pymol crashing under Qt on Catalina

Sun Oct 13 18:10:26 UTC 2019

A few more data points. Testing builds of the pymol with the +python34,
 +python35, +python36 and +python37 on Catalina built with Xcode 11.2 beta
2 shows that none of them have issues running under the Qt interface. So
this crash seems entirely specific to the +python27 variant of pymol.
            Jack

On Sun, Oct 13, 2019 at 12:07 PM Chris Jones <jonesc at hep.phy.cam.ac.uk>
wrote:

>
>
> 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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