Trying to open any notebook/lab v5-7 makes terminal completely unresponsive #7429
Description
- I checked the documentation and found no answer
- I checked to make sure that this issue has not already been filed
- ["no way to be sure" ] I'm reporting the issue to the correct repository
Description
I run Jupyter on a supermicro CentOS 8 machine. I create an ssh tunnel and work on the machine from my browser. I had a running v6 installed through conda, but after a powerout, my notebooks would not open. Since then, I have installed several different version of notebook from 5 to 7 with the correct listed dependency versions (as far as I can tell) through both pypi and conda. I uninstalled and reinstalled every major release of python from 3.5 for the kernel trying to get it to work, but to no avail. I installed a python 2 kernel, and the same behavior persists. Soon as I try to create a new notebook or open a new one, the terminal on the HPC hangs and becomes unresponsive to everything including ctrl C.
In versions 5 and 6, there is no error message. But on the latest version of jupyterlab 4.2.4, I get this:
[I 2024-07-22 09:25:03.635 ServerApp] 302 GET / (@127.0.0.1) 0.39ms
[W 2024-07-22 09:25:03.689 ServerApp] Clearing invalid/expired login cookie username-localhost-8890
[I 2024-07-22 09:25:03.689 LabApp] 302 GET /lab? (@127.0.0.1) 0.93ms
[I 2024-07-22 09:25:08.305 ServerApp] User e62304d5eea34aecb7e9d1f9ce082bcc logged in.
[I 2024-07-22 09:25:08.305 ServerApp] 302 POST /login?next=%2Flab%3F (e62304d5eea34aecb7e9d1f9ce082bcc@127.0.0.1) 1.17ms
[I 2024-07-22 09:25:09.549 LabApp] Build is up to date
[W 2024-07-22 09:25:10.603 ServerApp] 404 GET /api/contents/r5?1721665510103 (e62304d5eea34aecb7e9d1f9ce082bcc@127.0.0.1) 0.98ms referer=http://localhost:8890/lab?
[W 2024-07-22 09:25:10.603 ServerApp] 404 GET /api/contents/r5?1721665510103 (127.0.0.1): No such file or directory: r5
[I 2024-07-22 09:25:12.432 ServerApp] Creating new notebook in
This is strange, because it points to my r5 directory, even when I run the server in a completely different folder mounted on another node. Before trying to open a notebook, the web interface in my browser runs fine and can create text files and folders. But after the terminal becomes unresponsive, the browser tab does so as well.
Reproduce
I run jupyter notebook --no-browser or jupyter lab --no-browser .
I create an ssh tunnel by running:
ssh -N -f -L localhost:8890:localhost:8888 username@domain
This problem is machine specific. All triggered by a powerout and reboot. My best guess is that it's a network file system issue.
Expected behavior
Context
- Operating System and version: CentOS Linux 8
- Browser and version: Any browser
IPython : 8.26.0
ipykernel : 6.29.5
ipywidgets : 8.1.3
jupyter_client : 8.6.2
jupyter_core : 5.7.2
jupyter_server : 2.14.2
jupyterlab : 4.2.4
nbclient : 0.10.0
nbconvert : 7.16.4
nbformat : 5.10.4
notebook : 7.2.1
qtconsole : 5.5.2
traitlets : 5.14.3
Troubleshoot Output
Paste the output from running `jupyter troubleshoot` from the command line here.
$PATH:
/cm/shared/apps/slurm/19.05.8/bin
/wing2/users/mdalam/perl5/bin
/data2/cat/ncbi-blast-2.12.0+/bin
/data2/cat/te/EvoPipes-master/scripts
/wing2/users/mdalam/miniconda3/bin
/opt/sbanalyzer/bin
/usr/share/Modules/bin
/opt/marbl/meryl/meryl-1.3/bin
/usr/condabin
/cm/local/apps/gcc/9.2.0/bin
/opt/arq5x/bedtools
/usr/local/bin
/usr/bin
/usr/local/sbin
/usr/sbin
/usr/local/src/HiFiAdapterFilt
/usr/local/src/HiFiAdapterFilt/DB
/opt/phoenix-2.2.0/bin
/wing2/users/mdalam/bin
sys.path:
/newwing/wing2/users/mdalam/miniconda3/bin
/data2/scratch/cat
/opt/phoenix-2.2.0/lib
/wing2/users/mdalam/miniconda3/lib/python312.zip
/wing2/users/mdalam/miniconda3/lib/python3.12
/wing2/users/mdalam/miniconda3/lib/python3.12/lib-dynload
/wing2/users/mdalam/miniconda3/lib/python3.12/site-packages
sys.executable:
/wing2/users/mdalam/miniconda3/bin/python
sys.version:
3.12.4 | packaged by Anaconda, Inc. | (main, Jun 18 2024, 15:12:24) [GCC 11.2.0]
platform.platform():
Linux-4.18.0-305.25.1.el8_4.x86_64-x86_64-with-glibc2.28
which -a jupyter:
/wing2/users/mdalam/miniconda3/bin/jupyter
pip list:
Package Version
------------------------- --------------
anaconda-anon-usage 0.4.4
anyio 4.4.0
archspec 0.2.3
argon2-cffi 23.1.0
argon2-cffi-bindings 21.2.0
arrow 1.3.0
asttokens 2.4.1
async-lru 2.0.4
attrs 23.2.0
Babel 2.15.0
beautifulsoup4 4.12.3
bleach 6.1.0
boltons 23.0.0
Brotli 1.0.9
certifi 2024.7.4
cffi 1.16.0
charset-normalizer 2.0.4
comm 0.2.2
conda 24.5.0
conda-content-trust 0.2.0
conda-libmamba-solver 24.1.0
conda-package-handling 2.3.0
conda_package_streaming 0.10.0
cryptography 42.0.5
debugpy 1.8.2
decorator 5.1.1
defusedxml 0.7.1
distro 1.9.0
executing 2.0.1
fastjsonschema 2.20.0
fqdn 1.5.1
frozendict 2.4.2
h11 0.14.0
httpcore 1.0.5
httpx 0.27.0
idna 3.7
ipykernel 6.29.5
ipython 8.26.0
ipywidgets 8.1.3
isoduration 20.11.0
jedi 0.19.1
Jinja2 3.1.4
json5 0.9.25
jsonpatch 1.33
jsonpointer 2.1
jsonschema 4.23.0
jsonschema-specifications 2023.12.1
jupyter_client 8.6.2
jupyter_core 5.7.2
jupyter-events 0.10.0
jupyter-lsp 2.2.5
jupyter_server 2.14.2
jupyter_server_terminals 0.5.3
jupyterlab 4.2.4
jupyterlab_pygments 0.3.0
jupyterlab_server 2.27.3
jupyterlab_widgets 3.0.11
libmambapy 1.5.8
MarkupSafe 2.1.5
matplotlib-inline 0.1.7
menuinst 2.1.1
mistune 3.0.2
nbclient 0.10.0
nbconvert 7.16.4
nbformat 5.10.4
nest-asyncio 1.6.0
notebook 7.2.1
notebook_shim 0.2.4
overrides 7.7.0
packaging 24.1
pandocfilters 1.5.1
parso 0.8.4
pexpect 4.9.0
pip 24.0
platformdirs 3.10.0
pluggy 1.0.0
prometheus_client 0.20.0
prompt_toolkit 3.0.47
psutil 6.0.0
ptyprocess 0.7.0
pure_eval 0.2.3
pycosat 0.6.6
pycparser 2.21
Pygments 2.18.0
PySocks 1.7.1
python-dateutil 2.9.0.post0
python-json-logger 2.0.7
PyYAML 6.0.1
pyzmq 26.0.3
qtconsole 5.5.2
QtPy 2.4.1
referencing 0.35.1
requests 2.32.2
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rpds-py 0.19.0
ruamel.yaml 0.17.21
Send2Trash 1.8.3
setuptools 69.5.1
six 1.16.0
sniffio 1.3.1
soupsieve 2.5
stack-data 0.6.3
terminado 0.18.1
tinycss2 1.3.0
tornado 6.4.1
tqdm 4.66.4
traitlets 5.14.3
truststore 0.8.0
types-python-dateutil 2.9.0.20240316
uri-template 1.3.0
urllib3 2.2.2
wcwidth 0.2.13
webcolors 24.6.0
webencodings 0.5.1
websocket-client 1.8.0
wheel 0.43.0
widgetsnbextension 4.0.11
zstandard 0.22.0
conda list:
# packages in environment at /wing2/users/mdalam/miniconda3:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
anaconda-anon-usage 0.4.4 py312hfc0e8ea_100
anyio 4.4.0 pypi_0 pypi
archspec 0.2.3 pyhd3eb1b0_0
argon2-cffi 23.1.0 pypi_0 pypi
argon2-cffi-bindings 21.2.0 pypi_0 pypi
arrow 1.3.0 pypi_0 pypi
asttokens 2.4.1 pypi_0 pypi
async-lru 2.0.4 pypi_0 pypi
attrs 23.2.0 pypi_0 pypi
babel 2.15.0 pypi_0 pypi
beautifulsoup4 4.12.3 pypi_0 pypi
bleach 6.1.0 pypi_0 pypi
boltons 23.0.0 py312h06a4308_0
brotli-python 1.0.9 py312h6a678d5_8
bzip2 1.0.8 h5eee18b_6
c-ares 1.19.1 h5eee18b_0
ca-certificates 2024.7.2 h06a4308_0
certifi 2024.7.4 py312h06a4308_0
cffi 1.16.0 py312h5eee18b_1
charset-normalizer 2.0.4 pyhd3eb1b0_0
comm 0.2.2 pypi_0 pypi
conda 24.5.0 py312h06a4308_0
conda-content-trust 0.2.0 py312h06a4308_1
conda-libmamba-solver 24.1.0 pyhd3eb1b0_0
conda-package-handling 2.3.0 py312h06a4308_0
conda-package-streaming 0.10.0 py312h06a4308_0
cryptography 42.0.5 py312hdda0065_1
debugpy 1.8.2 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
defusedxml 0.7.1 pypi_0 pypi
distro 1.9.0 py312h06a4308_0
executing 2.0.1 pypi_0 pypi
expat 2.6.2 h6a678d5_0
fastjsonschema 2.20.0 pypi_0 pypi
fmt 9.1.0 hdb19cb5_1
fqdn 1.5.1 pypi_0 pypi
frozendict 2.4.2 py312h06a4308_0
h11 0.14.0 pypi_0 pypi
httpcore 1.0.5 pypi_0 pypi
httpx 0.27.0 pypi_0 pypi
icu 73.1 h6a678d5_0
idna 3.7 py312h06a4308_0
ipykernel 6.29.5 pypi_0 pypi
ipython 8.26.0 pypi_0 pypi
ipywidgets 8.1.3 pypi_0 pypi
isoduration 20.11.0 pypi_0 pypi
jedi 0.19.1 pypi_0 pypi
jinja2 3.1.4 pypi_0 pypi
json5 0.9.25 pypi_0 pypi
jsonpatch 1.33 py312h06a4308_1
jsonpointer 2.1 pyhd3eb1b0_0
jsonschema 4.23.0 pypi_0 pypi
jsonschema-specifications 2023.12.1 pypi_0 pypi
jupyter-client 8.6.2 pypi_0 pypi
jupyter-core 5.7.2 pypi_0 pypi
jupyter-events 0.10.0 pypi_0 pypi
jupyter-lsp 2.2.5 pypi_0 pypi
jupyter-server 2.14.2 pypi_0 pypi
jupyter-server-terminals 0.5.3 pypi_0 pypi
jupyterlab 4.2.4 pypi_0 pypi
jupyterlab-pygments 0.3.0 pypi_0 pypi
jupyterlab-server 2.27.3 pypi_0 pypi
jupyterlab-widgets 3.0.11 pypi_0 pypi
krb5 1.20.1 h143b758_1
ld_impl_linux-64 2.38 h1181459_1
libarchive 3.6.2 h6ac8c49_3
libcurl 8.7.1 h251f7ec_0
libedit 3.1.20230828 h5eee18b_0
libev 4.33 h7f8727e_1
libffi 3.4.4 h6a678d5_1
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libmamba 1.5.8 hfe524e5_2
libmambapy 1.5.8 py312h2dafd23_2
libnghttp2 1.57.0 h2d74bed_0
libsolv 0.7.24 he621ea3_1
libssh2 1.11.0 h251f7ec_0
libstdcxx-ng 11.2.0 h1234567_1
libuuid 1.41.5 h5eee18b_0
libxml2 2.10.4 hfdd30dd_2
lz4-c 1.9.4 h6a678d5_1
markupsafe 2.1.5 pypi_0 pypi
matplotlib-inline 0.1.7 pypi_0 pypi
menuinst 2.1.1 py312h06a4308_0
mistune 3.0.2 pypi_0 pypi
nbclient 0.10.0 pypi_0 pypi
nbconvert 7.16.4 pypi_0 pypi
nbformat 5.10.4 pypi_0 pypi
ncurses 6.4 h6a678d5_0
nest-asyncio 1.6.0 pypi_0 pypi
notebook 7.2.1 pypi_0 pypi
notebook-shim 0.2.4 pypi_0 pypi
openssl 3.0.14 h5eee18b_0
overrides 7.7.0 pypi_0 pypi
packaging 24.1 py312h06a4308_0
pandocfilters 1.5.1 pypi_0 pypi
parso 0.8.4 pypi_0 pypi
pcre2 10.42 hebb0a14_1
pexpect 4.9.0 pypi_0 pypi
pip 24.0 py312h06a4308_0
platformdirs 3.10.0 py312h06a4308_0
pluggy 1.0.0 py312h06a4308_1
prometheus-client 0.20.0 pypi_0 pypi
prompt-toolkit 3.0.47 pypi_0 pypi
psutil 6.0.0 pypi_0 pypi
ptyprocess 0.7.0 pypi_0 pypi
pure-eval 0.2.3 pypi_0 pypi
pybind11-abi 5 hd3eb1b0_0
pycosat 0.6.6 py312h5eee18b_1
pycparser 2.21 pyhd3eb1b0_0
pygments 2.18.0 pypi_0 pypi
pysocks 1.7.1 py312h06a4308_0
python 3.12.4 h5148396_1
python-dateutil 2.9.0.post0 pypi_0 pypi
python-json-logger 2.0.7 pypi_0 pypi
pyyaml 6.0.1 pypi_0 pypi
pyzmq 26.0.3 pypi_0 pypi
qtconsole 5.5.2 pypi_0 pypi
qtpy 2.4.1 pypi_0 pypi
readline 8.2 h5eee18b_0
referencing 0.35.1 pypi_0 pypi
reproc 14.2.4 h6a678d5_2
reproc-cpp 14.2.4 h6a678d5_2
requests 2.32.2 py312h06a4308_0
rfc3339-validator 0.1.4 pypi_0 pypi
rfc3986-validator 0.1.1 pypi_0 pypi
rpds-py 0.19.0 pypi_0 pypi
ruamel.yaml 0.17.21 py312h5eee18b_0
send2trash 1.8.3 pypi_0 pypi
setuptools 69.5.1 py312h06a4308_0
six 1.16.0 pypi_0 pypi
sniffio 1.3.1 pypi_0 pypi
soupsieve 2.5 pypi_0 pypi
sqlite 3.45.3 h5eee18b_0
stack-data 0.6.3 pypi_0 pypi
terminado 0.18.1 pypi_0 pypi
tinycss2 1.3.0 pypi_0 pypi
tk 8.6.14 h39e8969_0
tornado 6.4.1 pypi_0 pypi
tqdm 4.66.4 py312he106c6f_0
traitlets 5.14.3 pypi_0 pypi
truststore 0.8.0 py312h06a4308_0
types-python-dateutil 2.9.0.20240316 pypi_0 pypi
tzdata 2024a h04d1e81_0
uri-template 1.3.0 pypi_0 pypi
urllib3 2.2.2 py312h06a4308_0
wcwidth 0.2.13 pypi_0 pypi
webcolors 24.6.0 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.8.0 pypi_0 pypi
wheel 0.43.0 py312h06a4308_0
widgetsnbextension 4.0.11 pypi_0 pypi
xz 5.4.6 h5eee18b_1
yaml-cpp 0.8.0 h6a678d5_1
zlib 1.2.13 h5eee18b_1
zstandard 0.22.0 py312h2c38b39_0
zstd 1.5.5 hc292b87_2
conda env:
name: base
channels:
- defaults
dependencies:
- _libgcc_mutex=0.1=main
- _openmp_mutex=5.1=1_gnu
- anaconda-anon-usage=0.4.4=py312hfc0e8ea_100
- archspec=0.2.3=pyhd3eb1b0_0
- boltons=23.0.0=py312h06a4308_0
- brotli-python=1.0.9=py312h6a678d5_8
- bzip2=1.0.8=h5eee18b_6
- c-ares=1.19.1=h5eee18b_0
- ca-certificates=2024.7.2=h06a4308_0
- certifi=2024.7.4=py312h06a4308_0
- cffi=1.16.0=py312h5eee18b_1
- charset-normalizer=2.0.4=pyhd3eb1b0_0
- conda=24.5.0=py312h06a4308_0
- conda-content-trust=0.2.0=py312h06a4308_1
- conda-libmamba-solver=24.1.0=pyhd3eb1b0_0
- conda-package-handling=2.3.0=py312h06a4308_0
- conda-package-streaming=0.10.0=py312h06a4308_0
- cryptography=42.0.5=py312hdda0065_1
- distro=1.9.0=py312h06a4308_0
- expat=2.6.2=h6a678d5_0
- fmt=9.1.0=hdb19cb5_1
- frozendict=2.4.2=py312h06a4308_0
- icu=73.1=h6a678d5_0
- idna=3.7=py312h06a4308_0
- jsonpatch=1.33=py312h06a4308_1
- jsonpointer=2.1=pyhd3eb1b0_0
- krb5=1.20.1=h143b758_1
- ld_impl_linux-64=2.38=h1181459_1
- libarchive=3.6.2=h6ac8c49_3
- libcurl=8.7.1=h251f7ec_0
- libedit=3.1.20230828=h5eee18b_0
- libev=4.33=h7f8727e_1
- libffi=3.4.4=h6a678d5_1
- libgcc-ng=11.2.0=h1234567_1
- libgomp=11.2.0=h1234567_1
- libmamba=1.5.8=hfe524e5_2
- libmambapy=1.5.8=py312h2dafd23_2
- libnghttp2=1.57.0=h2d74bed_0
- libsolv=0.7.24=he621ea3_1
- libssh2=1.11.0=h251f7ec_0
- libstdcxx-ng=11.2.0=h1234567_1
- libuuid=1.41.5=h5eee18b_0
- libxml2=2.10.4=hfdd30dd_2
- lz4-c=1.9.4=h6a678d5_1
- menuinst=2.1.1=py312h06a4308_0
- ncurses=6.4=h6a678d5_0
- openssl=3.0.14=h5eee18b_0
- packaging=24.1=py312h06a4308_0
- pcre2=10.42=hebb0a14_1
- pip=24.0=py312h06a4308_0
- platformdirs=3.10.0=py312h06a4308_0
- pluggy=1.0.0=py312h06a4308_1
- pybind11-abi=5=hd3eb1b0_0
- pycosat=0.6.6=py312h5eee18b_1
- pycparser=2.21=pyhd3eb1b0_0
- pysocks=1.7.1=py312h06a4308_0
- python=3.12.4=h5148396_1
- readline=8.2=h5eee18b_0
- reproc=14.2.4=h6a678d5_2
- reproc-cpp=14.2.4=h6a678d5_2
- requests=2.32.2=py312h06a4308_0
- ruamel.yaml=0.17.21=py312h5eee18b_0
- setuptools=69.5.1=py312h06a4308_0
- sqlite=3.45.3=h5eee18b_0
- tk=8.6.14=h39e8969_0
- tqdm=4.66.4=py312he106c6f_0
- truststore=0.8.0=py312h06a4308_0
- tzdata=2024a=h04d1e81_0
- urllib3=2.2.2=py312h06a4308_0
- wheel=0.43.0=py312h06a4308_0
- xz=5.4.6=h5eee18b_1
- yaml-cpp=0.8.0=h6a678d5_1
- zlib=1.2.13=h5eee18b_1
- zstandard=0.22.0=py312h2c38b39_0
- zstd=1.5.5=hc292b87_2
- pip:
- anyio==4.4.0
- argon2-cffi==23.1.0
- argon2-cffi-bindings==21.2.0
- arrow==1.3.0
- asttokens==2.4.1
- async-lru==2.0.4
- attrs==23.2.0
- babel==2.15.0
- beautifulsoup4==4.12.3
- bleach==6.1.0
- comm==0.2.2
- debugpy==1.8.2
- decorator==5.1.1
- defusedxml==0.7.1
- executing==2.0.1
- fastjsonschema==2.20.0
- fqdn==1.5.1
- h11==0.14.0
- httpcore==1.0.5
- httpx==0.27.0
- ipykernel==6.29.5
- ipython==8.26.0
- ipywidgets==8.1.3
- isoduration==20.11.0
- jedi==0.19.1
- jinja2==3.1.4
- json5==0.9.25
- jsonschema==4.23.0
- jsonschema-specifications==2023.12.1
- jupyter-client==8.6.2
- jupyter-core==5.7.2
- jupyter-events==0.10.0
- jupyter-lsp==2.2.5
- jupyter-server==2.14.2
- jupyter-server-terminals==0.5.3
- jupyterlab==4.2.4
- jupyterlab-pygments==0.3.0
- jupyterlab-server==2.27.3
- jupyterlab-widgets==3.0.11
- markupsafe==2.1.5
- matplotlib-inline==0.1.7
- mistune==3.0.2
- nbclient==0.10.0
- nbconvert==7.16.4
- nbformat==5.10.4
- nest-asyncio==1.6.0
- notebook==7.2.1
- notebook-shim==0.2.4
- overrides==7.7.0
- pandocfilters==1.5.1
- parso==0.8.4
- pexpect==4.9.0
- prometheus-client==0.20.0
- prompt-toolkit==3.0.47
- psutil==6.0.0
- ptyprocess==0.7.0
- pure-eval==0.2.3
- pygments==2.18.0
- python-dateutil==2.9.0.post0
- python-json-logger==2.0.7
- pyyaml==6.0.1
- pyzmq==26.0.3
- qtconsole==5.5.2
- qtpy==2.4.1
- referencing==0.35.1
- rfc3339-validator==0.1.4
- rfc3986-validator==0.1.1
- rpds-py==0.19.0
- send2trash==1.8.3
- six==1.16.0
- sniffio==1.3.1
- soupsieve==2.5
- stack-data==0.6.3
- terminado==0.18.1
- tinycss2==1.3.0
- tornado==6.4.1
- traitlets==5.14.3
- types-python-dateutil==2.9.0.20240316
- uri-template==1.3.0
- wcwidth==0.2.13
- webcolors==24.6.0
- webencodings==0.5.1
- websocket-client==1.8.0
- widgetsnbextension==4.0.11
prefix: /../miniconda3
You may want to sanitize the paths in the output.
Command Line Output
Paste the output from your command line running `jupyter notebook` here, use `--debug` if possible. The output is very long. I'm creating a google doc instead: https://docs.google.com/document/d/1uwYin83aNIo1Mafy2-g9bnhckLTODSCRVl6pGFlF1XI/edit?usp=sharing
Browser Output
Paste the output from your browser Javascript console here, if applicable.
Activity