Opened 9 years ago

Last modified 9 years ago

#13588 closed enhancement

libGAP! -- create a Cython library interface to gap — at Version 34

Reported by: vbraun Owned by: joyner
Priority: major Milestone: sage-5.7
Component: group theory Keywords:
Cc: mmarco, tfeulner, iandrus, SimonKing Merged in:
Authors: Volker Braun Reviewers:
Report Upstream: N/A Work issues:
Branch: Commit:
Dependencies: #13211, #13880 Stopgaps:

Status badges

Description (last modified by jdemeyer)

Currently, libGAP doesn't give useful errors if something goes wrong during initialization.

Also, the GAP SIGINT handler got installed, this is fixed in the new spkg. Now Ctrl-C works as expected.

The trac_6391_* patches have already been reviewed at #6391, I'm just attaching them to this ticket for convenience.

Change History (38)

comment:1 Changed 9 years ago by vbraun

  • Authors set to Volker Braun
  • Cc mmarco added
  • Dependencies set to #6391, #13211
  • Status changed from new to needs_review

Miguel, you said that you had some mysterious error. Can you try this patch? It depends on the recently-updated patches on #6391, #13211.

comment:2 Changed 9 years ago by mmarco

I have been checking the different updates of libgap, and the error seemed to go away several versions ago. Anyways, i will keep testing it.

comment:3 Changed 9 years ago by mmarco

I don't know if it is an issue related with this patch or if it comes from libgap itself, but i have experienced some problems when i use tab completion in a session in the command line (i haven't checked it in the notebook).

An example:

sage: F=libgap.eval('FreeGroup(2)')
sage: (a,b)=F.GeneratorsOfGroup()
sage: H=F/libgap([a^2,b^2,a*b*a*b])
sage: H
<fp group on the generators [ f1, f2 ]>
sage: H.IsomorphismSimplifiedFpGroup()
[ f1, f2 ] -> [ f1, f2 ]
sage: H=F/libgap([a^2,b^2,a*b])    
sage: c=H.Gene
H.GeneralLinearGroup      H.GeneralisedEigenspaces  H.GeneralizedEigenvalues  H.GeneratorsOfIdeal
H.GeneralOrthogonalGroup  H.GeneralisedEigenvalues  H.GeneratorsOfField       
H.GeneralUnitaryGroup     H.GeneralizedEigenspaces  H.GeneratorsOfGroup       
sage: c=H.GeneratorsOfGroup()[0]
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/home/mmarco/sage-5.4/<ipython console> in <module>()

/home/mmarco/sage-5.4/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement.__getattr__ (sage/libs/gap/element.c:3555)()

AttributeError: Name "GeneratorsOfGroup" is not defined in GAP.
sage: c=H.GeneratorsOfGroup()   
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/home/mmarco/sage-5.4/<ipython console> in <module>()

/home/mmarco/sage-5.4/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement.__getattr__ (sage/libs/gap/element.c:3555)()

AttributeError: Name "GeneratorsOfGroup" is not defined in GAP.
sage: H
Exception RuntimeError: 'Entered a critical block twice' in 'sage.libs.gap.util.error_handler' ignored
<fp group on the generators [ f1, f2 ]>
sage: H.GeneratorsOfGroup()
[ f1, f2 ]
sage: c=H.GeneratorsOfGroup()[0]
sage: c
f1
sage: c=H.Generat
H.GeneratorsOfField  H.GeneratorsOfGroup  H.GeneratorsOfIdeal  
sage: c=H.GeneratorsOfGroup()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/home/mmarco/sage-5.4/<ipython console> in <module>()

/home/mmarco/sage-5.4/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement.__getattr__ (sage/libs/gap/element.c:3555)()

AttributeError: Name "GeneratorsOfGroup" is not defined in GAP.
sage: c=H.GeneratorsOfGroup()
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/home/mmarco/sage-5.4/<ipython console> in <module>()

/home/mmarco/sage-5.4/local/lib/python2.7/site-packages/sage/libs/gap/element.so in sage.libs.gap.element.GapElement.__getattr__ (sage/libs/gap/element.c:3555)()

AttributeError: Name "GeneratorsOfGroup" is not defined in GAP.
sage: H
Exception RuntimeError: 'Entered a critical block twice' in 'sage.libs.gap.util.error_handler' ignored
<fp group on the generators [ f1, f2 ]>
sage: c=H.GeneratorsOfGroup()

comment:4 Changed 9 years ago by mmarco

This same behaviour appears when i don't use this patch, so reported in the libgap ticket.

comment:5 Changed 9 years ago by vbraun

  • Description modified (diff)

comment:6 Changed 9 years ago by vbraun

Updated patch fixes the issue with the command line completion

comment:7 Changed 9 years ago by vbraun

  • Cc tfeulner added

Updated spkg fixes long input lines (>32k characters):

sage: S = SymmetricGroup(10000)
sage: s = S.random_element()
sage: len(str(s._gap_()))
61673
sage: libgap(s)
(1,5243,8582,5012,6862,7477,1681,7423,8405,3101,...,5257,9362,2495,8500)( [...] )

comment:8 Changed 9 years ago by vbraun

  • Description modified (diff)

comment:9 Changed 9 years ago by vbraun

I've added the same workaround for the gap command line option issue as just discussed in #13211

comment:10 Changed 9 years ago by vbraun

I've added __nonzero__ for wrapped GAP booleans for easier use.

Changed 9 years ago by vbraun

Updated patch

comment:11 Changed 9 years ago by vbraun

The new patch allows to change the comparison method for libgap objects since not all GAP objects can be compared. This is important if you want use them as cache keys.

Also, the comparison was not properly wrapped in sig_on/sig_off

comment:12 Changed 9 years ago by vbraun

I forgot to package aclocal.m4, updated spkg adds that file.

comment:13 Changed 9 years ago by vbraun

  • Description modified (diff)

comment:14 Changed 9 years ago by vbraun

  • Description modified (diff)

comment:15 Changed 9 years ago by vbraun

Updated to libGap-4.5.7

comment:16 Changed 9 years ago by vbraun

  • Dependencies changed from #6391, #13211 to #13211
  • Description modified (diff)

Changed 9 years ago by vbraun

patch from #6391

Changed 9 years ago by vbraun

patch from #6391

comment:17 Changed 9 years ago by vbraun

  • Description modified (diff)

comment:18 Changed 9 years ago by vbraun

  • Description modified (diff)

comment:19 Changed 9 years ago by jdemeyer

  • Milestone changed from sage-5.6 to sage-5.7
  • Summary changed from Improve libGAP startup error handling to libGAP! -- create a Cython library interface to gap

comment:20 Changed 9 years ago by iandrus

  • Cc iandrus added

comment:21 Changed 9 years ago by mmarco

I still see the segfault when trying to execute "Exec" trough libgap. This seems to make it impossible to load gap packages that make use of external programs.

comment:22 Changed 9 years ago by vbraun

Thanks for reminding me, I completely forgot about the Exec thing.

In the meantime, can we get this reviewed and included into Sage before the next GAP version comes out?

comment:23 Changed 9 years ago by vbraun

  • Description modified (diff)

I've replaced the spkg with a new version that fixes the GAP Exec command.

Changed 9 years ago by vbraun

Updated patch

comment:24 Changed 9 years ago by mmarco

Thanks. Still i can't load the kbmag package :(

comment:25 Changed 9 years ago by vbraun

I've updated the spkg, now loading kbmag works for me. I had to install it by hand since your spkg at #13673 is offline.

comment:26 Changed 9 years ago by dimpase

I get a slew of errors in ptestlong after following the instructions of the ticket with Sage 5.5; e.g.:

sage -t  --long -force_lib devel/sage/sage/libs/gap/libgap.pyx
**********************************************************************
File "/usr/local/src/sage/sage-5.5/devel/sage-main/sage/libs/gap/libgap.pyx", line 11:
    sage: a = libgap(10)
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/src/sage/sage-5.5/local/bin/ncadoctest.py", line 1231, in run_one_test
        self.run_one_example(test, example, filename, compileflags)
      File "/usr/local/src/sage/sage-5.5/local/bin/sagedoctest.py", line 38, in run_one_example
        OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)
      File "/usr/local/src/sage/sage-5.5/local/bin/ncadoctest.py", line 1172, in run_one_example
        compileflags, 1) in test.globs
      File "<doctest __main__.example_0[2]>", line 1, in <module>
        a = libgap(Integer(10))###line 11:
    sage: a = libgap(10)
      File "lazy_import.pyx", line 244, in sage.misc.lazy_import.LazyImport.__call__ (sage/misc/lazy_import.c:2012)
      File "lazy_import.pyx", line 148, in sage.misc.lazy_import.LazyImport._get_object (sage/misc/lazy_import.c:1291)
      File "libgap.pyx", line 574, in init sage.libs.gap.libgap (sage/libs/gap/libgap.c:4157)
        libgap = Gap()
      File "libgap.pyx", line 395, in sage.libs.gap.libgap.Gap.__init__ (sage/libs/gap/libgap.c:2716)
        initialize()
      File "util.pyx", line 193, in sage.libs.gap.util.initialize (sage/libs/gap/util.c:3312)
        from sage.interfaces.gap import get_gap_memory_pool_size
    ImportError: cannot import name get_gap_memory_pool_size
**********************************************************************
File "/usr/local/src/sage/sage-5.5/devel/sage-main/sage/libs/gap/libgap.pyx", line 12:
    sage: a
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/src/sage/sage-5.5/local/bin/ncadoctest.py", line 1231, in run_one_test
        self.run_one_example(test, example, filename, compileflags)
      File "/usr/local/src/sage/sage-5.5/local/bin/sagedoctest.py", line 38, in run_one_example
        OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)
      File "/usr/local/src/sage/sage-5.5/local/bin/ncadoctest.py", line 1172, in run_one_example
        compileflags, 1) in test.globs
      File "<doctest __main__.example_0[3]>", line 1, in <module>
        a###line 12:
    sage: a
    NameError: name 'a' is not defined

are some patches missing or not up date?

comment:27 follow-up: Changed 9 years ago by vbraun

Did you apply the patches from #13211? The get_gap_memory_pool_size() function was added in trac_13211_fix_gap_doctests_vb.patch.

Last edited 9 years ago by vbraun (previous) (diff)

comment:28 in reply to: ↑ 27 Changed 9 years ago by dimpase

Replying to vbraun:

Did you apply the patches from #13211? The get_gap_memory_pool_size() function was added in trac_13211_fix_gap_doctests_vb.patch.

indeed, I overlooked that #13211 isn't merged in 5.5. Sorry for noise.

comment:29 Changed 9 years ago by dimpase

Does sig_on() need a matching sig_off() in case sig_on() is issued in a try block, which throws an exception?

Comparison functions returning -1, 0, +1... So FORTRAN |V... :-)

comment:30 Changed 9 years ago by vbraun

sig_on and sig_off must be paired, though ideally they enclose only C/Cython code which cannot raise Python exceptions. A C signal will jump back to sig_on and raise there.

http://www.sagemath.org/doc/developer/coding_in_cython.html#using-sig-on-and-sig-off

Last edited 9 years ago by vbraun (previous) (diff)

comment:31 Changed 9 years ago by dimpase

  • Dependencies changed from #13211 to #13211, #13880

patches from #13880 are needed for doctests to (eventually) pass here.

comment:32 Changed 9 years ago by dimpase

  • Status changed from needs_review to positive_review

comment:33 Changed 9 years ago by jdemeyer

  • Description modified (diff)

comment:34 Changed 9 years ago by jdemeyer

  • Description modified (diff)
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