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 <jon...@hep.phy.cam.ac.uk> wrote: > > > 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 >>>>> >>>>>