Sage 9.2.beta9 released

[Volker Braun]

As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html 

548666e9f2 (tag: 9.2.beta9, trac/develop) Updated SageMath version to 9.2.beta9

842a6866f1 Trac #29974: Make combinat doctests ready for random seeds

1de1d457b4 Trac #29971: Make categories doctests ready for random seeds

6864757e11 Trac #29968: Make algebras doctests ready for random seeds

b526019731 Trac #29963: Make geometry doctests ready for random seeds

719f9af12c Trac #29509: rational_points fails for some hyperelliptic curves

4d5ab773b5 Trac #29257: use solve_left for division operation of matrices

e18e84219d Trac #30365: Disable LTO in matplotlib build

01f536726d Trac #29989: fix random test failures in PSage interface

f531b354f7 Trac #30345: build/make/Makefile.in: Filter out "-j" from sub-make invocations to avoid excessive parallel load

8417e64af6 Trac #29511: Broken coercion between cyclotomic fields

b4a8c5745b Trac #29325: Set up permutahedron with both Vrep and Hrep (if backend supports it)

9b14ca3e86 Trac #29248: Index notation for tensors should allow for unicode characters

a331d47ef3 Trac #28966: Provide unicode aliases for some globals in Python 3

95d0cd5b9e Trac #28951: Fixing a bug in sage.schemes.cyclic_covers.charpoly_frobenius

4986d5ea7f Trac #28816: database_stein_watkins Python 3 issues

193e14365a Trac #30127: cygwin-minimal: pip-20.1.1 fails to install

a92871805f Trac #26919: Upgrade Jupyter notebook to latest (6.1.1) and its dependencies to latest

66472811de Trac #30251: ExtPowerFreeModule, ExtPowerDualFreeModule: Simplify _repr_

7030fa15a7 Trac #30175: Remove outdated spkg-src script for ecl

11bb005e98 Trac #30165: normalize_coordinates broken for p-adic fields

82568e3cbd Trac #30044: tox.ini: Test on voidlinux

294931e00b Trac #30339: tox.ini: Update for latest ubuntu, fedora versions

ea615c4ce6 Trac #30331: Issue with toric_substitute for Laurent polynomials

df3cf63875 Trac #30327: affine group element * a polytope raises KeyError

9cfaefb544 Trac #30303: Graphs: two families of distance-regular graphs

81a7e50cd2 Trac #30301: Italian translation of FAQ

48fb9141da Trac #30286: Graph: last sporadic distance-regular graphs

6f2561fdca Trac #30260: Graphs: more distance-regular graphs

29098c6af9 Trac #30240: Graphs: a few distance-regular graphs

1b8dff7172 Trac #30178: Manifolds: add orientability

24eb3aa28d Trac #29911: sage.rings.integer, integer_ring: Remove dependencies on sage.libs.ntl

8b9743d0af Trac #29654: Improve face generator of polyhedra by exposing `FaceIterator` class

c0b61fd5cf Trac #28904: Move reversed graph from backend to CGraph for sparse graphs

04c64492a6 Trac #30335: openblas: clear out .pc symlinks before installation

ef6132b817 Trac #25363: Add '--simple-prompt' argument for sage

3682402983 Trac #30277: Remove src/module_list.py

0cc658a1f9 Trac #30257: Fusion Ring - Rmatrix

6ffe4c9e55 Trac #30209: Action for Bundle Connections

eaa2f0a361 Trac #29950: Build sagelib from build/pkgs/sagelib/src, fix `setup.py sdist`, add spkg-src and tox.ini

e002ee071c Trac #29539: Bug in saturation of elliptic curves over number fields

a4b8705ae5 Trac #30330: `cdd` backend fails to initialize empty polyhedron from double description

c3e5ce6ea1 Trac #30292: is_pyramid returns a wrong certificate

3d594b5cc6 Trac #30262: Update e-antic to 0.1.8

415221a9a8 (tag: 9.2.beta8) Updated SageMath version to 9.2.beta8

[Steven Trogdon]

This beta fails on Gentoo, apparently when building the html-docs, as and upgrade from beta7 which built successfully.

[dochtml]   File "sage/rings/polynomial/polynomial_element.pyx", line 7893, in sage.rings.polynomial.polynomial_element.Polynomial.roots (build/cythonized/sage/rings/polynomial/polynomial_element.c:64031)

[dochtml]   File "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/rings/polynomial/complex_roots.py", line 246, in complex_roots

[dochtml]     factors = p.squarefree_decomposition()

[dochtml]   File "sage/rings/polynomial/polynomial_element.pyx", line 1815, in sage.rings.polynomial.polynomial_element.Polynomial.squarefree_decomposition (build/cythonized/sage/rings/polynomial/polynomial_element.c:18350)

[dochtml]   File "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/categories/fields.py", line 501, in _squarefree_decomposition_univariate_polynomial

[dochtml]     return Factorization(factors, unit=unit, sort=False)

[dochtml]   File "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/structure/factorization.py", line 299, in __init__

[dochtml]     self.__universe = Sequence(t[0] for t in x).universe()

[dochtml]   File "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/structure/sequence.py", line 255, in Sequence

[dochtml]     from sage.rings.polynomial.pbori import BooleanMonomialMonoid

[dochtml] ImportError: libm4ri-0.0.20200115.so: cannot open shared object file: No such file or directory

make[3]: *** [Makefile:1864: doc-html] Error 1

make[2]: *** [Makefile:1754: all-start] Error 2

I have system m4ri-2010115 and m4ri3-20200115 installed. From config.log

configure:36038: result: m4ri-20200115:                               using system package; SPKG will not be installed

configure:36038: result: m4rie-20200115:                              using system package; SPKG will not be installed

and

configure:24084: will use system package and not install SPKG lrcalc

## ------------------------------------------------------ ##

## Checking whether SageMath should install SPKG m4rie... ##

## ------------------------------------------------------ ##

configure:24184: checking whether any of m4ri is installed as or will be installed as SPKG

configure:24193: result: no

configure:24196: checking m4rie/m4rie.h usability

configure:24196: g++ -std=gnu++11 -c -g -O2   conftest.cpp >&5

configure:24196: $? = 0

configure:24196: result: yes

configure:24196: checking m4rie/m4rie.h presence

configure:24196: g++ -E -std=gnu++11   conftest.cpp

configure:24196: $? = 0

configure:24196: result: yes

configure:24196: checking for m4rie/m4rie.h

configure:24196: result: yes

So my system m4ri is not found even though installed.

[Steven Trogdon]

I stated things incorrectly. This was an incremental upgrade from beta8 not beta7.

[Thierry Dumont]

On my Ubuntu 20/04, migrating from 9.2 beta 8 to beta 9:

- compilation: no problem
- make ptestlong
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------

t.d.

[David Coudert]

incremental upgrade from 9.2.beta8 on macOS 10.14.6

- build OK

- docbuild OK

however, a non blocking error with sagetex:

[sagetex-3.4] Successfully built sagetex

[sagetex-3.4] Installing collected packages: sagetex

[sagetex-3.4]   Created temporary directory: /private/var/folders/l8/sxf193t11mvdyqq56f4w_6_80000gn/T/pip-unpacked-wheel-6tdncpf9

[sagetex-3.4]   *** Error compiling '/private/var/folders/l8/sxf193t11mvdyqq56f4w_6_80000gn/T/pip-unpacked-wheel-6tdncpf9/sagetex-3.4.data/data/share/texmf/tex/latex/sagetex/extractsagecode.py'...

[sagetex-3.4]     File "/private/var/folders/l8/sxf193t11mvdyqq56f4w_6_80000gn/T/pip-unpacked-wheel-6tdncpf9/sagetex-3.4.data/data/share/texmf/tex/latex/sagetex/extractsagecode.py", line 48

[sagetex-3.4]       except getopt.GetoptError, err:

[sagetex-3.4]                                ^

[sagetex-3.4]   SyntaxError: invalid syntax

[sagetex-3.4]   

[sagetex-3.4]   *** Error compiling '/private/var/folders/l8/sxf193t11mvdyqq56f4w_6_80000gn/T/pip-unpacked-wheel-6tdncpf9/sagetex-3.4.data/data/share/texmf/tex/latex/sagetex/makestatic.py'...

[sagetex-3.4]     File "/private/var/folders/l8/sxf193t11mvdyqq56f4w_6_80000gn/T/pip-unpacked-wheel-6tdncpf9/sagetex-3.4.data/data/share/texmf/tex/latex/sagetex/makestatic.py", line 48

[sagetex-3.4]       except getopt.GetoptError, err:

[sagetex-3.4]                                ^

[sagetex-3.4]   SyntaxError: invalid syntax

[sagetex-3.4]   

[sagetex-3.4] 

[sagetex-3.4] Successfully installed sagetex-3.4

[sagetex-3.4] Removed build tracker: '/private/var/folders/l8/sxf193t11mvdyqq56f4w_6_80000gn/T/pip-req-tracker-l6deu40y'

[sagetex-3.4] Removing old SageTex version(s)

[sagetex-3.4] 

[sagetex-3.4] real 0m3.307s

[sagetex-3.4] user 0m1.896s

[sagetex-3.4] sys 0m0.652s

[sagetex-3.4] Copying package files from temporary location /Users/dcoudert/sage/local/var/tmp/sage/build/sagetex-3.4/inst to /Users/dcoudert/sage/local

[sagetex-3.4] Successfully installed sagetex-3.4

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[David Coudert]

Incremental build from 9.2.beta8 on macOS 10.15.6

- build OK

- doc build failed even after make doc-clean

cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html ' logs/dochtml.log

[dochtml] 

[dochtml] Building reference manual, first pass.

[dochtml] 

[dochtml] [reference] Sphinx v3.1.2 en cours d'exécution

[dochtml] [reference] WARNING: l'entrée html_static_path '/Users/dcoudert/sage/src/doc/common/static' n'existe pas

[dochtml] [reference] WARNING: l'entrée html_static_path 'static' n'existe pas

[dochtml] [reference] WARNING: le fichier de favicon 'favicon.ico' n'existe pas

[dochtml] [reference] construction en cours [mo]:cibles pour les fichiers po 0 qui sont périmées

[dochtml] [reference] construction [inventory]:cibles pour les fichiers sources 1 qui sont périmées

[dochtml] [reference] mise-à-jour de l'environnement :[nouvelle configuration] 1 ajouté, 0 modifié, 0 supprimé

[dochtml] [reference] lecture des sources... [100%] index

[dochtml] [reference] recherche des fichiers périmés... aucun résultat

[dochtml] [reference] environnement de sérialisation... fait

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:36: WARNING: La citation [AAGMRZ2019] n'est pas référencée

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:40: WARNING: La citation [Ab1995] n'est pas référencée

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:46: WARNING: La citation [AB2007] n'est pas référencée

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:50: WARNING: La citation [AB2008] n'est pas référencée

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:54: WARNING: La citation [ABBDHR2019] n'est pas référencée

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:58: WARNING: La citation [ABBR2011] n'est pas référencée

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:62: WARNING: La citation [ABBR2012] n'est pas référencée

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:65: WARNING: La citation [ABCFHLLMRT2019] n'est pas référencée

….

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:5690: WARNING: La citation [Zor] n'est pas référencée

[dochtml] [reference] /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:5693: WARNING: La citation [ZZ2005] n'est pas référencée

[dochtml] [reference] vérification de la cohérence... fait

[dochtml] [reference] document en préparation... fait

[dochtml] [reference] écriture... [100%] index

[dochtml] [reference] dumping object inventory... fait

[dochtml] [reference] build a réussi, 1352 warnings.

[dochtml] [reference] The inventory files are in local/share/doc/sage/inventory/en/reference/references.

[dochtml] Error building the documentation.

[dochtml] Traceback (most recent call last):

[dochtml]   File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/python3.7/runpy.py", line 193, in _run_module_as_main

[dochtml]     "__main__", mod_spec)

[dochtml]   File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/python3.7/runpy.py", line 85, in _run_code

[dochtml]     exec(code, run_globals)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__main__.py", line 2, in <module>

[dochtml]     main()

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 1721, in main

[dochtml]     builder()

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 328, in _wrapper

[dochtml]     getattr(get_builder(document), 'inventory')(*args, **kwds)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 551, in _wrapper

[dochtml]     self._build_bibliography(lang, format, *args, **kwds)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 528, in _build_bibliography

[dochtml]     build_many(build_ref_doc, references)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", line 281, in build_many

[dochtml]     _build_many(target, args, processes=NUM_THREADS)

[dochtml]   File "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", line 283, in build_many

[dochtml]     raise worker_exc.original_exception

[dochtml] OSError: WARNING: l'entrée html_static_path '/Users/dcoudert/sage/src/doc/common/static' n'existe pas

make[3]: *** [doc-html] Error 1

make[2]: *** [all-start] Error 2

Le 19 août 2020 à 01:01, Volker Braun <vbrau...@gmail.com> a écrit :

[Dima Pasechnik]

please review https://trac.sagemath.org/ticket/30342 (update of sagetex)

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/B2CCFA52-DCFB-42FE-9A33-535A43EB6F56%40gmail.com.

[Sébastien Labbé]

Testing with various optional and external packages, I get:

Using --optional=4ti2,cbc,ccache,cryptominisat,dot2tex,e_antic,external,fricas,glucose,latte_int,lidia,lrslib,memlimit,normaliz,notedown,openssl,pandoc_attributes,pycosat,pynormaliz,rst2ipynb,sage,sage_numerical_backends_coin

----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------

External software detected for doctesting: ffmpeg,graphviz,imagemagick,latex,octave,pandoc

But *internet* doctests were not tested due to problem with my installation.

Sébastien

[Samuel Lelievre]

2020-08-19 12:43:58 UTC, Sébastien Labbé:

Testing with various optional and external packages, I get:

[...]

 

Speaking of optional packages, could someone review

- Sage Trac ticket 30390: Fix PyPI url

  https://trac.sagemath.org/ticket/30390

[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM, ugrading 9.2.beta8 + Trac#25363 + Trac#300Trac#3006363 to 9.2.beta9 + Trac#29456 + Trac#30063 and running ~ptestlong~ gives the same resulys as those reported since 9.2.beta5 (one transient timeout, three permanent failures).

HTH,

​

[Maxime Bombar]

Hi,

On a fresh install from sources on Debian Sid build and documentation
are ok, but tests sometimes fail :

make: *** [Makefile:190: ptestlong] Error 17

--
MB.

[Steven Trogdon]

Actually I have system m4ri-20200125 and not 20200115 installed. For me the info in config.log was somewhat misleading. I have been using the sage provided brial, so after rebuilding brial the html docs successfully built and sage starts.

On Tuesday, August 18, 2020 at 11:07:05 PM UTC-6, Steven Trogdon wrote:

[Kenji Iohara]

I have Mac OS X.15.6.   I could compile it with no problem, 

but I had some errors running ptestlong 

[David Coudert]

was it incremental build (and from which beta) or fresh build ?

Le 20 août 2020 à 02:55, Kenji Iohara <simplye...@gmail.com> a écrit :

I have Mac OS X.15.6.   I could compile it with no problem, 

but I had some errors running ptestlong 

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<ptestlong.log>

2020/08/19 18:17、Steven Trogdon <steven....@gmail.com>のメール:

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[Kenji Iohara]

It is a fresh build.

2020/08/20 9:33、David Coudert <david....@gmail.com>のメール:

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/E34E9924-6725-4370-8333-18A0BE8124C4%40gmail.com.

[Dima Pasechnik]

More details please - which tests have failed?
(normally there should be a summary report at the end of testing session)

Thanks
Dima
>
> --
> MB.

>
>
>
> --
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[Maxime Bombar]

Oh yes sure, sorry I didn't see it. It that the following ?

 sage -t --long --random-seed=0
src/doc/en/constructions/algebraic_geometry.rst  # 1 doctest failed
 sage -t --long --random-seed=0 src/doc/en/reference/sat/index.rst  #
Killed due to segmentation fault
 sage -t --long --random-seed=0 src/sage/crypto/mq/sr.py  # Killed due
to abort
 sage -t --long --random-seed=0 src/sage/modules/fg_pid/fgp_module.py  #
3 doctests failed
 sage -t --long --random-seed=0
src/sage/modules/free_module_morphism.py  # 3 doctests failed
 sage -t --long --random-seed=0 src/sage/rings/complex_arb.pyx  # 6
doctests failed
 sage -t --long --random-seed=0 src/sage/rings/polynomial/pbori.pyx  #
Killed due to abort
 sage -t --long --random-seed=0
src/sage/rings/polynomial/multi_polynomial_sequence.py  # Killed due to
abort
 sage -t --long --random-seed=0 src/sage/rings/real_arb.pyx  # 2
doctests failed
 sage -t --long --random-seed=0
src/sage/rings/polynomial/polynomial_ring_constructor.py  # Killed due
to abort
 sage -t --long --random-seed=0 src/sage/sat/boolean_polynomials.py  #
Killed due to abort
 sage -t --long --random-seed=0 src/sage/sat/solvers/dimacs.py  # Killed
due to abort
 sage -t --long --random-seed=0
src/sage/schemes/hyperelliptic_curves/monsky_washnitzer.py  # Killed due
to abort

I can be more specific by digging into the log file, for instance :

File "src/doc/en/constructions/algebraic_geometry.rst", line 145, in
doc.en.constructions.algebraic_geometry
Failed example:
    print(L)
Expected:
    [1]:
       _[1]=y   
       _[2]=x   
    ...
Got:
    [1]:
       _[1]=y^2+y+1
       _[2]=x+1
    [2]:
       _[1]=y^2+y+1
       _[2]=x+y+1
    [3]:
       _[1]=y^2+y+1
       _[2]=x+y
    [4]:
       _[1]=y^2+y+1
       _[2]=x
    [5]:
       _[1]=y+1
       _[2]=x^2+x+1
    [6]:
       _[1]=y+1
       _[2]=x+1
    [7]:
       _[1]=y+1
       _[2]=x
    [8]:
       _[1]=y
       _[2]=x^2+x+1
    [9]:
       _[1]=y
       _[2]=x+1
    [10]:
       _[1]=y
       _[2]=x


Best,

--
MB.

[Dima Pasechnik]

It would be good to know which of these still fail if you run them separately.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/4884af9a-7f02-a9a7-534a-338ecfe76700%40inria.fr.

[Maxime Bombar]

On 8/20/20 4:24 PM, Dima Pasechnik wrote:
> It would be good to know which of these still fail if you run them
> separately.

I have exactly the same result by running them separately.

I tried running those tests with sage9.1, and both
`src/sage/rings/real_arb.pyx` and `src/sage/rings/complex_arb.pyx`
failed with the same error as 9.2.beta9 but the other tests passed.

How can I be more helpful ?

Best,

--
Maxime Bombar

[Dima Pasechnik]

segfaults and aborts you get from tests are kind of worrying. Could it be that you have "rogue" libraries in /usr/local, which get picked up instead of system ones?

Perhaps, post the main config.log

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[Maxime Bombar]

On 8/20/20 5:05 PM, Dima Pasechnik wrote:
> segfaults and aborts you get from tests are kind of worrying. Could it
> be that you have "rogue" libraries in /usr/local, which get picked up
> instead of system ones?
>
> Perhaps, post the main config.log

sure, here it is.

--
MB.

[Justin C. Walker]

> On Aug 18, 2020, at 16:01, Volker Braun <vbrau...@gmail.com> wrote:
>
> As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html

Built from fresh clones of the 9.2.b8 branch, on two macOS systems: 10.13.6 (2019 iMac Pro, 18-core Xeon W); and 10.15.6 (2019 MBP, 8-core Core i9).

No problems with either of the builds, and testing (‘ptestlong’) on each completed with no failures.

Justin

[Steven Trogdon]

I've seen the following failures when doctesting Sage-on-Gentoo but I'm now seeing them when doctesting vanilla Sage:

sage -t --long --warn-long 165.2 --random-seed=0 src/sage/rings/integer.pyx

**********************************************************************

File "src/sage/rings/integer.pyx", line 3100, in sage.rings.integer.Integer.divisors

Failed example:

    for i in range(20):  # long time

        try:

            alarm(RDF.random_element(1e-3, 0.5))

            _ = n.divisors()

            cancel_alarm()  # we never get here

        except AlarmInterrupt:

            pass

Exception raised:

    Traceback (most recent call last):

      File "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 715, in _run

        self.compile_and_execute(example, compiler, test.globs)

      File "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1139, in compile_and_execute

        exec(compiled, globs)

      File "<doctest sage.rings.integer.Integer.divisors[20]>", line 4, in <module>

        _ = n.divisors()

      File "sage/rings/integer.pyx", line 3170, in sage.rings.integer.Integer.divisors (build/cythonized/sage/rings/integer.c:20840)

        ptr = <unsigned long*>check_allocarray(divisor_count, 3 * sizeof(unsigned long))

      File "memory.pxd", line 87, in cysignals.memory.check_allocarray (build/cythonized/sage/rings/integer.c:47465)

    MemoryError: failed to allocate 33554432 * 24 bytes

**********************************************************************

File "src/sage/rings/integer.pyx", line 3912, in sage.rings.integer.Integer.?

Failed example:

    n.factor(proof=True)

Exception raised:

    Traceback (most recent call last):

      File "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 715, in _run

        self.compile_and_execute(example, compiler, test.globs)

      File "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1139, in compile_and_execute

        exec(compiled, globs)

      File "<doctest sage.rings.integer.Integer.?[9]>", line 1, in <module>

        n.factor(proof=True)

      File "sage/rings/integer.pyx", line 3994, in sage.rings.integer.Integer.factor (build/cythonized/sage/rings/integer.c:25893)

        F = factor_using_pari(n, int_=int_, debug_level=verbose, proof=proof)

      File "sage/rings/factorint.pyx", line 345, in sage.rings.factorint.factor_using_pari (build/cythonized/sage/rings/factorint.c:6481)

        p, e = n.__pari__().factor(proof=proof)

      File "cypari2/gen.pyx", line 4311, in cypari2.gen.Gen.factor

    cysignals.signals.AlarmInterrupt

**********************************************************************

and

sage -t --long --warn-long 165.2 --random-seed=0 src/sage/doctest/test.py

**********************************************************************

File "src/sage/doctest/test.py", line 521, in sage.doctest.test

Failed example:

    if system() == "Linux":

        P = subprocess.Popen(["sage", "-t", "--warn-long", "0", "--random-seed=0", "--memlimit=2000", "memlimit.rst"], stdout=subprocess.PIPE, **kwds)

        out, err = P.communicate()

        ok = ("MemoryError: failed to allocate" in bytes_to_str(out))

Expected nothing

Got:

    Process DocTestWorker-1:

    Traceback (most recent call last):

      File "/local/sage-git/sage/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap

        self.run()

      File "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2185, in run

        task(self.options, self.outtmpfile, msgpipe, self.result_queue)

      File "/local/sage-git/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2535, in __call__

        result_queue.put(result, False)

      File "/local/sage-git/sage/local/lib/python3.7/multiprocessing/queues.py", line 87, in put

        self._start_thread()

      File "/local/sage-git/sage/local/lib/python3.7/multiprocessing/queues.py", line 170, in _start_thread

        self._thread.start()

      File "/local/sage-git/sage/local/lib/python3.7/threading.py", line 847, in start

        _start_new_thread(self._bootstrap, ())

    RuntimeError: can't start new thread

On Tuesday, August 18, 2020 at 5:01:42 PM UTC-6, Volker Braun wrote:

[jonatha...@googlemail.com]

I can confirm the rings/integer.pyx failure from running it in the shell.

sage: n = prod(primes_first_n(25))

sage: _ = n.divisors()

If I cancel the second line many time (after a few seconds each), I see an increase in memory usage.

There doesn't seem to be a limit to it.

I can immitate the problem by the following (this is what divisors does along the way):

sage: cython('''
....: from sage.rings.integer cimport Integer
....: from sage.ext.stdsage cimport PY_NEW
....: from cysignals.signals cimport sig_check
....: def foo():
....:     cdef list sorted = []
....:     cdef Integer apn
....:     cdef Py_ssize_t i
....:     for i in range(100000000):
....:         apn = <Integer>PY_NEW(Integer)
....:         sorted.append(apn) 
....:         sig_check()
....: ''')

If I cancel the function foo after a few seconds, it leaks.

Looks to me like this list isn't garbage collected at interrupt.

Btw, note that alarm might be triggered much later than expected:

sage: def test_alarm():
....:     n = prod(primes_first_n(25)) 
....:     try:
....:         alarm(RDF.random_element(1e-3,0.5))
....:         _ = n.divisors() 
....:         sleep(20)
....:     except AlarmInterrupt:
....:         pass
....:                                                                                                                                                                              
sage: %time test_alarm()                                                                                                                                                           
CPU times: user 127 ms, sys: 24 ms, total: 151 ms
Wall time: 150 ms
sage: %time test_alarm()                                                                                                                                                           
CPU times: user 1.22 s, sys: 88.1 ms, total: 1.31 s
Wall time: 1.31 s

[jonatha...@googlemail.com]

I have create https://trac.sagemath.org/ticket/30427 for the memory leak in divisors of integers.

[Maxime Bombar]

On 8/20/20 5:05 PM, Dima Pasechnik wrote:
> segfaults and aborts you get from tests are kind of worrying. Could it
> be that you have "rogue" libraries in /usr/local, which get picked up
> instead of system ones?
>
> Perhaps, post the main config.log
>

Hi,

I upgraded to beta10, and every segfault is now gone. I bet it was an
edge case of forbidding a recent version of some compiler like gcc.
There is only one abortion left
(src/sage/schemes/hyperelliptic_curves/monsky_washnitzer.py
), but it seems to be documented here
https://trac.sagemath.org/ticket/29719#comment:17, because on debian
unstable libflint-dev depends on libflint-2.6.3, and libflint-dev was
recommended in the installation guide for later version than debian buster.

It could be a good idea to ensure flint version to be less than 2.6.3,
as it was done for gcc and gfortran before beta10. How do you think ?
Should I open a ticket ?

I uninstalled this lib from my system, and the test now passes.

I will continue to look at the other failures.

Best,

--
MB.

[Dima Pasechnik]

On Mon, Aug 24, 2020 at 8:02 PM Maxime Bombar <maxime...@inria.fr> wrote:
>
> On 8/20/20 5:05 PM, Dima Pasechnik wrote:
> > segfaults and aborts you get from tests are kind of worrying. Could it
> > be that you have "rogue" libraries in /usr/local, which get picked up
> > instead of system ones?
> >
> > Perhaps, post the main config.log
> >
> Hi,
>
> I upgraded to beta10, and every segfault is now gone. I bet it was an
> edge case of forbidding a recent version of some compiler like gcc.
> There is only one abortion left
> (src/sage/schemes/hyperelliptic_curves/monsky_washnitzer.py
> ), but it seems to be documented here
> https://trac.sagemath.org/ticket/29719#comment:17, because on debian
> unstable libflint-dev depends on libflint-2.6.3, and libflint-dev was
> recommended in the installation guide for later version than debian buster.
>
> It could be a good idea to ensure flint version to be less than 2.6.3,
> as it was done for gcc and gfortran before beta10. How do you think ?

we certainly plan to upgrade to flint 2.6.3, it's just not going to
happen on 9.2, but has to wait till 9.3
See https://trac.sagemath.org/ticket/29719

I believe that the problem you report has been fixed on that ticket's
branch, so you might try to dig the fix up from there.
IIRC it's https://git.sagemath.org/sage.git/commit?id=a3981f6eb02a3d9e7a78aa5c81525fbd0e3fbc96

HTH
Dima

> Should I open a ticket ?
>
> I uninstalled this lib from my system, and the test now passes.
>
> I will continue to look at the other failures.
>
> Best,
>
> --
> MB.
>
>

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[Justin C. Walker]

> On Aug 18, 2020, at 16:01 , Volker Braun <vbrau...@gmail.com> wrote:
>
> As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html

Built from a fresh clone of 9.2.b9 on macOS 10.14.6 (2017 MBP, Quad Core Core i7).

No problems with the build, and all tests (‘ptestlong’) passed!

Justin

--
Justin C. Walker, Curmudgeon-At-Large
Institute for the Absorption of Federal Funds
--------
If you're not confused,
You're not paying attention
--------