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Re: Notebook cells don't execute in Windows

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Re: Notebook cells don't execute in Windows

David Hume
Hi, 
I've been running the iPython notebook now for several months and it has transformed my productivity.  Though I'm running on a Linux box, I'm so impressed with the notebook that I've been encouraging fellow work-mates (on Windows) to take the plunge from Matlab/R etc, to Python / iPython / NumPy / SciPy / Pandas, etc.  

Initially I set up a Server on a spare Linux box connected to our Corporate Windows environment which they could try out.  More recently I've helped install iPython on several Windows 7 machines locally.  

All was going well, until yesterday, when the output of the Notebook cells, all of a sudden, stopped being displayed in the browser!  Three of my colleges are effected, all on Windows 7 machines.  Bazaarly, I have a Windows HP laptop, connected to the same network which has so far been unaffected!? 

We are at a loss at the moment to explain what has caused this, other than that it is windows specific.  I've followed a few posts on this list back in September http://mail.scipy.org/pipermail/ipython-user/2012-September/011220.html and we have tried installing Chrome/Firefox and Opera, but, unfortunately with no success. 

It appears the Browser is not seeing/reading the output from iPython, or perhaps something is blocking this communacation, any existing code is displayed as we can run through Shift-Enter down the notebook cells and plots/etc will appear, just no output in the browser window. 

Any help or thoughts would be appreciated.

Thanks

Dave Hume
Wellington, NZ.










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Re: Notebook cells don't execute in Windows

Matthias Bussonnier

Hi dave.

Sorry if my answer is short, sent from my phone.

Could you have a look a javascript console on the concerned boxes? Does it state anything out of usual. (you should have at least message telling that websocket connexion are ok).

Do you have any kind of proxy? Can you try telling the boxes not to use proxy for localhost? ( i doubt this one will do anything as otherwise you would'nt be able to execute anything).

Any network security software/ antivirus update?

--
Matthias

Le 1 nov. 2012 00:48, "Dave Hume" <[hidden email]> a écrit :
Hi, 
I've been running the iPython notebook now for several months and it has transformed my productivity.  Though I'm running on a Linux box, I'm so impressed with the notebook that I've been encouraging fellow work-mates (on Windows) to take the plunge from Matlab/R etc, to Python / iPython / NumPy / SciPy / Pandas, etc.  

Initially I set up a Server on a spare Linux box connected to our Corporate Windows environment which they could try out.  More recently I've helped install iPython on several Windows 7 machines locally.  

All was going well, until yesterday, when the output of the Notebook cells, all of a sudden, stopped being displayed in the browser!  Three of my colleges are effected, all on Windows 7 machines.  Bazaarly, I have a Windows HP laptop, connected to the same network which has so far been unaffected!? 

We are at a loss at the moment to explain what has caused this, other than that it is windows specific.  I've followed a few posts on this list back in September http://mail.scipy.org/pipermail/ipython-user/2012-September/011220.html and we have tried installing Chrome/Firefox and Opera, but, unfortunately with no success. 

It appears the Browser is not seeing/reading the output from iPython, or perhaps something is blocking this communacation, any existing code is displayed as we can run through Shift-Enter down the notebook cells and plots/etc will appear, just no output in the browser window. 

Any help or thoughts would be appreciated.

Thanks

Dave Hume
Wellington, NZ.










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Re: Notebook cells don't execute in Windows

David Hume
Hi Matthias, thanks for the quick response and suggestions.  

I had a look at the javascript console and I can't see anything out of usual.  
We do have a proxy, (in fact we have several), and I've made sure the proxy is not used for localhost.

The weird thing is that it was all running so well.  I'm assuming an auto software update - either MS windows or our antivirus software may be the cause.   What is doubly weird is that it is talking in one direction as we see plot windows etc appear when we shift-enter down the cells!  Just no output back to the web browser.  

For the time being I've got one of my colleges using the Notebook server (which I've set up running on a Linux box) and this works fine.  Although not ideal as he really needs a more interactive plotting window rather than the inline plot.

I might have another chat with our system admin about our virus software/etc and see if I can temp disable the virus software to check if this is the cause?

Thanks again for your suggestions.  Will post again when we have it sorted (fingers crossed!)

cheers
Dave.
 

 

 
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Re: Notebook cells don't execute in Windows

MinRK


On Thu, Nov 1, 2012 at 7:37 PM, David Hume <[hidden email]> wrote:
Hi Matthias, thanks for the quick response and suggestions.

I had a look at the javascript console and I can't see anything out of
usual.
We do have a proxy, (in fact we have several), and I've made sure the proxy
is not used for localhost.

The weird thing is that it was all running so well.  I'm assuming an auto
software update - either MS windows or our antivirus software may be the
cause.   What is doubly weird is that it is talking in one direction as we
see plot windows etc appear when we shift-enter down the cells!  Just no
output back to the web browser.

For the time being I've got one of my colleges using the Notebook server
(which I've set up running on a Linux box) and this works fine.  Although
not ideal as he really needs a more interactive plotting window rather than
the inline plot.

I might have another chat with our system admin about our virus software/etc
and see if I can temp disable the virus software to check if this is the
cause?

Thanks again for your suggestions.  Will post again when we have it sorted
(fingers crossed!)

I saw somewhere the suggestion that telling it to listen on all IPs (--ip='*') may be a workaround,
can you check if this is the case for you?  I don't remember where that was, so it may be nonsense.

-MinRK
 

cheers
Dave.








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Re: Notebook cells don't execute in Windows

klo uo
I tried that, and it had no impact here, although it seems my reported problem (linked in first mail in this thread) is different, but with same outcome.

I wanted to add more notes on this problem, which hopefully will help you track this issue.

Couple of days after I had this problem and resolved it by using Opera, I removed whole Python installation and packages and installed again. After that IPython was working fine in all browsers, so I thought it must have been some package that caused this. But just right now I see the problem again. To let you know, I don't have thousands packages. Standard ones like numpy/scipy... some scikits, h5py, mayavi, pyqt, wx, and their dependencies.

I used IPython dev version, so occasionally update IPython directory cloned from git, and play with it, mostly in qtconsole.
Now I wanted again to make notebook file, but no joy. After launching Firefox I see well known portal at http://127.0.0.1:8888/ and choose to make new notebook. However screen was just blank. Looking at html source it seems fine, I mean there is some content but nothing is shown. OK, I launch Chrome, then I launch Opera to witness the same.

At this point I decided I stop using IPython dev version. I removed all traces of IPython and went ahead to download latest stable version. I build 13.1 from source and BTW I noticed that download links in menu and side menu on IPython main page are empty, and that Win32 installer from pypi makes 64 bit executables.

Now launching notebook in Firefox is as reported previously  - I see the notebook, but commands aren't executed. Using Opera again saved me, luckily for me.

I don't know what are the changes in 0.13 but with 0.12 there were no this kind of issues on Windows. And yes, I know that majority of IPython devs don't use Windows.


On Fri, Nov 2, 2012 at 2:59 AM, MinRK wrote:
I saw somewhere the suggestion that telling it to listen on all IPs (--ip='*') may be a workaround,
can you check if this is the case for you?  I don't remember where that was, so it may be nonsense.

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Re: Notebook cells don't execute in Windows

klo uo
Please ignore this line ;)

On Sat, Nov 3, 2012 at 9:47 AM, klo uo wrote:
I noticed that download links in menu and side menu on IPython main page are empty


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Re: Notebook cells don't execute in Windows

Patrick Marsh
I would like to chime in here and say that one of my students has a similar problem on her Windows 7 machine. The difference is that she is not connecting to a network; she's using her local EPD distribution and updated IPython.

In her case, everything loads, but none of the Python cells work. I tried making a function call (import numpy) with the QTConsole, as well, on her laptop and that doesn't work either. However, the standard IPython works fine.


Patrick

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Cooperative Institute for Mesoscale Meteorological Studies
National Severe Storms Laboratory
http://www.patricktmarsh.com



On Sat, Nov 3, 2012 at 3:55 AM, klo uo <[hidden email]> wrote:
Please ignore this line ;)


On Sat, Nov 3, 2012 at 9:47 AM, klo uo wrote:
I noticed that download links in menu and side menu on IPython main page are empty


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Re: Notebook cells don't execute in Windows

David Hume
Hi all,  thanks very much for the feedback so far.
 
My colleagues (who's computers run in our corporate Windows environment) have had no notebook access for the best part of a week (poor windows users...)  

So today, in frustration (and out of sympathy on my part) we started a trial and error procedure of removing processes, one by one, from one of the windows machines in question.  

Our procedure was this:

while notebook does not return an output:
    remove a process (being careful to not kill any system processes)
    close/kill any open iPython and the web browser sessions (note: restarting the kernel was not enough)
    re-run iPython notebook with new web browser session
    Shift enter in a code cell  

Doing this we have managed to get the windows notebook back up and running!  

We just haven't quite nailed down the exact process which is causing this (as we did this in batches to save time....)  

Oddly, if we reboot the machine and quickly open the iPython notebook we can obtain a working notebook.  If we restart the kernel a few minutes (maybe seconds?) later the notebook output stops.

I think we almost have this nailed.

I'll post here again tomorrow, once we track the exact rogue process/program that is causing this mischief.

cheers
Dave Hume
Wellington, NZ.
     
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Re: Notebook cells don't execute in Windows

Matthias Bussonnier
Hi Dave,

Happy to see you might have find a solution.

I'll see if I can come up with a notebook that auto execute during lunch break so that you don't have to manually press shift enter.
I think it might need some code tweak on server side, so maybe we could design a 'diagnostic' mode for the notebook, that just
pop up a page that constantly probe the kernel connexion and report the status of different actions.

Good luck for debugging,
--
Matthias

Le 8 nov. 2012 à 06:09, David Hume a écrit :

> Hi all,  thanks very much for the feedback so far.
>
> My colleagues (who's computers run in our corporate Windows environment)
> have had no notebook access for the best part of a week (poor windows
> users...)  
>
> So today, in frustration (and out of sympathy on my part) we started a trial
> and error procedure of removing processes, one by one, from one of the
> windows machines in question.  
>
> Our procedure was this:
>
> while notebook does not return an output:
>    remove a process (being careful to not kill any system processes)
>    close/kill any open iPython and the web browser sessions (note:
> restarting the kernel was not enough)
>    re-run iPython notebook with new web browser session
>    Shift enter in a code cell  
>
> Doing this we have managed to get the windows notebook back up and running!  
>
> We just haven't quite nailed down the exact process which is causing this
> (as we did this in batches to save time....)  
>
> Oddly, if we reboot the machine and quickly open the iPython notebook we can
> obtain a working notebook.  If we restart the kernel a few minutes (maybe
> seconds?) later the notebook output stops.
>
> I think we almost have this nailed.
>
> I'll post here again tomorrow, once we track the exact rogue process/program
> that is causing this mischief.
>
> cheers
> Dave Hume
> Wellington, NZ.
>
>
>
>
>
> --
> View this message in context: http://python.6.n6.nabble.com/Re-Notebook-cells-don-t-execute-in-Windows-tp4994309p4995181.html
> Sent from the IPython - User mailing list archive at Nabble.com.
> _______________________________________________
> IPython-User mailing list
> [hidden email]
> http://mail.scipy.org/mailman/listinfo/ipython-user

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Re: Notebook cells don't execute in Windows

Brian Granger-3
It would be nice to have a debug mode that logs lots of things to the JS console.


On Thu, Nov 8, 2012 at 12:45 AM, Matthias BUSSONNIER <[hidden email]> wrote:
Hi Dave,

Happy to see you might have find a solution.

I'll see if I can come up with a notebook that auto execute during lunch break so that you don't have to manually press shift enter.
I think it might need some code tweak on server side, so maybe we could design a 'diagnostic' mode for the notebook, that just
pop up a page that constantly probe the kernel connexion and report the status of different actions.

Good luck for debugging,
--
Matthias

Le 8 nov. 2012 à 06:09, David Hume a écrit :

> Hi all,  thanks very much for the feedback so far.
>
> My colleagues (who's computers run in our corporate Windows environment)
> have had no notebook access for the best part of a week (poor windows
> users...)
>
> So today, in frustration (and out of sympathy on my part) we started a trial
> and error procedure of removing processes, one by one, from one of the
> windows machines in question.
>
> Our procedure was this:
>
> while notebook does not return an output:
>    remove a process (being careful to not kill any system processes)
>    close/kill any open iPython and the web browser sessions (note:
> restarting the kernel was not enough)
>    re-run iPython notebook with new web browser session
>    Shift enter in a code cell
>
> Doing this we have managed to get the windows notebook back up and running!
>
> We just haven't quite nailed down the exact process which is causing this
> (as we did this in batches to save time....)
>
> Oddly, if we reboot the machine and quickly open the iPython notebook we can
> obtain a working notebook.  If we restart the kernel a few minutes (maybe
> seconds?) later the notebook output stops.
>
> I think we almost have this nailed.
>
> I'll post here again tomorrow, once we track the exact rogue process/program
> that is causing this mischief.
>
> cheers
> Dave Hume
> Wellington, NZ.
>
>
>
>
>
> --
> View this message in context: http://python.6.n6.nabble.com/Re-Notebook-cells-don-t-execute-in-Windows-tp4994309p4995181.html
> Sent from the IPython - User mailing list archive at Nabble.com.
> _______________________________________________
> IPython-User mailing list
> [hidden email]
> http://mail.scipy.org/mailman/listinfo/ipython-user

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Re: Notebook cells don't execute in Windows

Brian Granger-3
In reply to this post by David Hume
Almost sounds like a virus/security software issue that is eventually detecting the notebook traffic and shuts it down.


On Wed, Nov 7, 2012 at 9:09 PM, David Hume <[hidden email]> wrote:
Hi all,  thanks very much for the feedback so far.

My colleagues (who's computers run in our corporate Windows environment)
have had no notebook access for the best part of a week (poor windows
users...)

So today, in frustration (and out of sympathy on my part) we started a trial
and error procedure of removing processes, one by one, from one of the
windows machines in question.

Our procedure was this:

while notebook does not return an output:
    remove a process (being careful to not kill any system processes)
    close/kill any open iPython and the web browser sessions (note:
restarting the kernel was not enough)
    re-run iPython notebook with new web browser session
    Shift enter in a code cell

Doing this we have managed to get the windows notebook back up and running!

We just haven't quite nailed down the exact process which is causing this
(as we did this in batches to save time....)

Oddly, if we reboot the machine and quickly open the iPython notebook we can
obtain a working notebook.  If we restart the kernel a few minutes (maybe
seconds?) later the notebook output stops.

I think we almost have this nailed.

I'll post here again tomorrow, once we track the exact rogue process/program
that is causing this mischief.

cheers
Dave Hume
Wellington, NZ.





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Re: Notebook cells don't execute in Windows

Fernando Perez
On Thu, Nov 8, 2012 at 9:30 AM, Brian Granger <[hidden email]> wrote:
> Almost sounds like a virus/security software issue that is eventually
> detecting the notebook traffic and shuts it down.

My bet exactly.  Some over-aggressive firewall that's killing the zmq
ports or the websocket traffic.

Does the Qt console work? That would let us know whether the problem
is on the zmq side or the http one...

f
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Re: Notebook cells don't execute in Windows

klo uo
I don't have virus scanner, while system (XP) has it's own firewall
If you have ideas how to take advantage of the fact that I can execute notebooks in Opera, but not in other browsers, let me know.

Another strange thing is that I can't use Opera to delete or shutdown Notebooks - buttons just don't work there, and I can only create new Notebook. But if I open Firefox I can manage Notebooks from there. So notebook managing in Firefox, and execution in Opera - hilarious :)


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Re: Notebook cells don't execute in Windows

David Hume
In reply to this post by Fernando Perez
Hi everyone,

I think we have cracked this.  Hopefully for good.   And yes your bets were on the money - thank you.  

We have identified the problem (as suspected) as an anti-virus program called Sophos.

But...

after killing all Sophos processes they magically, (like a virus or perhaps Zombie), reappear after 10-30 seconds, or so.   We currently can't uninstall the software as, although we have admin rights, we are not (yet..) in the Zombie killer "Sophos Admin group"....

In the mean time, this window of time while Sophos is temporarily dead,  allows us to sneak in and get a working notebook session up and running.  We first kill all Sophos processes, then we run the ipython notebook.   This seems to work with no problems (yet).

I've yet to talk with our IT person about this,  so in the mean time, we have created the following simple, rather crude, but effective, zombie killing batch file:

taskkill /f /im ManagementAgentNT.exe
taskkill /f /im RouterNT.exe
taskkill /f /im swc_service.exe
taskkill /f /im swi_service.exe
C:\Python27\Scripts\ipython.exe notebook --pylab

I'll post again if we continue to have any issues.  

We have yet to try Qt console, if we do, I'll post results here.

Thanks everyone, and thanks to iPython!

cheers
Dave Hume
Wellington, NZ

 

 

 
 
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Re: Notebook cells don't execute in Windows

Fernando Perez
On Thu, Nov 8, 2012 at 3:26 PM, David Hume <[hidden email]> wrote:
>
> We have identified the problem (as suspected) as an anti-virus program
> called Sophos.

Wow, that's really nasty behavior...  Please do let us know of
anything else you learn, as at least it may help us find workarounds
for our Windows users.

Cheers,

f
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Re: Notebook cells don't execute in Windows

Darren Govoni
I read somewhere (forget where) in the past week that Sophos itself was
exploited to deliver virus'

On 11/08/2012 06:30 PM, Fernando Perez wrote:

> On Thu, Nov 8, 2012 at 3:26 PM, David Hume <[hidden email]> wrote:
>> We have identified the problem (as suspected) as an anti-virus program
>> called Sophos.
> Wow, that's really nasty behavior...  Please do let us know of
> anything else you learn, as at least it may help us find workarounds
> for our Windows users.
>
> Cheers,
>
> f
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Re: Notebook cells don't execute in Windows

Brian Granger-3
In reply to this post by David Hume
Ouch, I hate crap like this.

I am sorry you have had to deal with this, hopefully you can work with your IT folks to come up with a better solution.  Glad you figured it out.

Cheers,

Brian


On Thu, Nov 8, 2012 at 3:26 PM, David Hume <[hidden email]> wrote:
Hi everyone,

I think we have cracked this.  Hopefully for good.   And yes your bets were
on the money - thank you.

We have identified the problem (as suspected) as an anti-virus program
called Sophos.

But...

after killing all Sophos processes they magically, (like a virus or perhaps
Zombie), reappear after 10-30 seconds, or so.   We currently can't uninstall
the software as, although we have admin rights, we are not (yet..) in the
Zombie killer "Sophos Admin group"....

In the mean time, this window of time while Sophos is temporarily dead,
allows us to sneak in and get a working notebook session up and running.  We
first kill all Sophos processes, then we run the ipython notebook.   This
seems to work with no problems (yet).

I've yet to talk with our IT person about this,  so in the mean time, we
have created the following simple, rather crude, but effective, zombie
killing batch file:

taskkill /f /im ManagementAgentNT.exe
taskkill /f /im RouterNT.exe
taskkill /f /im swc_service.exe
taskkill /f /im swi_service.exe
C:\Python27\Scripts\ipython.exe notebook --pylab

I'll post again if we continue to have any issues.

We have yet to try Qt console, if we do, I'll post results here.

Thanks everyone, and thanks to iPython!

cheers
Dave Hume
Wellington, NZ










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Re: Notebook cells don't execute in Windows

klo uo
In reply to this post by David Hume
I'm sure they would be very happy that you want to remove anti-virus software to be able to run IPython.
I've never heard about that program, but there sure must be a better way, which will allow you to unblock IPython, instead terminating Windows services - it just looks brutal to me


On Fri, Nov 9, 2012 at 12:26 AM, David Hume <[hidden email]> wrote:
I've yet to talk with our IT person about this,  so in the mean time, we
have created the following simple, rather crude, but effective, zombie
killing batch file:

taskkill /f /im ManagementAgentNT.exe
taskkill /f /im RouterNT.exe
taskkill /f /im swc_service.exe
taskkill /f /im swi_service.exe
C:\Python27\Scripts\ipython.exe notebook --pylab


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Re: Notebook cells don't execute in Windows

Pedro A. Tonelli
There is a recept for by Joran Beasley involving sophos at

http://stackoverflow.com/questions/13036197/ipython-notebook-getting-output


"So the solution is to
  1. open your Sophos Endpoint Security and Control Panel from your tray or start menu

  2. Select "configure" > "Anti-virus" > "Authorization" from the menu at the top

  3. Select the websites tab

  4. click the "Add" button and add 127.0.0.1 and localhost to the "Authorized websites" list

  5. restart computer

  6. output works now :) "







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Re: Notebook cells don't execute in Windows

Brian Granger-3
Oh fantastic!


On Thu, Nov 8, 2012 at 7:04 PM, Pedro A. Tonelli <[hidden email]> wrote:
There is a recept for by Joran Beasley involving sophos at

http://stackoverflow.com/questions/13036197/ipython-notebook-getting-output


"So the solution is to
  1. open your Sophos Endpoint Security and Control Panel from your tray or start menu

  2. Select "configure" > "Anti-virus" > "Authorization" from the menu at the top

  3. Select the websites tab

  4. click the "Add" button and add 127.0.0.1 and localhost to the "Authorized websites" list

  5. restart computer

  6. output works now :) "







_______________________________________________
IPython-User mailing list
[hidden email]
http://mail.scipy.org/mailman/listinfo/ipython-user





--
-- Pedro Aladar Tonelli --

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Brian E. Granger
Cal Poly State University, San Luis Obispo
[hidden email] and [hidden email]


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