Segfault testing src/sage/libs/gap/element.pyx on python 3.12 #37026

tornaria · 2024-01-07T14:31:25Z

Concerning the error in src/sage/libs/gap/element.pyx, it happens in line 2489:

for i in range(100):
        rnd = [ randint(-10,10) for i in range(randint(0,7)) ]
        # compute the sum in GAP
        _ = libgap.Sum(rnd)
        try:
            libgap.Sum(*rnd)
            print('This should have triggered a ValueError')
            print('because Sum needs a list as argument')
        except ValueError:
            pass

getting Killed due to segmentation fault. Running this code in the terminal works, the error appears only in tests and with python 3.12.

Originally posted by @enriqueartal in #37011 (comment)

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

dimpase · 2024-01-07T19:09:10Z

my eyes bleed from this line:

        rnd = [ randint(-10,10) for i in range(randint(0,7)) ]

How about

        rnd = random.choices(range(-10,10), k=randint(0,7))

?

See https://docs.python.org/3/library/random.html#random.choices

dimpase · 2024-01-07T19:51:56Z

maybe it segfaults on libgap.Sum(*rnd) when rnd==[] ?

dimpase · 2024-03-11T13:07:14Z

This also pops up on Fedora 39 with system Python 3.12, see e.g. https://groups.google.com/g/sage-release/c/oTnTrEnB3YU/m/tZiLm66ZAwAJ

dimpase · 2024-03-11T14:36:03Z

But I can't reproduce this with Python 3.12.2

enriqueartal · 2024-03-12T09:02:38Z

Is it possible that both @jaapspies and me are missing some python3 system package?

enriqueartal · 2024-03-12T09:45:27Z

At some point this segfault occured only in tests, now it happens also in the command line

kiwifb · 2024-04-22T21:13:50Z

my eyes bleed from this line:
        rnd = [ randint(-10,10) for i in range(randint(0,7)) ]
How about
        rnd = random.choices(range(-10,10), k=randint(0,7))
?

See https://docs.python.org/3/library/random.html#random.choices

Tried that but it does not have an effect

sage: import random ## line 2490 ##
sage: for i in range(100):
    rnd = random.choices(range(-10,10), k=randint(0,7))
    # compute the sum in GAP
    _ = libgap.Sum(rnd)
    try:
        libgap.Sum(*rnd)
        print('This should have triggered a ValueError')
        print('because Sum needs a list as argument')
    except ValueError:
        pass ## line 2491 ##
------------------------------------------------------------------------
/usr/lib/python3.12/site-packages/cysignals/signals.cpython-312-x86_64-linux-gnu.so(+0xa0d4)[0x7fbe2865c0d4]
/usr/lib/python3.12/site-packages/cysignals/signals.cpython-312-x86_64-linux-gnu.so(+0xa196)[0x7fbe2865c196]
/usr/lib/python3.12/site-packages/cysignals/signals.cpython-312-x86_64-linux-gnu.so(+0xcbf6)[0x7fbe2865ebf6]
/usr/lib64/libc.so.6(+0x3a210)[0x7fbe2945f210]

tornaria · 2024-04-22T21:21:32Z

There's a more detailed trace in #36407 (comment)

antonio-rojas · 2024-05-01T09:11:04Z

Caused by GCC commit https://gcc.gnu.org/git/?p=gcc.git;a=commit;h=049ec9b981d1f4f97736061d5cf7d0ae990b57d7

Upstream report: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=114872

Can be reproduced by calling any libgap function in exactly 3 parameters, eg. libgap.AbelianGroup(0,0,0)

dimpase · 2024-05-03T13:31:20Z

@sheerluck has kindly disassembled broken element....so, resulting from compilation of element.c. I report the result here:
https://gcc.gnu.org/bugzilla/show_bug.cgi?id=114872#c12
(that is, code generation is broken, the call to GAP_CallFunc3Args() is formed with one parameter less than it should be)

Fixing gcc is above my payrate, though :-)

This appears to fix sagemath#37026

dimpase · 2024-05-08T18:03:40Z

more discussion on https://gcc.gnu.org/bugzilla/show_bug.cgi?id=114872 seems to indicate that gcc is actually not broken, it's our code that is (missing volatile declarations).
See also https://stackoverflow.com/questions/7996825/why-volatile-works-for-setjmp-longjmp

If I am not mistaken, we have

sig_on()
...
GAP_CallFunc3Args(foo0,...,foo3)
...
sign_off()

and the longmp() triggered somewhere in libgap, called by GAP_CallFunc3Args, invalidates the registers' contents.
Now, if foo3, say, was held in a register, it is gone for good. Thus unwinding this call, which involves a GAP object
held in foo3, is no longer possible, and triggers a segfault.

Looks like a lot of volatile to add all over the place: (anywhere libgap, singular (which also uses setjmp/longjmp) is called, any other setjmp/longjmp-ing upstream code?

dimpase · 2024-05-13T12:51:33Z

See https://trofi.github.io/posts/312-the-sagemath-saga.html for a detailed analysis. Not sure whether the detail that GAP uses setjmp/longjmp to return from GAP_CallFunc3Args() here in the 1st place.

dimpase · 2024-05-13T14:10:45Z

By the way, the Python 3.12 is only needed to produce a crash. Otherwise, we get a memory leak, as these temporary GAP objects are not cleared.

$ ./sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 10.4.beta6, Release Date: 2024-05-12              │
│ Using Python 3.11.9. Type "help()" for help.                       │
└────────────────────────────────────────────────────────────────────┘

 sage: libgap.count_GAP_objects()
0
sage: libgap.Sum(1,2,42)
---------------------------------------------------------------------------
GAPError                                  Traceback (most recent call last)
Cell In[2], line 1
----> 1 libgap.Sum(Integer(1),Integer(2),Integer(42))

File /home/scratch/scratch2/dimpase/sage/sage/src/sage/libs/gap/element.pyx:2514, in sage.libs.gap.element.GapElement_Function.__call__()
   2512 try:
   2513     sig_GAP_Enter()
-> 2514     sig_on()
   2515     if n == 0:
   2516         result = GAP_CallFunc0Args(self.value)

GAPError: Error, no method found! Error, no 1st choice method found for `SumOp' on 3 arguments
sage: libgap.count_GAP_objects()
4
sage: libgap.Sum(3,5,7)
---------------------------------------------------------------------------
GAPError                                  Traceback (most recent call last)
Cell In[4], line 1
----> 1 libgap.Sum(Integer(3),Integer(5),Integer(7))

File /home/scratch/scratch2/dimpase/sage/sage/src/sage/libs/gap/element.pyx:2514, in sage.libs.gap.element.GapElement_Function.__call__()
   2512 try:
   2513     sig_GAP_Enter()
-> 2514     sig_on()
   2515     if n == 0:
   2516         result = GAP_CallFunc0Args(self.value)

GAPError: Error, no method found! Error, no 1st choice method found for `SumOp' on 3 arguments
sage: libgap.count_GAP_objects()
7

This appears to fix sagemath#37026

This appears to fix sagemath#37026 (segfaults in src/sage/libs/gap/element.pyx with Python 3.12 and gcc 13.2.1) See also sagemath#36407 (comment) The corresponding gcc 13.2.1's bug (or feature) is being dealt with here: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=114872 ### 📝 Checklist  - [x] The title is concise and informative. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation and checked the documentation preview. ### ⌛ Dependencies    URL: sagemath#37951 Reported by: Dima Pasechnik Reviewer(s): Dima Pasechnik, Gonzalo Tornaría

tornaria changed the title ~~Segfault testing src/sage/libs/gap/element.pyx~~ Segfault testing src/sage/libs/gap/element.pyx on python 3.12 Jan 7, 2024

tornaria added the t: bug label Jan 7, 2024

mkoeppe mentioned this issue Jan 7, 2024

m4/pyproject_toml_metadata.m4: Allow Python 3.12 #36869

Merged

5 tasks

tornaria mentioned this issue Feb 12, 2024

Segfaults in sage.libs.gap.element #37289

Open

tornaria mentioned this issue Apr 22, 2024

Support python 3.12 on sagemath-standard #36407

Merged

mkoeppe mentioned this issue Apr 23, 2024

Added some documentation in the developer's guide regarding deprecation #37807

Merged

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mkoeppe mentioned this issue May 1, 2024

build/pkgs/python3: Update to 3.12.3; declare support of Python 3.12.x stable #37834

Open

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mkoeppe added this to the sage-10.4 milestone May 3, 2024

dimpase added a commit to dimpase/sage that referenced this issue May 6, 2024

declare the last arg to GAP_CallFunc3Args volatile

483474a

This appears to fix sagemath#37026

dimpase linked a pull request May 6, 2024 that will close this issue

declare the last arg to GAP_CallFunc3Args volatile #37951

Open

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dimpase mentioned this issue May 10, 2024

volatile's to be used in libgap-calling functions? gap-system/gap#5714

Open

dimpase added a commit to dimpase/sage that referenced this issue May 14, 2024

declare the last arg to GAP_CallFunc3Args volatile

72e6b66

This appears to fix sagemath#37026

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Segfault testing src/sage/libs/gap/element.pyx on python 3.12 #37026

Segfault testing src/sage/libs/gap/element.pyx on python 3.12 #37026

tornaria commented Jan 7, 2024

dimpase commented Jan 7, 2024 •

edited

dimpase commented Jan 7, 2024

dimpase commented Mar 11, 2024

dimpase commented Mar 11, 2024

enriqueartal commented Mar 12, 2024

enriqueartal commented Mar 12, 2024

kiwifb commented Apr 22, 2024

tornaria commented Apr 22, 2024

antonio-rojas commented May 1, 2024 •

edited

dimpase commented May 3, 2024

dimpase commented May 8, 2024

dimpase commented May 13, 2024

dimpase commented May 13, 2024

Segfault testing src/sage/libs/gap/element.pyx on python 3.12 #37026

Segfault testing src/sage/libs/gap/element.pyx on python 3.12 #37026

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tornaria commented Jan 7, 2024

dimpase commented Jan 7, 2024 • edited

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dimpase commented Mar 11, 2024

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