<div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">I've also been able to test the python27 variant of pymol against both py27-pyqt5 and python27 packages built with -fno-stack-check passed to clang and clang++ in Xcode 11.2 beta 2 and the crash in the Qt interface of pymol remains. The crashing thread shows the following in the crash log...</div><div dir="ltr"><br></div><div dir="ltr"><div dir="ltr">Thread 0 Crashed:: Dispatch queue: com.apple.main-thread</div><div dir="ltr">0 org.qt-project.QtCore <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x00000001081ac641 0x107ffd000 + 1766977</div><div dir="ltr">1 org.qt-project.QtCore <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x000000010808c6c3 QString::fromUtf16(unsigned short const*, int) + 53</div><div dir="ltr">2 QtCore.so <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x000000010990ff1d qpycore_PyObject_AsQString(_object*) + 24</div><div dir="ltr">3 QtCore.so <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x000000010990ff83 qpycore_qt_conf() + 91</div><div dir="ltr">4 QtCore.so <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000109802965 qpycore_post_init(_object*) + 665</div><div dir="ltr">5 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104227b36 _PyImport_LoadDynamicModule + 150</div><div dir="ltr">6 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x000000010422654d import_submodule + 285</div><div dir="ltr">7 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104225fde load_next + 270</div><div dir="ltr">8 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104224e5b PyImport_ImportModuleLevel + 843</div><div dir="ltr">9 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x00000001041fe8a9 builtin___import__ + 137</div><div dir="ltr">10 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104157f6e PyObject_CallFunction + 318</div><div dir="ltr">11 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x00000001042249c1 PyImport_Import + 353</div><div dir="ltr">12 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x00000001042227dc PyImport_ImportModule + 28</div><div dir="ltr">13 sip.so <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x000000010870512f sip_api_export_module + 82</div><div dir="ltr">14 QtGui.so <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000107a3f78e initQtGui + 225</div><div dir="ltr">15 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104227b36 _PyImport_LoadDynamicModule + 150</div><div dir="ltr">16 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x000000010422654d import_submodule + 285</div><div dir="ltr">17 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x000000010422633f ensure_fromlist + 575</div><div dir="ltr">18 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104224f0f PyImport_ImportModuleLevel + 1023</div><div dir="ltr">19 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x00000001041fe8a9 builtin___import__ + 137</div><div dir="ltr">20 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104157dc1 PyObject_Call + 97</div><div dir="ltr">21 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104207f26 PyEval_EvalFrameEx + 16198</div><div dir="ltr">22 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104203d44 PyEval_EvalCodeEx + 2004</div><div dir="ltr">23 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104203562 PyEval_EvalCode + 34</div><div dir="ltr">24 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104223756 PyImport_ExecCodeModuleEx + 230</div><div dir="ltr">25 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104226a78 load_source_module + 968</div><div dir="ltr">26 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104226df1 load_package + 321</div><div dir="ltr">27 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x000000010422654d import_submodule + 285</div><div dir="ltr">28 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104225fde load_next + 270</div><div dir="ltr">29 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104224e5b PyImport_ImportModuleLevel + 843</div><div dir="ltr">30 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x00000001041fe8a9 builtin___import__ + 137</div><div dir="ltr">31 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104157dc1 PyObject_Call + 97</div><div dir="ltr">32 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104207f26 PyEval_EvalFrameEx + 16198</div><div dir="ltr">33 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104203d44 PyEval_EvalCodeEx + 2004</div><div dir="ltr">34 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104203562 PyEval_EvalCode + 34</div><div dir="ltr">35 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104223756 PyImport_ExecCodeModuleEx + 230</div><div dir="ltr">36 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104226a78 load_source_module + 968</div><div dir="ltr">37 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x000000010422654d import_submodule + 285</div><div dir="ltr">38 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x000000010422633f ensure_fromlist + 575</div><div dir="ltr">39 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104224f0f PyImport_ImportModuleLevel + 1023</div><div dir="ltr">40 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x00000001041fe8a9 builtin___import__ + 137</div><div dir="ltr">41 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104157dc1 PyObject_Call + 97</div><div dir="ltr">42 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104207f26 PyEval_EvalFrameEx + 16198</div><div dir="ltr">43 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104203d44 PyEval_EvalCodeEx + 2004</div><div dir="ltr">44 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x000000010420e96a fast_function + 106</div><div dir="ltr">45 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104209298 PyEval_EvalFrameEx + 21176</div><div dir="ltr">46 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104203d44 PyEval_EvalCodeEx + 2004</div><div dir="ltr">47 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104203562 PyEval_EvalCode + 34</div><div dir="ltr">48 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104232131 PyRun_FileExFlags + 161</div><div dir="ltr">49 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104231c2f PyRun_SimpleFileExFlags + 751</div><div dir="ltr">50 org.python.python <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x0000000104249acf Py_Main + 3279</div><div dir="ltr">51 libdyld.dylib <span class="gmail-Apple-tab-span" style="white-space:pre"> </span>0x00007fff6539d405 start + 1</div><div><br></div><div>So I guess rebuilding QtCore.so with -fno-stack-check is the next step.</div><div> Jack </div></div></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Oct 13, 2019 at 2:10 PM Jack Howarth <<a href="mailto:howarth.at.macports@gmail.com">howarth.at.macports@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr">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.<div> Jack</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Oct 13, 2019 at 12:07 PM Chris Jones <<a href="mailto:jonesc@hep.phy.cam.ac.uk" target="_blank">jonesc@hep.phy.cam.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="auto"><div dir="ltr"><br></div><div dir="ltr"><br><blockquote type="cite">On 13 Oct 2019, at 4:57 pm, Jack Howarth <<a href="mailto:howarth.at.macports@gmail.com" target="_blank">howarth.at.macports@gmail.com</a>> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">Another data point. Rebuilding python27 with this addition to the Portfile...<div><br></div>if { ([vercmp ${os.major} 19] >= 0) && ([vercmp $xcodeversion 11.3] < 0) } {<br> if {[string match clang ${configure.compiler}]} {<br> configure.cc-append -fno-stack-check<br> }<br>}</div><div dir="ltr"><br></div><div>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?</div></div></div></div></div></blockquote><div><br></div>Maybe. Or perhaps this is something different to the stack check issue. ....<div><div><br><blockquote type="cite"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div> Jack</div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Oct 13, 2019 at 11:38 AM Jack Howarth <<a href="mailto:howarth.at.macports@gmail.com" target="_blank">howarth.at.macports@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr">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.<br><br># Workaround for test failure :-<br># > ./sblat2 < ./sblat2.dat<br># Program received signal SIGSEGV: Segmentation fault - invalid memory reference.<br># Current information is that this should be fixed in Xcode 11.2<br>if { ([vercmp ${os.major} 19] >= 0) && ([vercmp $xcodeversion 11.2] < 0) } {<br> if {[string match clang ${configure.compiler}]} {<br> configure.cc-append -fno-stack-check<br> }<br>}<br><br>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?</div><div> Jack</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Oct 13, 2019 at 11:08 AM Chris Jones <<a href="mailto:jonesc@hep.phy.cam.ac.uk" target="_blank">jonesc@hep.phy.cam.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="auto"><div dir="ltr"><br></div><div dir="ltr"><br><blockquote type="cite">On 13 Oct 2019, at 4:02 pm, Jack Howarth <<a href="mailto:howarth.at.macports@gmail.com" target="_blank">howarth.at.macports@gmail.com</a>> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><div dir="ltr"><div dir="ltr">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...<div><br></div><div><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">:info:build OPENBLAS_NUM_THREADS=1 OMP_NUM_THREADS=1 ./sblat2 < ./sblat2.dat</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">:info:build Program received signal SIGSEGV: Segmentation fault - invalid memory reference.</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">:info:build Backtrace for this error:</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">:info:build #0 0x1029863e4</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">:info:build #1 0x102985b06</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">:info:build #2 0x7fff688fab1c</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">:info:build /bin/sh: line 1: 22671 Segmentation fault: 11 OPENBLAS_NUM_THREADS=1 OMP_NUM_THREADS=1 ./sblat2 < ./sblat2.dat</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">:info:build make[1]: *** [level2] Error 139</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">:info:build make[1]: *** Waiting for unfinished jobs....</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">: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'</span></p></div></div></div></div></blockquote><div><br></div>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.<div><br><blockquote type="cite"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="font-variant-ligatures:no-common-ligatures"><br></span></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Oct 13, 2019 at 10:49 AM Jack Howarth <<a href="mailto:howarth.at.macports@gmail.com" target="_blank">howarth.at.macports@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr">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?<div> Jack</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Oct 13, 2019 at 10:13 AM Chris Jones <<a href="mailto:jonesc@hep.phy.cam.ac.uk" target="_blank">jonesc@hep.phy.cam.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><br>
<br>
> On 13 Oct 2019, at 3:11 pm, Joshua Root <<a href="mailto:jmr@macports.org" target="_blank">jmr@macports.org</a>> wrote:<br>
> <br>
> On 2019-10-14 00:59 , Jack Howarth wrote:<br>
>> <br>
>> <br>
>>> On Sun, Oct 13, 2019 at 9:49 AM Chris Jones <<a href="mailto:jonesc@hep.phy.cam.ac.uk" target="_blank">jonesc@hep.phy.cam.ac.uk</a><br>
>>> <mailto:<a href="mailto:jonesc@hep.phy.cam.ac.uk" target="_blank">jonesc@hep.phy.cam.ac.uk</a>>> wrote:<br>
>>> <br>
>>> <br>
>>> <br>
>>> On 13 Oct 2019, at 2:46 pm, Joshua Root <<a href="mailto:jmr@macports.org" target="_blank">jmr@macports.org</a><br>
>>> <mailto:<a href="mailto:jmr@macports.org" target="_blank">jmr@macports.org</a>>> wrote:<br>
>>> <br>
>>> On 2019-10-14 00:35 , Chris Jones wrote:<br>
>>>> <br>
>>>> After that, my next guess would perhaps another issue related to the<br>
>>>> stack-check issue with Xcode 11. See e.g. the fix I added for<br>
>>>> OpenBLAS<br>
>>>> <br>
>>>> <a href="https://github.com/macports/macports-ports/commit/6e78e5c9495b4dc4e7e050fae2b41dd5b9accfdd#diff-a755de84ca7f97ab071328807d829e0b" rel="noreferrer" target="_blank">https://github.com/macports/macports-ports/commit/6e78e5c9495b4dc4e7e050fae2b41dd5b9accfdd#diff-a755de84ca7f97ab071328807d829e0b</a><br>
>>> <br>
>>> I'd be wary of removing a hardening measure and leaving it at that. It<br>
>>> could be revealing a genuine stack-smashing bug.<br>
>> <br>
>> Agreed. Accordingly to Jeremy though its a Xcode bug expected to be<br>
>> fixed in 11.2. Thats why I subsequently added a version check, see e.g.<br>
> <br>
> Ah, good to know. Do you have a link to Jeremy's statement out of curiosity?<br>
<br>
No I don’t, I only know this second hand from a comment by Ken...<br>
<br>
> <br>
>> <a href="https://github.com/macports/macports-ports/blob/master/math/OpenBLAS/Portfile" rel="noreferrer" target="_blank">https://github.com/macports/macports-ports/blob/master/math/OpenBLAS/Portfile</a><br>
>> <br>
>> Line 109.<br>
>> <br>
>>> <br>
>>> - Josh<br>
>> <br>
>> <br>
>> Josh,<br>
>> Does anyone know if this is already fixed in the posted Xcode 11.2<br>
>> beta 2? If so, would rebuilding the OpenBLAS package with it be<br>
>> sufficient or aren't we sure where the offending code lies?<br>
>> Jack<br>
> <br>
> I don't know sorry.<br>
> <br>
> - Josh<br>
<br>
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