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conda: segmentation fault during doctest of crypto/mq/sr and pbori #35595

Closed
2 tasks done
Tracked by #35597
tobiasdiez opened this issue May 2, 2023 · 3 comments
Closed
2 tasks done
Tracked by #35597

conda: segmentation fault during doctest of crypto/mq/sr and pbori #35595

tobiasdiez opened this issue May 2, 2023 · 3 comments
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t: bug t: tests

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@tobiasdiez
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Is there an existing issue for this?

  • I have searched the existing issues for a bug report that matches the one I want to file, without success.

Did you read the documentation and troubleshoot guide?

  • I have read the documentation and troubleshoot guide

Environment

- **OS**: Windows, WSL 2.0
- **Sage Version**: dev branch

Steps To Reproduce

Run ./sage -t src/sage/crypto/mq/sr.py in conda enviroment. See also github workflow: https://github.com/sagemath/sage/actions/runs/4846009227/jobs/8635274790

Expected Behavior

No error

Actual Behavior

Get error

too many failed tests, not using stored timings
Running doctests with ID 2023-05-02-20-08-00-d8b98e86.
Git branch: lin_symplectic
Git ref: 10.0.rc1-17-gb439ea140b-dirty
Running with SAGE_LOCAL='/home/tobias/miniconda3/envs/sage-dev' and SAGE_VENV='/home/tobias/miniconda3/envs/sage-dev'
Using --optional=conda,pip,sage
Features to be detected: 4ti2,benzene,bliss,buckygen,conway_polynomials,csdp,cvxopt,cvxopt,database_cremona_ellcurve,database_cremona_mini_ellcurve,database_cubic_hecke,database_jones_numfield,database_knotinfo,dvipng,fpylll,gfan,graphviz,imagemagick,ipython,jupymake,kenzo,latte_int,lrcalc_python,lrslib,mcqd,meataxe,mpmath,msolve,nauty,networkx,numpy,palp,pandoc,pdf2svg,pdftocairo,pexpect,phitigra,pillow,plantri,polytopes_db,polytopes_db_4d,pplpy,primecountpy,ptyprocess,pynormaliz,python_igraph,requests,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.libs.gap,sage.libs.pari,sage.libs.singular,sage.misc.cython,sage.modules,sage.plot,sage.rings.finite_rings,sage.rings.function_field,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.rings.real_mpfr,sage.symbolic,sage_numerical_backends_coin,sagemath_doc_html,scipy,singular,sphinx,sympy,tdlib
Doctesting 1 file.
sage -t --random-seed=152125203327691848610921166990507833546 src/sage/crypto/mq/sr.py
    Killed due to segmentation fault
**********************************************************************
Tests run before process (pid=1361) failed:
sage: sr = mq.SR(1, 1, 1, 4) ## line 29 ##
sage: sr.n, sr.r, sr.c, sr.e ## line 37 ##
(1, 1, 1, 4)
sage: print(sr.R.repr_long()) ## line 42 ##
Polynomial Ring
  Base Ring : Finite Field in a of size 2^4
       Size : 20 Variables
   Block  0 : Ordering : deglex
              Names    : k100, k101, k102, k103, x100, x101, x102, x103, w100, w101, w102, w103, s000, s001, s002, s003, k000, k001, k002, k003

sage: sr.ShiftRows ## line 53 ##
[1 0 0 0]
[0 1 0 0]
[0 0 1 0]
[0 0 0 1]
sage: sr.MixColumns ## line 61 ##
[1 0 0 0]
[0 1 0 0]
[0 0 1 0]
[0 0 0 1]
sage: sr.Lin ## line 69 ##
[          a^2 + 1                 1         a^3 + a^2           a^2 + 1]
[                a                 a                 1 a^3 + a^2 + a + 1]
[          a^3 + a               a^2               a^2                 1]
[                1               a^3             a + 1             a + 1]
sage: sr.M ## line 77 ##
[          a^2 + 1                 1         a^3 + a^2           a^2 + 1]
[                a                 a                 1 a^3 + a^2 + a + 1]
[          a^3 + a               a^2               a^2                 1]
[                1               a^3             a + 1             a + 1]
sage: sr.Mstar ## line 85 ##
[          a^2 + 1                 1         a^3 + a^2           a^2 + 1]
[                a                 a                 1 a^3 + a^2 + a + 1]
[          a^3 + a               a^2               a^2                 1]
[                1               a^3             a + 1             a + 1]
sage: sr = mq.SR(10,4,4,8) ## line 94 ##
sage: sr.Mstar == ~sr.MixColumns * sr.M ## line 95 ##
True
sage: sr = mq.SR(1,1,1,4, gf2=True, polybori=True) ## line 101 ##
sage: K = sr.base_ring() ## line 102 ##
sage: a = K.gen() ## line 103 ##
sage: K = [a] ## line 104 ##
sage: P = [1] ## line 105 ##
sage: F,s = sr.polynomial_system(P=P, K=K) ## line 106 ##
sage: F.groebner_basis() ## line 107 ##
------------------------------------------------------------------------
/home/tobias/miniconda3/envs/sage-dev/lib/python3.10/site-packages/cysignals/signals.cpython-310-x86_64-linux-gnu.so(+0x76cd)[0x7fa350dd06cd]
/home/tobias/miniconda3/envs/sage-dev/lib/python3.10/site-packages/cysignals/signals.cpython-310-x86_64-linux-gnu.so(+0x778c)[0x7fa350dd078c]
/home/tobias/miniconda3/envs/sage-dev/lib/python3.10/site-packages/cysignals/signals.cpython-310-x86_64-linux-gnu.so(+0x9bc7)[0x7fa350dd2bc7]
/lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7fa351db7520]
/home/tobias/miniconda3/envs/sage-dev/lib/libbrial_groebner.so.3(+0x39cc3)[0x7fa2fbb7bcc3]
/home/tobias/miniconda3/envs/sage-dev/lib/libbrial_groebner.so.3(+0x44669)[0x7fa2fbb86669]
/home/tobias/miniconda3/envs/sage-dev/lib/libbrial_groebner.so.3(_ZN8polybori8groebner16GroebnerStrategy16faugereStepDenseERKSt6vectorINS_15BoolePolynomialESaIS3_EE+0x136)[0x7fa2fbb81236]
/home/tobias/sage-conda/src/sage/rings/polynomial/pbori/pbori.cpython-310-x86_64-linux-gnu.so(+0x7c67a)[0x7fa2fbf4367a]
python3(+0x14012b)[0x564eff00f12b]
python3(_PyEval_EvalFrameDefault+0x4d0d)[0x564eff00423d]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x332)[0x564efefff862]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyObject_FastCallDictTstate+0x185)[0x564eff0080b5]
python3(_PyObject_Call_Prepend+0x69)[0x564eff019ae9]
python3(+0x2177b9)[0x564eff0e67b9]
python3(PyObject_Call+0x209)[0x564eff01c209]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyObject_FastCallDictTstate+0x185)[0x564eff0080b5]
python3(_PyObject_Call_Prepend+0x69)[0x564eff019ae9]
python3(+0x2177b9)[0x564eff0e67b9]
python3(PyObject_Call+0x209)[0x564eff01c209]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyObject_FastCallDictTstate+0x185)[0x564eff0080b5]
python3(_PyObject_Call_Prepend+0x69)[0x564eff019ae9]
python3(+0x2177b9)[0x564eff0e67b9]
python3(PyObject_Call+0x209)[0x564eff01c209]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyObject_FastCallDictTstate+0x185)[0x564eff0080b5]
python3(_PyObject_Call_Prepend+0x69)[0x564eff019ae9]
python3(+0x2177b9)[0x564eff0e67b9]
python3(PyObject_Call+0x209)[0x564eff01c209]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyObject_FastCallDictTstate+0x185)[0x564eff0080b5]
python3(_PyObject_Call_Prepend+0x69)[0x564eff019ae9]
python3(+0x2177b9)[0x564eff0e67b9]
python3(PyObject_Call+0x209)[0x564eff01c209]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyObject_FastCallDictTstate+0x185)[0x564eff0080b5]
python3(_PyObject_Call_Prepend+0x69)[0x564eff019ae9]
python3(+0x2177b9)[0x564eff0e67b9]
python3(PyObject_Call+0x209)[0x564eff01c209]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyObject_FastCallDictTstate+0x185)[0x564eff0080b5]
python3(_PyObject_Call_Prepend+0x69)[0x564eff019ae9]
python3(+0x2177b9)[0x564eff0e67b9]
python3(PyObject_Call+0x209)[0x564eff01c209]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyObject_Call+0xb8)[0x564eff01c0b8]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(PyVectorcall_Call+0xb9)[0x564eff01c419]
/home/tobias/sage-conda/src/sage/rings/polynomial/pbori/pbori.cpython-310-x86_64-linux-gnu.so(+0x3079f)[0x7fa2fbef779f]
/home/tobias/sage-conda/src/sage/rings/polynomial/pbori/pbori.cpython-310-x86_64-linux-gnu.so(+0x88926)[0x7fa2fbf4f926]
python3(_PyObject_MakeTpCall+0x26b)[0x564eff008cdb]
python3(+0x14c874)[0x564eff01b874]
python3(PyVectorcall_Call+0xb9)[0x564eff01c419]
/home/tobias/sage-conda/src/sage/rings/polynomial/pbori/pbori.cpython-310-x86_64-linux-gnu.so(+0x3079f)[0x7fa2fbef779f]
/home/tobias/sage-conda/src/sage/rings/polynomial/pbori/pbori.cpython-310-x86_64-linux-gnu.so(+0x4b8f0)[0x7fa2fbf128f0]
python3(_PyObject_MakeTpCall+0x26b)[0x564eff008cdb]
python3(+0x14cac2)[0x564eff01bac2]
python3(_PyEval_EvalFrameDefault+0x2ec3)[0x564eff0023f3]
python3(+0x14c581)[0x564eff01b581]
python3(_PyEval_EvalFrameDefault+0x4d0d)[0x564eff00423d]
python3(+0x1db6a2)[0x564eff0aa6a2]
python3(PyEval_EvalCode+0x87)[0x564eff0aa5e7]
python3(+0x1e2c30)[0x564eff0b1c30]
python3(+0x140d14)[0x564eff00fd14]
python3(_PyEval_EvalFrameDefault+0x332)[0x564efefff862]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x735)[0x564efefffc65]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x735)[0x564efefffc65]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x735)[0x564efefffc65]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x735)[0x564efefffc65]
python3(_PyObject_FastCallDictTstate+0xd1)[0x564eff008001]
python3(_PyObject_Call_Prepend+0x69)[0x564eff019ae9]
python3(+0x2177b9)[0x564eff0e67b9]
python3(_PyObject_MakeTpCall+0x26b)[0x564eff008cdb]
python3(_PyEval_EvalFrameDefault+0x4fb1)[0x564eff0044e1]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x735)[0x564efefffc65]
python3(+0x14c581)[0x564eff01b581]
python3(_PyEval_EvalFrameDefault+0x13d0)[0x564eff000900]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x735)[0x564efefffc65]
python3(_PyObject_FastCallDictTstate+0xd1)[0x564eff008001]
python3(+0x14a0fb)[0x564eff0190fb]
python3(_PyObject_MakeTpCall+0x2bb)[0x564eff008d2b]
python3(_PyEval_EvalFrameDefault+0x4fb1)[0x564eff0044e1]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x4d0d)[0x564eff00423d]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x4d0d)[0x564eff00423d]
python3(+0x14c581)[0x564eff01b581]
python3(_PyEval_EvalFrameDefault+0x4d0d)[0x564eff00423d]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x735)[0x564efefffc65]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x735)[0x564efefffc65]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x735)[0x564efefffc65]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x735)[0x564efefffc65]
python3(_PyFunction_Vectorcall+0x6f)[0x564eff00fb1f]
python3(_PyEval_EvalFrameDefault+0x735)[0x564efefffc65]
python3(+0x1db6a2)[0x564eff0aa6a2]
python3(PyEval_EvalCode+0x87)[0x564eff0aa5e7]
python3(+0x20e3fc)[0x564eff0dd3fc]
python3(+0x2092d4)[0x564eff0d82d4]
python3(+0x9758d)[0x564efef6658d]
python3(_PyRun_SimpleFileObject+0x1b5)[0x564eff0d24f5]
python3(_PyRun_AnyFileObject+0x43)[0x564eff0d20a3]
python3(Py_RunMain+0x399)[0x564eff0cf279]
python3(Py_BytesMain+0x39)[0x564eff09cdc9]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7fa351d9ed90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7fa351d9ee40]
python3(+0x1cdcc1)[0x564eff09ccc1]

Additional Information

@isuruf @mkoeppe

(There is also #32083 but this doesn't seem to be the same issue)

Full debug log:
log.txt
@tobiasdiez tobiasdiez mentioned this issue May 2, 2023
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@mkoeppe
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mkoeppe commented May 2, 2023 •
edited
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That's all polybori (brial); any insights @kiwifb?

@kiwifb
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kiwifb commented May 2, 2023

It looks like cschwan/sage-on-gentoo#733 which seems to be related to have compiled brial with gcc-11 and then sage with gcc-12. It is a very weird, should not happen, incompatibility if it is really the root cause.

@tobiasdiez tobiasdiez changed the title conda: segmentation fault during doctest of crypto/mq/sr conda: segmentation fault during doctest of crypto/mq/sr and pbori Oct 1, 2023
@tobiasdiez
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Seems to be gone by now.

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