opt/conda/lib/python3.6/site-packages/absl/logging/__init__.py", line 776, in flush self.stream.flush() File "/opt/conda/lib/python3.6/site-packages/ipykernel/iostream.py", line 341, in flush if self.pub_thread.thread.is_alive(): AttributeError: 'NoneType' object has no attribute 'thread'
243.20 15 [NbConvertApp] Writing 34252 bytes to __notebook__.ipynb
244.06 16 [NbConvertApp] Converting notebook __notebook__.ipynb to html
244.57 17 [NbConvertApp] Writing 319262 bytes to __results__.html

[jaideep11061982]

kaggle notebook error ...

[BLaurent]

Hi,
I used to have this issue as well:

jupyter              1.0.0
jupyter-client       5.3.1
jupyter-console      6.0.0
jupyter-core         4.5.0
jupyterlab           1.1.1
jupyterlab-server    1.0.6
ipykernel            5.1.1
ipython              7.8.0
ipython-genutils     0.2.0
ipywidgets           7.5.1

Downgrading ipykernel to 5.1.1 fixed it.

[dobos]

Same issue here. It used to work a few days ago before I ran a conda update --all

I execute notebooks from my own python script, not with nbconvert but it's the same library.

jupyter_client            5.3.1                      py_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
ipykernel                 5.1.2            py36h5ca1d4c_0    conda-forge
ipython                   7.8.0            py36h5ca1d4c_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.5.1                      py_0    conda-forge

Downgrading to 5.1.1 works for me too.

[miss1997yuan]

it is sad because the competition i join is required to submit an offline kernel ,so i cannot connect the internet to downgrad my ipykernel

[GetCurious]

Sad...when will this be fixed?

[hadim]

Bumping here as I have the same issue.

$ conda list |grep jupyter
jupyter-archive           0.5.5                      py_0    conda-forge
jupyter_client            5.3.3                    py37_1    conda-forge
jupyter_conda             3.1.1                      py_1    conda-forge
jupyter_core              4.6.1                    py37_0    conda-forge
jupyterlab                1.2.3                      py_0    conda-forge
jupyterlab_server         1.0.6                      py_0    conda-forge
$ conda list |grep ipy
ipykernel                 5.1.3            py37h5ca1d4c_0    conda-forge
ipython                   7.9.0            py37h5ca1d4c_1    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.5.1                      py_0    conda-forge

Pinging @blink1073 as I am not sure any of the core devs saw that issue.

[pcko1]

Downgrading ipykernel to 5.1.1 fixed it.

Thanks man, you're hero.