Opened 9 years ago
Last modified 9 years ago
#13588 closed enhancement
libGAP! -- create a Cython library interface to gap — at Version 51
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: | Dmitrii Pasechnik |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | #13211, #13880 | Stopgaps: |
Description (last modified by )
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.
- Start with sage-5.6.beta3 or later.
- Install http://www.stp.dias.ie/~vbraun/Sage/spkg/libgap-4.5.7.spkg
- Apply trac_6391_libGAP_root.patch to the root repository
- Apply trac_6391_libGAP.patch to the Sage library
- Apply trac_13588_improve_libGAP.patch to the Sage library
- Apply trac_13588_exec_fix.patch to the Sage library
- Apply trac_13588_manifest.patch to the Sage library
The trac_6391_*
patches have already been reviewed at #6391, I'm just attaching them to this ticket for convenience.
Change History (57)
comment:1 Changed 9 years ago by
- Cc mmarco added
- Dependencies set to #6391, #13211
- Status changed from new to needs_review
comment:2 Changed 9 years ago by
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
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
This same behaviour appears when i don't use this patch, so reported in the libgap ticket.
comment:5 Changed 9 years ago by
- Description modified (diff)
comment:6 Changed 9 years ago by
Updated patch fixes the issue with the command line completion
comment:7 Changed 9 years ago by
- 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
- Description modified (diff)
comment:9 Changed 9 years ago by
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
I've added __nonzero__
for wrapped GAP booleans for easier use.
comment:11 Changed 9 years ago by
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
I forgot to package aclocal.m4
, updated spkg adds that file.
comment:13 Changed 9 years ago by
- Description modified (diff)
comment:14 Changed 9 years ago by
- Description modified (diff)
comment:15 Changed 9 years ago by
Updated to libGap-4.5.7
comment:16 Changed 9 years ago by
- Dependencies changed from #6391, #13211 to #13211
- Description modified (diff)
comment:17 Changed 9 years ago by
- Description modified (diff)
comment:18 Changed 9 years ago by
- Description modified (diff)
comment:19 Changed 9 years ago by
- 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
- Cc iandrus added
comment:21 Changed 9 years ago by
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
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
- Description modified (diff)
I've replaced the spkg with a new version that fixes the GAP Exec command.
comment:24 Changed 9 years ago by
Thanks. Still i can't load the kbmag package :(
comment:25 Changed 9 years ago by
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
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: ↓ 28 Changed 9 years ago by
Did you apply the patches from #13211? The get_gap_memory_pool_size()
function was added in trac_13211_fix_gap_doctests_vb.patch
.
comment:28 in reply to: ↑ 27 Changed 9 years ago by
comment:29 Changed 9 years ago by
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
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
comment:31 Changed 9 years ago by
- 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
- Status changed from needs_review to positive_review
comment:33 Changed 9 years ago by
- Description modified (diff)
comment:34 Changed 9 years ago by
- Description modified (diff)
comment:35 Changed 9 years ago by
Is the test program sage/libs/gap/test/main.c
used anywhere in the Sage library? I don't mind having such a program, but I'd say it belongs in the libgap spkg and not in the Sage library. It could be run when installing libGAP.
comment:36 Changed 9 years ago by
- Reviewers set to Dmitrii Pasechnik
comment:37 Changed 9 years ago by
sage/libs/gap/test/main.c
is not used anywhere. As the readme file explains, it is there if you need an example for how to link with libGAP without Sage. This can be useful for debugging. LibGAP has its own testsuite.
comment:38 Changed 9 years ago by
- Status changed from positive_review to needs_work
libgap tries to run various autotools, which should be avoided (as it can lead to build errors). Probably this is simply timestamps were clobbered during the packaging.
libgap-4.5.7.log:WARNING: 'aclocal-1.12' is missing on your system. You should only need it if libgap-4.5.7.log:WARNING: 'automake-1.12' is missing on your system. You should only need it if libgap-4.5.7.log:WARNING: 'autoconf' is missing on your system. You should only need it if libgap-4.5.7.log:WARNING: 'autoheader' is missing on your system. You should only need it if
comment:39 Changed 9 years ago by
- Status changed from needs_work to positive_review
Ok I've regenerated the files and checked that it builds without the WARNING on an older machine. Spkg at the same place.
comment:40 follow-up: ↓ 41 Changed 9 years ago by
While building the documentation with this patch included, twice something went wrong.
- First time, I got an "unhandled SIGSEGV" in Sage while reading the sources of some elliptic curve file (sorry, forgot which one) for the PDF documentation. I didn't store the exact logs since I thought it was a cosmic ray or something...
- Next attempt, building from scratch again during the build of the HTML documentation:
reading sources... [ 86%] sage/schemes/elliptic_curves/cm reading sources... [ 87%] sage/schemes/elliptic_curves/constructor reading sources... [ 87%] sage/schemes/elliptic_curves/ec_database reading sources... [ 87%] sage/schemes/elliptic_curves/ell_curve_isogeny reading sources... [ 87%] sage/schemes/elliptic_curves/ell_field reading sources... [ 87%] sage/schemes/elliptic_curves/ell_finite_field reading sources... [ 87%] sage/schemes/elliptic_curves/ell_generic Exception occurred: File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/environment.py", line 831, in read_doc pickle.dump(doctree, f, pickle.HIGHEST_PROTOCOL) MemoryError The full traceback has been saved in /tmp/release/sphinx-err-QDcECu.log, if you want to report the issue to the developers.
Full traceback:
# Sphinx version: 1.1.2 # Python version: 2.7.3 # Docutils version: 0.7 release # Jinja2 version: 2.5.5 Traceback (most recent call last): File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/cmdline.py", line 189, in main app.build(force_all, filenames) File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/application.py", line 204, in build self.builder.build_update() File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/builders/__init__.py", line 196, in build_update 'out of date' % len(to_build)) File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/builders/__init__.py", line 216, in build purple, length): File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/builders/__init__.py", line 120, in status_iterator for item in iterable: File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/environment.py", line 616, in update_generator self.read_doc(docname, app=app) File "/release/merger/sage-5.7.alpha0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/environment.py", line 831, in read_doc pickle.dump(doctree, f, pickle.HIGHEST_PROTOCOL) MemoryError
I cannot say for sure that this ticket is to blame, but the MemoryError
certainly made me suspect GAP. And I also saw some "halving pool size" messages appear during the docbuilding.
comment:41 in reply to: ↑ 40 ; follow-up: ↓ 42 Changed 9 years ago by
Replying to jdemeyer:
While building the documentation with this patch included, twice something went wrong.
- First time, I got an "unhandled SIGSEGV" in Sage while reading the sources of some elliptic curve file (sorry, forgot which one) for the PDF documentation. I didn't store the exact logs since I thought it was a cosmic ray or something...
- Next attempt, building from scratch again during the build of the HTML documentation:
if this happens on one host only, I'd blame the RAM there.
comment:42 in reply to: ↑ 41 Changed 9 years ago by
Replying to dimpase:
if this happens on one host only, I'd blame the RAM there.
If this happens only with the libGAP patches, I'd blame libGAP. Besides, why would faulty RAM lead to a MemoryError
exception?
comment:43 follow-up: ↓ 44 Changed 9 years ago by
All GAP/libGAP processes should be terminated by the time we are building the manual, so I don't see how we could possibly impact that.
Is this a 32-bit machine? There you might run into warts caused by the limited address space, and the halving pool size would support that. Sphinx uses quite a lot of memory and might fail to load its pickles if there is no memory left or no contiguous address space block available.
comment:44 in reply to: ↑ 43 ; follow-up: ↓ 45 Changed 9 years ago by
Replying to vbraun:
All GAP/libGAP processes should be terminated by the time we are building the manual
Not really, as building the manual runs Sage code (as witnessed for example that Segmentation Faults run the Sage signal handler and display "Unhandled SIGSEGV...")
comment:45 in reply to: ↑ 44 ; follow-up: ↓ 46 Changed 9 years ago by
Replying to jdemeyer:
Not really, as building the manual runs Sage code (as witnessed for example that Segmentation Faults run the Sage signal handler and display "Unhandled SIGSEGV...")
Theoretically true, but a normal Sage session won't start GAP until it has to and libGAP is lazily imported as well. Even then, none of that has anything to do with the elliptic curve stuff.
Right now the only thing in this ticket that seems to actually influence the docbuild is that the documentation becomes larger.
comment:46 in reply to: ↑ 45 ; follow-up: ↓ 47 Changed 9 years ago by
Replying to vbraun:
Theoretically true, but a normal Sage session won't start GAP until it has to and libGAP is lazily imported as well.
The fact that I'm seeing "halving pool size" messages during the docbuilding proves that GAP is started.
comment:47 in reply to: ↑ 46 Changed 9 years ago by
Replying to jdemeyer:
The fact that I'm seeing "halving pool size" messages during the docbuilding proves that GAP is started.
That indeed means that something is wonky. We are trying hard to pick a pool size that should fit into memory yet it doesn't. As I said before, this means that either there is very little memory to start with or the available address space is so fragmented that there is no contiguous piece left (32-bit only).
comment:48 Changed 9 years ago by
I guess sphinx has to resolve the lazy imports in order to get at the docstrings? That would pull in libGAP, which then subtracts ~250MB from the available address space. On a 32-bit machine that might push you over the cliff since sphinx is the most memory-demanding piece of the whole sage build process. Can you tell us which architecture we are talking about?
comment:49 Changed 9 years ago by
Sorry, I wasn't immediately aware of this, but this was with ulimit -v 2500000
(2.5GB) set on a 64-bit system.
comment:50 Changed 9 years ago by
- Status changed from positive_review to needs_work
This needs a patch to MANIFEST.in
to add the Makefile
(but again: I doubt that this really belongs in the Sage library).
comment:51 Changed 9 years ago by
- Description modified (diff)
- Status changed from needs_work to positive_review
I've added it to the manifest. I do think it is useful, when I started working on libgap that was one of the first things that I had to figure out.
Miguel, you said that you had some mysterious error. Can you try this patch? It depends on the recently-updated patches on #6391, #13211.