Opened 4 years ago
Closed 4 years ago
#22677 closed defect (fixed)
Polybori segfaults when built with clang on OS X
Reported by:  fbissey  Owned by:  

Priority:  major  Milestone:  sage8.0 
Component:  porting  Keywords:  
Cc:  Merged in:  
Authors:  François Bissey, Dima Pasechnik  Reviewers:  François Bissey, Dima Pasechnik 
Report Upstream:  Fixed upstream, in a later stable release.  Work issues:  
Branch:  382b25c (Commits, GitHub, GitLab)  Commit:  382b25cc1c348d8503fdcaaf122499dc6b255c70 
Dependencies:  Stopgaps: 
Description (last modified by )
Split from #12426. Doctest involving polybori
segfault when everything is built with clang
sage t long warnlong 62.3 src/sage/rings/polynomial/multi_polynomial_sequence.py ********************************************************************** File "src/sage/rings/polynomial/multi_polynomial_sequence.py", line 106, in sage.rings.polynomial.multi_polynomial_sequence Failed example: C[0].groebner_basis() Exception raised: Traceback (most recent call last): File "/Users/fbissey/build/sageclang/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 498, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/fbissey/build/sageclang/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 861, in compile_and_execute exec(compiled, globs) File "<doctest sage.rings.polynomial.multi_polynomial_sequence[7]>", line 1, in <module> C[Integer(0)].groebner_basis() File "/Users/fbissey/build/sageclang/local/lib/python2.7/sitepackages/sage/rings/polynomial/multi_polynomial_sequence.py", line 518, in groebner_basis return self.ideal().groebner_basis(*args, **kwargs) File "sage/rings/polynomial/pbori.pyx", line 5080, in sage.rings.polynomial.pbori.BooleanPolynomialIdeal.groebner_basis (/Users/fbissey/build/sageclang/src/build/cythonized/sage/rings/polynomial/pbori.cpp:42498) sig_on() File "src/cysignals/signals.pyx", line 109, in cysignals.signals.sig_raise_exception (build/src/cysignals/signals.c:1695) SignalError: Segmentation fault Killed due to segmentation fault
Backtrace
sage: F.eliminate_linear_variables() # everything vanishes ## line 1147 ##  0 signals.so 0x000000010589c5d1 print_backtrace + 65 1 signals.so 0x000000010589fc0c sigdie + 60 2 signals.so 0x000000010589fb7f cysigs_signal_handler + 351 3 libsystem_platform.dylib 0x00007fffd0769bba _sigtramp + 26 4 ??? 0x00000001052a9a00 0x0 + 4381645312 5 pbori.so 0x000000010f0257ef _ZN8polybori8groebner11linalg_stepERNSt3__16vectorINS_15BoolePolynomialENS1_9allocatorIS3_EEEENS_8BooleSetES8_bbPKc + 479 6 pbori.so 0x000000010f0252d3 _ZN8polybori8groebner14gauss_on_polysERKNSt3__16vectorINS_15BoolePolynomialENS1_9allocatorIS3_EEEE + 275 7 pbori.so 0x000000010f024fe0 _ZL58__pyx_pw_4sage_5rings_10polynomial_5pbori_39gauss_on_polysP7_objectS0_ + 192 8 libpython2.7.dylib 0x000000010514cfdc PyEval_EvalFrameEx + 29500 9 libpython2.7.dylib 0x0000000105151e02 fast_function + 338
Similarly sage/rings/polynomial/pbori.pyx
Assertion failed: (result != map.end()), function get, file ../../groebner/include/polybori/groebner/PolyEntryIndices.h, line 115.  0 signals.so 0x000000010bc6a5d1 print_backtrace + 65 1 signals.so 0x000000010bc6dc0c sigdie + 60 2 signals.so 0x000000010bc6db5d cysigs_signal_handler + 317 3 libsystem_platform.dylib 0x00007fffd0769bba _sigtramp + 26 4 ??? 0x00007fd399cbd6a0 0x0 + 140546795099808 5 libsystem_c.dylib 0x00007fffd05f0420 abort + 129 6 libsystem_c.dylib 0x00007fffd05b7893 basename_r + 0 7 libbrial_groebner.0.dylib 0x0000000115658737 _ZNK8polybori8groebner16PolyEntryIndices3getINSt3__13mapINS_13BooleExponentEiNS_13MapComparatorIS5_EENS3_9allocatorINS3_4pairIKS5_iEEEEEES5_EEiRKT_RKT0_NS1_7uncheckE + 551 8 libbrial_groebner.0.dylib 0x00000001156584ff _ZNK8polybori8groebner16PolyEntryIndices3getINS1_7uncheckEEEiRKNS_13BooleExponentET_ + 47 9 libbrial_groebner.0.dylib 0x00000001156584bd _ZNK8polybori8groebner16PolyEntryIndicesclINS_13BooleExponentEEEiRKT_ + 29 10 libbrial_groebner.0.dylib 0x000000011561105c _ZNK8polybori8groebner15PolyEntryVector5indexINS_13BooleExponentEEEmRKT_ + 44 11 libbrial_groebner.0.dylib 0x00000001156609ad _ZN8polybori8groebner15PolyEntryVectorclINS_13BooleExponentEEENS0_18PolyEntryReferenceERKT_ + 61 12 libbrial_groebner.0.dylib 0x0000000115692ea7 _ZNK8polybori8groebner20SetAssociatedMinimalINS_13BooleExponentELb0EEclERKS2_ + 39 13 libbrial_groebner.0.dylib 0x000000011569108a _ZN8polybori8groebner17ReductionStrategy28unmarkNonMinimalLeadingTermsENS_8BooleSetE + 186 14 libbrial_groebner.0.dylib 0x0000000115690e16 _ZN8polybori8groebner17ReductionStrategy19setupSetsForElementERKNS0_9PolyEntryE + 262 15 pbori.so 0x00000001153af381 _ZL76__pyx_pw_4sage_5rings_10polynomial_5pbori_17ReductionStrategy_5add_generatorP7_objectS0_ + 177 16 pbori.so 0x000000011533967a _ZL25__Pyx_PyObject_CallOneArgP7_objectS0_ + 154 17 pbori.so 0x00000001153974b1 _ZL71__pyx_pw_4sage_5rings_10polynomial_5pbori_17BooleanPolynomial_129reduceP7_objectS0_ + 2289 18 libpython2.7.dylib 0x000000010b51bfdc PyEval_EvalFrameEx + 29500 19 libpython2.7.dylib 0x000000010b514927 PyEval_EvalCodeEx + 2119
finally the failures in
sage t long src/sage/crypto/mq/sr.py # 7 doctests failed
are consequences of segfaults above.
tarball https://github.com/BRiAl/BRiAl/releases/download/0.8.7/brial0.8.7.tar.bz2
Change History (21)
comment:1 Changed 4 years ago by
 Report Upstream changed from N/A to Fixed upstream, but not in a stable release.
comment:2 Changed 4 years ago by
 Branch set to u/dimpase/brial086
 Commit set to a3e4c6ba6ef28ad7eb8db010224e1c18a36b02df
comment:3 Changed 4 years ago by
 Description modified (diff)
 Status changed from new to needs_review
comment:4 Changed 4 years ago by
I know, sorry I cannot seem to move my ass to make a proper release. On it now.
comment:5 Changed 4 years ago by
 Description modified (diff)
 Report Upstream changed from Fixed upstream, but not in a stable release. to Fixed upstream, in a later stable release.
 Status changed from needs_review to needs_work
Need to fix the checksum to the properly released tarball. I'll put it back in review once it is done.
comment:6 Changed 4 years ago by
 Branch changed from u/dimpase/brial086 to u/fbissey/brial0.8.6
 Commit changed from a3e4c6ba6ef28ad7eb8db010224e1c18a36b02df to 0943ae5079ff302ac31b89b27be3f83174f3762d
 Reviewers set to François Bissey
 Status changed from needs_work to needs_review
I'll put it in positive review but can you double check that the new tarball works for you.
New commits:
0943ae5  updating checksum for official release

comment:7 Changed 4 years ago by
 Status changed from needs_review to needs_work
ironically, it does not work on gentoo Lunix with gcc 5.4.0.
sage t long warnlong 118.6 src/sage/rings/polynomial/multi_polynomial_sequence.py # Killed due to segmentation fault
and two more brialrelated errors. While numerous
warning: comparison between signed and unsigned integer expressions [Wsigncompare]
are probably OK,
[sagelib7.6] In file included from /home/dima/Sage/sagedev/src/sage/libs/polybori/pb_wrap.h:22:0, from /home/dima/Sage/sagedev/src/build/cythonized/sage/rings/polynomial/pbori.cpp:517: /home/dima/Sage/sagedev/src/sage/ext/ccobject.h: In instantiation of ‘void Delete(T*) [with T = polybori::groebner::ReductionStrategy]’: /home/dima/Sage/sagedev/src/build/cythonized/sage/rings/polynomial/pbori.cpp:50398:51: required from here /home/dima/Sage/sagedev/src/sage/ext/ccobject.h:77:3: warning: deleting object of polymorphic class type ‘polybori::groebner::ReductionStrategy’ which has nonvirtual destructor might cause undefined behaviour [Wdeletenonvirtualdtor] delete mem; ^
might spell trouble. It could also be that we must switch to gcc 6. Can you check in what Linux configuration this works for you?
(meahwhile I'll do distclean and a full rebuild, just to see if this still persists)
comment:8 Changed 4 years ago by
I confirm, it breaks things here too with gcc5.4.0. I think it may be down to https://github.com/BRiAl/BRiAl/issues/11#issuecomment269957098 I'll have to check on that.
comment:9 followup: ↓ 10 Changed 4 years ago by
I'll have a look at how it plays together with #22554 (which isn't in this branch yet).
comment:10 in reply to: ↑ 9 Changed 4 years ago by
comment:11 Changed 4 years ago by
OK I have a fix. I cut a bit too much stuff. Actually adding one character would have been sufficient to fix gcc6 compilation. It is still worth cleaning some stuff that wouldn't work anyway. I am not sure when I will have time to push the fix, I am rather busy this week end.
comment:12 Changed 4 years ago by
 Description modified (diff)
brial0.8.7
(now linked to in the ticket description) should work for all reasonably recent compilers. I am not sure about keeping std=c++98
in CXXFLAGS
as it could cause problem in the near future I think. I haven't updated the branch yet, feel free to beat me to it.
comment:13 Changed 4 years ago by
0.8.7 works well on FreeBSD+clang. I'm happy to give it positive review once we have a branch...
comment:14 Changed 4 years ago by
Did you try on gentoo as well? Since 0.8.6 was working on FreeBSD+clang but not on Gentoo+gcc?
comment:15 Changed 4 years ago by
 Branch changed from u/fbissey/brial0.8.6 to u/dimpase/brial0.8.6
 Commit 0943ae5079ff302ac31b89b27be3f83174f3762d deleted
 Status changed from needs_work to needs_review
checking now on Linux. Will take a whiledoing a clean rebuild of sage 8.0.beta...
comment:16 Changed 4 years ago by
OK, it works on Linux too. No idea why the branch is red though.
comment:17 Changed 4 years ago by
Interesting message: "branch doesn't exist".
comment:18 Changed 4 years ago by
 Branch changed from u/dimpase/brial0.8.6 to u/dimpase/brial086
 Commit set to 382b25cc1c348d8503fdcaaf122499dc6b255c70
oops...
comment:19 Changed 4 years ago by
 Status changed from needs_review to positive_review
comment:20 Changed 4 years ago by
 Reviewers changed from François Bissey to François Bissey, Dima Pasechnik
comment:21 Changed 4 years ago by
 Branch changed from u/dimpase/brial086 to 382b25cc1c348d8503fdcaaf122499dc6b255c70
 Resolution set to fixed
 Status changed from positive_review to closed
All the above are solved by upgrading
BRiAl
to git master. I'll prepare a release ofBRiAl
.