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 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 *Date: *Thursday, September 28, 2023 at 11:24 AM *To: *Kizziah, James *Cc: *[email protected] *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 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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 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/c7f6feadfdb866d672f317452eb97e...) 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 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 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 *Date: *Thursday, September 28, 2023 at 11:24 AM *To: *Kizziah, James *Cc: *[email protected] *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 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]