Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
Here's a quite popular service to share Jupyter notebooks together with a preset environment (e.g., a SageMath kernel) : http://mybinder.org/ Quite a different workflow compared to sharing a notebook on a SageNB server, though. Luca On Thu, Oct 27, 2016 at 7:11 AM, Jori Mäntysalo wrote: > On Sun, 23 Oct 2016, Luca De Feo wrote: > >> When I want to share a notebook with the students, I share a static >> .ipynb file via gist, and visualize it via nbviewer. e.g.: >> >> http://nbviewer.jupyter.org/gist/defeo/4adb727f7608dfd2c75eb7699d670fb7 >> >> When I want to see the student's work, I ask them to send me the >> .ipynb by mail, or directly access their notebooks using my admin >> account. >> >> Works like a charm. > > > OK, sounds possible to do. But document sharing between researchers still > does not work. (But to be honest, only sharing so far here has been me > replying to request like "Can you test this hypothesis?". Maybe some day...) > > -- > Jori Mäntysalo -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
On Sun, 23 Oct 2016, Luca De Feo wrote: When I want to share a notebook with the students, I share a static .ipynb file via gist, and visualize it via nbviewer. e.g.: http://nbviewer.jupyter.org/gist/defeo/4adb727f7608dfd2c75eb7699d670fb7 When I want to see the student's work, I ask them to send me the .ipynb by mail, or directly access their notebooks using my admin account. Works like a charm. OK, sounds possible to do. But document sharing between researchers still does not work. (But to be honest, only sharing so far here has been me replying to request like "Can you test this hypothesis?". Maybe some day...) -- Jori Mäntysalo
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
On Tue, 25 Oct 2016, Jori Mantysalo wrote:
https://jupyterhub.readthedocs.io/en/latest/getting-started.html
Got it installed and shown up in my browser. Good start. It rejected login
with wrong password, and with right password gave "Spawner failed to start
[status=1]". So next I guess I should somehow register Sage as a "kernel"(?)
for jupyterhub.
More progress. After
pip3 install jupyter
cd /usr/local/share/jupyter
ln -s /opt/sage-7.4/local/share/jupyter/kernels
ln -s /opt/sage-7.4/local/share/jupyter/nbextensions/
it almost work. Now when I modified
/opt/sage-7.4/local/share/jupyter/kernels/sagemath/kernel.json
by adding
"env": {"SAGE_ROOT": "/opt/sage-7.4/"}
to the dict I got this to work!
I used jupyterhub --no-ssl --port=80
Next move to https, then try ldap, and then combine ldap and local
accounts. And last look for worksheet sharing.
Thanks for help!
--
Jori Mäntysalo
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
On Mon, 24 Oct 2016, Volker Braun wrote: I have a setup helper for jupyterhup at https://github.com/vbraun/run-jupyter-hub Thanks. Stopped with ffi.h missing, now installed libffi-dev and trying again... On Tue, 25 Oct 2016, Luca De Feo wrote: Can you give me some kind of Hello world! -example of Jupyter? I am not sure you realize that JupyterHub is not shipped with Sage. That explains quite much. No, I did not realize that. If you want to try out JupyterHub, you will have to install it separately, and link the Sage kernel to it. I find the JupyterHub docs pretty well written and easy to follow for a Hello world test https://jupyterhub.readthedocs.io/en/latest/getting-started.html Got it installed and shown up in my browser. Good start. It rejected login with wrong password, and with right password gave "Spawner failed to start [status=1]". So next I guess I should somehow register Sage as a "kernel"(?) for jupyterhub. * * * I tested on Ubuntu 16.04 LTS. I did apt-get install npm nodejs-legacy apt-get install python3-pip npm install -g configurable-http-proxy export LC_ALL="en_US.UTF-8" export LC_CTYPE="en_US.UTF-8" dpkg-reconfigure locales pip3 install jupyterhub Noticed that it used IPv6, got a headache when googling, found the instruction to put GRUB_CMDLINE_LINUX_DEFAULT="ipv6.disable=1 quiet" on /etc/default/grub, said update-grub and got the login prompt. -- Jori Mäntysalo
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
> Can you give me some kind of Hello world! -example of Jupyter? ./sage > --notebook=jupyter will open a server to port --- how to change the > port or, more general, is there some help file? First I would like to see a > way to have two local user using Sage and not seeing each other files. I am not sure you realize that JupyterHub is not shipped with Sage. Running ./sage --notebook=jupyter will run the Jupyter server, NOT JupyterHub. This is a single-user setting: the Jupyter server runs as your user, and can acces any file your user can access (the file explorer is rooted in your working dir, but you can go anywhere in the file system using Python). JupyterHub is a different beast: it is a server that waits for connections and spawns Jupyter servers under different userids. So this is similar to running ./sage --notebook=jupyter as two different users in their respective homedirs. If you want to try out JupyterHub, you will have to install it separately, and link the Sage kernel to it. I find the JupyterHub docs pretty well written and easy to follow for a Hello world test https://jupyterhub.readthedocs.io/en/latest/getting-started.html You can test them in a virtualenv for an easy throwaway setup. Volker's scripts may be another good starting point, although I haven't tested them. Alternatively, there is a docker container here : https://hub.docker.com/r/jupyterhub/jupyterhub/ which is also good for testing. I agree with Dima that a tutorial for setting up JupyterHub in a SageNB-like way would be much welcome. I have the feeling that the Jupyter/JupyterHub/SageMath integration is still a bit of a moving target ATM, but we should try to write this sooner than later. Luca -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
I have a setup helper for jupyterhup at https://github.com/vbraun/run-jupyter-hub It might be out of date, haven't tried it with the newest version of jupyterhub. But maybe its a starting point for you... On Monday, October 24, 2016 at 7:47:15 AM UTC-4, Jori Mäntysalo wrote: > > On Sun, 23 Oct 2016, Luca De Feo wrote: > > >> As far as I know, Jupyter(hub) does not have such a feature since it > >> completely relies on the OS for access checks. > > > > That's not correct. JupyterHub supports arbitrary authenticators: > > > > https://jupyterhub.readthedocs.io/en/latest/authenticators.html > > Can you give me some kind of Hello world! -example of Jupyter? ./sage > --notebook=jupyter will open a server to port --- how to change the > port or, more general, is there some help file? First I would like to see > a way to have two local user using Sage and not seeing each other files. > > -- > Jori Mäntysalo > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
On Monday, October 24, 2016 at 11:47:15 AM UTC, Jori Mäntysalo wrote: > > On Sun, 23 Oct 2016, Luca De Feo wrote: > > >> As far as I know, Jupyter(hub) does not have such a feature since it > >> completely relies on the OS for access checks. > > > > That's not correct. JupyterHub supports arbitrary authenticators: > > > > https://jupyterhub.readthedocs.io/en/latest/authenticators.html > > Can you give me some kind of Hello world! -example of Jupyter? ./sage > --notebook=jupyter will open a server to port --- how to change the > port or, more general, is there some help file? First I would like to see > a way to have two local user using Sage and not seeing each other files. > I mentioned this here: https://github.com/OpenDreamKit/OpenDreamKit/issues/94#issuecomment-255683103 > > -- > Jori Mäntysalo > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
On Sun, 23 Oct 2016, Luca De Feo wrote: As far as I know, Jupyter(hub) does not have such a feature since it completely relies on the OS for access checks. That's not correct. JupyterHub supports arbitrary authenticators: https://jupyterhub.readthedocs.io/en/latest/authenticators.html Can you give me some kind of Hello world! -example of Jupyter? ./sage --notebook=jupyter will open a server to port --- how to change the port or, more general, is there some help file? First I would like to see a way to have two local user using Sage and not seeing each other files. -- Jori Mäntysalo
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
On Sun, Oct 23, 2016 at 4:28 AM, Dima Pasechnik wrote: > > > On Sunday, October 23, 2016 at 7:48:43 AM UTC, Jori Mäntysalo wrote: >> >> On Sun, 23 Oct 2016, Jeroen Demeyer wrote: >> >> >> I must check if sharing worksheets works >> > >> > As far as I know, Jupyter(hub) does not have such a feature since it >> > completely relies on the OS for access checks. A notebook is just an >> > ordinary file owned by some Unix user. >> >> OK, then I am not going to try this (yet). >> >> How others teach Sage? Here I make a Sage account of the form >> "Coursecode-Year", and the teacher asks students to share worksheet with >> that account. > > > there are people who hack SMC into being installable and runnable on local > machines or other (non/GCE clouds). See e.g. > https://groups.google.com/d/msg/sage-cloud/og3tmsXK-K0/snB-7v2_CgAJ Or use our official docker image https://github.com/sagemathinc/smc/blob/master/src/dev/docker/README.md Our docker image is not perfect, secure, or totally robust yet, but it is easy to use. William >> >> -- >> Jori Mäntysalo > > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-devel@googlegroups.com. > Visit this group at https://groups.google.com/group/sage-devel. > For more options, visit https://groups.google.com/d/optout. -- William (http://wstein.org) -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
On Sunday, October 23, 2016 at 7:48:43 AM UTC, Jori Mäntysalo wrote: > > On Sun, 23 Oct 2016, Jeroen Demeyer wrote: > > >> I must check if sharing worksheets works > > > > As far as I know, Jupyter(hub) does not have such a feature since it > > completely relies on the OS for access checks. A notebook is just an > > ordinary file owned by some Unix user. > > OK, then I am not going to try this (yet). > > How others teach Sage? Here I make a Sage account of the form > "Coursecode-Year", and the teacher asks students to share worksheet with > that account. > there are people who hack SMC into being installable and runnable on local machines or other (non/GCE clouds). See e.g. https://groups.google.com/d/msg/sage-cloud/og3tmsXK-K0/snB-7v2_CgAJ > > -- > Jori Mäntysalo > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
> As far as I know, Jupyter(hub) does not have such a feature since it > completely relies on the OS for access checks. That's not correct. JupyterHub supports arbitrary authenticators: https://jupyterhub.readthedocs.io/en/latest/authenticators.html In particular, there is an LDAP authenticator: https://github.com/jupyterhub/ldapauthenticator If I understands Jori's loud thoughts, he wants to mix an LDAP authenticator with the default PAM authenticator. It shouldn't be too hard to write a class that tries them in some order, although I'm not sure that's the best solution. > A notebook is just an ordinary file owned by some Unix user. That is pretty much configurable too : https://jupyterhub.readthedocs.io/en/latest/spawners.html I think the hardest thing to achieve with jupyterhub is notebook sharing, at least in a fashion similar to the classic notebook. There is a concept of *admin account* in JupyterHub (disjoint from Unix admins). Admins can run the Jupyter notebook as any other user, so they can see and run all the students' notebooks. > How others teach Sage? Here I make a Sage account of the form > "Coursecode-Year", and the teacher asks students to share worksheet > with that account. For the first year this time, I set up a jupyterhub with a PAM authenticator. I create a unix user account for each student (and teacher). This is fine with us, because we want them to also have ssh access (and it's only ~10 students). They can use Python, Sage, and Julia via the Jupyter notebook, and can also run any of those and much more from a shell. Added bonuses: - There is an in-browser shell in JupyterHub. Very practical for those students who don't know how to run ssh on their home computers. - JupyterHub file view lets the students upload and download any kind of file from the server, not only noteboks. So this makes a very simple "cloud host" for them to have all their work available from anywhere (e.g., the C files they write in the system programming class). When I want to share a notebook with the students, I share a static .ipynb file via gist, and visualize it via nbviewer. e.g.: http://nbviewer.jupyter.org/gist/defeo/4adb727f7608dfd2c75eb7699d670fb7 When I want to see the student's work, I ask them to send me the .ipynb by mail, or directly access their notebooks using my admin account. Works like a charm. I'll be looking at custom authentication soon. Luca -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
On Sun, 23 Oct 2016, Jeroen Demeyer wrote: I must check if sharing worksheets works As far as I know, Jupyter(hub) does not have such a feature since it completely relies on the OS for access checks. A notebook is just an ordinary file owned by some Unix user. OK, then I am not going to try this (yet). How others teach Sage? Here I make a Sage account of the form "Coursecode-Year", and the teacher asks students to share worksheet with that account. -- Jori Mäntysalo
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
On 2016-10-23 08:47, Jori Mäntysalo wrote: I must check if sharing worksheets works As far as I know, Jupyter(hub) does not have such a feature since it completely relies on the OS for access checks. A notebook is just an ordinary file owned by some Unix user. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
On Sat, 22 Oct 2016, Volker Braun wrote: Yes, with jupyterhub you can have isolation with unix users. That is, there is a login screen and people can sign in with their normal unix username/password. Hmm... OK. Thinking aloud: As Sage may eat much CPU and/or memory, I want it to be on it's own server. That server should connect to our LDAP, and have normal Unix accounts. Also we need some local accounts for courses. Managing users is then not possible from Sage UI, but with normal Linux commands. But that's not a problem for us. Normal shell logins should be disabled for almost all users, but some researcher might use Sage from command line too. I must check if sharing worksheets works, see if I can run plain Python2, R and Octave too from UI. What else? Check how much memory every worksheet eats (no, we don't have memory ballooning in our virtualization environment) and so. (Besides that, University of Tampere, Technical University of Tampere and University of Applied Sciences of Tampere will be united from 1.1.2018. So check out what other two wants and be ready for that too. Maple to same server maybe?) -- Jori Mäntysalo
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
Yes, with jupyterhub you can have isolation with unix users. That is, there is a login screen and people can sign in with their normal unix username/password. On Saturday, October 22, 2016 at 4:27:55 PM UTC-4, Jori Mäntysalo wrote: > > Does it have multiuser support, so that A can't see worksheet for B with > some file(...) -command? > > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Notebook stuck on "N?" with a worksheet
On Sat, 22 Oct 2016, Volker Braun wrote: IMHO the best solution is to stop using SageNB asap and use "sage --notebook=jupyter" Does it have multiuser support, so that A can't see worksheet for B with some file(...) -command? * * * A quick test: make new worksheet, write "1+2", press Shift+Enter. Got "3". Press arrow up, correct text to "1+3", again Shift+Enter and arrow up. And now how to correct the line to "1+4" without mouse? This is 64-bit Ubuntu, Firefox from repository, all up-to-date. (OK, can do that, but is not quick and easy.) -- Jori Mäntysalo
[sage-devel] Re: Notebook stuck on "N?" with a worksheet
IMHO the best solution is to stop using SageNB asap and use "sage --notebook=jupyter" On Friday, October 7, 2016 at 11:24:02 AM UTC+2, Jori Mäntysalo wrote: > > Could someone try SageNB with http://www.sis.uta.fi/~jm58660/Broken.sws > > For me that stucks when I try to evaluate the first calculation cell, the > one with content > > #Katso komennon N helppi, erityisesti se, miten desimaalien määrää voidaan > säädellä > N? > > It is somehow related to some phrases or characters or something in text > cells before it, as the problem faded away when I remove those. Because of > that I did not clear the example from Finnish texts. > > -- > Jori Mäntysalo > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Re: Notebook stuck on "N?" with a worksheet (fwd)
On Friday, October 21, 2016 at 2:38:14 AM UTC-4, Jori Mäntysalo wrote: > > Anybody? > > One -- and only one -- of my users if having really big problems with > cells not responding. Somehow computation seems to work, but the result is > not got back to worksheet. Pressing refresh helps sometimes, not always. > > How to debug this? > That is a hard question, if it isn't due to some specific repeatable thing. You can use the developer tools in your browser to try to track what responses are coming, but if the sagenb log isn't showing anything unusual, I'm not sure what else to say. However, a workaround is to put the text into true text cells, rather than as comments in the compute cell. That is probably better anyway, since you can then style it. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
