pymol crashing under Qt on Catalina

[Jack Howarth]

On Sun, Oct 13, 2019 at 10:04 AM Chris Jones <jonesc at hep.phy.cam.ac.uk>
wrote:

>
>
> On 13 Oct 2019, at 2:56 pm, Jack Howarth <howarth.at.macports at gmail.com>
> wrote:
>
> 
> Chris,
>      This is a fresh build of all the MacPorts packages from last night's
> port files using Xcode 11.1.
>               Jack
>
>
> Ok, then next I would try either using the Xcode 11.2 beta, or patch
> python with the stack-check fix.
>
> P.s. side comment, but perhaps its also time to propose making python37
> the default variant for pymol ? We should anyway be looking to start
> weeding out 2.x usage, at least as the default version where 3.x
> alternatives are available.
>

At this point I'm pretty much agnostic on switching the default python
variant for pymol. The only reason that I left it at python2.7 is that the
pdb2pqr program used internally by the APBS plugin. The problem is that
pdb2pqr is not python3 compatible and the way the plugin calls it when
pymol is running under python3 results in it running against that python
instead of python2.7.

https://github.com/Electrostatics/apbs-pdb2pqr/pull/516
https://github.com/Electrostatics/apbs-pdb2pqr/pull/440

It seems one of the issues that have stymied progress there is that scons
isn't python 3 compatible.

https://github.com/SCons/scons/issues/3299

Under python 3, the APBS plugin is still usable but users have to manually
create a pdb to a pqr file using pdb2pdb on the command line or using a web
server.
                 Jack

>
>
> On Sun, Oct 13, 2019 at 9:31 AM Chris Jones <jonesc at hep.phy.cam.ac.uk>
> wrote:
>
>> Hi,
>>
>> What Xcode version are you using ? If 11.0, first try updating to 11.1
>> and then rebuild the various ports (including python).
>>
>> Chris
>>
>> > On 13 Oct 2019, at 1:52 pm, Jack Howarth <howarth.at.macports at gmail.com>
>> wrote:
>> >
>> > 
>> >       The +python37 variant of pymol runs fine under its Qt interface
>> on Catalina, however the stock +python27 variant crashes Qt as follows...
>> >
>> > Process:               Python [46230]
>> > Path:
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
>> > Identifier:            Python
>> > Version:               2.7.16 (2.7.16)
>> > Code Type:             X86-64 (Native)
>> > Parent Process:        zsh [907]
>> > Responsible:           Terminal [342]
>> > User ID:               501
>> >
>> > Date/Time:             2019-10-13 08:42:10.315 -0400
>> > OS Version:            Mac OS X 10.15 (19A583)
>> > Report Version:        12
>> > Anonymous UUID:        4A09CC71-7509-3F2D-8C77-BB546FDAFB8D
>> >
>> > Sleep/Wake UUID:       A3189974-D375-47A3-B65F-45F7E7DE5271
>> >
>> > Time Awake Since Boot: 16000 seconds
>> > Time Since Wake:       12000 seconds
>> >
>> > System Integrity Protection: disabled
>> >
>> > Crashed Thread:        0  Dispatch queue: com.apple.main-thread
>> >
>> > Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
>> > Exception Codes:       KERN_INVALID_ADDRESS at 0xffffffffffffffff
>> > Exception Note:        EXC_CORPSE_NOTIFY
>> >
>> > Termination Signal:    Segmentation fault: 11
>> > Termination Reason:    Namespace SIGNAL, Code 0xb
>> > Terminating Process:   exc handler [46230]
>> >
>> > The entire crash report is attached. Any idea what is going on here as
>> it seems to be specific to python2.7?
>> >           Jack
>> >
>> >
>> > <pymol_python27_crash.log>
>>
>>
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