> On 13 Oct 2019, at 4:57 pm, Jack Howarth <howarth.at.macpo...@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.macpo...@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 <jon...@hep.phy.cam.ac.uk>
>>> wrote:
>>>
>>>
>>>>> On 13 Oct 2019, at 4:02 pm, Jack Howarth <howarth.at.macpo...@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.macpo...@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 <jon...@hep.phy.cam.ac.uk>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>> > On 13 Oct 2019, at 3:11 pm, Joshua Root <j...@macports.org> wrote:
>>>>>> >
>>>>>> > On 2019-10-14 00:59 , Jack Howarth wrote:
>>>>>> >>
>>>>>> >>
>>>>>> >>> On Sun, Oct 13, 2019 at 9:49 AM Chris Jones <jon...@hep.phy.cam.ac.uk
>>>>>> >>> <mailto:jon...@hep.phy.cam.ac.uk>> wrote:
>>>>>> >>>
>>>>>> >>>
>>>>>> >>>
>>>>>> >>> On 13 Oct 2019, at 2:46 pm, Joshua Root <j...@macports.org
>>>>>> >>> <mailto:j...@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
>>>>>>
