<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr"><br></div><div dir="ltr"><br><blockquote type="cite">On 13 Oct 2019, at 4:38 pm, Jack Howarth <howarth.at.macports@gmail.com> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><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></div></blockquote><div><br></div>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.<div><br><blockquote type="cite"><div dir="ltr"><div dir="ltr"><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">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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