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MATLAB Login problems persist #105
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Hi @GlascherLab 4410 usually implies that your MathWorks account is not linked to the MATLAB release that's attempting to start with those credentials. I'll look deeper into this when i get in to office tomorrow, but in mean time could you please try the following
matlab -licmode online And login using the same credentials? Does MATLAB start?
Make sure you update the path to point to 24a after installing it, if you are trying this out. Finally two more pointers:
See https://github.com/mathworks-ref-arch/matlab-dockerfile/blob/main/MPM.md
The install steps listed in the main README of this repo should be the only thing you need to do to have this working on any platform. Thank you for trying the MATLAB integration for Jupyter! |
Dear Prabhakar,
thanks a lot for your super fast response and all the good tips. I installed R2024a and then I could start a MATLAB kernel in a Jupyter Lab session (started in the miniconda installation) and the tests worked! Thanks so much for this suggestion. This really made my day.
However, may I ask another question?
Originally, I wanted to install the MATLAB proxy in my system-wide homebrews installation of Python (version 3.11.10). I installed jupyterlab and the matlab proxy with
brew install jupyterlab
pip install jupyter-matlab-proxy
and it was successful. brew list jupyterlab shows
00:06 $ brew list jupyterlab
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jlpm
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-console
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-dejavu
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-events
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-execute
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-kernel
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-kernelspec
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-lab
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-labextension
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-labhub
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-migrate
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-nbconvert
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-run
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-server
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-troubleshoot
/opt/homebrew/Cellar/jupyterlab/4.3.1/bin/jupyter-trust
/opt/homebrew/Cellar/jupyterlab/4.3.1/etc/bash_completion.d/jupyter
/opt/homebrew/Cellar/jupyterlab/4.3.1/homebrew.jupyterlab.service
/opt/homebrew/Cellar/jupyterlab/4.3.1/homebrew.mxcl.jupyterlab.plist
/opt/homebrew/Cellar/jupyterlab/4.3.1/libexec/bin/ (35 files)
/opt/homebrew/Cellar/jupyterlab/4.3.1/libexec/etc/ (7 files)
/opt/homebrew/Cellar/jupyterlab/4.3.1/libexec/lib/ (8985 files)
/opt/homebrew/Cellar/jupyterlab/4.3.1/libexec/share/ (476 files)
/opt/homebrew/Cellar/jupyterlab/4.3.1/libexec/pyvenv.cfg
/opt/homebrew/Cellar/jupyterlab/4.3.1/sbom.spdx.json
/opt/homebrew/Cellar/jupyterlab/4.3.1/share/zsh/site-functions/_jupyter
and pip list
Package Version
--------------------------------- ————
...
jupyter_client 8.1.0
jupyter-contrib-core 0.4.2
jupyter-contrib-nbextensions 0.7.0
jupyter_core 5.3.0
jupyter-events 0.6.3
jupyter-highlight-selected-word 0.2.0
jupyter-matlab-proxy 0.15.3
jupyter-nbextensions-configurator 0.6.1
jupyter_server 2.5.0
jupyter-server-proxy 3.2.2
jupyter_server_terminals 0.4.4
jupyterlab-pygments 0.2.2
...
The malt proxy is installed into home-brew tree:
00:10 $ find /opt/homebrew/ -name "jupyter_matlab*"
/opt/homebrew//lib/python3.11/site-packages/jupyter_matlab_proxy-0.15.3.dist-info
/opt/homebrew//lib/python3.11/site-packages/jupyter_matlab_proxy
/opt/homebrew//lib/python3.11/site-packages/jupyter_matlab_kernel
/opt/homebrew//share/jupyter/labextensions/jupyter_matlab_labextension
/opt/homebrew//share/jupyter/kernels/jupyter_matlab_kernel
However, when I start the JupyterLab (using /opt/homebrew/bin/jupyter-lab) the Launcher does not show the MATLAB kernel icon or the Open MATLAB icon.
Does this suggest that the matlab proxy is not installed in the correct part the homebrew tree, since the Launcher appear not to be able to find the MATLAB kernel?
Thanks a lo,t for your help,
Jan
… On 20. Nov 2024, at 17:53, Prabhakar Kumar ***@***.***> wrote:
Hi @GlascherLab <https://github.com/GlascherLab>
4410 usually implies that your MathWorks account is not linked to the MATLAB release that's attempting to start with those credentials.
I'll look deeper into this when i get in to office tomorrow, but in mean time could you please try the following
start MATLAB from your terminal using
matlab -licmode online
And login using the same credentials?
Does MATLAB start?
Could you try using the jupyter integration with an older version of MATLAB? Say 24a?
Make sure you update the path to point to 24a after installing it, if you are trying this out.
Finally two more pointers:
MATLAB can now be installed using the MATLAB package manager (mpm)
See https://github.com/mathworks-ref-arch/matlab-dockerfile/blob/main/MPM.md
One doesn't need to install the MATLAB engine for python to use the jupyter integration as shown in the stack overflow answer.
You could install it only if you need to use it.
The install steps listed in the main README of this repo should be the only thing you need to do to have this working on any platform.
Thank you for trying the MATLAB integration for Jupyter!
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Dear Jan (@GlascherLab), The issue which you are seeing seems to be coming from Jupyter not registering MATLAB Kernel from the correct path. We can follow below steps to get it to a working state.
We would verify that the above was successful by running
This hopefully gets you to a place where you are able to see MATLAB Kernel as well as Open MATLAB tiles in the Jupyterlab launcher interface. Please let me know if this doesn't solve the issue with the system-wide Python and other packages. Regards, |
Dear Jan (@GlascherLab), I'll be closing this issue as it is considered resolved from our end. Please feel free to leave a comment in case the above instructions don't fully answer your questions and I'll reopen it. Thanks! |
Dear Krishnan,
thanks for these detailed instruction and apologies for not getting to try them earlier. It’s been a busy to weeks …
I followed your instructions, but encountered an error, when enabling the server extensions (see below)
Here are my steps:
Checking Phython installation
12:36 $ echo $PATH
/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/X11/bin:/Library/Apple/usr/bin:/usr/local/MacGPG2/bin:/Applications/MATLAB_R2024a.app/bin
12:39 $ which python3
/opt/homebrew/bin/python3
Installing packages
12:42 $ /opt/homebrew/bin/python3 -m pip install --no-cache-dir jupyterlab
Collecting jupyterlab
Downloading jupyterlab-4.3.2-py3-none-any.whl.metadata (16 kB)
Requirement already satisfied: async-lru>=1.0.0 in /opt/homebrew/lib/python3.11/site-packages (from jupyterlab) (2.0.4)
...
Downloading jupyterlab-4.3.2-py3-none-any.whl (11.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.7/11.7 MB 11.7 MB/s eta 0:00:00
Installing collected packages: jupyterlab
Successfully installed jupyterlab-4.3.2
12:42 $ /opt/homebrew/bin/python3 -m pip install --no-cache-dir jupyter-matlab-proxy
DEPRECATION: Loading egg at /opt/homebrew/lib/python3.11/site-packages/matlabengine-24.2-py3.11.egg is deprecated. pip 25.1 will enforce this behaviour change. A possible replacement is to use pip for package installation. Discussion can be found at pypa/pip#12330
Collecting jupyter-matlab-proxy
Downloading jupyter_matlab_proxy-0.15.4-py3-none-any.whl.metadata (15 kB)
Requirement already satisfied: aiohttp in /opt/homebrew/lib/python3.11/site-packages (from jupyter-matlab-proxy) (3.8.4)
…
Downloading jupyter_matlab_proxy-0.15.4-py3-none-any.whl (108 kB)
Installing collected packages: jupyter-matlab-proxy
Successfully installed jupyter-matlab-proxy-0.15.4
Setting JUPYTER_PATH
I added the export line to my .bashrc
12:44 $ echo $JUPYTER_PATH
/opt/homebrew/share/jupyter
Enable server extensions
/opt/homebrew/bin/jupyter server extension enable --py jupyter_server_proxy --sys-prefix
I got this message, but in the end it says that the extension was successfully enabled …
12:48 $ /opt/homebrew/bin/jupyter server extension enable --py jupyter_server_proxy --sys-prefix
jupyter_server_proxy | error adding extension (enabled: True): The module 'jupyter_server_proxy' could not be found (No module named 'jupyter_server_proxy'). Are you sure the extension is installed?
Traceback (most recent call last):
File "/opt/homebrew/Cellar/jupyterlab/4.3.1/libexec/lib/python3.12/site-packages/jupyter_server/extension/manager.py", line 323, in add_extension
extpkg = ExtensionPackage(name=extension_name, enabled=enabled)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/jupyterlab/4.3.1/libexec/lib/python3.12/site-packages/jupyter_server/extension/manager.py", line 187, in __init__
self._load_metadata()
File "/opt/homebrew/Cellar/jupyterlab/4.3.1/libexec/lib/python3.12/site-packages/jupyter_server/extension/manager.py", line 202, in _load_metadata
raise ExtensionModuleNotFound(msg) from None
jupyter_server.extension.utils.ExtensionModuleNotFound: The module 'jupyter_server_proxy' could not be found (No module named 'jupyter_server_proxy'). Are you sure the extension is installed?
Enabling: jupyter_server_proxy
- Writing config: /opt/homebrew/Cellar/jupyterlab/4.3.1/libexec/etc/jupyter
- Validating jupyter_server_proxy...
jupyter_server_proxy OK
- Extension successfully enabled.
Starting JupyterLab (as you suggested)
/opt/homebrew/bin/jupyter-lab --app-dir=/opt/homebrew/share/jupyter/lab
12:48 $ /opt/homebrew/bin/jupyter-lab --app-dir=/opt/homebrew/share/jupyter/lab
[I 2024-12-06 12:50:17.998 ServerApp] jupyterlab | extension was successfully linked.
[I 2024-12-06 12:50:18.075 LabApp] JupyterLab extension loaded from /opt/homebrew/lib/python3.11/site-packages/jupyterlab
[I 2024-12-06 12:50:18.075 LabApp] JupyterLab application directory is /opt/homebrew/share/jupyter/lab
[I 2024-12-06 12:50:18.075 LabApp] Extension Manager is 'pypi'.
[I 2024-12-06 12:50:18.094 ServerApp] jupyterlab | extension was successfully loaded.
[I 2024-12-06 12:50:18.095 ServerApp] Serving notebooks from local directory: /Users/glaescher
[I 2024-12-06 12:50:18.095 ServerApp] Jupyter Server 2.5.0 is running at:
[I 2024-12-06 12:50:18.095 ServerApp] http://localhost:8888/lab?token=e8a28dbec83dd7656c498e8ea6331be75b1f13a0a57089b7
[I 2024-12-06 12:50:18.095 ServerApp] http://127.0.0.1:8888/lab?token=e8a28dbec83dd7656c498e8ea6331be75b1f13a0a57089b7
[I 2024-12-06 12:50:18.095 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 2024-12-06 12:50:18.100 ServerApp]
To access the server, open this file in a browser:
file:///Users/glaescher/Library/Jupyter/runtime/jpserver-83410-open.html
Or copy and paste one of these URLs:
http://localhost:8888/lab?token=e8a28dbec83dd7656c498e8ea6331be75b1f13a0a57089b7
http://127.0.0.1:8888/lab?token=e8a28dbec83dd7656c498e8ea6331be75b1f13a0a57089b7
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
[W 2024-12-06 12:50:20.028 ServerApp] 404 GET /lsp/status?1733485820020 (114ca4bb1c014ea4974144cc9e01f849@::1) 7.30ms referer=http://localhost:8888/lab
[W 2024-12-06 12:50:20.129 ServerApp] 404 GET /server-proxy/servers-info?1733485820125 (114ca4bb1c014ea4974144cc9e01f849@::1) 0.83ms referer=http://localhost:8888/lab
[W 2024-12-06 12:50:20.130 ServerApp] 404 GET /server-proxy/servers-info (114ca4bb1c014ea4974144cc9e01f849@::1) 1.17ms referer=http://localhost:8888/lab
[I 2024-12-06 12:50:20.276 LabApp] Build is up to date
looking good so far. I can see the MATLAB kernel button in Jupyterlab, but when I click on it, I get
[I 2024-12-06 12:59:41.602 ServerApp] Creating new notebook in
[I 2024-12-06 12:59:41.880 ServerApp] Kernel started: 5dfe86da-601b-4171-a2a6-297a10e6554b
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
INFO:MATLABKernel:Initializing logger with log_level: INFO
INFO:MATLABKernel:Starting the kernel at pid: 83529
INFO:MATLABKernel:To connect another client to this kernel, use:
INFO:MATLABKernel: --existing kernel-5dfe86da-601b-4171-a2a6-297a10e6554b.json
[I 2024-12-06 12:59:42.535 ServerApp] Generating new user for token-authenticated request: 4b5f271391124b828cc5319d2f74e42a
[W 2024-12-06 12:59:42.536 ServerApp] 404 GET /matlab (4b5f271391124b828cc5319d2f74e42a@::1) 0.83ms referer=None
[W 2024-12-06 12:59:42.537 ServerApp] 404 GET /matlab (@::1) 0.25ms referer=None
[W 2024-12-06 12:59:42.539 ServerApp] 404 GET /matlab (@::1) 0.26ms referer=None
ERROR:MATLABKernel.5dfe86da-601b-4171-a2a6-297a10e6554b:MATLABKernel could not communicate with matlab-proxy through Jupyter server
ERROR:MATLABKernel.5dfe86da-601b-4171-a2a6-297a10e6554b:Jupyter server:
{'base_url': '/', 'hostname': 'localhost', 'password': False, 'pid': 83410, 'port': 8888, 'root_dir': '/Users/glaescher', 'secure': False, 'sock': '', 'token': 'e8a28dbec83dd7656c498e8ea6331be75b1f13a0a57089b7', 'url': 'http://localhost:8888/', 'version': '2.5.0'}
[I 2024-12-06 12:59:42.542 ServerApp] Connecting to kernel 5dfe86da-601b-4171-a2a6-297a10e6554b.
[I 2024-12-06 12:59:42.543 ServerApp] Connecting to kernel 5dfe86da-601b-4171-a2a6-297a10e6554b.
[I 2024-12-06 12:59:42.555 ServerApp] Connecting to kernel 5dfe86da-601b-4171-a2a6-297a10e6554b.
Entering a simple “x = 1:10”, I get the following error message
Error: MATLAB Kernel could not communicate with MATLAB.
Reason: Possibly due to invalid jupyter security tokens.
ERROR:MATLABKernel.5dfe86da-601b-4171-a2a6-297a10e6554b:Found a startup error:
Error: MATLAB Kernel could not communicate with MATLAB.
Reason: Possibly due to invalid jupyter security tokens.
ERROR:MATLABKernel.5dfe86da-601b-4171-a2a6-297a10e6554b:Exception occurred while processing execution request:
Error: MATLAB Kernel could not communicate with MATLAB.
Reason: Possibly due to invalid jupyter security tokens.
Any clues about what is going wrong here? Is the jupyter-matlab-prox looking in the correct place for the kernel?
Thanks a lot,
Jan
… On 6. Dec 2024, at 06:37, Krishan Sharma ***@***.***> wrote:
Dear Jan ***@***.*** <https://github.com/GlascherLab>),
I'll be closing this issue as it is considered resolved from our end. Please feel free to leave a comment in case the above instructions don't fully answer your questions and I'll reopen it. Thanks!
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Thanks for your reply, Jan! When running the command to enable the
followed by re-running the step to enable the jupyter_server_proxy extension (which should now ideally enable the extension from right location - /opt/homebrew/lib/python3.11/site-packages)
This should enable If this doesn't resolve your issue, kindly share the output of below command to help diagnose this further.
HTH! |
Dear Krishnan,
thanks for you reply.
Removing the homebrew installation of jupyterlab as you suggested also removes the “jupyter” script/binary in /opt/homebrew/bin and thus I cannot use it to enable the server extensions. There is, however, a script /opt/homebrew/bin/jupyter-lab. Can that be used instead?
Here is the output if the “pip list” command that you mentioned in your email:
DEPRECATION: Loading egg at /opt/homebrew/lib/python3.11/site-packages/matlabengine-24.2-py3.11.egg is deprecated. pip 25.1 will enforce this behaviour change. A possible replacement is to use pip for package installation. Discussion can be found at pypa/pip#12330
jupyter_client 8.1.0
jupyter-contrib-core 0.4.2
jupyter-contrib-nbextensions 0.7.0
jupyter_core 5.3.0
jupyter-events 0.6.3
jupyter-highlight-selected-word 0.2.0
jupyter-lsp 2.2.5
jupyter-matlab-proxy 0.15.4
jupyter-nbextensions-configurator 0.6.1
jupyter_server 2.5.0
jupyter-server-proxy 3.2.2
jupyter_server_terminals 0.4.4
jupyterlab 4.3.2
jupyterlab-pygments 0.2.2
jupyterlab_server 2.27.3
Thanks for you help!
Jan
… On 9. Dec 2024, at 09:53, Krishan Sharma ***@***.***> wrote:
Thanks for your reply, Jan!
When running the command to enable the jupyter_server_proxy extension, it seems like the preference is given to the jupyterlab package which was downloaded previously using brew. To troubleshoot, I would suggest we start with removing that package by running this command:
brew remove jupyterlab
followed by re-running the step to enable the jupyter_server_proxy extension (which should now ideally enable the extension from right location - /opt/homebrew/lib/python3.11/site-packages)
/opt/homebrew/bin/jupyter server extension enable --py jupyter_server_proxy --sys-prefix
This should enable jupyter_server_proxy extension in the same location as jupyter_matlab_proxy and help with progressing in the workflow.
If this doesn't resolve your issue, kindly share the output of below command to help diagnose this further.
/opt/homebrew/bin/python3 -m pip list | grep -i "jupyter"
HTH!
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Hello Jan, We need
It is perhaps a case of mixed environments here. In these logs that you shared earlier and referenced right above, you can see that I would start with removing the jupyterlab cask and performing
This would drop a jupyter executable in /opt/homebrew/bin which won't be linked to the cask and possibly help you with moving forward. Thanks! |
Hi Krishnan,
the jupyterlab casks was never installed. it was only installed as a formula, which I remove with “brew remove jupyterlab”.
When I tried to install the jupyter-core, I got the message that all requirements were already satisfied and they are referring to Python 3.11
13:55 $ /opt/homebrew/bin/python3 -m pip install --no-cache-dir jupyter-core
DEPRECATION: Loading egg at /opt/homebrew/lib/python3.11/site-packages/matlabengine-24.2-py3.11.egg is deprecated. pip 25.1 will enforce this behaviour change. A possible replacement is to use pip for package installation. Discussion can be found at pypa/pip#12330
Requirement already satisfied: jupyter-core in /opt/homebrew/lib/python3.11/site-packages (5.3.0)
Requirement already satisfied: platformdirs>=2.5 in /opt/homebrew/lib/python3.11/site-packages (from jupyter-core) (3.2.0)
Requirement already satisfied: traitlets>=5.3 in /opt/homebrew/lib/python3.11/site-packages (from jupyter-core) (5.9.0)
But still no jupyter binary in /opt/homebrew/bin
Also, Python 3.11 is the default version that homebrew links to:
14:05 $ python --version
Python 3.11.10
Do you think it would help to uninstall Python 3.12?
Thanks,
Jan
… On 9. Dec 2024, at 12:38, Krishan Sharma ***@***.***> wrote:
Hello Jan,
We need jupyter executable to enable/disable the jupyter_server_proxy extension. It appears to me that jupyter executable present in /opt/homebrew/bin was placed there by the jupyterlab cask and not when you performed jupyterlab package installation using pip.
12:48 $ /opt/homebrew/bin/jupyter server extension enable --py jupyter_server_proxy --sys-prefix
jupyter_server_proxy | error adding extension (enabled: True): The module 'jupyter_server_proxy' could not be found (No module named 'jupyter_server_proxy'). Are you sure the extension is installed?
Traceback (most recent call last):
File "/opt/homebrew/Cellar/jupyterlab/4.3.1/libexec/lib/python3.12/site-packages/jupyter_server/extension/manager.py", line 323, in add_extension
extpkg = ExtensionPackage(name=extension_name, enabled=enabled)
It is perhaps a case of mixed environments here. In these logs that you shared earlier and referenced right above, you can see that jupyter from brew is trying to update a different python environment (3.12) than your homebrew python (3.11), hence causing issues with finding jupyter_server_proxy which is a requirement for jupyter_matlab_proxy package.
I would start with removing the jupyterlab cask and performing
/opt/homebrew/bin/python3 -m pip install --no-cache-dir jupyter-core
This would drop a jupyter executable in /opt/homebrew/bin which won't be linked to the cask and possibly help you with moving forward.
Thanks!
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|
Dear Jan, Apologies for not providing complete instructions. A mere install of
This would delete the above-mentioned packages from system-wide Python environment.
At this point, you should have a
A virtual environment like Hope that helps in moving things along! |
To add to Krishan's answer, if you do want to use homebrew's installation of In a clean environment, (ie: no other conflicting PATH entries with other # Download and Install BREW
NONINTERACTIVE=1 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
if [[ "$(uname)" == "Darwin" ]]; then
BREW_BIN_DIR=/opt/homebrew/bin
elif [[ "$(uname)" == "Linux" ]]; then
BREW_BIN_DIR=/home/linuxbrew/.linuxbrew/bin
fi
# Add BREW to PATH
export PATH=$BREW_BIN_DIR:$PATH
# Install JupyterLab using brew
brew install jupyterlab
# Find the right Python to Use
PYTHON_USED_BY_JUPYTER=$(cat `which jupyter` | head -n 1 | cut -d '!' -f 2)
PATH_TO_PYTHON=$(echo $PYTHON_USED_BY_JUPYTER | xargs dirname)
export PATH=$PATH_TO_PYTHON:$PATH
# Install the MATLAB Integration for Jupyter
$PYTHON_USED_BY_JUPYTER -m pip install jupyter-matlab-proxy
# Start using JupyterLab
jupyter lab --ip 0.0.0.0
|
Dear Krishnan,
thanks for providing these more extended instructions.
I uninstalled and re-installed the different jupyter packages, but with the newly installed jupyter-core 5.7.2 the server subcommand is no longer supported, only the subcommand “serverextension”. With that I was able to start the server extensions. Yeah!
When I then start JupyterLab, I get the MATLAB Kernel button in the Launcher (but not the Start MATLAB button), and this on the Terminal
13:14 $ /opt/homebrew/bin/jupyter-lab --app-dir=/opt/homebrew/share/jupyter/lab
[I 2024-12-10 13:15:04.413 ServerApp] jupyterlab | extension was successfully linked.
[I 2024-12-10 13:15:04.461 LabApp] JupyterLab extension loaded from /opt/homebrew/lib/python3.11/site-packages/jupyterlab
[I 2024-12-10 13:15:04.461 LabApp] JupyterLab application directory is /opt/homebrew/share/jupyter/lab
[I 2024-12-10 13:15:04.461 LabApp] Extension Manager is 'pypi'.
[I 2024-12-10 13:15:04.480 ServerApp] jupyterlab | extension was successfully loaded.
[I 2024-12-10 13:15:04.480 ServerApp] Serving notebooks from local directory: /Users/glaescher
[I 2024-12-10 13:15:04.480 ServerApp] Jupyter Server 2.5.0 is running at:
[I 2024-12-10 13:15:04.480 ServerApp] http://localhost:8888/lab?token=116e6c41e5369c5160479ab19ae30910c85047003be61dca
[I 2024-12-10 13:15:04.480 ServerApp] http://127.0.0.1:8888/lab?token=116e6c41e5369c5160479ab19ae30910c85047003be61dca
[I 2024-12-10 13:15:04.480 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 2024-12-10 13:15:04.486 ServerApp]
To access the server, open this file in a browser:
file:///Users/glaescher/Library/Jupyter/runtime/jpserver-10376-open.html
Or copy and paste one of these URLs:
http://localhost:8888/lab?token=116e6c41e5369c5160479ab19ae30910c85047003be61dca
http://127.0.0.1:8888/lab?token=116e6c41e5369c5160479ab19ae30910c85047003be61dca
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
[W 2024-12-10 13:15:06.397 ServerApp] 404 GET /lsp/status?1733832906389 (114ca4bb1c014ea4974144cc9e01f849@::1) 6.84ms referer=http://localhost:8888/lab
[W 2024-12-10 13:15:06.539 ServerApp] 404 GET /server-proxy/servers-info?1733832906533 (114ca4bb1c014ea4974144cc9e01f849@::1) 1.19ms referer=http://localhost:8888/lab
[I 2024-12-10 13:15:06.694 LabApp] Build is up to date
[W 2024-12-10 13:15:06.776 ServerApp] 404 GET /api/contents/Untitled.ipynb?content=0&hash=0&1733832906773 (::1): No such file or directory: Untitled.ipynb
[W 2024-12-10 13:15:06.777 ServerApp] wrote error: 'No such file or directory: Untitled.ipynb'
Traceback (most recent call last):
File "/opt/homebrew/lib/python3.11/site-packages/tornado/web.py", line 1713, in _execute
result = await result
^^^^^^^^^^^^
File "/opt/homebrew/lib/python3.11/site-packages/jupyter_server/services/contents/handlers.py", line 121, in get
model = await ensure_async(
^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 198, in ensure_async
result = await obj
^^^^^^^^^
File "/opt/homebrew/lib/python3.11/site-packages/jupyter_server/services/contents/filemanager.py", line 877, in get
raise web.HTTPError(404, "No such file or directory: %s" % path)
tornado.web.HTTPError: HTTP 404: Not Found (No such file or directory: Untitled.ipynb)
[W 2024-12-10 13:15:06.779 ServerApp] 404 GET /api/contents/Untitled.ipynb?content=0&hash=0&1733832906773 (114ca4bb1c014ea4974144cc9e01f849@::1) 2.88ms referer=http://localhost:8888/lab
[W 2024-12-10 13:15:06.780 ServerApp] 404 GET /api/contents/Untitled.ipynb?content=0&hash=0&1733832906773 (::1): No such file or directory: Untitled.ipynb
[W 2024-12-10 13:15:06.780 ServerApp] wrote error: 'No such file or directory: Untitled.ipynb'
Traceback (most recent call last):
File "/opt/homebrew/lib/python3.11/site-packages/tornado/web.py", line 1713, in _execute
result = await result
^^^^^^^^^^^^
File "/opt/homebrew/lib/python3.11/site-packages/jupyter_server/services/contents/handlers.py", line 121, in get
model = await ensure_async(
^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 198, in ensure_async
result = await obj
^^^^^^^^^
File "/opt/homebrew/lib/python3.11/site-packages/jupyter_server/services/contents/filemanager.py", line 877, in get
raise web.HTTPError(404, "No such file or directory: %s" % path)
tornado.web.HTTPError: HTTP 404: Not Found (No such file or directory: Untitled.ipynb)
[W 2024-12-10 13:15:06.780 ServerApp] 404 GET /api/contents/Untitled.ipynb?content=0&hash=0&1733832906773 (114ca4bb1c014ea4974144cc9e01f849@::1) 0.74ms referer=http://localhost:8888/lab
Pressing the MATLAB Kernel button, then provides this Terminal output
[I 2024-12-10 13:18:40.913 ServerApp] Creating new notebook in
[I 2024-12-10 13:18:41.241 ServerApp] Kernel started: d3a99574-d421-4217-94e6-997cb92698a4
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
INFO:MATLABKernel:Initializing logger with log_level: INFO
INFO:MATLABKernel:Starting the kernel at pid: 10422
INFO:MATLABKernel:To connect another client to this kernel, use:
INFO:MATLABKernel: --existing kernel-d3a99574-d421-4217-94e6-997cb92698a4.json
[I 2024-12-10 13:18:41.849 ServerApp] Generating new user for token-authenticated request: 659b03963ab34f10b6b5a399ae972394
[W 2024-12-10 13:18:41.850 ServerApp] 404 GET /matlab (659b03963ab34f10b6b5a399ae972394@::1) 0.72ms referer=None
[W 2024-12-10 13:18:41.852 ServerApp] 404 GET /matlab (@::1) 0.28ms referer=None
[W 2024-12-10 13:18:41.853 ServerApp] 404 GET /matlab (@::1) 0.27ms referer=None
ERROR:MATLABKernel.d3a99574-d421-4217-94e6-997cb92698a4:MATLABKernel could not communicate with matlab-proxy through Jupyter server
ERROR:MATLABKernel.d3a99574-d421-4217-94e6-997cb92698a4:Jupyter server:
{'base_url': '/', 'hostname': 'localhost', 'password': False, 'pid': 10376, 'port': 8888, 'root_dir': '/Users/glaescher', 'secure': False, 'sock': '', 'token': '116e6c41e5369c5160479ab19ae30910c85047003be61dca', 'url': 'http://localhost:8888/', 'version': '2.5.0'}
[I 2024-12-10 13:18:41.857 ServerApp] Connecting to kernel d3a99574-d421-4217-94e6-997cb92698a4.
[I 2024-12-10 13:18:41.858 ServerApp] Connecting to kernel d3a99574-d421-4217-94e6-997cb92698a4.
[I 2024-12-10 13:18:41.869 ServerApp] Connecting to kernel d3a99574-d421-4217-94e6-997cb92698a4.
And the executing “x = 1:10” in a code block, give this error message
ERROR:MATLABKernel.d3a99574-d421-4217-94e6-997cb92698a4:Found a startup error:
Error: MATLAB Kernel could not communicate with MATLAB.
Reason: Possibly due to invalid jupyter security tokens.
ERROR:MATLABKernel.d3a99574-d421-4217-94e6-997cb92698a4:Exception occurred while processing execution request:
Error: MATLAB Kernel could not communicate with MATLAB.
Reason: Possibly due to invalid jupyter security tokens.
I found this conversation from last year <#23> on your GitHub Issues. Does this also apply in my case?
Thanks a lot,
Jan
… On 10. Dec 2024, at 10:52, Krishan Sharma ***@***.***> wrote:
Dear Jan,
Apologies for not providing complete instructions. A mere install of jupyter-core will simply will ignore the install process if site-packages are already present. Let's try first getting into a clean state before performing install step.
Remove existing installs of various jupyter-related packages:
/opt/homebrew/bin/python3 -m pip uninstall -y jupyter-core jupyterlab jupyter-server-proxy jupyter-matlab-proxy
This would delete the above-mentioned packages from system-wide Python environment.
Perform re-install of the required packages:
/opt/homebrew/bin/python3 -m pip install jupyter-core jupyterlab jupyter-server-proxy jupyter-matlab-proxy
At this point, you should have a jupyter executable dropped under /opt/homebrew/bin.
Enable jupyter-server-proxy extension:
/opt/homebrew/bin/jupyter server extension enable --py jupyter_server_proxy --sys-prefix
Finally, try launching jupyter-lab:
/opt/homebrew/bin/jupyter-lab --app-dir=/opt/homebrew/share/jupyter/lab
A virtual environment like miniconda, venv, pyenv makes things easy by isolating Python environments and ensuring that all the packages are installed and launched from same location. With the usage of System Python, the end-user is responsible for ensuring the isolation and that's where these issues seems to be stemming from.
Hope that helps in moving things along!
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Thanks, Prabhakar for these insightful instructions. But this would mean that I have reinstall my entire Homebrew tree with all the other packages, no? I would try to avoid that as it will quite a bit time to get it back to the state where it is now.
… On 10. Dec 2024, at 12:49, Prabhakar Kumar ***@***.***> wrote:
To add to Krishan's answer, if you do want to use homebrew's installation of jupyterlab directly, then you have to make sure that you install jupyter-matlab-proxy into the python environment that is installed by brew install jupyterlab.
In a clean environment, (ie: no other conflicting PATH entries with other jupyter or matlab-proxy-app executables.) one could run the following sequence of commands starting from homebrew installation:
# Download and Install BREW
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
if [[ "$(uname)" == "Darwin" ]]; then
BREW_BIN_DIR=/opt/homebrew/bin
elif [[ "$(uname)" == "Linux" ]]; then
BREW_BIN_DIR=/home/linuxbrew/.linuxbrew/bin
fi
# Add BREW to PATH
export PATH=$BREW_BIN_DIR:$PATH
# Install JupyterLab using brew
brew install jupyterlab
# Find the right Python to Use
PYTHON_USED_BY_JUPYTER=$(cat `which jupyter` | head -n 1 | cut -d '!' -f 2)
PATH_TO_PYTHON=$(echo $PYTHON_USED_BY_JUPYTER | xargs dirname)
export PATH=$PATH_TO_PYTHON:$PATH
# Install the MATLAB Integration for Jupyter
$PYTHON_USED_BY_JUPYTER -m pip install jupyter-matlab-proxy
# Start using JupyterLab
jupyter lab --ip 0.0.0.0
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You could simply skip the line that installs HOWEBREW. Just make sure that Because we want to be sure that |
Would this interfere with Krishnan’s manual re-installation the jupyter packages (core and server-proxy) using python -m pip install (outside of homebrew?)
… On 10. Dec 2024, at 13:41, Prabhakar Kumar ***@***.***> wrote:
@GlascherLab <https://github.com/GlascherLab>
You could simply skip the line that installs HOWEBREW.
And try running the rest?
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It might be easier help resolve this over a call, I've sent an invite to the email address on your github profile |
Dear Prabhakar,
thanks so much for our offer to work this out in a call. I could be available tomorrow (Dec 12 at 1pm CET). Would that fit your schedule or is this too early? (I am not sure which time zone you are on.)
Also, even though I would like to use the system-wide Phyton installation with the MATLAB proxy, if this turns out to be too complicated, I could also create a conda environment and run it form there, if that is any easier in your opinion. Please let me know.
Thanks,
Jan
… On 10. Dec 2024, at 14:23, Prabhakar Kumar ***@***.***> wrote:
@GlascherLab <https://github.com/GlascherLab>
It might be easier help resolve this over a call, I've sent an invite to the email address on your github profile
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Dear Jan, At the end of the day, the choice of python installation and environment configuration is based on your usecase, and both configurations (global or env based) are easily done. It would however require care on your part to know what to expect when you are dealing with each environment. We can discuss more on this in the call tomorrow. Thank you for using the MATLAB integration for Jupyter! Sincerely |
Excellent. I look forward to this. Just responded from the other email to which my GitHub is linked.
See you tomorrow. And thanks!
Jan
… On 11. Dec 2024, at 13:14, Prabhakar Kumar ***@***.***> wrote:
Dear Jan,
I've sent the updated meeting invite for Dec 12, 1pm CET. That time works beautifully for my time zone.
At the end of the day, the choice of python installation and environment configuration is based on your usecase, and both configurations (global or env based) are easily done. It would however require care on your part to know what to expect when you are dealing with each environment. We can discuss more on this in the call tomorrow.
Thank you for using the MATLAB integration for Jupyter!
Sincerely
Prabhakar
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Dear Prabhakar and Krishnan,
in preparation for our meeting call today, I tried Prabhakar’s suggestion of installing jupyterlab from the homebrew tree and carefully selecting the corresponding Python version … and I got it up and running. Thanks so much for your continued support in getting the MATLAB proxy running with the system-wide installation of Python. For what it's worth (maybe for inclusion in the installation instruction), here are the steps that worked for me.
1. Remove pip installation of jupyter-related packages
/opt/homebrew/bin/python3 -m pip uninstall -y jupyter-core jupyterlab jupyter-server-proxy jupyter-matlab-proxy
2. Confirm that homebrew/bin and $MATLABROOT/bin folder is on system path
echo $PATH
10:42 $ echo $PATH
/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/Apple/usr/bin:/usr/local/MacGPG2/bin:/Applications/MATLAB_R2024a.app/bin
3. Install jupyterlab from homebrew distribution
brew install jupyterlab
During the installation, I was told to link jupyterlab
brew link jupyterlab
However, on my system this pulled Python 3.13 as a dependency and installed it as the default Python version.
3a. Switch to Python 3.11 as default version
brew unlink ***@***.*** && brew link ***@***.***
This removes the symlink python3 in /opt/homebrew/bin, so I relinked it
cd /opt/homebrew/bin
ln -s python3.11 python3
4a. Check the version of jupyter-related package
jupyter —version
10:57 $ jupyter --version
Selected Jupyter core packages...
IPython : 8.30.0
ipykernel : 6.29.5
ipywidgets : not installed
jupyter_client : 8.6.3
jupyter_core : 5.7.2
jupyter_server : 2.14.2
jupyterlab : 4.3.3
nbclient : 0.10.1
nbconvert : 7.16.4
nbformat : 5.10.4
notebook : 7.3.1
qtconsole : not installed
traitlets : 5.14.3
5. Determine Python version
PYTHON_USED_BY_JUPYTER=$(cat `which jupyter` | head -n 1 | cut -d '!' -f 2)
PATH_TO_PYTHON=$(echo $PYTHON_USED_BY_JUPYTER | xargs dirname)
export PATH=$PATH_TO_PYTHON:$PATH
11:02 $ echo $PATH_TO_PYTHON
/opt/homebrew/Cellar/jupyterlab/4.3.3/libexec/bin
6. Install server and MATLAB proxy (using homebrew python)
/opt/homebrew/bin/python3 -m pip install --no-cache-dir jupyter-server-proxy jupyter-matlab-proxy
This also re-installed the jupyter-core package
7. Enable server extensions
/opt/homebrew/bin/jupyter server extension enable --py jupyter_server_proxy --sys-prefix
11:09 $ /opt/homebrew/bin/jupyter server extension enable --py jupyter_server_proxy --sys-prefix
Enabling: jupyter_server_proxy
- Writing config: /opt/homebrew/Cellar/jupyterlab/4.3.3/libexec/etc/jupyter
- Validating jupyter_server_proxy...
jupyter_server_proxy OK
- Extension successfully enabled.
8. Start JupyterLab
jupyter lab
This now starts the Launcher with the MATLAB Kernel and the Open MATLAB button and both seem to work.
Looking forward to out meeting in a few minutes.
Jan
… On 11. Dec 2024, at 13:14, Prabhakar Kumar ***@***.***> wrote:
Dear Jan,
I've sent the updated meeting invite for Dec 12, 1pm CET. That time works beautifully for my time zone.
At the end of the day, the choice of python installation and environment configuration is based on your usecase, and both configurations (global or env based) are easily done. It would however require care on your part to know what to expect when you are dealing with each environment. We can discuss more on this in the call tomorrow.
Thank you for using the MATLAB integration for Jupyter!
Sincerely
Prabhakar
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That's great news, Jan! Thank you for listing out the steps that worked in your case. Glad we could help. Closing this issue as completed. |
Summary
I have installed a miniconda python setup on a Macbookd Pro (Apple M3 Silicon chipset) and a MATLAB R2024b installed and added to my system path. Following this descriptions, I ran
cd /Applications/MATLAB_R2024b.app/extern/engines/python/; python setup.py install
and then ued miniconda's
pip
to install jupyter-matlab-proxy and jupyterlabpip install jupyter-matlab-proxy; pip install jupyterlab
When I choose the MATLAB kernel in the Laucher, I get to the MATLAB login page, where I entered my credentials using the Online License Manager for individaul licenses. I then get
when I enter any command. Clicking on "Open MATLAB" I see
Any hints on how to solve this isseu would be highly appreciated.
Thanks.
PS: The throbleshooting scripts alerts me that Python is not installed. However, I rand the script with miniconda Python as well as with my other homebrew Python installation. Not sure if this is somehow related ...
Browser(s) used
Chrome
Issue found in
MATLAB Kernel
Script output
17:28 $ python troubleshooting.py
matlab - /Applications/MATLAB_R2024b.app/bin/matlab OK
matlab-proxy-app - /opt/homebrew/bin/matlab-proxy-app OK
jupyter - /opt/homebrew/bin/jupyter OK
python - None X
Recommendation: python is not installed. Please install python.
pip - /opt/homebrew/bin/pip OK
pip 24.3.1 from /opt/homebrew/lib/python3.11/site-packages/pip (python 3.11)
python3 - /opt/homebrew/bin/python3 OK
Python 3.11.10
Darwin
23.5.0
macOS-14.5-arm64-arm-64bit
uname_result(system='Darwin', node='synapse.local', release='23.5.0', version='Darwin Kernel Version 23.5.0: Wed May 1 20:13:18 PDT 2024; root:xnu-10063.121.3~5/RELEASE_ARM64_T6030', machine='arm64')
conda - None
/bin/sh: python: command not found
Config dir: /Users/glaescher/.jupyter
Config dir: /opt/homebrew/Cellar/jupyterlab/4.3.1/libexec/etc/jupyter
jupyter_lsp enabled
- Validating jupyter_lsp...
jupyter_lsp 2.2.5 OK
jupyter_server_terminals enabled
- Validating jupyter_server_terminals...
jupyter_server_terminals 0.5.3 OK
jupyterlab enabled
- Validating jupyterlab...
jupyterlab 4.3.1 OK
notebook enabled
- Validating notebook...
notebook 7.0.7 OK
notebook_shim enabled
- Validating notebook_shim...
notebook_shim OK
Config dir: /usr/local/etc/jupyter
JupyterLab v4.3.1
/opt/homebrew/Cellar/jupyterlab/4.3.1/libexec/share/jupyter/labextensions
jupyterlab_pygments v0.3.0 enabled OK (python, jupyterlab_pygments)
@jupyter-notebook/lab-extension v7.0.7 enabled OK
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