> On 13 Oct 2019, at 4:38 pm, 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?
Yes. Thats what I originally was suggesting when I pointed you at OpenBlAS, to
try the same with python, not that openblas itself was the problem.
> 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
>>>>>
