pymol crashing under Qt on Catalina

[Jack Howarth]

Another data point. Rebuilding python27 with this addition to the
Portfile...

if { ([vercmp ${os.major} 19] >= 0) && ([vercmp $xcodeversion 11.3] < 0) } {
    if {[string match clang ${configure.compiler}]} {
        configure.cc-append -fno-stack-check
    }
}

successfully passes -fno-stack-check to the build but the resulting
python2.7 doesn't suppress the pymol crashes with the QT interface. Maybe
the problem code is in py27-pyqt5?
          Jack

On Sun, Oct 13, 2019 at 11:38 AM Jack Howarth <howarth.at.macports at gmail.com>
wrote:

> It would seem that this failure under Xcode 11.2 beta 2 is due to the
> current patch dropping -fno-stack-check for Xcode 11.2 in anticipation of a
> fix.
>
> # Workaround for test failure :-
> # > ./sblat2 < ./sblat2.dat
> # Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
> # Current information is that this should be fixed in Xcode 11.2
> if { ([vercmp ${os.major} 19] >= 0) && ([vercmp $xcodeversion 11.2] < 0) }
> {
>     if {[string match clang ${configure.compiler}]} {
>         configure.cc-append -fno-stack-check
>     }
> }
>
> So this would seem to rule out OpenBLAS as the source of the pymol crashes
> under python2.7 with the QT interface as, under Xcode 11.1, OpenBLAS
> already built with -fno-stack-check. Perhaps the problem is in python2.7
> when -fstack-check is used?
>            Jack
>
> On Sun, Oct 13, 2019 at 11:08 AM Chris Jones <jonesc at hep.phy.cam.ac.uk>
> wrote:
>
>>
>>
>> On 13 Oct 2019, at 4:02 pm, Jack Howarth <howarth.at.macports at gmail.com>
>> wrote:
>>
>> 
>> Well this is interesting. After installing Xcode 11 Beta 2, Command Line
>> tools and setting the Xcode-select path to the Xcode-beta.app, I find that
>> 'sudo port build OpenBLAS' now fails with...
>>
>> :info:build OPENBLAS_NUM_THREADS=1 OMP_NUM_THREADS=1 ./sblat2 <
>> ./sblat2.dat
>>
>> :info:build Program received signal SIGSEGV: Segmentation fault - invalid
>> memory reference.
>>
>> :info:build Backtrace for this error:
>>
>> :info:build #0  0x1029863e4
>>
>> :info:build #1  0x102985b06
>>
>> :info:build #2  0x7fff688fab1c
>>
>> :info:build /bin/sh: line 1: 22671 Segmentation fault: 11
>> OPENBLAS_NUM_THREADS=1 OMP_NUM_THREADS=1 ./sblat2 < ./sblat2.dat
>>
>> :info:build make[1]: *** [level2] Error 139
>>
>> :info:build make[1]: *** Waiting for unfinished jobs....
>>
>> :info:build make[1]: Leaving directory
>> `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_OpenBLAS/OpenBLAS/work/xianyi-OpenBLAS-5f36f18/test'
>>
>>
>> That just means the stack check issue is in fact not addressed in 11.2,
>> or there is in fact a real issue with the openblas source.
>>
>>
>>
>> On Sun, Oct 13, 2019 at 10:49 AM Jack Howarth <
>> howarth.at.macports at gmail.com> wrote:
>>
>>> Okay, I have Xcode 11.2 beta 2 and the associated Command Line Tools
>>> installed. Is there some permutation of options to pass to 'port' that will
>>> rebuild and reinstall a currently installed MacPorts package without
>>> uninstalling it first?
>>>             Jack
>>>
>>> On Sun, Oct 13, 2019 at 10:13 AM Chris Jones <jonesc at hep.phy.cam.ac.uk>
>>> wrote:
>>>
>>>>
>>>>
>>>> > On 13 Oct 2019, at 3:11 pm, Joshua Root <jmr at macports.org> wrote:
>>>> >
>>>> > On 2019-10-14 00:59 , Jack Howarth wrote:
>>>> >>
>>>> >>
>>>> >>> On Sun, Oct 13, 2019 at 9:49 AM Chris Jones <
>>>> jonesc at hep.phy.cam.ac.uk
>>>> >>> <mailto:jonesc at hep.phy.cam.ac.uk>> wrote:
>>>> >>>
>>>> >>>
>>>> >>>
>>>> >>>    On 13 Oct 2019, at 2:46 pm, Joshua Root <jmr at macports.org
>>>> >>>    <mailto:jmr at macports.org>> wrote:
>>>> >>>
>>>> >>>    On 2019-10-14 00:35 , Chris Jones wrote:
>>>> >>>>
>>>> >>>>    After that, my next guess would perhaps another issue related
>>>> to the
>>>> >>>>    stack-check issue with Xcode 11. See e.g. the fix I added for
>>>> >>>>    OpenBLAS
>>>> >>>>
>>>> >>>>
>>>> https://github.com/macports/macports-ports/commit/6e78e5c9495b4dc4e7e050fae2b41dd5b9accfdd#diff-a755de84ca7f97ab071328807d829e0b
>>>> >>>
>>>> >>>    I'd be wary of removing a hardening measure and leaving it at
>>>> that. It
>>>> >>>    could be revealing a genuine stack-smashing bug.
>>>> >>
>>>> >>    Agreed. Accordingly to Jeremy though its a Xcode bug expected to
>>>> be
>>>> >>    fixed in 11.2. Thats why I subsequently added a version check,
>>>> see e.g.
>>>> >
>>>> > Ah, good to know. Do you have a link to Jeremy's statement out of
>>>> curiosity?
>>>>
>>>> No I don’t, I only know this second hand from a comment by Ken...
>>>>
>>>> >
>>>> >>
>>>> https://github.com/macports/macports-ports/blob/master/math/OpenBLAS/Portfile
>>>> >>
>>>> >>    Line 109.
>>>> >>
>>>> >>>
>>>> >>>    - Josh
>>>> >>
>>>> >>
>>>> >> Josh,
>>>> >>      Does anyone know if this is already fixed in the posted Xcode
>>>> 11.2
>>>> >> beta 2? If so, would rebuilding the OpenBLAS package with it be
>>>> >> sufficient or aren't we sure where the offending code lies?
>>>> >>             Jack
>>>> >
>>>> > I don't know sorry.
>>>> >
>>>> > - Josh
>>>>
>>>>
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