segmentation fault in pexpect for singular #30945

fchapoton · 2020-11-22T19:15:05Z

At least two patchbots, one Linux and one macOS, meet a failure
related to pexpect interface for Singular, namely:

sage -t --long --random-seed=0 src/sage/interfaces/singular.py  # Killed due to segmentation fault

The tested file also fails when run alone, but the copy-pasted test works fine.

See https://groups.google.com/d/msgid/sage-devel/54c8dd1f-5efa-4a9f-b17f-4225ef9c6c91n%40googlegroups.com.

The following test fails:

sage: try:
    alarm(0.5)
    singular._expect_expr('>')  # interrupt this
except KeyboardInterrupt:
    pass ## line 505 ##
Control-C pressed. Interrupting Singular. Please wait a few seconds...
sage: 2*a ## line 514 ##
------------------------------------------------------------------------
/home/chapoton/sage/local/lib/python3.8/site-packages/cysignals/signals.cpython-38-x86_64-linux-gnu.so(+0x7df4)[0x7f7c33af8df4]
...

For full logs, see:

CC: @dimpase @slel @sagetrac-tmonteil @kiwifb

Component: interfaces

Keywords: singular, segfault

Reviewer: Michael Orlitzky

Issue created by migration from https://trac.sagemath.org/ticket/30945

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

fchapoton · 2020-11-22T19:15:40Z

comment:1

changing alarm(0.5) to either alarm(0.5*256) or alarm(0.5/256) does not fix the issue

slel · 2020-11-23T11:23:14Z

comment:3

I have sometimes seen that failure too.

slel · 2020-11-23T11:23:14Z

Changed keywords from none to singular, segfault

fchapoton · 2020-11-23T13:19:55Z

comment:4

Je suis preneur de toute suggestion.

egourgoulhon · 2020-11-26T06:53:46Z

comment:6

Some date points, in case it might be useful: on my Ubuntu 20.04 computer, running sage -t --long src/sage/interfaces/singular.py

triggers the segfault with Sage 9.3.beta2 and 9.2
returns "All tests passed!" with Sage 9.1

fchapoton · 2020-11-26T13:10:16Z

comment:7

pexpect was last updated in #29240, included in Sage 9.2.beta11

dimpase · 2020-11-26T14:51:09Z

comment:8

Perhaps this test failure has nothing to do Singular.

singular's is the only pexpect interface on which this test is carried out. One could also have same for GAP, say:

sage: a = gap(1)
sage: _ = gap._expect.sendline('1+')  # unfinished input
sage: try:
....:     alarm(0.5)
....:     gap._expect_expr('gap>')  # interrupt this
....: except KeyboardInterrupt:
....:     pass                                                                                                                                                                                
Control-C pressed. Interrupting Gap. Please wait a few seconds...
sage: 2*a                                                                                                                                                                      
2

Could someone who has a box where this is reliably reproduced, try adding somewhere the doctest for GAP above, and see if it fails too?

fchapoton · 2020-11-26T15:43:52Z

comment:9

Bug fails with gap too, when running doctests. In the command line, provokes a very bad crash of sage.

running in the doctests:

File "src/sage/interfaces/singular.py", line 511, in sage.interfaces.singular.Singular._send_interrupt
Failed example:
    2*a
Exception raised:
    Traceback (most recent call last):
      File "/home/chapoton/sage/local/lib/python3.8/site-packages/sage/interfaces/gap.py", line 763, in _eval_line
        raise RuntimeError("%s produced error output\n%s\n   executing %s"%(self, error,line))
    RuntimeError: Gap produced error output
    Error, no method found! For debugging hints type ?Recovery from NoMethodFound
    Error, no 1st choice method found for `*' on 2 arguments

       executing \$sage3:=\$sage2 * \$sage1;;

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/home/chapoton/sage/local/lib/python3.8/site-packages/sage/interfaces/expect.py", line 1469, in __init__
        self._name = parent._create(value, name=name)
      File "/home/chapoton/sage/local/lib/python3.8/site-packages/sage/interfaces/interface.py", line 501, in _create
        self.set(name, value)
      File "/home/chapoton/sage/local/lib/python3.8/site-packages/sage/interfaces/gap.py", line 1422, in set
        self._eval_line(cmd, allow_use_file=True)
      File "/home/chapoton/sage/local/lib/python3.8/site-packages/sage/interfaces/gap.py", line 797, in _eval_line
        raise RuntimeError(exc)
    RuntimeError: Gap produced error output
    Error, no method found! For debugging hints type ?Recovery from NoMethodFound
    Error, no 1st choice method found for `*' on 2 arguments

       executing \$sage3:=\$sage2 * \$sage1;;
etc

in the console, one gets

sage: a                                                                                                                                     
(invalid Gap object -- The gap session in which this object was defined is no longer running.)
sage: 2*a
big mess as above

dimpase · 2020-11-26T17:01:16Z

comment:10

OK, actually I should have checked, for me such GAP pexpect test in Sage console also results in
(invalid Gap object -- The gap session in which this object was defined is no longer running.)

This makes me wonder why it's important to have such a test in Singular. Only Singular has a custom _send_interrupt; GAP
uses the default one, below, and you see it sends _quit_string; it kills the GAP session if it lands in the main loop, rather than in the break loop (doing quit; in GAP's break loop brings you to the main loop, so in this case it's OK).

    def _send_interrupt(self):
        """
        Send an interrupt to the application.  This is used internally
        by :meth:`interrupt`.

        First CTRL-C to stop the current command, then quit.
        """
        self._expect.sendline(chr(3))
        self._expect.sendline(self._quit_string())

Singular custom one was added along with the test in question, and no _quit_string() is sent (which is quit; for GAP, as
you can see by looking at the value of gap._quit_string()).
For Singular one has the following in _send_interrupt():

        sleep(0.1)

        E = self._expect
        E.sendline(chr(3))
        for i in range(5):
            try:
                E.expect_upto(self._prompt, timeout=1.0)
                return
            except Exception:
                pass
            E.sendline(";")

We can try just to erase Singular's _send_interrupt(), set its _quit_string() to proper value (it's quit rather than quit;,
as it should be) and be done with.

fchapoton · 2020-11-26T19:20:36Z

comment:11

here is a tentative, just removing the _send_interrupt method

New commits:

`95e1efd`	`remove custom _send_interrupt in singular pexpect interface`

fchapoton · 2020-11-26T19:20:36Z

Branch: public/singular_pexpect

fchapoton · 2020-11-26T19:20:36Z

Commit: 95e1efd

fchapoton · 2020-11-27T07:58:48Z

comment:12

Did you mean that exit is the singular quit command ??

sagetrac-git · 2020-11-28T07:36:21Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`85f65bf`	`remove custom _send_interrupt in singular pexpect interface`

sagetrac-git · 2020-11-28T07:36:21Z

Changed commit from 95e1efd to 85f65bf

fchapoton · 2020-11-28T16:53:22Z

comment:14

hmm, this seems to have a side effect, see the latest patchbot report

dimpase · 2020-11-29T08:49:09Z

comment:15

the side effect could be that hitting ^C during a computation involving a session with pexpect Singular is no longer only (probably) interrupted, but the whole session is killed.

I am not sure it is safe do interrupt Singular - note the warning at the end

^C// ** Interrupt at cmd:`load` in line:';return();'
abort after this command(a), abort immediately(r), print backtrace(b), continue(c) or quit Singular(q) ?// ** Interrupt at cmd:`load` in line:';return();'
abort after this command(a), abort immediately(r), print backtrace(b), continue(c) or quit Singular(q) ?r
** Warning: Singular should be restarted as soon as possible **

in a console Singular session.

embray · 2021-03-04T17:52:23Z

comment:16

I encountered this in #31404 as well. I believe I have isolated it to a possible bug in cysignals: sagemath/cysignals#126

embray · 2021-03-04T17:54:27Z

comment:17

I am able to reproduce this pretty reliably on the current develop branch with

./sage -t --file-iterations=2 -T 0 --verbose src/sage/interfaces/singular.py

embray · 2021-03-05T17:26:51Z

comment:18

This now has a possible fix at sagemath/cysignals#127

The segfault is not caused by Singular (if it were this would crash pexpect, not cause a segfault in Sage). It's caused by cysignals itself.

mkoeppe · 2021-03-16T17:21:45Z

Dependencies: #31474

slel · 2021-04-01T08:09:31Z

Changed commit from 85f65bf to none

slel · 2021-04-01T08:09:31Z

Changed branch from public/singular_pexpect to none

slel · 2021-04-01T08:09:31Z

comment:21

Likely solved by cysignals 1.10.3 upgrade at #31474,
merged in Sage 9.3.rc0, released 2021-03-24.

If we get no more reports on sage-release in a while,
this ticket should be closed.

Can the branch public/singular_pexpect improving
interfaces/singular.py go to a new ticket?

slel · 2021-05-22T17:11:45Z

comment:22

Branch improving the pexpect interface to Singular now at #31846.

slel · 2021-05-22T17:11:45Z

Changed dependencies from #31474 to none

orlitzky · 2021-10-04T23:33:46Z

Reviewer: Michael Orlitzky

orlitzky · 2021-10-04T23:33:46Z

comment:23

Addressed in #31474 and #31846.

This essentially reverts 85f65bf and a10d19d from trac sagemath#31846. It turns out this was originaly written for sagemath#30945, but that issue was fixed by upgrading cysignals. Singular really needs a custom `_send_interrupt()` method, because the default one will quit singular. Moreover, this handles two quirks of singular: - a small delay before sending `chr(3)` works around a bug in singular. - sometimes one needs to send `;` a few times after interrupt to get back a prompt. The original author of the custom `_send_interrupt()` is Jeroen Demeyer in commit 17d23e9 (trac sagemath#10476). I changed the timeout for a smaller one, and rewrote the doctest to call `interrupt()` explicitly instead of using `alarm()` which introduces more noise.

fchapoton added this to the sage-9.3 milestone Nov 22, 2020

fchapoton added c: interfaces labels Nov 22, 2020

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slel removed this from the sage-9.3 milestone Apr 1, 2021

slel added the s: needs review label Apr 1, 2021

orlitzky added s: positive review and removed s: needs review labels Oct 4, 2021

mkoeppe removed the s: positive review label Oct 4, 2021

mkoeppe closed this as completed Oct 4, 2021

embray mentioned this issue Mar 18, 2021

Upgrade cysignals to 1.10.3 #31474

Closed

slel mentioned this issue Dec 15, 2022

Improve pexpect interface to Singular #31846

Closed

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segmentation fault in pexpect for singular #30945

segmentation fault in pexpect for singular #30945

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