I want to view an image in Jupyter notebook. It's a 9.9MB .png file.
from IPython.display import Image
Image(filename='path_to_image/image.png')
I get the below error:
IOPub data rate exceeded.
The notebook server will temporarily stop sending output
to the client in order to avoid crashing it.
A bit surprising and reported elsewhere.
Is this expected and is there a simple solution?
(Error msg suggests changing limit in --NotebookApp.iopub_data_rate_limit.)
Try this:
jupyter notebook --NotebookApp.iopub_data_rate_limit=1.0e10
Or this:
yourTerminal:prompt> jupyter notebook --NotebookApp.iopub_data_rate_limit=1.0e10
I ran into this using networkx and bokeh
This works for me in Windows 7 (taken from here):
To create a jupyter_notebook_config.py file, with all the defaults commented out, you can use the following command line:
$ jupyter notebook --generate-config
Open the file and search for c.NotebookApp.iopub_data_rate_limit
Comment out the line c.NotebookApp.iopub_data_rate_limit = 1000000 and change it to a higher default rate. l used c.NotebookApp.iopub_data_rate_limit = 10000000
This unforgiving default config is popping up in a lot of places. See git issues:
jupyter
IOPub data rate exceeded
It looks like it might get resolved with the 5.1 release
Update:
Jupyter notebook is now on release 5.2.2. This problem should have been resolved. Upgrade using conda or pip.
Removing print statements can also fix the problem.
Apart from loading images, this error also happens when your code is printing continuously at a high rate, which is causing the error "IOPub data rate exceeded". E.g. if you have a print statement in a for loop somewhere that is being called over 1000 times.
By typing 'jupyter notebook --NotebookApp.iopub_data_rate_limit=1.0e10' in Anaconda PowerShell or prompt, the Jupyter notebook will open with the new configuration. Try now to run your query.
Some additional advice for Windows(10) users:
If you are using Anaconda Prompt/PowerShell for the first time, type "Anaconda" in the search field of your Windows task bar and you will see the suggested software.
Make sure to open the Anaconda prompt as administrator.
Always navigate to your user directory or the directory with your Jupyter Notebook files first before running the command. Otherwise you might end up somewhere in your system files and be confused by an unfamiliar file tree.
The correct way to open Jupyter notebook with new data limit from the Anaconda Prompt on my own Windows 10 PC is:
(base) C:\Users\mobarget\Google Drive\Jupyter Notebook>jupyter notebook --NotebookApp.iopub_data_rate_limit=1.0e10
I have the same problem in my Jupyter NB on Win 10 when querying from a MySQL database.
Removing any print statements solved my problem.
For already running docker containers, try editing the file name - ~/.jupyter/jupyter_notebook_config.py
uncomment the line - NotebookApp.iopub_data_rate_limit =
and set high number like 1e10.
Restart the docker, it should fix the problem
I ran into this problem running version 6.3.0. When I tried the top rated solution by Merlin the powershell prompt notified me that iopub_data_rate_limit has moved from NotebookApp to ServerApp. The solution still worked but wanted to mention the variation, especially as internal handling of the config may become deprecated.
Easy workaround is to create a for loop and print. Then there wont be any issue. Printing directly wcc would cause if graph is huge. Hence any of below code will work as workaround.
wcc=list(nx.weakly_connected_components(train_graph))
for i in range(1,10):
print(wcc[i])
for i in wcc):
print(wcc)
Like others pointed out, print statement at a high rate can cause this. Resolve it by printing modulo a number using if statement. Example in python:
k = 10
if (i % k == 0):
print("Something")
Increase k if the warning persists.
Using Visual Studio Code, the Jupyter extension will be able to handle big data. launch from anaconda navigator
In general, trying to print something that is too long will trigger this error. I tried to print a string that was 9221593 characters long (too long), and that triggered the error.
Related
Currently, a jupyter notebook does not show the lateral table of contents. All the other notebooks do.
In fact, for that notebook under menu->edit the nbextensions config disappeared, so, it looks like that notebook does not load the extension.
My jupyter version is 4.4.0.
How to fix that notebook?
I found the solution to this problem. All those advises like "close and then re-open", "clean output of the notebook" or "re-install extensions" won't work. The problem is in the javascript load timeouts.
In firefox press F12 and press on the red icon in the top right corner - you will see that you have an error
Load timeout for modules:
custom/custom,nbextensions/nbextensions_configurator/config_menu/main,
bla-bla-bla...
How to solve:
close the notebook in jupyter, open your ipynb file in any text editor, go to the end of it - you will find "metadata" section. Add the line
"setTimeout": 120
create a file ~/.jupyter/custom/custom.js if you don't have it (I have Linux, where it is in Windows - I have no idea, google for it) and put this contents into this file:
window.requirejs.config({
waitseconds: 90, // default is 30s
});
This page describes the problem in detail:
https://github.com/ipython-contrib/jupyter_contrib_nbextensions/issues/1195
In my case, disabling my ad-blocker brought the table of contents back.
Apparently, all it needs is to shutdown the notebook. After restarting it, all works fine. I suppose that problem happens when the notebook has been closed wrongly without the proper "close and halt" procedure.
My solution in these cases is, make a copy (File <Make a Copy), delete the original notebook and rename the copy (File <Rename)
For me it seems that one of the following steps worked:
Update all packages and jupyter notebook to the latest version using conda
Uninstall then install again the nbextensions configurator
Reboot the computer
For me the reason was 22 emojis in the headers, deleting 5 of them was enough for firefox to get toc back with no reloading and kernel operations.
I have the problem with Jupyter notebook version 6.1.4. After installing nbextensions and enabling extension "Table of Contents (2)" (as "toc" and "toc2" don't work), I cannot obtain the TOC of an a notebook (2.8 MB), while new notebooks have a table of contents.
Reloading, reopening, restarting jupyter does not help, even after a long wait (> 15 min).
I have tried with browsers Mozilla Firefox version 83 and Chromium version 87.
However, a workaround is to create a new notebook (with TOC), then copy all cells from old notebook to new notebook. In order to do this, this might be useful:
how to copy cells from notebook to notebook and
how to select all cells.
Actually I could not copy all cells at once, I had to do three partial copies.
Alas, my method is not only painful but also ineffective in the long term, as the TOC disappeared again.
Restarting the computer worked or did not work.
Opening a small notebook with a table of content and reloading the big notebook worked or did not work.
The problem concerns all Nbextensions, they are just not active for the big notebook. A Javascript console is shown in Google Chrome with Control Shift J.
Error: Load timeout for modules:
nbextensions/nbextensions_configurator/config_menu/main,nbextensions/init_cell/main,nbextensions/spellchecker/main,nbextensions/toc2/main,nbextensions/jupyter-js-widgets/extension
I'm trying to open a jupyter notebook and it takes a long time and I see at the bottom it's trying to load various [MathJax] extension, e.g. at the bottom left of the chrome browser it says:
Loading [MathJax]/extensions/safe.js
Eventually, the notebook loads, but it's frozen and then at the bottom left it keeps showing that it's trying to load other [MathJax] .js files.
Meanwhile, the "pages unresponsive do you want to kill them" pop up keeps popping up.
I have no equations or plots in my notebook so I can't understand what is going on. My notebook never did this before.
I googled this and some people said to delete the ipython checkpoints. Where would those be? I'm on Mac OS and using Anaconda.
conda install -c conda-forge nbstripout
nbstripout filename.ipynb. Make sure that there is no whitespace in the filename.
I had a feeling that the program in my Jupyter notebook was stuck trying to produce some output, so I restarted the kernel and cleared output and that seemed to do the trick!
If Jupyter crashes while opening the ipynb file, try "using nbstripout to clear output directly from the .ipynb file via command line"(bndwang). Install with pip install nbstripout
I was having the same problem with jupyter notebook. My recommendations to you are as follows:
First, check the size of the .ipynb file you are trying to open. Probably the file size is in MB and is large. One of the reasons for this might be the output of a dataset that you previously displayed all rows.
For example;
In order to check the dataset, sometimes I use pd.set_option('display.max_rows', None) instead of the .head() function. And so I view all the rows in the data set.
The large number of outputs increases the file size, making the notebook slower. Try to delete such outputs.
I think this will solve your problem.
Here restarting your kernel will not help. Instead use nbstripout to strip the output from command line.
Run this command -> nbstripout FILE.ipynb
Install nbstripout if it is not there
https://pypi.org/project/nbstripout/
It happened to me the time I decided to print a matrix for 100000 times. The notebook file became 150MB and Jupyter (in Chrome) was not able to open it: it said all the things you experienced and then the page died saying it was "OutOfMemory".
I solved the issue opening it in Visual Studio Code, there is a button "Clear All Output", then I saved the notebook again and it was back to some hundreds of KB, which I could open normally.
If you don't have Visual Studio Code installed, you can open the notebook with another editor (gedit if you use Linux or Notepad++ in Windows) and try to delete the output cells. This is more tricky since you have to pay a lot of attention in what you are deleting, otherwise the notebook will stop working.
I just installed Miniconda and the R Essentials bundle on my Windows 10 machine, following the instructions given here. Everything went swimmingly until I opened up an Anaconda command prompt and entered jupyter notebook and got an error. I then used ipython notebook which worked, so okay, no problem there.
However, after creating a new folder and trying to create a new R notebook within that folder, my Jupyter tabs started to hang. Whenever I try to do something, whether it is rename the notebook, run a block of code, basically anything, all of the Jupyter tabs sit there loading endlessly saying "Waiting for localhost..."
I try stopping the server and restarting it, but every time I try to do anything I get the same result. I also tried changing the port and running the command prompt as administrator--same result. I am using Chrome, which shouldn't be an issue.
Any ideas? I was really excited about using a Jupyter notebook to keep track of my analyses in R, but if I can't even get it to function out of the box I'll have to find a better solution.
I'm using OSX Yosemite.
I've update ipython via conda and turns out notebook also has updated version, which I'm very excited to try this.The notebook has been converted into jupyter.
I'm using python 2.X, and already have existing .ipynb files. When I open it, new window appears but there's blank and nothing. I can create first cell there, but I already have my notebook. And the kernel also loading forever. There isn't any error log in the console. What do I have to do? Please help!
Nevermind, this solve the problem https://github.com/ipython/ipython/issues/5746
I'm using ccp notebook extension, and as Ian Hawke mentioned in the thread, remove the call to the extention at profile/static/custom/custom.js
I am new to IPython Notebook. I am using the Anaconda distribution on CrunchBang (Waldorf). My development cycle is as follows:
1. Open Spyder.
2. Open the .py file if not already loaded
3. Start IPython Notebook
4. Open the specific notebook from the main IPython screen
5. Select Cell/Run All
6. Note errors. If none goto step 11.
7. Save and close the notebook
8. Shutdown the notebook from main IPython screen
9. Correct errors in Spyder and save
10. go to step 4
11. Move on to the next part of the project and start the process over.
Is there a better approach for a noob? This really gets monotonous although I am learning quite a bit.
Thanks in advance
Forget Spyder for the time being just use the IPython notebook.
1, write code in notebook
2. test it
3. when done if needed make a py file...
You really will only need Spyder later for starting out it just complicates things for no gain
Use Spyder and .py files for writing big functions, classes, modules, tests, etc.
Use IPython notebooks for interactive work where you want to keep the output together with the code (e.g. data processing and analysis, demos, etc.).
To add to Ian's answer, another useful tool is the autoreload extension, which reloads modules automatically when they are changed.
To use, type into your IPython console or notebook:
%load_ext autoreload
%autoreload 2
For example:
This way you can work on a Python file and an IPython notebook at the same time, without having to reload the Python file after each change.
In addition to #dartdog's answer about developing directly in the notebook, if you must edit .py files used by the notebook then note the reload function which allows you to re-import already imported modules without having to shutdown and reopen the notebook.