[phenixbb] Phenix installation on macOS 14 Sonoma

[Billy Poon]

Hi everyone,

The Phenix GUI should now work on macOS Sonoma with 1.21rc1-5109. There is
a separate tarball, sonoma_fix.tar.gz, that will fix earlier versions of
Phenix. Download the fix here (
https://phenix-online.org/download/sonoma_fix.tar.gz). You may need to run
"xattr -c" to convince macOS that the files are safe. Then run the
following steps for Phenix 1.20.1-4487 installed in /Applications.

1) tar -xf sonoma_fix.tar.gz
2) cd sonoma_fix
3) sudo ./fix_wxpython.sh /Applications/phenix-1.20.1-4487

You will see log output about removing the old version of wxPython and
installing the updated version. You will need "sudo" to modify files in
/Applications. If you have a Phenix installation somewhere else, you can
remove the "sudo" in step 3 and replace "/Applications/phenix-1.20.1-4487"
with your installation directory (e.g. ${HOME}/phenix-1.20.1-4487). The
"phenix-<version>-<build>" directory name is required.

Let us know if there are more GUI issues on macOS Sonoma. Thanks!

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Fax: (510) 486-5909
Web: https://phenix-online.org


On Tue, Oct 3, 2023 at 5:20 PM Billy Poon <BKPoon at lbl.gov> wrote:

> Hi everyone,
>
> I have a working fix (see attached screenshot). I'm doing some more
> testing and then coming up with instructions (or an installer) for updating
> the 1.20 release. The 1.21 release candidates will be updated to work with
> Sonoma. Essentially, i backported this commit (
> https://github.com/wxWidgets/wxWidgets/commit/c7f6feadfdb866d672f317452eb97e125c308231)
> to the wxWidgets in wxPython 3.0. The fix is encapsulated in an updated
> wxPython conda package.
>
> --
> Billy K. Poon
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Fax: (510) 486-5909
> Web: https://phenix-online.org
>
>
> On Sat, Sep 30, 2023 at 6:01 AM Billy Poon <BKPoon at lbl.gov> wrote:
>
>> I have narrowed down the segmentation fault to some code in wxWidgets
>> (from wxPython). It's a similar problem to this (
>> https://github.com/wxWidgets/wxWidgets/issues/19005)  I'm testing some
>> fixes and I think I can provide a way to update the wxPython package in
>> 1.20. The 1.21 release candidates will be updated to have the fixes.
>>
>> --
>> Billy K. Poon
>> Research Scientist, Molecular Biophysics and Integrated Bioimaging
>> Lawrence Berkeley National Laboratory
>> 1 Cyclotron Road, M/S 33R0345
>> Berkeley, CA 94720
>> Fax: (510) 486-5909
>> Web: https://phenix-online.org
>>
>>
>> On Thu, Sep 28, 2023 at 9:29 AM Kizziah, James <kizziah4 at uab.edu> wrote:
>>
>>> Hi Billy,
>>>
>>>
>>>
>>> Thanks for your help. I’m using the v1.20.1-4487 graphical installer
>>> currently listed for macOS on the main download page:
>>> https://phenix-online.org/download/phenix/release/
>>>
>>>
>>>
>>> Best,
>>>
>>> James
>>>
>>>
>>>
>>>
>>>
>>> *From: *Billy Poon <BKPoon at lbl.gov>
>>> *Date: *Thursday, September 28, 2023 at 11:24 AM
>>> *To: *Kizziah, James <kizziah4 at uab.edu>
>>> *Cc: *phenixbb at phenix-online.org <phenixbb at phenix-online.org>
>>> *Subject: *Re: [phenixbb] Phenix installation on macOS 14 Sonoma
>>>
>>> Hi James,
>>>
>>>
>>>
>>> Which installer are you using (version and graphical or command-line)? I
>>> have not updated my laptop to Sonoma yet, so I am not able to test.
>>>
>>>
>>>
>>> --
>>>
>>> Billy K. Poon
>>>
>>> Research Scientist, Molecular Biophysics and Integrated Bioimaging
>>>
>>> Lawrence Berkeley National Laboratory
>>>
>>> 1 Cyclotron Road, M/S 33R0345
>>>
>>> Berkeley, CA 94720
>>>
>>> Fax: (510) 486-5909
>>>
>>> Web: https://phenix-online.org
>>>
>>>
>>>
>>>
>>>
>>> On Thu, Sep 28, 2023 at 8:54 AM Kizziah, James <kizziah4 at uab.edu> wrote:
>>>
>>> Hi all,
>>>
>>>
>>>
>>> I am having trouble getting Phenix to open on a new mac.
>>>
>>> I downloaded the latest official release of the point-and-click
>>> installer, ran xattr -c on it, and installed without issue. Initially, I
>>> can create the first project directory (or recreate it if I remove the
>>> .phenix directory), but then I get a notice that another instance of Phenix
>>> is running with the associated PID. If I continue anyway, python quits
>>> unexpectedly, and if Phenix is opened in the command line, this reply is
>>> given:
>>>
>>> “python[9678:116756] It's not legal to call -layoutSubtreeIfNeeded on a
>>> view which is already being laid out.  If you are implementing the
>>> view's -layout method, you can call -[super layout] instead. Break on void
>>> _NSDetectedLayoutRecursion(void) to debug.  This will be logged only
>>> once.  This may break in the future.
>>>
>>>
>>>
>>> [3]    segmentation fault  phenix”
>>>
>>>
>>>
>>> However, the PID for this supposed other instance doesn’t exist. This
>>> occurs every time Phenix is run from Applications or in the command line,
>>> even after restarting the laptop (without resuming programs) or deleting
>>> and reinstalling Phenix.
>>>
>>>
>>>
>>> Any ideas how to solve this problem?
>>>
>>>
>>>
>>> Thanks,
>>>
>>> James
>>>
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
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>>>
>>>
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