Bug 1895038

Summary: Cannot get sage to start
Product: [Fedora] Fedora Reporter: Ariel S. <ariels.boiardi>
Component: sagemathAssignee: Paulo Andrade <paulo.cesar.pereira.de.andrade>
Status: CLOSED ERRATA QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: urgent Docs Contact:
Priority: unspecified    
Version: 33CC: ariels.boiardi, gmaxwell, jorgecszabo, loganjerry, paulo.cesar.pereira.de.andrade, trpost, woutersj
Target Milestone: ---   
Target Release: ---   
Hardware: x86_64   
OS: Linux   
Whiteboard:
Fixed In Version: sagemath-9.0-8.fc32 Doc Type: If docs needed, set a value
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2020-11-25 01:42:31 UTC Type: Bug
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: --- Target Upstream Version:
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Description Flags
crash_report none

Description Ariel S. 2020-11-05 15:49:02 UTC 
Created attachment 1726937 [details]
crash_report

Description of problem:
sage does not start and crashes


Version-Release number of selected component (if applicable):
Latest version, i.e. 9.1-4


How reproducible:
Install and launch sage

Actual results:
sage crashes with a long list error in Python execution. The traceback is attached to this report. 

The first error seems to occur while setting up GP/PARI, but I really don't know. The binaries compiled for Debian from https://www.sagemath.org/download.html works for me. 
I guess there must be some incompatibility with some python library after F33 update, as it used to work before the update.
Comment 1 Jerry James 2020-11-06 16:47:35 UTC 
I've been trying to figure out that same problem for the last couple of days.  I don't understand what is going on yet, but I'm working on it.  Wish me luck!
Comment 2 Ariel S. 2020-11-07 12:57:56 UTC 
At least I'm glad to know that it is not a ghost in my machine! 
If I can be of any help please let me know. Thanks for your work!
Comment 3 Jerry James 2020-11-09 16:54:18 UTC 
*** Bug 1895556 has been marked as a duplicate of this bug. ***
Comment 4 Jerry James 2020-11-09 16:56:37 UTC 
This started happening when giac was updated from version 1.6.0-7 to version 1.6.0-25. The way giac initializes pari was changed. Sagemath starts up and initializes cypari2, which stores the value of avma. Later, giac is loaded. It initializes pari a second time, creating an entirely new value of avma. When cypari2 is next used, it tries to use values on the old stack, but they are not valid stack slots because giac made a new pari stack.

I'm trying to decide on the best approach to take. I think we will have to prevent giac from calling either pari_init_opts or pari_close if avma is nonzero when giac starts up.
Comment 5 Jerry James 2020-11-09 17:00:32 UTC 
Hmmmm, or maybe we need to build pari with TLS support.  That might be enough.  I will try it.
Comment 6 Jerry James 2020-11-10 22:13:52 UTC 
Building pari with TLS support does appear to be the key.  That involves rebuilding or updating several other packages.  I am trying to get the full scope of the necessary changes worked out.  I also figured I might as well update to sagemath 9.2 while I'm at it.  Please bear with me as I try to get the whole thing figured out and built.  Given the build times for some of these packages, it is likely going to be a few days before I have anything ready for all of you to try.

If you are feeling adventurous, you might try downgrading giac to see if that lets you get some work done in the meantime.
Comment 7 Gregory Maxwell 2020-11-10 22:29:11 UTC 
FWIW, I switched to running sage 9.2 compiled from source so I wouldn't be totally dead in the water.  Unfortunately, the sage source builds use lots of bundled libraries-- some older than Fedora some newer than Fedora so the fact that it works for me isn't of any particular use.

For other stuck folks if downgrading giac doesn't work building Sage 9.2 from source was essentially painless.
Comment 8 Ariel S. 2020-11-10 23:26:11 UTC 
(In reply to Jerry James from comment #6)

> If you are feeling adventurous, you might try downgrading giac to see if
> that lets you get some work done in the meantime.

I can confirm that downgrading giac seems to work.
Comment 9 Fedora Update System 2020-11-16 16:12:26 UTC 
FEDORA-2020-f16abf2fb5 has been submitted as an update to Fedora 33. https://bodhi.fedoraproject.org/updates/FEDORA-2020-f16abf2fb5
Comment 10 Fedora Update System 2020-11-16 16:12:26 UTC 
FEDORA-2020-6994abfc21 has been submitted as an update to Fedora 32. https://bodhi.fedoraproject.org/updates/FEDORA-2020-6994abfc21
Comment 11 Fedora Update System 2020-11-17 02:05:33 UTC 
FEDORA-2020-6994abfc21 has been pushed to the Fedora 32 testing repository.
In short time you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --advisory=FEDORA-2020-6994abfc21`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-6994abfc21

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
Comment 12 Fedora Update System 2020-11-17 02:34:01 UTC 
FEDORA-2020-f16abf2fb5 has been pushed to the Fedora 33 testing repository.
In short time you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --advisory=FEDORA-2020-f16abf2fb5`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-f16abf2fb5

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
Comment 13 Ariel S. 2020-11-17 14:23:07 UTC 
I tried to install the update trough the testing repository as in the message above, but dnf gives a bunch of conflicts:
  file /usr/share/doc/sagemath/html/en/_static/config from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/_static/extensions from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/_static/fonts from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/_static/jax from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/_static/localization from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/_static/test from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/a_tour_of_sage/_static/config from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/a_tour_of_sage/_static/extensions from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/a_tour_of_sage/_static/fonts from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/a_tour_of_sage/_static/jax from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/a_tour_of_sage/_static/localization from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/a_tour_of_sage/_static/test from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/constructions/_static/config from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/constructions/_static/extensions from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/constructions/_static/fonts from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/constructions/_static/jax from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/constructions/_static/localization from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/constructions/_static/test from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/developer/_static/config from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
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  file /usr/share/doc/sagemath/html/en/developer/_static/localization from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/developer/_static/test from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/faq/_static/config from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/faq/_static/extensions from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/faq/_static/fonts from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/faq/_static/jax from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/faq/_static/localization from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
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  file /usr/share/doc/sagemath/html/en/installation/_static/jax from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/installation/_static/localization from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/installation/_static/test from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/prep/_static/config from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/prep/_static/extensions from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/prep/_static/fonts from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/prep/_static/jax from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/prep/_static/localization from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/prep/_static/test from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
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  file /usr/share/doc/sagemath/html/en/reference/_static/fonts from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
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  file /usr/share/doc/sagemath/html/en/reference/_static/localization from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/reference/_static/test from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/thematic_tutorials/_static/config from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/thematic_tutorials/_static/extensions from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/thematic_tutorials/_static/fonts from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/thematic_tutorials/_static/jax from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/thematic_tutorials/_static/localization from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/thematic_tutorials/_static/test from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/tutorial/_static/config from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/tutorial/_static/extensions from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/tutorial/_static/fonts from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/tutorial/_static/jax from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/tutorial/_static/localization from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/tutorial/_static/test from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/website/_static/config from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/website/_static/extensions from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
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  file /usr/share/doc/sagemath/html/en/website/_static/localization from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
  file /usr/share/doc/sagemath/html/en/website/_static/test from install of sagemath-doc-en-9.2-1.fc33.x86_64 conflicts with file from package sagemath-doc-en-9.1-4.fc33.x86_64
Comment 14 Jerry James 2020-11-17 16:39:41 UTC 
(In reply to Ariel S. from comment #13)
> I tried to install the update trough the testing repository as in the
> message above, but dnf gives a bunch of conflicts:

That's due to the fix for bug 1875606, which replaces directories with symlinks.  RPM has never been able to handle directory replacements automatically.  I should have remembered that.

If you completely uninstall sagemath, then reinstall from the testing repository, that should work.  I will add a fix for this to the sagemath package and rebuild.  Sorry for the trouble.
Comment 15 Ariel S. 2020-11-17 17:04:38 UTC 
(In reply to Jerry James from comment #14)
 
> If you completely uninstall sagemath, then reinstall from the testing
> repository, that should work.  I will add a fix for this to the sagemath
> package and rebuild.  Sorry for the trouble.

Yea I know, but thanks for advising! I wanted to report before pushing to the stable repository. 
And again thank you for the superb work!
Comment 16 Fedora Update System 2020-11-19 15:41:15 UTC 
FEDORA-2020-f16abf2fb5 has been submitted as an update to Fedora 33. https://bodhi.fedoraproject.org/updates/FEDORA-2020-f16abf2fb5
Comment 17 Fedora Update System 2020-11-19 17:15:49 UTC 
FEDORA-2020-f16abf2fb5 has been submitted as an update to Fedora 33. https://bodhi.fedoraproject.org/updates/FEDORA-2020-f16abf2fb5
Comment 18 Fedora Update System 2020-11-20 02:14:40 UTC 
FEDORA-2020-f16abf2fb5 has been pushed to the Fedora 33 testing repository.
In short time you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --advisory=FEDORA-2020-f16abf2fb5`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-f16abf2fb5

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
Comment 19 Fedora Update System 2020-11-25 01:42:31 UTC 
FEDORA-2020-6994abfc21 has been pushed to the Fedora 32 stable repository.
If problem still persists, please make note of it in this bug report.
Comment 20 Fedora Update System 2020-11-30 01:08:35 UTC 
FEDORA-2020-f16abf2fb5 has been pushed to the Fedora 33 stable repository.
If problem still persists, please make note of it in this bug report.
Comment 21 Jerry James 2020-11-30 18:27:28 UTC 
*** Bug 1902423 has been marked as a duplicate of this bug. ***