pymol crashing under Qt on Catalina

[Chris Jones]

> On 13 Oct 2019, at 4:57 pm, Jack Howarth <howarth.at.macports at gmail.com> wrote:
> 
> 
> 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?

Maybe.  Or perhaps this is something different to the stack check issue. ....

>           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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