upgrade GAP to 4.11.1 or newer #31498

dimpase · 2021-03-15T11:40:42Z

the current GAP release is 4.11.1. Time to upgrade - previous upgrade
was in #29314.

Here we also upgrade libsemigroups, in lockstep with GAP, to 1.1.0.

GAP tarball is now hosted on GitHub; we also need to install more GAP packages to satsify needs of updated GAP package digraph and semigroups.

Finally, we fix a bug in TestSuite for abelian groups

CC: @antonio-rojas @embray @kiwifb @mkoeppe @slel @tobihan @videlec

Component: packages: standard

Keywords: upgrade, gap

Author: Dima Pasechnik

Branch: 82f3fa7

Reviewer: Volker Braun, Travis Scrimshaw

Issue created by migration from https://trac.sagemath.org/ticket/31498

The text was updated successfully, but these errors were encountered:

slel · 2021-03-16T01:29:24Z

Changed keywords from none to upgrade, gap

dimpase · 2021-05-13T21:51:25Z

Commit: 37466dd

dimpase · 2021-05-13T21:51:25Z

Author: Dima Pasechnik

dimpase · 2021-05-13T21:51:25Z

New commits:

`37466dd`	`GAP version bump to 4.11.1`

dimpase · 2021-05-13T21:51:25Z

Branch: u/dimpase/packages/gap4111

sagetrac-git · 2021-05-13T23:04:09Z

Branch pushed to git repo; I updated commit sha1. New commits:

`8367f8e`	`ctbl versions now numbered`

sagetrac-git · 2021-05-13T23:04:09Z

Changed commit from 37466dd to 8367f8e

sagetrac-git · 2021-05-14T08:45:47Z

Changed commit from 8367f8e to 246664d

sagetrac-git · 2021-05-14T08:45:47Z

Branch pushed to git repo; I updated commit sha1. New commits:

`1d113f8`	`update libsemigroup`
`246664d`	`more GAP packages are deps`

dimpase · 2021-05-14T08:51:19Z

comment:5

what remains is to fix this weird error - something is emitting that string of * whcih overrides the test output. Not reproducible at sage: prompt:

File "src/sage/tests/gap_packages.py", line 8, in sage.tests.gap_packages
Failed example:
    test_packages(pkgs, only_failures=True)    # optional - gap_packages
Expected:
    ...
      Status   Package   GAP Output
    +--------+---------+------------+
Got:
      Status   Package   GAP Output
    +--------+---------+------------+
**********************************************************************

but

sage: from sage.tests.gap_packages import all_installed_packages, test_packages                                                                                                                                                                                                   
sage: pkgs = all_installed_packages(ignore_dot_gap=True)                                                                                                                                                                                                                          
sage: test_packages(pkgs, only_failures=True)                                                                                                                                                                                                                                     
  Status   Package   GAP Output
+--------+---------+------------+
sage:

antonio-rojas · 2021-05-14T09:09:15Z

comment:6

Replying to @dimpase:

what remains is to fix this weird error - something is emitting that string of * whcih overrides the test output.

Isn't that just the usual test failure output? It seems to me that the actual issue is the "..." wildcard on the first line - there is no newline before the "Status" line so it doesn't match.

sagetrac-git · 2021-05-14T09:19:30Z

Changed commit from 246664d to 7170197

sagetrac-git · 2021-05-14T09:19:30Z

Branch pushed to git repo; I updated commit sha1. New commits:

`7170197`	`modify the test so that Sage's "table" is not used`

dimpase · 2021-05-14T09:20:00Z

comment:8

another test to fix:

sage -t --warn-long 50.1 --random-seed=0 src/sage/groups/abelian_gps/abelian_group_gap.py
**********************************************************************
File "src/sage/groups/abelian_gps/abelian_group_gap.py", line 201, in sage.groups.abelian_gps.abelian_group_gap.AbelianGroupElement_polycyclic
Failed example:
    TestSuite(G.an_element()).run()       # optional - gap_packages
Expected nothing
Got:
    Failure in _test_pickling:
    Traceback (most recent call last):
      File "/home/scratch2/dimpase/sage/sage/local/lib64/python3.8/site-packages/sage/misc/sage_unittest.py", line 297, in run
        test_method(tester=tester)
      File "sage/structure/sage_object.pyx", line 647, in sage.structure.sage_object.SageObject._test_pickling (build/cythonized/sage/structure/sage_object.c:5023)
        tester.assertEqual(loads(dumps(self)), self)
      File "sage/misc/persist.pyx", line 935, in sage.misc.persist.loads (build/cythonized/sage/misc/persist.c:7536)
        return unpickler.load()
      File "sage/structure/parent.pyx", line 898, in sage.structure.parent.Parent.__call__ (build/cythonized/sage/structure/parent.c:9335)
        return mor._call_(x)
      File "sage/structure/coerce_maps.pyx", line 161, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (build/cythonized/sage/structure/coerce_maps.c:4622)
        raise
      File "sage/structure/coerce_maps.pyx", line 156, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (build/cythonized/sage/structure/coerce_maps.c:4514)
        return C._element_constructor(x)
      File "/home/scratch2/dimpase/sage/sage/local/lib64/python3.8/site-packages/sage/groups/abelian_gps/abelian_group_gap.py", line 368, in _element_constructor_
        x *= gens_gap[i]**(exp[i] % orders[i])
      File "sage/rings/integer.pyx", line 3413, in sage.rings.integer.Integer.__mod__ (build/cythonized/sage/rings/integer.c:22616)
        raise ZeroDivisionError("Integer modulo by zero")
    ZeroDivisionError: Integer modulo by zero
    ------------------------------------------------------------
    The following tests failed: _test_pickling
**********************************************************************

sagetrac-git · 2021-05-14T11:49:55Z

Changed commit from 7170197 to 5c885dd

sagetrac-git · 2021-05-14T11:49:55Z

Branch pushed to git repo; I updated commit sha1. New commits:

`5c885dd`	`do not take "mod 0", skip "mod"`

dimpase · 2021-05-27T11:15:50Z

comment:11

please review...

kiwifb · 2021-05-27T11:31:35Z

comment:12

I won't lie, I am not quite ready for this in sage-on-gentoo. I have been under rather heavy stress so far this year and I am not doing as much as I want.

vbraun · 2021-05-30T09:24:47Z

comment:13

Tell me about it ;-)

But I think we should have people bang away at this asap and not later in the release cycle.

dimpase · 2021-05-30T11:54:19Z

comment:14

Thanks!

vbraun · 2021-05-30T16:02:53Z

Reviewer: Volker Braun

vbraun · 2021-05-30T16:57:32Z

comment:16

There is a small merge conflict with #31489, and a failure

sage -t --long --warn-long 43.1 --random-seed=0 src/sage/tests/gap_packages.py
**********************************************************************
File "src/sage/tests/gap_packages.py", line 9, in sage.tests.gap_packages
Failed example:
    for p in pkgs:
        pkg = p.split('-')[0]
        if not libgap.LoadPackage(pkg):
            raise
Exception raised:
    Traceback (most recent call last):
      File "/home/release/Sage/local/lib64/python3.9/site-packages/sage/doctest/forker.py", line 714, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/release/Sage/local/lib64/python3.9/site-packages/sage/doctest/forker.py", line 1133, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.tests.gap_packages[3]>", line 4, in <module>
        raise
    RuntimeError: No active exception to reraise
**********************************************************************
1 item had failures:
   1 of   6 in sage.tests.gap_packages
    [12 tests, 1 failure, 0.26 s]
----------------------------------------------------------------------
sage -t --long --warn-long 43.1 --random-seed=0 src/sage/tests/gap_packages.py  # 1 doctest failed
----------------------------------------------------------------------

dimpase · 2021-06-01T11:24:51Z

comment:18

these test_packages stuff is a mess. We have two different functions
that both claim to Return list of all installed packages., test_packages(), and all_installed_packages() which differ in the output format - the former outputs table (sic!)
and the latter does not check whether these packages actually may be loaded (so it's largely meaningless).

May we do it on another ticket?

sagetrac-git · 2021-06-01T23:46:50Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`a9ac506`	`GAP version bump to 4.11.1`
`f8c87d4`	`ctbl versions now numbered`
`a2bc010`	`update libsemigroup`
`40e6105`	`more GAP packages are deps`
`8d44ad0`	`modify the test so that Sage's "table" is not used`
`05b434a`	`do not take "mod 0", skip "mod"`
`7ee7b58`	`better fix for the test`

sagetrac-git · 2021-06-01T23:46:50Z

Changed commit from 5c885dd to 7ee7b58

dimpase · 2021-06-01T23:50:56Z

comment:20

I believe the test is fixed now.

dimpase · 2021-06-02T00:01:33Z

Dependencies: #31489

sagetrac-git · 2021-06-02T00:02:18Z

Branch pushed to git repo; I updated commit sha1. New commits:

`101bd74`	`use the change from #31489`

sagetrac-git · 2021-06-02T00:02:18Z

Changed commit from 7ee7b58 to 101bd74

dimpase · 2021-06-02T00:03:47Z

comment:23

OK, now it depends on #31489 and should cleanly merge: the only change from #31489 is done in comment:22

dimpase · 2021-06-02T00:06:00Z

comment:24

I have not merged the full branch of #31489 here, though.

sagetrac-git · 2021-06-08T15:41:13Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`96df458`	`GAP version bump to 4.11.1`
`91a695f`	`ctbl versions now numbered`
`79b3bde`	`update libsemigroup`
`1116073`	`more GAP packages are deps`
`7469042`	`modify the test so that Sage's "table" is not used`
`82f3fa7`	`better fix for the test`

sagetrac-git · 2021-06-08T15:41:13Z

Changed commit from 101bd74 to 82f3fa7

dimpase · 2021-06-08T15:41:57Z

comment:26

rebased on 9.4.beta1

dimpase · 2021-06-08T15:42:20Z

Changed dependencies from #31489 to none

tscrim · 2021-06-11T03:46:16Z

comment:28

Let's try to get this into the next beta.

tscrim · 2021-06-11T03:46:16Z

Changed reviewer from Volker Braun to Volker Braun, Travis Scrimshaw

vbraun · 2021-06-20T08:14:22Z

Changed branch from u/dimpase/packages/gap4111 to 82f3fa7

kiwifb · 2021-06-20T10:57:40Z

comment:30

I am a bit dumbfounded by this upgrade in a way. There are strange particulars to it in sage-on-gentoo. I cannot build the doc.

[categorie] /var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/categories/finite_coxeter_groups.py:docstring of sage.categories.finite_coxeter_groups.FiniteCoxeterGroups.ParentMethods.permutahedron:50: WARNING: Exception occurred in plotting finite_coxeter_groups-1
[categorie]  from /var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/doc/en/reference/categories/sage/categories/finite_coxeter_groups.rst:
[categorie] Traceback (most recent call last):
[categorie]   File "/usr/lib/python3.9/site-packages/matplotlib/sphinxext/plot_directive.py", line 483, in run_code
[categorie]     exec(code, ns)
[categorie]   File "<string>", line 1, in <module>
[categorie]   File "sage/misc/lazy_import.pyx", line 362, in sage.misc.lazy_import.LazyImport.__call__ (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/misc/lazy_import.c:4041)
[categorie]     return self.get_object()(*args, **kwds)
[categorie]   File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/combinat/root_system/coxeter_group.py", line 135, in CoxeterGroup
[categorie]     return CoxeterMatrixGroup(cartan_type, base_ring, index_set)
[categorie]   File "sage/misc/classcall_metaclass.pyx", line 322, in sage.misc.classcall_metaclass.ClasscallMetaclass.__call__ (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/misc/classcall_metaclass.c:1743)
[categorie]     return cls.classcall(cls, *args, **kwds)
[categorie]   File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/groups/matrix_gps/coxeter_group.py", line 230, in __classcall_private__
[categorie]     return super(CoxeterMatrixGroup, cls).__classcall__(cls,
[categorie]   File "sage/misc/cachefunc.pyx", line 1001, in sage.misc.cachefunc.CachedFunction.__call__ (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/misc/cachefunc.c:6087)
[categorie]     w = self.f(*args, **kwds)
[categorie]   File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/structure/unique_representation.py", line 1007, in __classcall__
[categorie]     instance = typecall(cls, *args, **options)
[categorie]   File "sage/misc/classcall_metaclass.pyx", line 486, in sage.misc.classcall_metaclass.typecall (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/misc/classcall_metaclass.c:2207)
[categorie]     return (<PyTypeObject*>type).tp_call(cls, args, kwds)
[categorie]   File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/groups/matrix_gps/coxeter_group.py", line 273, in __init__
[categorie]     one = MS.one()
[categorie]   File "sage/misc/cachefunc.pyx", line 2310, in sage.misc.cachefunc.CachedMethodCallerNoArgs.__call__ (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/misc/cachefunc.c:12918)
[categorie]     self.cache = f(self._instance)
[categorie]   File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/matrix/matrix_space.py", line 1608, in identity_matrix
[categorie]     A = self.zero_matrix().__copy__()
[categorie]   File "sage/misc/cachefunc.pyx", line 2310, in sage.misc.cachefunc.CachedMethodCallerNoArgs.__call__ (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/misc/cachefunc.c:12918)
[categorie]     self.cache = f(self._instance)
[categorie]   File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/matrix/matrix_space.py", line 1766, in zero_matrix
[categorie]     zero = self.base_ring().zero()
[categorie]   File "sage/misc/cachefunc.pyx", line 2310, in sage.misc.cachefunc.CachedMethodCallerNoArgs.__call__ (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/misc/cachefunc.c:12918)
[categorie]     self.cache = f(self._instance)
[categorie]   File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/rings/universal_cyclotomic_field.py", line 1397, in zero
[categorie]     return self.element_class(self, libgap.zero())
[categorie]   File "sage/libs/gap/libgap.pyx", line 618, in sage.libs.gap.libgap.Gap.zero (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/gap/libgap.c:6277)
[categorie]     return self(0)
[categorie]   File "sage/structure/parent.pyx", line 898, in sage.structure.parent.Parent.__call__ (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/structure/parent.c:9342)
[categorie]     return mor._call_(x)
[categorie]   File "sage/structure/coerce_maps.pyx", line 161, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/structure/coerce_maps.c:4628)
[categorie]     raise
[categorie]   File "sage/structure/coerce_maps.pyx", line 156, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/structure/coerce_maps.c:4520)
[categorie]     return C._element_constructor(x)
[categorie]   File "sage/libs/gap/libgap.pyx", line 298, in sage.libs.gap.libgap.Gap._element_constructor_ (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/gap/libgap.c:3391)
[categorie]     initialize()
[categorie]   File "sage/libs/gap/util.pyx", line 314, in sage.libs.gap.util.initialize (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/gap/util.c:5897)
[categorie]     with atomic_write(workspace) as f:
[categorie]   File "sage/libs/gap/util.pyx", line 316, in sage.libs.gap.util.initialize (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/gap/util.c:5852)
[categorie]     gap_eval('SaveWorkspace("{0}")'.format(f.name))
[categorie]   File "sage/libs/gap/util.pyx", line 398, in sage.libs.gap.util.gap_eval (/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/cythonized/sage/libs/gap/util.c:6068)
[categorie]     GAP_Enter()
[categorie] sage.libs.gap.util.GAPError: Error, reached the pre-set memory limit
[categorie] (change it with the -o command line option)
[graphs   ] The inventory files are in ../../build_doc/inventory/en/reference/graphs.
Build finished. The built documents can be found in /var/tmp/portage/sci-mathematics/sage-9999/work/build_doc/inventory/en/reference/graphs
[functions] building [inventory]: targets for 20 source files that are out of date
[functions] updating environment: [new config] 20 added, 0 changed, 0 removed
[finite_ri] The inventory files are in ../../build_doc/inventory/en/reference/finite_rings.
Build finished. The built documents can be found in /var/tmp/portage/sci-mathematics/sage-9999/work/build_doc/inventory/en/reference/finite_rings
[function_] The inventory files are in ../../build_doc/inventory/en/reference/function_fields.
Build finished. The built documents can be found in /var/tmp/portage/sci-mathematics/sage-9999/work/build_doc/inventory/en/reference/function_fields
[game_theo] building [inventory]: targets for 6 source files that are out of date
[game_theo] updating environment: [new config] 6 added, 0 changed, 0 removed
[games    ] building [inventory]: targets for 5 source files that are out of date
[games    ] updating environment: [new config] 5 added, 0 changed, 0 removed
[game_theo] The inventory files are in ../../build_doc/inventory/en/reference/game_theory.
Build finished. The built documents can be found in /var/tmp/portage/sci-mathematics/sage-9999/work/build_doc/inventory/en/reference/game_theory
[categorie] The inventory files are in ../../build_doc/inventory/en/reference/categories.
Error building the documentation.
Traceback (most recent call last):
  File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/sage_docbuild/__main__.py", line 2, in <module>
    main()
  File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/sage_docbuild/__init__.py", line 1813, in main
    builder()
  File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/sage_docbuild/__init__.py", line 345, in _wrapper
    getattr(get_builder(document), 'inventory')(*args, **kwds)
  File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/sage_docbuild/__init__.py", line 582, in _wrapper
    self._build_everything_except_bibliography(format, *args, **kwds)
  File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/sage_docbuild/__init__.py", line 565, in _build_everything_except_bibliography
    build_many(build_ref_doc, non_references)
  File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/sage_docbuild/__init__.py", line 297, in build_many
    _build_many(target, args, processes=processes)
  File "/var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/sage_docbuild/utils.py", line 289, in build_many
    raise worker_exc.original_exception
OSError: /var/tmp/portage/sci-mathematics/sage-9999/work/sage-9999/src-python3_9/build/lib/sage/categories/finite_coxeter_groups.py:docstring of sage.categories.finite_coxeter_groups.FiniteCoxeterGroups.ParentMethods.permutahedron:50: WARNING: Exception occurred in plotting finite_coxeter_groups-1

In sage-on-gentoo, I do separate gap packages and the source of error is more precisely ctbllib-1.3.1+ (I say + because there is a 1.3.2 now in its upstream and the result is the same with it). If I downgrade ctbllib to 1.2_p2 the documentation builds.

The error message suggests to increase the memory limit. This is set somewhere in sage/interface/gap.py and I pushed it from the current 400MB to 2000MB without improvement.

I am probably missing something but what?

kiwifb · 2021-06-20T10:57:40Z

Changed commit from 82f3fa7 to none

vbraun · 2021-06-20T13:26:45Z

comment:31

Whats the output of _get_gap_memory_pool_size_MB?

GAP needs swap due to how they reserve the memory pool.

kiwifb · 2021-06-20T21:39:42Z

comment:32

Replying to @vbraun:

Whats the output of _get_gap_memory_pool_size_MB?

GAP needs swap due to how they reserve the memory pool.

568MB if I leave it to the default. With the changes for my last attempt, it should be 2001MB. But what puzzles me is the influence of ctbllib. So, I am wondering if the message is in fact unhelpful for the issue at hand.

upgrades our corresponding spkgs: * gap * gap_packages * libsemigroups * Previous upgrades: - #31498: GAP 4.11.1 - #29314: GAP 4.11, libsemigroup 1.0.9 * Upstream: Completely fixed; Fix reported upstream Closes #34391 URL: #35093 Reported by: Dima Pasechnik Reviewer(s): Gonzalo Tornaría, Matthias Köppe

dimpase added this to the sage-9.4 milestone Mar 15, 2021

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dimpase added the s: needs review label May 14, 2021

vbraun added s: positive review and removed s: needs review labels May 30, 2021

dimpase added s: needs review and removed s: needs work labels Jun 1, 2021

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vbraun closed this as completed in 05de389 Jun 20, 2021

dimpase mentioned this issue May 27, 2021

Random failure: sage.libs.gap.util.GAPError: Error, OnSets: <set> must be a set #31848

Closed

slel mentioned this issue Jan 27, 2023

Upgrade: GAP 4.12 #34391

Closed

dimpase mentioned this issue Feb 12, 2023

update GAP to 4.12.2 #35093

Merged

upgrade GAP to 4.11.1 or newer #31498

upgrade GAP to 4.11.1 or newer #31498

Comments

dimpase commented Mar 15, 2021

slel commented Mar 16, 2021

dimpase commented May 13, 2021

dimpase commented May 13, 2021

dimpase commented May 13, 2021

dimpase commented May 13, 2021

sagetrac-git mannequin commented May 13, 2021

sagetrac-git mannequin commented May 13, 2021

sagetrac-git mannequin commented May 14, 2021

sagetrac-git mannequin commented May 14, 2021

dimpase commented May 14, 2021

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