Re: SageManifolds Install Issue

208 views
Skip to first unread message

Jan Groenewald

unread,
Jun 12, 2015, 11:53:53 AM6/12/15
to Gérard JASTRZEB, sage-devel, Jonathan Carter
Hi

The more important drop is the whole src folder, which I think is needed for rebuilds. We did it to save space and bandwidth, and most importantly you should not be compiling as root which is necessary to install optional packages, which we intentially dropped now.. Perhaps a poll on this is necessary.

In principle the PPA supports easy install and upgrades, and I am not sure how to safely install, except perhaps to have all files owned by a new sagemath user we'd have to create and  incorporate, and also the deb is built from prebuilt binaries, see a recent thread about sagemath binaries unsuitable for development.

https://groups.google.com/forum/#!searchin/sage-devel/binaries$20development/sage-devel/QdwdT8J8q50/TyLCIeAF37cJ

At the moment we don't want to immediately revert. We could have a package sagemath-source which installs the latest source, but you are probably better of with a source tree of your own. How big is the need for optional packages via the PPA? We have a need for gap_packages at our institution, and a few others.

Regards,
Jan

On 12 June 2015 at 17:13, Gérard JASTRZEB <gerard....@free.fr> wrote:
First of all, I let me thank you for maintaining a PPA for SAGEMATH.
But since v6.7 there is a problem for those who want to install
SAGEMANIFOLDS as well.
You dropped Makefile and .git from /usr/lib/sagemath (system install),
which are mandatory for SAGEMANIFOLDS, as the install script (stable
version) triggers a re-build of sage and the development version
installs via git. Here is the link for it :
http://sagemanifolds.obspm.fr/download.html

Thank you for having a look at it.
Gérard JASTRZEB
gerard,jast...@free.fr
--
This message was sent from Launchpad by
=?utf-8?q?G=C3=A9rard_JASTRZEB?= (https://launchpad.net/~gerard-jastrzeb)
using the "Contact this team's admins" link on the AIMS team page
(https://launchpad.net/~aims).
For more information see
https://help.launchpad.net/YourAccount/ContactingPeople

Jan Groenewald

unread,
Jun 12, 2015, 12:03:51 PM6/12/15
to Gérard JASTRZEB, sage-devel, Jonathan Carter
Also, to revert in the meantime, do

wget https://launchpad.net/~aims/+archive/ubuntu/sagemath/+build/7499250/+files/sagemath-upstream-binary_6.7ppa10revert6.6.aims6-2_amd64.deb
sudo dpkg -i sagemath-upstream-binary_6.7ppa10revert6.6.aims6-2_amd64.deb
sudo apt-mark hold sagemath-upstream-binary

Regards,
Jan

Jan Groenewald

unread,
Jun 13, 2015, 4:20:02 AM6/13/15
to Gérard JASTRZEB, sage-devel, Jonathan Carter
Another side effect in 6.7 PPA is any foo? or foo?? in the sage command line says ImportError: no module named conf, but it seems help(foo) still works. In the notebook foo? and foo?? still works. Not sure whether this is PPA or 6.7 specific.

Another option is to have another PPA with a deb with a copy of sage.tar.gz build dependencies, and a sage-install-from-source script that does not run as root, installs per-user, owned by user, in /home/user/, i.e. fully developer friendly. This will massively increase the deb size and in multi-user systems even more massively increase the install size (think NFS in our computer lab). Users will also be able to accidentally delete or break their install. But this might be not too hard and able to do fairly quickly for those that need it.

Regards,
Jan

Eric Gourgoulhon

unread,
Jun 22, 2015, 4:12:38 PM6/22/15
to sage-...@googlegroups.com, jona...@aims.ac.za, gerard....@free.fr
Hi,

In order to avoid any confusion before some solution is found, we have updated the download page to tell that it is no longer possible to install SageManifolds atop of the sagemath Ubuntu package from the PPA.

Best wishes,

Eric.

Jan Groenewald

unread,
Sep 8, 2015, 10:30:54 AM9/8/15
to sage-devel, Jonathan Carter, Gérard JASTRZEB, egourg...@gmail.com
Hi Eric,

We now have an updated 6.8 in the *dev* version of our PPA (ppa:aims/sagemath-dev) with two packages

1) sagemath-upstream-binary
2) sagemath-upstream-binary-full (also depends on (1) )

where full again contains the src, git, etc. folders. It should support optional packages again. While it is a bad idea to install files and especially to compile as root in a apt-managed folder like /usr/lib/sagemath. But this gives you some time to make a better plan, or for us to have a sagemath user own that folder; which won't stop people running sudo sage -i anyway. The apt-managed files are less of an issue as sagemath already changes/moves files at first startup when fixing hardcoded path of the install, and we run that first sage call as root in the postinst script of the deb package from the PPA. So that is already broken.

To test these before we copy them to the stable PPA,

sudo apt-add-repository -y ppa:aims/sagemath-dev
sudo apt-get update
sudo apt-get install sagemath-upstream-binary-full

to revert go

sudo apt-get purge sagemath-upstream-binary-full
sudo apt-get install sagemath-upstream-binary=6.7ppa23
sudo mv /etc/apt/sources.list.d/aims-sagemath-dev-trusty.list{,.disabled}

Regards,
Jan



--
  .~.
  /V\     Jan Groenewald
 /( )\    www.aims.ac.za
 ^^-^^ 

Thierry

unread,
Sep 8, 2015, 11:55:50 AM9/8/15
to sage-...@googlegroups.com, Jonathan Carter, Gérard JASTRZEB, egourg...@gmail.com
Hi,

somehow related to that issue, i just gave some tutorials about Sage in
Esfahan (Iran) for a research school about tilings [1]. Since windows was
deployed there, we used the Sage Debian Live USB to run Sage [2]. I was
requested by some participants to install SageManifolds. Here is a way,
open a terminal and type:

cd /opt/sagemath/sage
wget http://sagemanifolds.obspm.fr/spkg/sm-install.sh
chmod +x sm-install.sh
./sm-install.sh
keep dir /opt/sagemath

The last line adds a squashfs layer to the current one(s) so that the
changes related to SageManifolds will remain available for further
reboots. Note that the (compressed) layer takes slightly less than 100M
because the documentation is rebuilt.

If you just want to try SageManifolds without modifying the default Sage
install, it suffice to type the first four lines, so that the changes
won't be kept for next reboot.

Note also that this installation will not be transferred during a clone or
upgrade of the key, since those operations aim at providing an unmodified
version of SDL to the target key.

Ciao,
Thierry

[1] http://isfahan.sciencesconf.org/
[2] http://sagedebianlive.metelu.net/
http://www.sagemath.org/download-liveusb.html



On Tue, Sep 08, 2015 at 04:30:30PM +0200, Jan Groenewald wrote:
> On 22 June 2015 at 22:12, Eric Gourgoulhon <egourg...@gmail.com> wrote:
> Hi,
>
> In order to avoid any confusion before some solution is found, we have
> updated the download page <http://sagemanifolds.obspm.fr/download.html> to
> --
> 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+...@googlegroups.com.
> To post to this group, send email to sage-...@googlegroups.com.
> Visit this group at http://groups.google.com/group/sage-devel.
> For more options, visit https://groups.google.com/d/optout.

Eric Gourgoulhon

unread,
Sep 8, 2015, 4:18:52 PM9/8/15
to sage-devel, jona...@aims.ac.za, gerard....@free.fr, egourg...@gmail.com
Hi Jan,

Thank you for having prepared a Ubuntu package with the sources included!
I've tried to install it but the step
sudo apt-get install sagemath-upstream-binary-full
results in the following error:

Décompactage de sagemath-upstream-binary-full (6.8~aimsppa11) ...
dpkg: error processing archive /var/cache/apt/archives/sagemath-upstream-binary-full_6.8~aimsppa11_amd64.deb (--unpack):
 tentative de remplacement de « /usr/lib/sagemath/local/libexec/git-core/git-merge-resolve », qui appartient aussi au paquet sagemath-upstream-binary 6.8~aimsppa11
dpkg-deb : erreur : le sous-processus coller a été tué par le signal (Relais brisé (pipe))

Sorry the message is in French, but it says basically that there is some attempt to replace  /usr/lib/sagemath/local/libexec/git-core/git-merge-resolve, which belongs also to the package sagemath-upstream-binary 6.8~aimsppa11.
(I'd say there seems to be a conflict between sagemath-upstream-binary-full and sagemath-upstream-binary).
My system is Ubuntu 14.04. I am attaching the full log for reference.

Regards,

Eric.
install_sagemath.log

Eric Gourgoulhon

unread,
Sep 8, 2015, 5:32:07 PM9/8/15
to sage-devel, egourg...@gmail.com
Hi Thierry,


Le mardi 8 septembre 2015 17:55:50 UTC+2, Thierry (sage-googlesucks@xxx) a écrit :

    cd /opt/sagemath/sage
    wget http://sagemanifolds.obspm.fr/spkg/sm-install.sh
    chmod +x sm-install.sh
    ./sm-install.sh
    keep dir /opt/sagemath


Thank you for these instructions. I've added them in a "Sage Debian Live" section at the download page
http://sagemanifolds.obspm.fr/download.html

Best regards,

Eric.

Jonathan Carter

unread,
Sep 9, 2015, 5:10:49 AM9/9/15
to Eric Gourgoulhon, sage-devel, gerard....@free.fr
Hi Eric
Thanks for the feedback, we'll need to add some extra fields in the
package to allow it to cross over from the old format.

In the meantime, there are two alternative options.

1. Allow the new package to overwrite paths from the old package:

This will download the packages without installing them:
sudo apt-get -d install sagemath-upstream-binary
sagemath-upstream-binary-full

This will allow dpkg to ignore package ownership while transitioning to
the new packages:
sudo dpkg --force-overwrite -i
/var/cache/apt/archives/sagemath-upstream-binary_6.8~aimsppa11_amd64.deb
/var/cache/apt/archives/sagemath-upstream-binary-full_6.8~aimsppa11_amd64.deb

2. Remove the old package completely and then install the new package(s).

We'll upload a new package to the dev ppa that contains the proper
fields in the control file that will specify that the new -full package
replaces files in the old package name that will allow for a smoother
transition.

-Jonathan

Jonathan Carter

unread,
Sep 9, 2015, 10:49:06 AM9/9/15
to Eric Gourgoulhon, sage-devel
Hi Again!
This is all fixed now in the ~aimsppa12 version, so doing and apt-get
update and installing the new version should also do the trick.

Next week we're also planning to enable automated daily packages in that
-dev PPA, so we'll be able to pick up anything that breaks faster and
avoid anything nasty from landing in the stable PPA.

-Jonathan

Eric Gourgoulhon

unread,
Sep 9, 2015, 5:16:59 PM9/9/15
to sage-devel, egourg...@gmail.com
Hi Jonathan,

Le mercredi 9 septembre 2015 16:49:06 UTC+2, Jonathan Carter a écrit :
This is all fixed now in the ~aimsppa12 version, so doing and apt-get
update and installing the new version should also do the trick.



Thanks!
It works now. I could install the package sagemath-upstream-binary-full and SageManifolds atop of it as follows:

cd /usr/lib/sagemath
sudo wget http://sagemanifolds.obspm.fr/spkg/sm-install.sh
sudo bash sm-install.sh

However, for some reason, the sources files in src/sage/tensor/modules updated by the script sm-install.sh have not been copied to the build directory (build/lib.linux-x86_64-2.7/sage/tensor/modules) during the 'sage -b' performed by sm-install.sh. To force this, I had to run the extra commands:

sudo touch src/sage/tensor/modules/*.py
sudo sage -b

Then SageManifolds was fully installed and everything went fine:
- the html documentation was produced
- SageManifolds doctests are passed (modulo a few unimportant failures in output due to changes in Sage 6.8 w.r.t. Sage 6.7; this will be fixed in the next version of SageManifolds)
- SageManifolds worksheets could be run in the Sage notebook.

Thanks again.
Best wishes,

Eric.

Jan Groenewald

unread,
Sep 10, 2015, 5:28:12 AM9/10/15
to sage-devel, Eric Gourgoulhon
Hi Eric,

You might want to disable the dev PPA. Within a week or two we will copy a sage 6.8 to the stable PPA. The dev PPA will get automated uploads as we do testing (probably weekly):

sudo mv /etc/apt/sources.list.d/aims-sagemath-dev-trusty.list{,.disabled}

Regards,
Jan

--
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+...@googlegroups.com.
To post to this group, send email to sage-...@googlegroups.com.
Visit this group at http://groups.google.com/group/sage-devel.
For more options, visit https://groups.google.com/d/optout.

Eric Gourgoulhon

unread,
Sep 10, 2015, 10:15:35 AM9/10/15
to sage-devel, egourg...@gmail.com

Hi Jan,

Le jeudi 10 septembre 2015 11:28:12 UTC+2, Jan Groenewald a écrit :
Hi Eric,

You might want to disable the dev PPA. Within a week or two we will copy a sage 6.8 to the stable PPA. The dev PPA will get automated uploads as we do testing (probably weekly):

sudo mv /etc/apt/sources.list.d/aims-sagemath-dev-trusty.list{,.disabled}


OK thanks.

Best regards,

Eric.
Reply all
Reply to author
Forward
0 new messages