Dead kernel #159

carloslesmes · 2014-03-19T05:05:54Z

After a few days I opened a note and found this message:

Dead kernel
The kernel has died, and the automatic restart has failed. It is possible the kernel cannot be restarted. If you are not able to restart the kernel, you will still be able to save the notebook, but running code will no longer work until the notebook is reopened.

Kernel Restarting
The kernel appears to have died. It will restart automatically.

Alternating...

I can't find a way to restart the kernel, please help.

The text was updated successfully, but these errors were encountered:

Keno · 2014-03-19T05:11:22Z

You can restart the kernel in the Kernel menu. As to why it failed, that's hard to say, there may be lots of reasons from bugs in Julia over bugs in IJulia to bugs in IPython.

carloslesmes · 2014-03-19T05:14:22Z

I get the same messages repeatedly...

Any idea of what to do?

stevengj · 2014-03-19T13:58:33Z

Did your Julia installation change? If you installed a new version of Julia (e.g. you changed the path to Julia), then you will need to quit IPython completely (stop the IPython server), rerun Pkg.build("IJulia") at the Julia command-line, then re-run ipython notebook --profile julia.

QCaudron · 2014-03-24T14:26:47Z

My kernels keep dying as well. I wasn't able to run anything at all, things just kept dying.

This was a brand new install of Julia and IJulia. Error messages are uninformative :

2014-03-24 10:25:17.484 [NotebookApp] The IPython Notebook is running at: http://127.0.0.1:8998/
2014-03-24 10:25:17.484 [NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
2014-03-24 10:25:20.307 [NotebookApp] Connecting to: tcp://127.0.0.1:59844
2014-03-24 10:25:20.309 [NotebookApp] Kernel started: a414a11a-99aa-407a-9571-fa9f2b77e377
2014-03-24 10:25:20.520 [NotebookApp] Connecting to: tcp://127.0.0.1:59841
2014-03-24 10:25:20.576 [NotebookApp] Connecting to: tcp://127.0.0.1:59843
2014-03-24 10:25:20.584 [NotebookApp] Connecting to: tcp://127.0.0.1:59842
2014-03-24 10:25:23.308 [NotebookApp] KernelRestarter: restarting kernel (1/5)
WARNING:root:kernel a414a11a-99aa-407a-9571-fa9f2b77e377 restarted
2014-03-24 10:25:26.313 [NotebookApp] KernelRestarter: restarting kernel (2/5)
WARNING:root:kernel a414a11a-99aa-407a-9571-fa9f2b77e377 restarted
2014-03-24 10:25:29.317 [NotebookApp] KernelRestarter: restarting kernel (3/5)
WARNING:root:kernel a414a11a-99aa-407a-9571-fa9f2b77e377 restarted
2014-03-24 10:25:32.322 [NotebookApp] KernelRestarter: restarting kernel (4/5)
2014-03-24 10:25:35.334 [NotebookApp] WARNING | KernelRestarter: restart failed
2014-03-24 10:25:35.335 [NotebookApp] WARNING | Kernel a414a11a-99aa-407a-9571-fa9f2b77e377 died, removing from map.

Thanks for any help !

stevengj · 2014-03-24T15:32:44Z

Does Pkg.build("IJulia") at the Julia command-line succeed?

QCaudron · 2014-03-24T15:37:36Z

Yes, the build was fine, no errors.
On 24 Mar 2014 11:32, "Steven G. Johnson" [email protected] wrote:

Does Pkg.build("IJulia") at the Julia command-line succeed?

Reply to this email directly or view it on GitHubhttps://github.com//issues/159#issuecomment-38458640
.

stevengj · 2014-03-24T18:36:23Z

What is the output of versioninfo() in Julia?

QCaudron · 2014-03-24T21:21:48Z

julia> versioninfo()
Julia Version 0.3.0-prerelease+2154
Commit 96fb7e1* (2014-03-24 13:35 UTC)
Platform Info:
  System: Darwin (x86_64-apple-darwin13.1.0)
  CPU: Intel(R) Core(TM) i7-3840QM CPU @ 2.80GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY)
  LAPACK: libopenblas
  LIBM: libopenlibm

carloslesmes · 2014-03-25T16:11:28Z

Why don't you stay in 0.2.0 for while?

QCaudron · 2014-03-26T14:27:17Z

Mostly because this is what built when I cloned the git repo and built from source two days ago ( commit code 96fb7e1 ). The binary didn't seem to work under Mavericks.

TransGirlCodes · 2014-07-28T16:50:04Z

I keep getting a restart message too. The python console log being:

ERROR: could not open file /Users/axolotlfan9250/.julia/v0.3/IJulia/src/kernel.jl
in include at ./boot.jl:245
in include_from_node1 at loading.jl:128
in process_options at ./client.jl:285
in _start at ./client.jl:354

I did Pkg.build("IJulia") but it does not stop the message from coming up.

I'll do a reinstall and see if it works.

Ahah! It works!

stonebig · 2014-08-23T17:12:40Z

I get the same issue currently. not sure what can be the root cause.
Trying to delete/re-install just Julia and .julia setting didn't work at first.

It seems I'm back in order, when I did

remove a julia_profile that was at C:\Users\my_windows_profile_.ipython

(as I want it to use a more particular \settings.ipython)
then launch julia and redo
- Pkg.rm("IJulia")
- Pkg.add("IJulia")

stevengj · 2015-11-27T19:06:59Z

Seems no longer applicable to the latest version.

luisjavierhernandez · 2015-12-11T08:24:25Z

I have been working with my instance of JuliaBox with the kernel Julia 0.4.1 without problems, but
some days ago, a new Kernel Julia 0.4.2 has been installed. My problem is that in my instance of
JuliaBox this Kernel Julia 0.4.2 has died and it is not possible for me to restart this kernel. Therefore I have returned to Kernel Julia 0.3 , but this a problem because I have to modify the code of many functions.

Any idea to solve my problem?

Thanks

Luis Javier Hernandez

tanmaykm · 2015-12-11T13:39:09Z

@luisjavierhernandez this is most likely because of some conflicting locally installed/precompiled packages. Clearing them from ~/.julia should resolve the issue, e.g.:
mv ~/.julia ~/oldpkgs

There's a button on the JuliaBox settings tab to do it as well.

luisjavierhernandez · 2015-12-11T16:46:56Z

Thanks Tanmay,

Your instruction is correct.
When I remove the packages the Kernel of Julia 0.4.2 works
properly.

However, my program uses PyPlot and this package
needs PyCall. The problem appears again when I try
to install the package PyCall.

If I work with the Kernel Julia 0.3
I do not have any problems with the installation of PyPlot and PyCall.

Is it possible to install PyCall without having
conflicts with the Kernel of Julia 0.4.2?

With my best wishes

stevengj · 2015-12-11T17:02:19Z

I think this is related to JuliaPy/PyPlot.jl#185, which in turn seems like some underlying problem with Julia's caching mechanism on JuliaBox, nothing specific to IJulia or PyPlot per se.

stevengj · 2015-12-11T17:03:39Z

In particular, I see a clearer error message in the JuliaBox console:

juser@juliabox:~$ /opt/julia-0.4.2/bin/julia                                                                                                                       
INFO: Recompiling stale cache file /opt/julia_packages/.julia/lib/v0.4/Compat.ji for module Compat.                                                                
               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org
   _ _   _| |_  __ _   |  Type "?help" for help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.4.2 (2015-12-06 21:47 UTC)
 _/ |\__'_|_|_|\__'_|  |  Official http://julialang.org/ release
|__/                   |  x86_64-unknown-linux-gnu

julia> using IJulia                                                                                                                                                
INFO: Precompiling module IJulia...                                                                                                                                
INFO: Recompiling stale cache file /opt/julia_packages/.julia/lib/v0.4/Compat.ji for module Compat.                                                                
ERROR: LoadError: unlink: read-only file system (EROFS)                                                                                                            
 in unlink at fs.jl:102                                                                                                                                            
 in rm at file.jl:59                                                                                                                                               
 in create_expr_cache at loading.jl:330                                                                                                                            
 in recompile_stale at loading.jl:461                                                                                                                              
 in _require_from_serialized at loading.jl:83                                                                                                                      
 in _require_from_serialized at ./loading.jl:109                                                                                                                   
 in require at ./loading.jl:219                                                                                                                                    
 in include at ./boot.jl:261                                                                                                                                       
 in include_from_node1 at ./loading.jl:304                                                                                                                         
 [inlined code] from none:2                                                                                                                                        
 in anonymous at no file:0                                                                                                                                         
 in process_options at ./client.jl:257                                                                                                                             
 in _start at ./client.jl:378                                                                                                                                      
while loading /opt/julia_packages/.julia/v0.4/IJulia/src/IJulia.jl, in expression starting on line 4                                                               
ERROR: Failed to precompile IJulia to /home/juser/.julia/lib/v0.4/IJulia.ji                                                                                        
 in error at ./error.jl:21                                                                                                                                         
 in compilecache at loading.jl:384                                                                                                                                 
 in require at ./loading.jl:250

stevengj · 2015-12-11T17:15:39Z

See the abovementioned Julia issue.

stevengj · 2015-12-11T17:16:59Z

In general, continuing to comment on this issue is not fruitful. Not all causes of "dead kernel" messages are created equal — each issue should be tied to a specific problem in IJulia (or, in this case, in Julia and JuliaBox).

So, in the future, if you see a "dead kernel" message, please file a new issue (and try first to diagnose the source of the launch failure by following the "debugging IJulia" instructions in the README).

samirOs · 2017-06-12T05:13:04Z

I had a similar issue on centos, however, the issue was coming from a bad packaging of IJulia, as i didn't have cmake so i saw the error during the Pkg.add("IJulia").
the solution was to make sure to yum install cmake
then
do Pkg.build("IJulia")
this will build IJulia, make sure there are no errors.
Once this is ok, try launching your notebook and check

saurabh2804 · 2018-10-04T17:01:10Z

I had the same issue on Manjaro linux recently. I was using the version available in the Manajaro repository (1.01). I simply uninstalled it and downloaded Julia from the Julia website, extracted it and added it to my path. It is working without any problem. Installed IJulia and using it with Jupyter notebook.

quinnj mentioned this issue Mar 24, 2014

***Kernel Died*** OS 10.9.2 quinnj/Sublime-IJulia#42

Closed

jiahao mentioned this issue Feb 14, 2015

Receive the message "The kernel appears to have died" when running #273

Closed

stevengj closed this as completed Nov 27, 2015

stevengj mentioned this issue Dec 11, 2015

precompile shouldn't try to overwrite stale read-only cache files JuliaLang/julia#14368

Closed

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Dead kernel #159

Dead kernel #159

carloslesmes commented Mar 19, 2014

Keno commented Mar 19, 2014

carloslesmes commented Mar 19, 2014

stevengj commented Mar 19, 2014

QCaudron commented Mar 24, 2014

stevengj commented Mar 24, 2014

QCaudron commented Mar 24, 2014

stevengj commented Mar 24, 2014

QCaudron commented Mar 24, 2014

carloslesmes commented Mar 25, 2014

QCaudron commented Mar 26, 2014

TransGirlCodes commented Jul 28, 2014

stonebig commented Aug 23, 2014

stevengj commented Nov 27, 2015

luisjavierhernandez commented Dec 11, 2015

tanmaykm commented Dec 11, 2015

luisjavierhernandez commented Dec 11, 2015

stevengj commented Dec 11, 2015

stevengj commented Dec 11, 2015

stevengj commented Dec 11, 2015

stevengj commented Dec 11, 2015

samirOs commented Jun 12, 2017

saurabh2804 commented Oct 4, 2018

Dead kernel #159

Dead kernel #159

Comments

carloslesmes commented Mar 19, 2014

Keno commented Mar 19, 2014

carloslesmes commented Mar 19, 2014

stevengj commented Mar 19, 2014

QCaudron commented Mar 24, 2014

stevengj commented Mar 24, 2014

QCaudron commented Mar 24, 2014

stevengj commented Mar 24, 2014

QCaudron commented Mar 24, 2014

carloslesmes commented Mar 25, 2014

QCaudron commented Mar 26, 2014

TransGirlCodes commented Jul 28, 2014

stonebig commented Aug 23, 2014

stevengj commented Nov 27, 2015

luisjavierhernandez commented Dec 11, 2015

tanmaykm commented Dec 11, 2015

luisjavierhernandez commented Dec 11, 2015

stevengj commented Dec 11, 2015

stevengj commented Dec 11, 2015

stevengj commented Dec 11, 2015

stevengj commented Dec 11, 2015

samirOs commented Jun 12, 2017

saurabh2804 commented Oct 4, 2018