ffmpeg on OSX 10.11: dyld: Symbol not found: _clock_gettime

[eddimpri@…]

Dear ChimeraX team,

I’ve been following the great tutorial of Tom Goddard on youtube from sbgrid. Everything worked smoothly until I tried to make movies of the morphs. Movie record works ok but when it goes to movie encode ChimeraX reports an error in the log (please see attachment). I thought was my “old version” form october so I dowloaded and installed the most recent one (version 0.1 (2017-12-20)) but the error still pops out both from command line and from the GUI if I click on the camera button. 

My ChimeraX app is located in /Applications/ChimeraX.app 

I am using  Mac OS 10.11.6 x86_64 with Python version is: 2.7.10 . Please find also attached the specs of my laptop. 

Could you please help me to fix this? 

Many thanks in advance,

Edoardo 




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Edoardo D'Imprima
PhD Student
Max Planck Institute of Biophysics
Structural Biology Department
Max-von-Laue Straße 3
60438 Frankfurt am Main
Germany

Tel: +49 (0) 69 6303 3015

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chimerax_error.rtf​

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[Eric Pettersen]

The issue is that the build machine is clemens (running 10.12) and when ffmpeg configures itself it finds the clock_gettime() system call, which does not exist on 10.11. Therefore, ffmpeg fails to run on 10.11 systems.

[eddimpri@…]

Thank you for the quick reply, so the easiest fix would be to upgrade my operative system?

 One quick thing I’ve done yesterday is to download ffmpeg compiled for OSX 10.11 and soft link it to ffmpeg brought by ChimeraX and that solved the problem. however I still suffer of the problem already encountered before when generating images (issue: #890: save image/supersample possible bug?). The movie is off-center. I solved that by using the trick suggest to my by Tom (width 2000 for images; size xxx for movies) however, this generates very large movies. 

Is it currently possible to just save the raw frames so that I can interpolate them in ffmpeg aside?

Best,

Edoardo
---------------------------------------------------
Edoardo D'Imprima
PhD Student
Max Planck Institute of Biophysics
Structural Biology Department
Max-von-Laue Straße 3
60438 Frankfurt am Main
Germany

Tel: +49 (0) 69 6303 3015

[goddard@…]

Didn't realize you are running macOS from two years ago.  The graphics driver is part of macOS so the only way the image save problem will be fixed is my moving to a newer macOS version where Apple has fixed it.  But the chances are not especially good that Apple will ever fix it unless it impairs some major application.

You don't have to use "width 2000" when saving images to avoid the problem, you can use "width 500" or however may pixels wide you want the image to be.  The value does not matter, any value you use will cause image save to an off-screen framebuffer which does not exhibit the bug.

Upgrading macOS would fix the ffmpeg problem.

The movie command has options to let you just save the image frames so you can create a movie from them on your own using ffmpeg or iMovie or whatever tool --  see the ChimeraX movie command documentation, in particular the "movie record" directory option, and the movie encode resetMode option.

[eddimpri@…]

Dear ChimeraX team,

my apologies for the very late reply. I know that the width number per-se does not matter, I only wanted to report how I worked around the issue that I also have when saving images. Thanks for your feedback about the movie encode option, I must have over-read it!

Best,

Edoardo
---------------------------------------------------
Edoardo D'Imprima
PhD Student
Max Planck Institute of Biophysics
Structural Biology Department
Max-von-Laue Straße 3
60438 Frankfurt am Main
Germany

Tel: +49 (0) 69 6303 3015

[Conrad Huang]

Fixing this requires some effort because we would have to work around an macOS problem that Apple has so far ignored. With the impending release of macOS 10.14 (Mojave), we will only (officially) support 10.12 and newer (3 releases back), where this problem does not occur.

That said, the workaround is to find an old copy of ffmpeg, preferably built for MacOS X 10.8 or older and copy it into the ChimeraX.app Contents/bin folder. (We chose not to do this for the ChimeraX distribution because we try always to use the most current versions of software that we can.)