I originally sent this to sage-release when 9.1 was released. I see the
same test failures under 9.2.beta0. I didn't see a way to make
exceptions for which system packages are used if installed, based on the
OS release. Maybe the best option is to simply document the configure
options under "known issues" with Ubuntu 19.10.
Regards, Andy
All the tests pass under Ubuntu 19.10 after building with sage's
internal versions of eclib, nauty and glpk. I did this by doing:
./configure --with-system-eclib=no -with-system-nauty=no
--with-system-glpk=no
The gory details:
I rebuilt sage after doing:
./configure --with-system-eclib=no -with-system-nauty=no
Previous fails now pass, but there were two other tests that failed hard:
sage -t --long --warn-long 65.8 src/sage/numerical/backends/glpk_backend.pyx #
1 doctest failed
sage -t --long --warn-long 65.8 src/sage/libs/glpk/error.pyx # 1 doctest failed
Using the sage's glpk fixed those:
./configure --with-system-eclib=no -with-system-nauty=no -with-system-glpk=no
Here are the details for the system installed libs. Note that the system
eclib-tools says that it breaks sagemath < 8.4. I don't know if that is
the same error with 9.1
Package: eclib-tools
Architecture: amd64
Version: 20190226-3
Priority: optional
Section: universe/math
Source: eclib
Origin: Ubuntu
Maintainer: Ubuntu Developers <ubuntu-devel-disc...@lists.ubuntu.com>
Original-Maintainer: Debian Science Maintainers
<debian-science-maintain...@lists.alioth.debian.org>
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 45
Depends: libec5 (= 20190226-3), libc6 (>= 2.4), libgcc1 (>= 1:3.0),
libntl35, libstdc++6 (>= 4.4.0)
Breaks: sagemath (<< 8.4~)
Filename: pool/universe/e/eclib/eclib-tools_20190226-3_amd64.deb
Size: 10476
MD5sum: 78cec4b65cf967544656508be512d631
SHA1: f057770c95e8f499f4a62ab659c7086902b988bb
SHA256: f229f2e674d8ce87e9afee8959144396acdbd42f51b41179c68acd004b1aca1e
Homepage: https://github.com/JohnCremona/eclib/
Description-en: Programs for modular symbols and elliptic curves over Q
This package includes several programs to compute with elliptic curves
over Q ; most notably mwrank (for 2-descent on elliptic curves over Q)
and the modular symbol tools used to create the elliptic curve database.
Description-md5: 0eb561b8bbb6cb2cb47894e7198e0b99
apt-cache show nauty
Package: nauty
Architecture: amd64
Version: 2.6r10+ds-1
Priority: extra
Section: universe/math
Origin: Ubuntu
Maintainer: Ubuntu Developers <ubuntu-devel-disc...@lists.ubuntu.com>
Original-Maintainer: Debian Science Maintainers
<debian-science-maintain...@lists.alioth.debian.org>
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 1094
Depends: libnauty2 (= 2.6r10+ds-1), libc6 (>= 2.14), libgmp10, zlib1g
(>= 1:1.1.4)
Suggests: graphviz, nauty-doc
Filename: pool/universe/n/nauty/nauty_2.6r10+ds-1_amd64.deb
Size: 306768
MD5sum: 8f4aee5709523b491f2ca71195f4e402
SHA1: 5df98416734668ace6d17c165ef1227d3acafd82
SHA256: 6c37a6542532750950046cbd46f613668449aa9e4be8a3e9e9221cc4ed0ec952
Homepage: http://pallini.di.uniroma1.it
Description-en: library for graph automorphisms -- interface and tools
nauty (No AUTomorphisms, Yes?) is a set of procedures for computing
automorphism groups of graphs and digraphs. This mathematical software
suite is developed by Brendan McKay and Adolfo Piperno:
http://pallini.di.uniroma1.it
.
nauty computes graph information in the form of a set of generators,
the size of the group, and the orbits of the group; it can also
produce a canonical label. The nauty suite is written in C and comes
with a command-line interface, a collection of command-line tools,
and an Application Programming Interface (API).
.
This package provides the nauty interface named dreadnaut, and a
small collection of utilities called gtools.
Description-md5: 44ae986d51bccb00a481cefd3d38bbfa
apt-cache show libglpk40
Package: libglpk40
Architecture: amd64
Version: 4.65-2
Multi-Arch: same
Priority: optional
Section: universe/math
Source: glpk
Origin: Ubuntu
Maintainer: Ubuntu Developers <ubuntu-devel-disc...@lists.ubuntu.com>
Original-Maintainer: Debian Science Team
<debian-science-maintain...@lists.alioth.debian.org>
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 922
Depends: libamd2 (>= 1:4.5.2), libc6 (>= 2.14), libcolamd2 (>= 1:4.5.2),
libgmp10, libltdl7 (>= 2.4.6), zlib1g (>= 1:1.1.4)
Suggests: libiodbc2-dev, default-libmysqlclient-dev
Filename: pool/universe/g/glpk/libglpk40_4.65-2_amd64.deb
Size: 378136
MD5sum: c8040d41297bbb6c7cbf19078fc98b86
SHA1: a9674a96de975a8050c9d53f55a804479337196f
SHA256: 428c28560e488d452ce066ac4c4c5c0b910ee8c8f0dd35131c82e8f1f042c88e
Homepage: http://www.gnu.org/software/glpk/glpk.html
Description-en: linear programming kit with integer (MIP) support
GLPK (GNU Linear Programming Kit) is intended for solving large-scale
linear programming (LP), mixed integer programming (MIP), and other
related problems. It is a set of routines written in ANSI C and
organized in the form of a callable library.
.
GLPK supports the GNU MathProg language, which is a subset of the
AMPL language. GLPK also supports the standard MPS and LP formats.
.
The GLPK package includes the following main components:
* Revised simplex method.
* Primal-dual interior point method.
* Branch-and-bound method.
* Translator for GNU MathProg modeling language.
* Application program interface (API).
.
In order to get connections between the internal MathProg model
objects and external database tables, please install the
libiodbc2-dev (for the iODBC table driver) and libmysqlclient-dev
(for the MySQL table driver).
Description-md5: a59dfd97ae7c98fa4132822ad0935832
apt-cache show libglpk-dev
Package: libglpk-dev
Architecture: amd64
Version: 4.65-2
Multi-Arch: same
Priority: optional
Section: universe/devel
Source: glpk
Origin: Ubuntu
Maintainer: Ubuntu Developers <ubuntu-devel-disc...@lists.ubuntu.com>
Original-Maintainer: Debian Science Team
<debian-science-maintain...@lists.alioth.debian.org>
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 1985
Depends: libglpk40 (= 4.65-2), libgmp-dev, zlib1g-dev, libsuitesparse-dev
Filename: pool/universe/g/glpk/libglpk-dev_4.65-2_amd64.deb
Size: 444944
MD5sum: 4e46f8149b17e6ac4b90b571472db3df
SHA1: 4115db795433f951c4152c1b82e97cc5a1ce2683
SHA256: aea3fc972ef3200c25f323cc6c5271dd2db75fe8a95ded1da3f561fdbc227df8
Homepage: http://www.gnu.org/software/glpk/glpk.html
Description-en: linear programming kit - development files
GLPK (GNU Linear Programming Kit) is intended for solving large-scale
linear programming (LP), mixed integer programming (MIP), and other
related problems. It is a set of routines written in ANSI C and
organized in the form of a callable library.
.
This package contains static library, headers, and the development
manpage for libvc.
Description-md5: 1a3290298c2e8e1d80e4bf1609c09ab9
On 5/21/20 4:15 PM, Andy Howell wrote:
On Ubuntu 19.10, I had the following hard errors after a clean build:
sage -t --long --warn-long 63.4 src/sage/libs/eclib/interface.py # 2
doctests failed
sage -t --long --warn-long 63.4
src/sage/numerical/backends/glpk_backend.pyx # 1 doctest failed
sage -t --long --warn-long 63.4 src/sage/libs/glpk/error.pyx # 1
doctest failed
Results of manual test runs below. I did receive a system error report
about mwrank core dumping. The system eclib-tools version is 20190226-3.
./sage -t --long --warn-long 63.4 src/sage/libs/eclib/interface.py
Running doctests with ID 2020-05-21-15-49-48-9a6627ba.
Git branch: develop
Using --optional=build,dochtml,memlimit,sage
Doctesting 1 file.
sage -t --long --warn-long 63.4 src/sage/libs/eclib/interface.py
**********************************************************************
File "src/sage/libs/eclib/interface.py", line 359, in
sage.libs.eclib.interface.mwrank_EllipticCurve.?
Failed example:
EllipticCurve([0,
prod(prime_range(100))]).mwrank_curve().two_descent()
Expected:
Traceback (most recent call last):
...
RuntimeError: A 2-descent did not complete successfully.
Got:
Basic pair: I=0, J=-62250335026528997468333757977957413890
disc=-3875104210915102959939644358548402200900731760187126282616072842416764932100
2-adic index bound = 2
2-adic index = 2
Two (I,J) pairs
Looking for quartics with I = 0, J =
-62250335026528997468333757977957413890
Looking for Type 3 quartics:
Trying positive a from 1 up to 1144080564738 (square a first...)
Traceback (most recent call last):
File
"/home/andy/bin/sage-9.1/lib/python3.7/site-packages/sage/doctest/forker.py",
line 681, in _run
self.compile_and_execute(example, compiler, test.globs)
File
"/home/andy/bin/sage-9.1/lib/python3.7/site-packages/sage/doctest/forker.py",
line 1123, in compile_and_execute
exec(compiled, globs)
File "<doctest
sage.libs.eclib.interface.mwrank_EllipticCurve.?[1]>", line 1, in <module>
EllipticCurve([Integer(0),
prod(prime_range(Integer(100)))]).mwrank_curve().two_descent()
File
"/home/andy/bin/sage-9.1/lib/python3.7/site-packages/sage/libs/eclib/interface.py",
line 386, in two_descent
second_descent)
File "sage/libs/eclib/mwrank.pyx", line 1062, in
sage.libs.eclib.mwrank._two_descent.do_descent
(build/cythonized/sage/libs/eclib/mwrank.cpp:5092)
sig_on()
RuntimeError: Aborted
**********************************************************************
File "src/sage/libs/eclib/interface.py", line 597, in
sage.libs.eclib.interface.mwrank_EllipticCurve.saturate
Failed example:
E.saturation([Q1,Q2])
Expected:
([(1 : -27 : 1), (157 : 1950 : 1)], 3, 0.801588644684981)
Got:
Attempt to round -0.2617840677e25 to a long int fails, aborting!
([(1 : -27 : 1), (157 : 1950 : 1)], 3, 0.801588644684981)
**********************************************************************
2 items had failures:
1 of 6 in sage.libs.eclib.interface.mwrank_EllipticCurve.?
1 of 9 in sage.libs.eclib.interface.mwrank_EllipticCurve.saturate
[192 tests, 2 failures, 4.81 s]
----------------------------------------------------------------------
sage -t --long --warn-long 63.4 src/sage/libs/eclib/interface.py # 2
doctests failed
----------------------------------------------------------------------
Total time for all tests: 4.9 seconds
cpu time: 4.7 seconds
cumulative wall time: 4.8 seconds
./sage -t --long --warn-long 63.4
src/sage/numerical/backends/glpk_backend.pyx
Running doctests with ID 2020-05-21-15-56-47-2364f65a.
Git branch: develop
Using --optional=build,dochtml,memlimit,sage
Doctesting 1 file.
sage -t --long --warn-long 63.4
src/sage/numerical/backends/glpk_backend.pyx
**********************************************************************
File "src/sage/numerical/backends/glpk_backend.pyx", line 2287, in
sage.numerical.backends.glpk_backend.GLPKBackend.print_ranges
Failed example:
p.print_ranges()
Expected:
glp_print_ranges: optimal basic solution required
1
Got:
1
**********************************************************************
1 item had failures:
1 of 13 in
sage.numerical.backends.glpk_backend.GLPKBackend.print_ranges
[554 tests, 1 failure, 3.65 s]
----------------------------------------------------------------------
sage -t --long --warn-long 63.4
src/sage/numerical/backends/glpk_backend.pyx # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 3.7 seconds
cpu time: 3.5 seconds
cumulative wall time: 3.6 seconds
./sage -t --long --warn-long 63.4 src/sage/libs/glpk/error.pyx
Running doctests with ID 2020-05-21-15-58-09-961e045f.
Git branch: develop
Using --optional=build,dochtml,memlimit,sage
Doctesting 1 file.
sage -t --long --warn-long 63.4 src/sage/libs/glpk/error.pyx
**********************************************************************
File "src/sage/libs/glpk/error.pyx", line 100, in
sage.libs.glpk.error.setup_glpk_error_handler
Failed example:
res = p.solve()
Expected:
0: obj = ...
Got:
<BLANKLINE>
**********************************************************************
1 item had failures:
1 of 11 in sage.libs.glpk.error.setup_glpk_error_handler
[12 tests, 1 failure, 1.11 s]
----------------------------------------------------------------------
sage -t --long --warn-long 63.4 src/sage/libs/glpk/error.pyx # 1
doctest failed
----------------------------------------------------------------------
Total time for all tests: 1.1 seconds
cpu time: 0.6 seconds
cumulative wall time: 1.1 seconds
On 5/20/20 5:53 PM, Volker Braun wrote:
The "master" git branch has been updated to Sage-9.1. 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
There was no change over 9.1.rc5
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