TLDR:
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 <[email protected]>
Original-Maintainer: Debian Science Maintainers
<[email protected]>
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 <[email protected]>
Original-Maintainer: Debian Science Maintainers
<[email protected]>
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 <[email protected]>
Original-Maintainer: Debian Science Team
<[email protected]>
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 <[email protected]>
Original-Maintainer: Debian Science Team
<[email protected]>
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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