Ubuntu PPA package and Jupyter notebook

[Eric Gourgoulhon]

Hi,

While testing the Ubuntu package sagemath-upstream-binary-full from AIMS PPA (cf. this thread), I've tried to run sage in Jupyter notebook via the command
sage -n ipython
The result is

┌────────────────────────────────────────────────────────────────────┐
│ SageMath Version 6.8, Release Date: 2015-07-26                     │
│ Type "notebook()" for the browser-based notebook interface.        │
│ Type "help()" for help.                                            │
└────────────────────────────────────────────────────────────────────┘
Please wait while the Sage Notebook server starts...

The IPython notebook requires ssl, even if you do not use
https. Install the openssl development packages in your system and
then rebuild Python (sage -f python).

Now, I do have the openssl dev package installed (on the same computer, the Jupyter notebook works well with local (i.e. installed manually in user home directory) versions of Sage 6.8). If, as suggested, I run
sudo sage -f python
I got the error message:
/usr/lib/sagemath/build/make/pipestatus: ligne 39: sage-spkg : commande introuvable

Am I missing something ? It would be nice to have the Jupyter notebook work in the Ubuntu package.

Eric.

[Jan Groenewald]

Hi Eric

Do you NOT get this error when using a binary from http://www.sagemath.org/download.html ? Or do you NOT get this error with from-source builds? When you say "installed manually".

I would like to know about the binaries.

Regards,

Jan

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[Eric Gourgoulhon]

Hi Jan,

Le vendredi 11 septembre 2015 07:31:18 UTC+2, pipedream a écrit :

Hi Eric

Do you NOT get this error when using a binary from http://www.sagemath.org/download.html ? Or do you NOT get this error with from-source builds? When you say "installed manually".

I do NOT get it from source builds (Sage 6.8). Regarding binaries, I don't have a Sage 6.8 binary at hand at the moment, but on a Sage 6.6 binary, I do NOT get the error either. Can somebody confirm it is fine for Sage 6.8 binary ?

Regards,

Eric.

[Samuel Lelièvre]

To rebuild python, use

sudo sage -f python2
sudo sage -f python3

and NOT

sudo sage -f python

[Jan Groenewald]

Hi

We seem to be missing something in the full package. Do you have the /usr/lib/sagemath/build/bin folder in your -full installation?

Regards,

Jan

On 10 September 2015 at 22:28, Eric Gourgoulhon <egourg...@gmail.com> wrote:

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[Eric Gourgoulhon]

Hi Samuel,

Le vendredi 11 septembre 2015 08:42:42 UTC+2, Samuel Lelievre a écrit :

To rebuild python, use

    sudo sage -f python2
    sudo sage -f python3

and NOT

    sudo sage -f python

I've tried
sudo sage -f python2
and got the same error message:

/usr/lib/sagemath/build/make/pipestatus: ligne 39: sage-spkg : commande introuvable

Regards,

Eric.

[Eric Gourgoulhon]

Le vendredi 11 septembre 2015 09:03:42 UTC+2, pipedream a écrit :

Hi

We seem to be missing something in the full package. Do you have the /usr/lib/sagemath/build/bin folder in your -full installation?

No I don't: the subfolders of  /usr/lib/sagemath/build/ are make and pkgs, there is no bin.

Regards,

Eric.

[Jan Groenewald]

Hi

We will update the package soon. We have an autobuild uploading to the dev PPA daily, though we plan to change that to weekly soon.

But this should go through tonight:
https://bitbucket.org/aims_za/sagemath-upstream-binary/commits/30a4b479c406c87666857185c855a13514bfefb2

Regards,

Jan

[Eric Gourgoulhon]

Hi Jan,

Le vendredi 11 septembre 2015 10:04:49 UTC+2, pipedream a écrit :

But this should go through tonight:
https://bitbucket.org/aims_za/sagemath-upstream-binary/commits/30a4b479c406c87666857185c855a13514bfefb2

I've reinstalled the package yesterday, with

sudo apt-get update

sudo apt-get install sagemath-upstream-binary-full
but there is still no /usr/lib/sagemath/build/bin directory and
sudo sage -f python2
still result in

/usr/lib/sagemath/build/make/pipestatus: ligne 39: sage-spkg : commande introuvable

Best regards,

Eric.

 

[Jan Groenewald]

Hi Eric,

I was mistaken, the daily autobuild is not enabled. We'll push it through during this week, probably tomorrow.

Regards,

Jan

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[Jan Groenewald]

Hi Eric,

A new -full package with the missing build folders is now uploaded and published on the sagemath-dev PPA.

You can turn this PPA on and off by renaming /etc/apt/sources.list.d/aims-sagemath-dev.list.disabled with or without the .disabled.

Regards,

Jan

[Eric Gourgoulhon]

Hi Jan,

I have uninstalled the package and reinstalled it with

sudo apt-get update

sudo apt-get install sagemath-upstream-binary-full

But the problem is still there: no folder /usr/lib/sagemath/build/bin and the same error message after sudo sage -f python2.

Best wishes,

Eric.

[Jan Groenewald]

Hi Eric

We had a typo in the install file. Now there is a new package here in the dev PPA.:

https://launchpad.net/~aims/+archive/ubuntu/sagemath-dev/+packages

Regards,

Jan

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[Jan Groenewald]

Apologies, we had some version mismatches, that version has the same error. Working on building the right one now.

Regards,

Jan

[Henri Girard]

Hi,
I was very happy after a fresh install sage /jupyter were working perfectly (I installed sage by hand, but I din't notice I had AIMS ppa selected and after doing today's update... I got too the ssl error, that's why after hours of googling I found this answer... Well I wait and see...
Regards
Henri

[Henri Girard]

Installing the LTS 6.8 manually solved the problem waiting for AIMS deb

Le jeudi 10 septembre 2015 22:28:39 UTC+2, Eric Gourgoulhon a écrit :

[Jan Groenewald]

Hi

A fixed 6.8 deb is now in the sagemath-dev PPA. I will test today since we are teaching a Sage class I will notice soon if it is broken, and upload to the stable PPA.

What is the SSL procedure? Is it

sudo apt-get install libssl-dev

sudo sage -f python

(while this is bad practice: compiling as root and writing over apt-managed files, we did make the sagemath-upstream-binary-full package to preserve this and cython functionality. Note the sizes (-full depends on sagemath-upstream-binary, and adds these folders https://bitbucket.org/aims_za/sagemath-upstream-binary/src/472bba7ef41379b61e03e216c1bb4a96e1ca604d/sagemath-upstream-binary/debian/sagemath-upstream-binary-full.install.in?at=master&fileviewer=file-view-default )

• sagemath-upstream-binary-full_6.8~aimsppa13~qa201509221157151_amd64.deb (315.0 MiB)
• sagemath-upstream-binary-full_6.8~aimsppa13~qa201509221157151_i386.deb (295.5 MiB)

• sagemath-upstream-binary_6.8~aimsppa13~qa201509221157151_amd64.deb (498.2 MiB)
• sagemath-upstream-binary_6.8~aimsppa13~qa201509221157151_i386.deb (445.9 MiB)

If we (finally) have 32 bit and 64 bit sage 6.8 trimmed and full in the stable PPA, we will enable weekly automated uploads to the dev PPA, so you'll want to stop using that.

Regards,

Jan

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[Henri Girard]

I just test it, ssl is always lacking
But I am not sure this is the reason because libssl-dev is installed.
Why not put in deb the sage-6.8 LTS, I installed it and it works (that's just a suggestion, but sorry if it's a bad idea ?)
Before I could compile sage but now I got errors that's why I like your deb and it's automatically updated.

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[Jan Groenewald]

Hi

On 23 September 2015 at 10:40, Henri Girard <henri....@gmail.com> wrote:

I just test it, ssl is always lacking
But I am not sure this is the reason because libssl-dev is installed.
Why not put in deb the sage-6.8 LTS, I installed it and it works (that's just a suggestion, but sorry if it's a bad idea ?)
Before I could compile sage but now I got errors that's why I like your deb and it's automatically updated.

I think due to other problems on many platforms the ssl is disabled by default in the Sage binaries.  Other sage developers are more qualified to discuss that and answer that.

What is the "sage 6.8 LTS"?  Do you mean include something other than http://sagemath.mirror.ac.za/linux/64bit/Ubuntu_14.04_LTS_sage-6.8-x86_64-Linux.tar.lrz in the PPA? Or do you mean depend on libssl-dev and include a rebuilt sage with pyopenssl in the deb? I coudl then be introducing errors/bugs to the downstream users if I include a rebuilt python with ssl. I want to confirm that it is possible though, with one or two lines, to add SSL capability.

Our (AIMS) main use case, by the way, is standalone laptop installs, that can work offline, so we use a per-user installation, not a multi-user server, so the https is irrelevant for us. I'd like to stay close to the upstream with the PPA. We do however have students ssh from a laptop into their own account on a campus desktop to use a notebook on a more powerful machine or just to access their worksheets conveniently from their rooms.

Right now we cannot on the -full package do either of

sage -i pyopenssl

or

sage -pip install pyopenssl

even though we did

sudo apt-get install python-dev libffi-dev libssl-dev libxml2-dev libxslt1-dev

Our

sage -f python was succcesful though.

What exactly are the commands and output of what you are trying to do?

Regards,

Jan

[Henri Girard]

In fact we must obtain (sagemanifolds and I... maybe more...(I guess but i don't want to speak in name of Eric) the following : sage --notebook=ipython so we have access to sage kernel.
With the following link you sent to me it works. Apparently ssl is inside or at least it doesn't ask for !
  I too installed all the libs you mentioned. But no way to get the deb working (pity but not dramatic), I have to install it by hand sudo mv sage /usr/share/sage and sudo ln -s /usr/share/sage/sage /usr/bin/sage (before delete sage in bin sudo rm /usr/bin/sage), but that's not ubuntu original installation : /usr/lib/sagemath (but it's helping me when something get wrong like at the moment !), so I have two sage installed in different location and when there is a problem I connect to the working version.
Anticipating a little wily seems to have problems with dir path python but I might be working properly when ready.
Anyway thanks for your great job. For me it's not too annoying and I don't want to give you more work than necessary, it's a only a whish that maybe others can have. I am not qualified enaugh to tell you what's the problem with ssl (In my opinion it's more a problem of right or directory than ssl as I have put all lib ?)
Kind regards
Henri

[Jan Groenewald]

Hi

I think that it now works because our latest PPA package includes all the build/bin folder in /usr/lib/sagemath.

Then when you have libssl-dev installed and do sudo sage -f python it is installed with ssl. I'm guessing though.

Regards,

Jan

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[Jan Groenewald]

The same working package is now uploading to the stable PPA. It is already in the dev PPA. We will probably next week turn on weekly autouploads to the dev PPA. And then release whenever there is a new sage and it is ready, to the stable PPA.

Regards,

Jan

[Henri Girard]

I noticed something : Your version compile python sage -f python
sage 6.8 LTS failed sage -f python
Now I will try make and see if it works
Regards
Henri

[Jan Groenewald]

Hi

What is Sage 6.8 LTS?

Regards,

Jan

[Henri Girard]

http://sagemath.mirror.ac.za/linux/64bit/Ubuntu_14.04_LTS_sage-6.8-x86_64-Linux.tar.lrz

[Henri Girard]

Sorry this one (ubuntu)
http://www-ftp.lip6.fr/pub/math/sagemath/linux/64bit/Ubuntu_14.04_LTS_sage-6.8-x86_64-Linux.tar.lrz
I don't know if it's the same ?

[Jan Groenewald]

Yes, that is the package we use to build the PPA deb.

The latest PPA version is supposed to be the same.

Regards,

Jan

[Henri Girard]

You said it could be easy to integrate ssl can you tell me how to do ?
sage - f python works in your version but while trying to run it, it doesn't work and I alway get ssl missing.
But if you haven't time don't worry I still can use ubuntu version. Just to see if it would work and integrate ssl

[Henri Girard]

Weird ...

[Thierry]

Hi,

sorry to enter the discussion late, i did not know i was involved there (i
built this binary). As you can see in the source of the builder, Sage is
built with openssl support (line 36):

http://sagebuilder.metelu.net/gitweb/?p=sagebuilder.git;a=blob;f=sage_deps.target;h=b18de8b4d7a2ad49fe2a905d689dc24b63bfe7da;hb=HEAD

So, you do not have to install libssl-dev nor rebuild python2. Instead,
just install the 'openssl' package and run Sage. Note that SSL is not only
required to run the notebook with https, but also to install PIP packages
(with the 'sage -pip install <pkg>' command), since the repository is
fetched via https.

I did ot look at the PPA recently, but if you use this binary, you should
add openssl as a dependency (probably also recommend or suggest : tk
texlive imagemagick dvipng libav-tools|ffmpeg openjdk-7-jre
icedtea-7-plugin runsnakerun linux-tools google-perftools graphviz
gnuplot).

If you need pyopenssl (a Python interface to openssl, which is not
required to let Sage work), note that it is not packaged anymore
(new-style packages), but the latest version is available via pip, so if
you need it, you just have to do:

sage -pip install pyopenssl

Ciao,
Thierry

On Wed, Sep 23, 2015 at 06:53:35PM +0200, Henri Girard wrote:
> Weird ...
>
> Le 23/09/2015 18:50, Jan Groenewald a écrit :
> >Yes, that is the package we use to build the PPA deb.
> >The latest PPA version is supposed to be the same.
> >
> >Regards,
> >Jan
> >
> >On 23 September 2015 at 18:45, Henri Girard

> ><henri....@gmail.com <mailto:henri....@gmail.com>> wrote:
> >
> > Sorry this one (ubuntu)
> > http://www-ftp.lip6.fr/pub/math/sagemath/linux/64bit/Ubuntu_14.04_LTS_sage-6.8-x86_64-Linux.tar.lrz
> > I don't know if it's the same ?
> >
> >
> >
> > Le 23/09/2015 18:43, Jan Groenewald a écrit :
> >> Hi
> >>
> >> What is Sage 6.8 LTS?
> >>
> >> Regards,
> >> Jan
> >>
> >> On 23 September 2015 at 18:42, Henri Girard

> >> <henri....@gmail.com <mailto:henri....@gmail.com>> wrote:
> >>
> >> I noticed something : Your version compile python sage -f python
> >> sage 6.8 LTS failed sage -f python
> >> Now I will try make and see if it works
> >> Regards
> >> Henri
> >>
> >>
> >> Le 23/09/2015 17:43, Jan Groenewald a écrit :
> >>> The same working package is now uploading to the stable PPA.
> >>> It is already in the dev PPA. We will probably next week
> >>> turn on weekly autouploads to the dev PPA. And then release
> >>> whenever there is a new sage and it is ready, to the stable PPA.
> >>>
> >>> Regards,
> >>> Jan
> >>>
> >>> On 23 September 2015 at 17:41, Jan Groenewald

> >>> <j...@aims.ac.za <mailto:j...@aims.ac.za>> wrote:
> >>>
> >>> Hi
> >>>
> >>> I think that it now works because our latest PPA package
> >>> includes all the build/bin folder in /usr/lib/sagemath.
> >>> Then when you have libssl-dev installed and do sudo sage
> >>> -f python it is installed with ssl. I'm guessing though.
> >>>
> >>> Regards,
> >>> Jan
> >>>
> >>> On 23 September 2015 at 17:00, Henri Girard

> >>> <henri....@gmail.com <mailto:henri....@gmail.com>>

> >>>> /( )\ www.aims.ac.za <http://www.aims.ac.za>

> >>>> ^^-^^
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[Jan Groenewald]

Hi

So the buildslaves we host did not have libssl-dev installed. This has now been fixed. From sage 6.9 the debs in the PPA will support SSL, if you do

sudo sage -pip install pyopenssl

(I'm looking into adding a user sagemath and changing all files in /usr/lib/sagemath to be owned by that user, so the command could change to

su - sagemath -c "sage -pip install pyopenssl"

in future to prevent compiling packages as root)

In the meantime on sagemath-upstream-binary-full 6.8 from the PPA, I think this will work

sudo -Es

sage -f python

cd /usr/lib/sagemath/

make

sage -pip install pyopenssl

Regards,

Jan

 ^^-^^