matlab_kernel
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Calysto
kernel keeps crashing
I am able to start a notebook and evaluate a few cells. But I usually can't get too far before the kernel crashes (there is no predictability to it). If I use Cell -> run all, it will die every time. The terminal window shows no error messages. Just notes that the kernel is restarting. Ideas ?
You can run jupyter notebook --debug to get more error messages in the terminal. What versions of jupyter, matlab_kernel, and matlab are you running?
Thanks, I tried that and the random crash occurred again. Here is what I am seeing now in the terminal right before the crash:
Assertion failed: nbytes == sizeof dummy (/Volumes/100GB/conda/conda-bld/zeromq_1505916310977/work/src/signaler.cpp:206)
I can do all the same commands in Matlab directly with no issue. Sometimes I get further than this in the notebook.
FYI, I used conda install zeromq=4.2.1 but that did not fix the issue. Same error message under the debug.
I ran the same notebook on my Windows device today. In runs perfectly. So it's something to do with my Mac.
I am starting to believe (but don't know for sure) that autosave is somehow related. Is there a way anyone knows to disable it when running a matlab kernel? There is no %autosave magic available
Here are the instructions for turning off autosave: https://stackoverflow.com/a/45980165/2814123
Thanks again. It appears that disabling the autosave has stopped the random crashing. Not perfect, but it's a work around for now. Going to leave this open though.
Crud! I spoke too soon. I just got further than ever before. Still crashes randomly.
Ah, it looks like this is a known issue with libzmq on Windows: https://github.com/zeromq/libzmq/issues/1808
Thanks. I am not sure how to interpret that. I have a mac and I have a somewhat different error message (" nbytes == sizeof dummy" vs "Connection reset by peer"). I tried updating a few packages, but eventually that just prevented Jupyter from launching at all. So I reinstalled Anaconda but am back where I started: Matlab kernel randomly crashes (every few evaluations).
Do you mind trying with Calysto Bash? It is also based on metakernel, and we could narrow down our potential sources of error.
Thanks for continuing to help me. I installed Calysto Bash, but I am not sure to do from there. The notebook doesn't display output like in the sample notebook. I ran the command command jupyter notebook --debug in a cell and in the session thereby generated opened a notebook with the matlab kernel and evaluated cells until the crash occurred (never takes very long). Anyway, the cell is just showing a * instead of a number meaning that it's busy. But I don't know to do next.
Here is a screenshot.
Oh wow, you are quite right. Looks like that kernel needs some updating. In the mean time you could try https://github.com/Calysto/calysto_prolog.
Thank you again. I am not sure what I am supposed to do with a prolog kernel. One thing I did try tonight was to spend a good deal of time sending commands and variables to and from MATLAB via the matlab engine (using the console in Spyder). No crashes. So I am pretty sure it's related to either Jupyter or the kernel. But I thought I should check that it is not a bug in Python engine for matlab. I don't think it is. But of course, since the error is random, who knows? I just know the error happen frequent enough in Jupyter that I can get it to happens usually after less than 5 minutes.
Hello I get the same error:
[D 12:20:20.395 NotebookApp] activity on c564caaa-43f2-403e-92a4-c890683b5ff7: execute_input
Assertion failed: nbytes == sizeof (dummy) (/Volumes/100GB/conda/conda-bld/zeromq_1505916310977/work/src/signaler.cpp:364)
It also crashes randomly when I try to execute a command on the matlab kernel
I also followed the instructions detaled above but I was not able to solve this
I'm running into the same problem, it looks a little bit different:
Assertion failed: nbytes == sizeof dummy (src/signaler.cpp:196)
I'm using a Linux system with Matlab 2016b, Python 3.5.4, installed using Miniconda. And the following Python packages: matlab-kernel==0.15.0 matlabengineforpython===R2016b metakernel==0.20.11 pyzmq==16.0.2
For me it's usable to some extent, sometimes I can use the notebook for an hour or so without issues, but sometimes it just crashes and does not recover for a while.
Apologies, I'm not sure what else to try and I don't have a Matlab license to try and reproduce.
I solved it by reinstalling zeromq, however not by pip install. This method of installation did not work for some reason. Follow it’s github instructions
@JuanRdBO Great news! We can put a note on the README. Can you say a bit about your situation? On WIndows? Which instructions did you follow? Was it this: https://github.com/zeromq/pyzmq/wiki/Building-and-Installing-PyZMQ#building-pyzmq-from-source
This issue occurred in a macbook pro mid 2012 with macOS High Sierra v. 10.13. I installed jupyter following the instructions on this github, so a standard installation. Then I installed the matlab kernel following this GitHub.
The solution was installing zeromq using the instructions provided here in zeromq.org's website. Actually it was just a line of code: brew install zmq. After that i restarted jupyter and it worked fine. However, there are still crashes sometimes, but the amount of them has decreased to an acceptable value. I'd say one every 2 hours or so. When it crashes, it does not show any output (Even in debugging mode).
I had the same with my Macbook and Matlab R2017b installed on my machine. Apparently, running with --debug makes it more robus O_o. While before the kernel would crash every 3/4 minutes, now it still hasn't crashed yet.
Just to keep this issue alive, I can report that I have the same issue on my Mac with a similar set up to @JuanRdBO. @2dvisio's suggestion to run with --debug doesn't appear to work for me.
It might be out there but I wonder if the issue is with the cases where the output is suppressed on Matlab. I ran the example notebook and noted that the crash always occurred around
b = a + 3;
So I removed the semicolon, re-ran and the notebook executed to the end without a crash.
Just a thought!
P.S. I am creating setup instructions (as a Jupyter notebook) for a class I am teaching in February. Here is a link to the notebook cpjobling/EG-247-Resources/setup.
