jupyterhub error

[jvonau]

Noted jupyterhub error open an issue or I will.

Originally posted by @jvonau in #3549 (comment)

[jvonau]

psutil could not be installed from sources

Long story short is that this error is very similar to #3538 solved with #3503 with PR coming

[holta]

Not sure if this applies to OS's beyond Ubuntu 23.04 and/or Python 3.11+ ?

In any case here's an example, excerpted from http://sprunge.us/r0BpIy?en :

2296 /opt/iiab/iiab/iiab-install.log-2023-04-25 20:12:41,271 p=5540 u=root n=ansible | TASK [jupyterhub : Break up jupyterhub/jupyterlab pip installs into 2 parts (3 packages above + 4 packages here) due to mutual dependency deadlock on some OS's] ***
2297 /opt/iiab/iiab/iiab-install.log-2023-04-25 20:13:28,310 p=5540 u=root n=ansible | fatal: [127.0.0.1]: FAILED! => {"changed": false, "cmd": ["/opt/iiab/jupyterhub/bin/pip3", "install", "--no-cache-dir", "jupyterlab", "jupyterhub_firstuseauthenticator", "jupyterhub-systemdspawner", "ipywidgets"], "msg": "stdout: Collecting jupyterlab\n Downloading jupyterlab-3.6.3-py3-none-any.whl (8.9 MB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.9/8.9 MB 4.5 MB/s eta 0:00:00\nCollecting jupyterhub_firstuseauthenticator\n Downloading jupyterhub_firstuseauthenticator-1.0.0-py3-none-any.whl (9.6 kB)\nCollecting jupyterhub-systemdspawner\n Downloading jupyterhub_systemdspawner-0.17.0-py3-none-any.whl (14 kB)\nCollecting ipywidgets\n Downloading ipywidgets-8.0.6-py3-none-any.whl (138 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 138.3/138.3 kB 6.4 MB/s eta 0:00:00\nCollecting ipython\n Downloading ipython-8.12.0-py3-none-any.whl (796 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 796.4/796.4 kB 5.6 MB/s eta 0:00:00\nRequirement already satisfied: packaging in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterlab) (23.1)\nRequirement already satisfied: tornado>=6.1.0 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterlab) (6.3.1)\nCollecting jupyter-core\n Downloading jupyter_core-5.3.0-py3-none-any.whl (93 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.2/93.2 kB 6.1 MB/s eta 0:00:00\nCollecting jupyterlab-server~=2.19\n Downloading jupyterlab_server-2.22.1-py3-none-any.whl (57 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.0/57.0 kB 5.9 MB/s eta 0:00:00\nCollecting jupyter-server<3,>=1.16.0\n Downloading jupyter_server-2.5.0-py3-none-any.whl (366 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 366.8/366.8 kB 5.7 MB/s eta 0:00:00\nCollecting jupyter-ydoc~=0.2.3\n Downloading jupyter_ydoc-0.2.4-py3-none-any.whl (5.9 kB)\nCollecting jupyter-server-ydoc~=0.8.0\n Downloading jupyter_server_ydoc-0.8.0-py3-none-any.whl (11 kB)\nCollecting nbclassic\n Downloading nbclassic-0.5.5-py3-none-any.whl (10.0 MB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.0/10.0 MB 5.3 MB/s eta 0:00:00\nCollecting notebook<7\n Downloading notebook-6.5.4-py3-none-any.whl (529 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 529.8/529.8 kB 5.8 MB/s eta 0:00:00\nRequirement already satisfied: jinja2>=2.1 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterlab) (3.1.2)\nCollecting bcrypt\n Downloading bcrypt-4.0.1-cp36-abi3-manylinux_2_28_aarch64.whl (583 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 583.6/583.6 kB 5.6 MB/s eta 0:00:00\nRequirement already satisfied: jupyterhub>=1.3 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterhub_firstuseauthenticator) (4.0.0)\nCollecting ipykernel>=4.5.1\n Downloading ipykernel-6.22.0-py3-none-any.whl (149 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 150.0/150.0 kB 6.9 MB/s eta 0:00:00\nRequirement already satisfied: traitlets>=4.3.1 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from ipywidgets) (5.9.0)\nCollecting widgetsnbextension~=4.0.7\n Downloading widgetsnbextension-4.0.7-py3-none-any.whl (2.1 MB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 5.4 MB/s eta 0:00:00\nCollecting jupyterlab-widgets~=3.0.7\n Downloading jupyterlab_widgets-3.0.7-py3-none-any.whl (198 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 198.2/198.2 kB 6.2 MB/s eta 0:00:00\nCollecting comm>=0.1.1\n Downloading comm-0.1.3-py3-none-any.whl (6.6 kB)\nCollecting debugpy>=1.6.5\n Downloading debugpy-1.6.7-py2.py3-none-any.whl (4.9 MB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 5.3 MB/s eta 0:00:00\nCollecting jupyter-client>=6.1.12\n Downloading jupyter_client-8.2.0-py3-none-any.whl (103 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.2/103.2 kB 6.2 MB/s eta 0:00:00\nCollecting matplotlib-inline>=0.1\n Downloading matplotlib_inline-0.1.6-py3-none-any.whl (9.4 kB)\nCollecting nest-asyncio\n Downloading nest_asyncio-1.5.6-py3-none-any.whl (5.2 kB)\nCollecting psutil\n Downloading psutil-5.9.5.tar.gz (493 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 493.5/493.5 kB 5.6 MB/s eta 0:00:00\n Installing build dependencies: started\n Installing build dependencies: finished with status 'done'\n Getting requirements to build wheel: started\n Getting requirements to build wheel: finished with status 'done'\n Preparing metadata (pyproject.toml): started\n Preparing metadata (pyproject.toml): finished with status 'done'\nCollecting pyzmq>=20\n Downloading pyzmq-25.0.2-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (865 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 865.6/865.6 kB 5.6 MB/s eta 0:00:00\nCollecting backcall\n Downloading backcall-0.2.0-py2.py3-none-any.whl (11 kB)\nCollecting decorator\n Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB)\nCollecting jedi>=0.16\n Downloading jedi-0.18.2-py2.py3-none-any.whl (1.6 MB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 5.4 MB/s eta 0:00:00\nCollecting pickleshare\n Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)\nCollecting prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30\n Downloading prompt_toolkit-3.0.38-py3-none-any.whl (385 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 385.8/385.8 kB 5.6 MB/s eta 0:00:00\nCollecting pygments>=2.4.0\n Downloading Pygments-2.15.1-py3-none-any.whl (1.1 MB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 5.4 MB/s eta 0:00:00\nCollecting stack-data\n Downloading stack_data-0.6.2-py3-none-any.whl (24 kB)\nCollecting pexpect>4.3\n Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 59.0/59.0 kB 7.2 MB/s eta 0:00:00\nRequirement already satisfied: MarkupSafe>=2.0 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jinja2>=2.1->jupyterlab) (2.1.2)\nCollecting platformdirs>=2.5\n Downloading platformdirs-3.3.0-py3-none-any.whl (15 kB)\nCollecting anyio>=3.1.0\n Downloading anyio-3.6.2-py3-none-any.whl (80 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.6/80.6 kB 8.0 MB/s eta 0:00:00\nCollecting argon2-cffi\n Downloading argon2_cffi-21.3.0-py3-none-any.whl (14 kB)\nCollecting jupyter-events>=0.4.0\n Downloading jupyter_events-0.6.3-py3-none-any.whl (18 kB)\nCollecting jupyter-server-terminals\n Downloading jupyter_server_terminals-0.4.4-py3-none-any.whl (13 kB)\nCollecting nbconvert>=6.4.4\n Downloading nbconvert-7.3.1-py3-none-any.whl (284 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 284.1/284.1 kB 5.9 MB/s eta 0:00:00\nCollecting nbformat>=5.3.0\n Downloading nbformat-5.8.0-py3-none-any.whl (77 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.4/77.4 kB 7.8 MB/s eta 0:00:00\nRequirement already satisfied: prometheus-client in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyter-server<3,>=1.16.0->jupyterlab) (0.16.0)\nCollecting send2trash\n Downloading Send2Trash-1.8.0-py3-none-any.whl (18 kB)\nCollecting terminado>=0.8.3\n Downloading terminado-0.17.1-py3-none-any.whl (17 kB)\nCollecting websocket-client\n Downloading websocket_client-1.5.1-py3-none-any.whl (55 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 55.9/55.9 kB 5.5 MB/s eta 0:00:00\nCollecting jupyter-server-fileid<1,>=0.6.0\n Downloading jupyter_server_fileid-0.9.0-py3-none-any.whl (15 kB)\nCollecting ypy-websocket<0.9.0,>=0.8.2\n Downloading ypy_websocket-0.8.4-py3-none-any.whl (10 kB)\nCollecting y-py<0.6.0,>=0.5.3\n Downloading y_py-0.5.9-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (1.6 MB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 5.5 MB/s eta 0:00:00\nRequirement already satisfied: alembic>=1.4 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterhub>=1.3->jupyterhub_firstuseauthenticator) (1.10.4)\nRequirement already satisfied: async-generator>=1.9 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterhub>=1.3->jupyterhub_firstuseauthenticator) (1.10)\nRequirement already satisfied: certipy>=0.1.2 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterhub>=1.3->jupyterhub_firstuseauthenticator) (0.1.3)\nRequirement already satisfied: jupyter-telemetry>=0.1.0 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterhub>=1.3->jupyterhub_firstuseauthenticator) (0.1.0)\nRequirement already satisfied: oauthlib>=3.0 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterhub>=1.3->jupyterhub_firstuseauthenticator) (3.2.2)\nRequirement already satisfied: python-dateutil in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterhub>=1.3->jupyterhub_firstuseauthenticator) (2.8.2)\nRequirement already satisfied: requests in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterhub>=1.3->jupyterhub_firstuseauthenticator) (2.28.2)\nRequirement already satisfied: SQLAlchemy>=1.4 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterhub>=1.3->jupyterhub_firstuseauthenticator) (2.0.10)\nRequirement already satisfied: pamela in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterhub>=1.3->jupyterhub_firstuseauthenticator) (1.0.0)\nCollecting babel>=2.10\n Downloading Babel-2.12.1-py3-none-any.whl (10.1 MB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.1/10.1 MB 5.3 MB/s eta 0:00:00\nCollecting json5>=0.9.0\n Downloading json5-0.9.11-py2.py3-none-any.whl (19 kB)\nRequirement already satisfied: jsonschema>=4.17.3 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jupyterlab-server~=2.19->jupyterlab) (4.17.3)\nCollecting ipython-genutils\n Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)\nCollecting notebook-shim>=0.1.0\n Downloading notebook_shim-0.2.3-py3-none-any.whl (13 kB)\nRequirement already satisfied: Mako in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from alembic>=1.4->jupyterhub>=1.3->jupyterhub_firstuseauthenticator) (1.2.4)\nRequirement already satisfied: typing-extensions>=4 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from alembic>=1.4->jupyterhub>=1.3->jupyterhub_firstuseauthenticator) (4.5.0)\nRequirement already satisfied: idna>=2.8 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from anyio>=3.1.0->jupyter-server<3,>=1.16.0->jupyterlab) (3.4)\nCollecting sniffio>=1.1\n Downloading sniffio-1.3.0-py3-none-any.whl (10 kB)\nRequirement already satisfied: pyopenssl in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from certipy>=0.1.2->jupyterhub>=1.3->jupyterhub_firstuseauthenticator) (23.1.1)\nCollecting parso<0.9.0,>=0.8.0\n Downloading parso-0.8.3-py2.py3-none-any.whl (100 kB)\n ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.8/100.8 kB 6.3 MB/s eta 0:00:00\nRequirement already satisfied: attrs>=17.4.0 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jsonschema>=4.17.3->jupyterlab-server~=2.19->jupyterlab) (23.1.0)\nRequirement already satisfied: pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 in /opt/iiab/jupyterhub/lib/python3.11/site-packages (from jsonschema>=4.17.3->jupyterlab-server~=2.19->jupyterlab) (0.19.3)\nRequirement already satisfied: 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0:00:00\nBuilding wheels for collected packages: psutil\n Building wheel for psutil (pyproject.toml): started\n Building wheel for psutil (pyproject.toml): finished with status 'error'\nFailed to build psutil\n\n:stderr: error: subprocess-exited-with-error\n \n × Building wheel for psutil (pyproject.toml) did not run successfully.\n │ exit code: 1\n ╰─> [47 lines of output]\n running bdist_wheel\n running build\n running build_py\n creating build\n creating build/lib.linux-aarch64-cpython-311\n creating build/lib.linux-aarch64-cpython-311/psutil\n copying psutil/init.py -> build/lib.linux-aarch64-cpython-311/psutil\n copying psutil/_pssunos.py -> build/lib.linux-aarch64-cpython-311/psutil\n copying psutil/_common.py -> build/lib.linux-aarch64-cpython-311/psutil\n copying psutil/_psaix.py -> build/lib.linux-aarch64-cpython-311/psutil\n copying psutil/_psosx.py -> build/lib.linux-aarch64-cpython-311/psutil\n copying psutil/_psbsd.py -> build/lib.linux-aarch64-cpython-311/psutil\n copying psutil/_pswindows.py -> build/lib.linux-aarch64-cpython-311/psutil\n copying psutil/_compat.py -> build/lib.linux-aarch64-cpython-311/psutil\n copying psutil/_pslinux.py -> build/lib.linux-aarch64-cpython-311/psutil\n copying psutil/_psposix.py -> build/lib.linux-aarch64-cpython-311/psutil\n creating build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/runner.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/init.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_bsd.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_system.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_windows.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_connections.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/main.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_memleaks.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_sunos.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_contracts.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_osx.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_unicode.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_posix.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_process.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_linux.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_testutils.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_aix.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n copying psutil/tests/test_misc.py -> build/lib.linux-aarch64-cpython-311/psutil/tests\n running build_ext\n building 'psutil._psutil_linux' extension\n creating build/temp.linux-aarch64-cpython-311\n creating build/temp.linux-aarch64-cpython-311/psutil\n aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=595 -DPy_LIMITED_API=0x03060000 -DPSUTIL_LINUX=1 -I/opt/iiab/jupyterhub/include -I/usr/include/python3.11 -c psutil/_psutil_common.c -o build/temp.linux-aarch64-cpython-311/psutil/_psutil_common.o\n psutil/_psutil_common.c:9:10: fatal error: Python.h: No such file or directory\n 9 | #include <Python.h>\n | ^~~~~~~~~~\n compilation terminated.\n psutil could not be installed from sources. Perhaps Python header files are not installed. Try running:\n sudo apt-get install gcc python3-dev\n error: command '/usr/bin/aarch64-linux-gnu-gcc' failed with exit code 1\n [end of output]\n \n note: This error originates from a subprocess, and is likely not a problem with pip.\n ERROR: Failed building wheel for psutil\nERROR: Could not build wheels for psutil, which is required to install pyproject.toml-based projects\n"}
2298 /opt/iiab/iiab/iiab-install.log:2023-04-25 20:13:28,373 p=5540 u=root n=ansible | TASK [jupyterhub : SEE ERROR ABOVE (skip_role_on_error: False)] ****************

[jvonau]

side note nodejs repo should be removed if the curl install fails to install.

[jvonau]

https://pypi.org/project/psutil/#files

[jvonau]

giampaolo/psutil#2206
giampaolo/psutil#2163

[holta]

Resolved by:

• PR JupyterHub tightened up w/ python3-psutil, --system-site-packages [python3-venv also removed from Calibre-Web & Lokole] [Node.js apt source pollution detox] #3554

[whomobile]

In case any comes here to fix "#include <Python.h>" not found issue with psutils
you will need to install correct python dev lib for your python. (error message is not wrong but not correct " sudo apt-get install gcc python3-dev" if you have more than one python verion.)

e.g. use one of following

apt-get install -y python3.11-dev
apt-get install -y python3.10-dev
apt-get install -y python3.12-dev
apt-get install -y python3.13-dev