PARI/GP segfault with XCode 11.4 on local-homebrew-macos-standard

[mkoeppe]

First reported in https://groups.google.com/d/msg/sage-release/kU5M1QVuQQY/Zu10Q-CKAwAJ

PARI fails its testsuite with "bug in PARI/GP (Segmentation Fault), please report."

Consequently, also many sagelib doctest failures of this kind:

File "src/sage/arith/misc.py", line 5801, in sage.arith.misc.dedekind_sum
Failed example:
    dedekind_sum(3^54 - 1, 2^93 + 1, algorithm='pari')
Exception raised:
    Traceback (most recent call last):
      File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/.tox/local-homebrew-macos-standard-nokegonly-python3_xcode/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/.tox/local-homebrew-macos-standard-nokegonly-python3_xcode/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.arith.misc.dedekind_sum[6]>", line 1, in <module>
        dedekind_sum(Integer(3)**Integer(54) - Integer(1), Integer(2)**Integer(93) + Integer(1), algorithm='pari')
      File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/.tox/local-homebrew-macos-standard-nokegonly-python3_xcode/local/lib/python3.7/site-packages/sage/arith/misc.py", line 5839, in dedekind_sum
        x = sage.interfaces.gp.gp('sumdedekind(%s,%s)' % (p, q))
      File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/.tox/local-homebrew-macos-standard-nokegonly-python3_xcode/local/lib/python3.7/site-packages/sage/interfaces/interface.py", line 297, in __call__
        return cls(self, x, name=name)
      File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/.tox/local-homebrew-macos-standard-nokegonly-python3_xcode/local/lib/python3.7/site-packages/sage/interfaces/expect.py", line 1471, in __init__
        self._name = parent._create(value, name=name)
      File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/.tox/local-homebrew-macos-standard-nokegonly-python3_xcode/local/lib/python3.7/site-packages/sage/interfaces/interface.py", line 502, in _create
        self.set(name, value)
      File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/.tox/local-homebrew-macos-standard-nokegonly-python3_xcode/local/lib/python3.7/site-packages/sage/interfaces/gp.py", line 561, in set
        raise TypeError("Error executing code in GP:\nCODE:\n\t%s\nPARI/GP ERROR:\n%s"%(cmd, out))
    TypeError: Error executing code in GP:
    CODE:
    	sage[2]=sumdedekind(58149737003040059690390168,9903520314283042199192993793);
    PARI/GP ERROR:
      ***   bug in PARI/GP (Segmentation Fault), please report.
**********************************************************************

To reproduce (with #29417):

• tox -e local-homebrew-macos-standard-nokegonly-python3_xcode -- SAGE_CHECK=yes pari
• tox -e local-homebrew-macos-standard -- SAGE_CHECK=yes pari

CC: @jhpalmieri

Component: porting

Author: Matthias Koeppe

Branch/Commit: ef6ecf4

Reviewer: John Palmieri

Issue created by migration from https://trac.sagemath.org/ticket/29451

[mkoeppe]

Description changed:

--- 
+++ 
@@ -1,6 +1,8 @@
 First reported in https://groups.google.com/d/msg/sage-release/kU5M1QVuQQY/Zu10Q-CKAwAJ
 
-Many doctest failures of this kind:
+PARI fails its testsuite with "bug in PARI/GP (Segmentation Fault), please report."
+
+Consequently, also many sagelib doctest failures of this kind:
 
 ```
 File "src/sage/arith/misc.py", line 5801, in sage.arith.misc.dedekind_sum

[jhpalmieri]

comment:2

This appears to be specific to Xcode 11.4. I just installed 9.1.beta9 on a machine with Xcode 11.3.1 and (for example) the file schemes/elliptic_curves/ell_rational_field.py passed tests. I upgraded that machine to use Xcode 11.4, rebuilt Sage, and then I hit these segfaults.

The new Xcode also leads to this in the top-level config.log:

clang: error: unable to execute command: Broken pipe: 13
clang: error: clang frontend command failed due to signal (use -v to see invocation)
Apple clang version 11.0.3 (clang-1103.0.32.29)
Target: x86_64-apple-darwin19.3.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
clang: note: diagnostic msg: PLEASE submit a bug report to http://developer.apple.com/bugreporter/ and include the crash backtrace, preprocessed source, and associated run script.
clang: note: diagnostic msg: 
********************

PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
clang: note: diagnostic msg: /var/folders/cp/n8wtqs490tq5psknff1hv9qr0000gn/T/conftest-d428b4.cpp
clang: note: diagnostic msg: /var/folders/cp/n8wtqs490tq5psknff1hv9qr0000gn/T/conftest-d428b4.sh
clang: note: diagnostic msg: Crash backtrace is located in
clang: note: diagnostic msg: /Users/palmieri/Library/Logs/DiagnosticReports/clang_<YYYY-MM-DD-HHMMSS>_<hostname>.crash
clang: note: diagnostic msg: (choose the .crash file that corresponds to your crash)
clang: note: diagnostic msg: 

This message did not appear in 11.3.1. Is there a connection?

[mkoeppe]

comment:3

I also started to see the segfaults only after updating XCode.

[mkoeppe]

Description changed:

--- 
+++ 
@@ -34,5 +34,7 @@
 **********************************************************************
 ```
 
-To reproduce (with #29417): `tox -e local-homebrew-macos-standard-nokegonly-python3_xcode -- ptest`
+To reproduce (with #29417): 
+- `tox -e local-homebrew-macos-standard-nokegonly-python3_xcode -- SAGE_CHECK=yes pari`
+- `tox -e local-homebrew-macos-standard -- SAGE_CHECK=yes pari`
 

[jhpalmieri]

comment:6

I also don't see this if I use "--with-system-python3=no". Does that make any sense?

[mkoeppe]

comment:7

Replying to @jhpalmieri:

I also don't see this if I use "--with-system-python3=no".

Yes, I can confirm this. This configuration is now local-homebrew-macos-standard-python3_spkg in #29417.

[mkoeppe]

comment:8

MACOSX_DEPLOYMENT_TARGET is the problem. This is set in sage-env depending on whether we use system python3 or not. I'll investigate more.

[mkoeppe]

Branch: u/mkoeppe/pari_gp_segfault_with_xcode_11_4_on_local_homebrew_macos_standard

[mkoeppe]

comment:10

Related previous ticket:

• OSX Yosemite libtool version detection #17204: OSX Yosemite libtool version detection

---

New commits:

79cd878

build/pkgs/pari/spkg-install.in: Use fake MACOSX_DEPLOYMENT_TARGET

[mkoeppe]

Commit: 79cd878

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

ef6ecf4

fixup

[sagetrac-git]

Changed commit from 79cd878 to ef6ecf4

[mkoeppe]

Author: Matthias Koeppe

[jhpalmieri]

Changed author from Matthias Koeppe to none

[jhpalmieri]

comment:13

See also #18272.