Opened 2 years ago

Closed 23 months ago

Last modified 23 months ago

#10218 closed defect (fixed)

ffmpeg failure

Reported by: david.chalmers@… Owned by: Greg Couch
Priority: normal Milestone: 1.7
Component: Input/Output Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.14.21-150500.53-default-x86_64-with-glibc2.35
ChimeraX Version: 1.7.dev202308212127 (2023-08-21 21:27:52 UTC)
Description
Installed the flatpak version of chimerax on opensuse 15.5
The installed version seems to run OK, but the 'spin movie' function fails. It does not seem to write the image frames to /usr/tmp

Thanks

David

Log:
Startup Messages  
---  
warning | QCoreApplication::postEvent: Unexpected null receiver  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7.dev202308212127 (2023-08-21)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /vcp1/people/david/step2_orient_contacts_1.pdb

Summary of feedback from opening
/vcp1/people/david/step2_orient_contacts_1.pdb  
---  
warning | Duplicate atom serial number found: 2869  
  
Chain information for step2_orient_contacts_1.pdb #1  
---  
Chain | Description  
? | No description available  
  

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> movie record

> turn y 2 180

> wait 180

> movie encode /vcp1/people/david/Desktop/movie1.mp4

/usr/bin/ffmpeg -r 25 -i /tmp/chimovie_Jjjo-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 /vcp1/people/david/Desktop/movie1.mp4  
stdout:  
  
stderr:  
ffmpeg version 5.0.3 Copyright (c) 2000-2022 the FFmpeg developers  
built with gcc 12.2.0 (GCC)  
configuration: --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu
--optflags='-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS
-fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-
unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer
' --extra-ldflags='-Wl,-z,relro,-z,now -Wl,--as-needed ' --disable-stripping
--disable-doc --disable-static --enable-shared --disable-everything --enable-
ffplay --enable-ffprobe --enable-gnutls --enable-libaom --enable-libdav1d
--enable-libfdk-aac --enable-libmp3lame --enable-libfontconfig --enable-
libfreetype --enable-libopus --enable-libpulse --enable-libspeex --enable-
libtheora --enable-libvorbis --enable-libvpx --enable-libwebp --enable-openal
--enable-opengl --enable-sdl2 --enable-vulkan --enable-zlib --enable-libv4l2
--enable-libxcb --enable-vdpau --enable-vaapi --enable-pthreads --enable-
encoder='ac3,alac,flac,libfdk_aac,g723_1,mp2,libmp3lame,libopus,libspeex,pcm_alaw,pcm_mulaw,pcm_f32le,pcm_s16be,pcm_s24be,pcm_s16le,pcm_s24le,pcm_s32le,pcm_u8,tta,libvorbis,wavpack,'
--enable-
encoder='ass,ffv1,libaom_av1,libvpx_vp8,libvpx_vp9,mjpeg_vaapi,rawvideo,theora,vp8_vaapi,libopenh264'
--enable-
decoder='adpcm_g722,alac,flac,g723_1,g729,libfdk_aac,libopus,libspeex,mp2,mp3,m4a,pcm_alaw,pcm_mulaw,pcm_f16le,pcm_f24le,pcm_f32be,pcm_f32le,pcm_f64be,pcm_f64le,pcm_s16be,pcm_s16be_planar,pcm_s24be,pcm_s16le,pcm_s16le_planar,pcm_s24le,pcm_s24le_planar,pcm_s32le,pcm_s32le_planar,pcm_s64be,pcm_s64le,pcm_s8,pcm_s8_planar,pcm_u8,pcm_u24be,pcm_u24le,pcm_u32be,pcm_u32le,tta,vorbis,wavpack,'
--enable-
decoder='ass,ffv1,mjpeg,mjpegb,libaom_av1,libdav1d,libvpx_vp8,libvpx_vp9,rawvideo,theora,vp8,vp9,libopenh264'
--enable-encoder='bmp,gif,jpegls,png,tiff,webp,' --enable-
decoder='bmp,gif,jpegls,png,tiff,webp,' --enable-
hwaccel='vp8_vaapi,mjpeg_vaapi,' --enable-
parser='aac,ac3,flac,mjpeg,mpegaudio,mpeg4video,opus,vp3,vp8,vp9,vorbis,'
--enable-
muxer='ac3,ass,flac,g722,gif,matroska,mp3,mpegvideo,rtp,ogg,opus,pcm_s16be,pcm_s16le,wav,webm,'
--enable-
demuxer='aac,ac3,ass,flac,g722,gif,image_jpeg_pipe,image_png_pipe,image_webp_pipe,matroska,mjpeg,mov,mp3,mpegvideo,ogg,pcm_mulaw,pcm_alaw,pcm_s16be,pcm_s16le,rtp,wav,'
--enable-
filter='atempo,crop,scale,overlay,amix,amerge,aresample,format,aformat,fps,transpose,pad,'
--enable-indev='v4l2,xcbgrab,' --enable-
protocol='crypto,file,pipe,rtp,srtp,rtsp,tcp,udp,unix,' --arch=x86_64
--enable-libopenh264  
libavutil 57. 17.100 / 57. 17.100  
libavcodec 59. 18.100 / 59. 18.100  
libavformat 59. 16.100 / 59. 16.100  
libavdevice 59. 4.100 / 59. 4.100  
libavfilter 8. 24.100 / 8. 24.100  
libswscale 6. 4.100 / 6. 4.100  
libswresample 4. 3.100 / 4. 3.100  
/tmp/chimovie_Jjjo-%05d.ppm: No such file or directory  
  
An error occurred during encoding. See Reply Log for details.  
  
Error during MPEG encoding:  
\-----------------------------  
Exit value: 1  
Error message:  
stdout:  
  
stderr:  
ffmpeg version 5.0.3 Copyright (c) 2000-2022 the FFmpeg developers  
built with gcc 12.2.0 (GCC)  
configuration: --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu
--optflags='-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS
-fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-
unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer
' --extra-ldflags='-Wl,-z,relro,-z,now -Wl,--as-needed ' --disable-stripping
--disable-doc --disable-static --enable-shared --disable-everything --enable-
ffplay --enable-ffprobe --enable-gnutls --enable-libaom --enable-libdav1d
--enable-libfdk-aac --enable-libmp3lame --enable-libfontconfig --enable-
libfreetype --enable-libopus --enable-libpulse --enable-libspeex --enable-
libtheora --enable-libvorbis --enable-libvpx --enable-libwebp --enable-openal
--enable-opengl --enable-sdl2 --enable-vulkan --enable-zlib --enable-libv4l2
--enable-libxcb --enable-vdpau --enable-vaapi --enable-pthreads --enable-
encoder='ac3,alac,flac,libfdk_aac,g723_1,mp2,libmp3lame,libopus,libspeex,pcm_alaw,pcm_mulaw,pcm_f32le,pcm_s16be,pcm_s24be,pcm_s16le,pcm_s24le,pcm_s32le,pcm_u8,tta,libvorbis,wavpack,'
--enable-
encoder='ass,ffv1,libaom_av1,libvpx_vp8,libvpx_vp9,mjpeg_vaapi,rawvideo,theora,vp8_vaapi,libopenh264'
--enable-
decoder='adpcm_g722,alac,flac,g723_1,g729,libfdk_aac,libopus,libspeex,mp2,mp3,m4a,pcm_alaw,pcm_mulaw,pcm_f16le,pcm_f24le,pcm_f32be,pcm_f32le,pcm_f64be,pcm_f64le,pcm_s16be,pcm_s16be_planar,pcm_s24be,pcm_s16le,pcm_s16le_planar,pcm_s24le,pcm_s24le_planar,pcm_s32le,pcm_s32le_planar,pcm_s64be,pcm_s64le,pcm_s8,pcm_s8_planar,pcm_u8,pcm_u24be,pcm_u24le,pcm_u32be,pcm_u32le,tta,vorbis,wavpack,'
--enable-
decoder='ass,ffv1,mjpeg,mjpegb,libaom_av1,libdav1d,libvpx_vp8,libvpx_vp9,rawvideo,theora,vp8,vp9,libopenh264'
--enable-encoder='bmp,gif,jpegls,png,tiff,webp,' --enable-
decoder='bmp,gif,jpegls,png,tiff,webp,' --enable-
hwaccel='vp8_vaapi,mjpeg_vaapi,' --enable-
parser='aac,ac3,flac,mjpeg,mpegaudio,mpeg4video,opus,vp3,vp8,vp9,vorbis,'
--enable-
muxer='ac3,ass,flac,g722,gif,matroska,mp3,mpegvideo,rtp,ogg,opus,pcm_s16be,pcm_s16le,wav,webm,'
--enable-
demuxer='aac,ac3,ass,flac,g722,gif,image_jpeg_pipe,image_png_pipe,image_webp_pipe,matroska,mjpeg,mov,mp3,mpegvideo,ogg,pcm_mulaw,pcm_alaw,pcm_s16be,pcm_s16le,rtp,wav,'
--enable-
filter='atempo,crop,scale,overlay,amix,amerge,aresample,format,aformat,fps,transpose,pad,'
--enable-indev='v4l2,xcbgrab,' --enable-
protocol='crypto,file,pipe,rtp,srtp,rtsp,tcp,udp,unix,' --arch=x86_64
--enable-libopenh264  
libavutil 57. 17.100 / 57. 17.100  
libavcodec 59. 18.100 / 59. 18.100  
libavformat 59. 16.100 / 59. 16.100  
libavdevice 59. 4.100 / 59. 4.100  
libavfilter 8. 24.100 / 8. 24.100  
libswscale 6. 4.100 / 6. 4.100  
libswresample 4. 3.100 / 4. 3.100  
/tmp/chimovie_Jjjo-%05d.ppm: No such file or directory  
  
\-----------------------------  
  

> save /vcp1/people/david/Desktop/image1.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode /vcp1/people/david/Desktop/movie1.mp4

/usr/bin/ffmpeg -r 25 -i /tmp/chimovie_Jjjo-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 /vcp1/people/david/Desktop/movie1.mp4  
stdout:  
  
stderr:  
ffmpeg version 5.0.3 Copyright (c) 2000-2022 the FFmpeg developers  
built with gcc 12.2.0 (GCC)  
configuration: --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu
--optflags='-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS
-fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-
unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer
' --extra-ldflags='-Wl,-z,relro,-z,now -Wl,--as-needed ' --disable-stripping
--disable-doc --disable-static --enable-shared --disable-everything --enable-
ffplay --enable-ffprobe --enable-gnutls --enable-libaom --enable-libdav1d
--enable-libfdk-aac --enable-libmp3lame --enable-libfontconfig --enable-
libfreetype --enable-libopus --enable-libpulse --enable-libspeex --enable-
libtheora --enable-libvorbis --enable-libvpx --enable-libwebp --enable-openal
--enable-opengl --enable-sdl2 --enable-vulkan --enable-zlib --enable-libv4l2
--enable-libxcb --enable-vdpau --enable-vaapi --enable-pthreads --enable-
encoder='ac3,alac,flac,libfdk_aac,g723_1,mp2,libmp3lame,libopus,libspeex,pcm_alaw,pcm_mulaw,pcm_f32le,pcm_s16be,pcm_s24be,pcm_s16le,pcm_s24le,pcm_s32le,pcm_u8,tta,libvorbis,wavpack,'
--enable-
encoder='ass,ffv1,libaom_av1,libvpx_vp8,libvpx_vp9,mjpeg_vaapi,rawvideo,theora,vp8_vaapi,libopenh264'
--enable-
decoder='adpcm_g722,alac,flac,g723_1,g729,libfdk_aac,libopus,libspeex,mp2,mp3,m4a,pcm_alaw,pcm_mulaw,pcm_f16le,pcm_f24le,pcm_f32be,pcm_f32le,pcm_f64be,pcm_f64le,pcm_s16be,pcm_s16be_planar,pcm_s24be,pcm_s16le,pcm_s16le_planar,pcm_s24le,pcm_s24le_planar,pcm_s32le,pcm_s32le_planar,pcm_s64be,pcm_s64le,pcm_s8,pcm_s8_planar,pcm_u8,pcm_u24be,pcm_u24le,pcm_u32be,pcm_u32le,tta,vorbis,wavpack,'
--enable-
decoder='ass,ffv1,mjpeg,mjpegb,libaom_av1,libdav1d,libvpx_vp8,libvpx_vp9,rawvideo,theora,vp8,vp9,libopenh264'
--enable-encoder='bmp,gif,jpegls,png,tiff,webp,' --enable-
decoder='bmp,gif,jpegls,png,tiff,webp,' --enable-
hwaccel='vp8_vaapi,mjpeg_vaapi,' --enable-
parser='aac,ac3,flac,mjpeg,mpegaudio,mpeg4video,opus,vp3,vp8,vp9,vorbis,'
--enable-
muxer='ac3,ass,flac,g722,gif,matroska,mp3,mpegvideo,rtp,ogg,opus,pcm_s16be,pcm_s16le,wav,webm,'
--enable-
demuxer='aac,ac3,ass,flac,g722,gif,image_jpeg_pipe,image_png_pipe,image_webp_pipe,matroska,mjpeg,mov,mp3,mpegvideo,ogg,pcm_mulaw,pcm_alaw,pcm_s16be,pcm_s16le,rtp,wav,'
--enable-
filter='atempo,crop,scale,overlay,amix,amerge,aresample,format,aformat,fps,transpose,pad,'
--enable-indev='v4l2,xcbgrab,' --enable-
protocol='crypto,file,pipe,rtp,srtp,rtsp,tcp,udp,unix,' --arch=x86_64
--enable-libopenh264  
libavutil 57. 17.100 / 57. 17.100  
libavcodec 59. 18.100 / 59. 18.100  
libavformat 59. 16.100 / 59. 16.100  
libavdevice 59. 4.100 / 59. 4.100  
libavfilter 8. 24.100 / 8. 24.100  
libswscale 6. 4.100 / 6. 4.100  
libswresample 4. 3.100 / 4. 3.100  
/tmp/chimovie_Jjjo-%05d.ppm: No such file or directory  
  
An error occurred during encoding. See Reply Log for details.  
  
Error during MPEG encoding:  
\-----------------------------  
Exit value: 1  
Error message:  
stdout:  
  
stderr:  
ffmpeg version 5.0.3 Copyright (c) 2000-2022 the FFmpeg developers  
built with gcc 12.2.0 (GCC)  
configuration: --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu
--optflags='-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS
-fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-
unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer
' --extra-ldflags='-Wl,-z,relro,-z,now -Wl,--as-needed ' --disable-stripping
--disable-doc --disable-static --enable-shared --disable-everything --enable-
ffplay --enable-ffprobe --enable-gnutls --enable-libaom --enable-libdav1d
--enable-libfdk-aac --enable-libmp3lame --enable-libfontconfig --enable-
libfreetype --enable-libopus --enable-libpulse --enable-libspeex --enable-
libtheora --enable-libvorbis --enable-libvpx --enable-libwebp --enable-openal
--enable-opengl --enable-sdl2 --enable-vulkan --enable-zlib --enable-libv4l2
--enable-libxcb --enable-vdpau --enable-vaapi --enable-pthreads --enable-
encoder='ac3,alac,flac,libfdk_aac,g723_1,mp2,libmp3lame,libopus,libspeex,pcm_alaw,pcm_mulaw,pcm_f32le,pcm_s16be,pcm_s24be,pcm_s16le,pcm_s24le,pcm_s32le,pcm_u8,tta,libvorbis,wavpack,'
--enable-
encoder='ass,ffv1,libaom_av1,libvpx_vp8,libvpx_vp9,mjpeg_vaapi,rawvideo,theora,vp8_vaapi,libopenh264'
--enable-
decoder='adpcm_g722,alac,flac,g723_1,g729,libfdk_aac,libopus,libspeex,mp2,mp3,m4a,pcm_alaw,pcm_mulaw,pcm_f16le,pcm_f24le,pcm_f32be,pcm_f32le,pcm_f64be,pcm_f64le,pcm_s16be,pcm_s16be_planar,pcm_s24be,pcm_s16le,pcm_s16le_planar,pcm_s24le,pcm_s24le_planar,pcm_s32le,pcm_s32le_planar,pcm_s64be,pcm_s64le,pcm_s8,pcm_s8_planar,pcm_u8,pcm_u24be,pcm_u24le,pcm_u32be,pcm_u32le,tta,vorbis,wavpack,'
--enable-
decoder='ass,ffv1,mjpeg,mjpegb,libaom_av1,libdav1d,libvpx_vp8,libvpx_vp9,rawvideo,theora,vp8,vp9,libopenh264'
--enable-encoder='bmp,gif,jpegls,png,tiff,webp,' --enable-
decoder='bmp,gif,jpegls,png,tiff,webp,' --enable-
hwaccel='vp8_vaapi,mjpeg_vaapi,' --enable-
parser='aac,ac3,flac,mjpeg,mpegaudio,mpeg4video,opus,vp3,vp8,vp9,vorbis,'
--enable-
muxer='ac3,ass,flac,g722,gif,matroska,mp3,mpegvideo,rtp,ogg,opus,pcm_s16be,pcm_s16le,wav,webm,'
--enable-
demuxer='aac,ac3,ass,flac,g722,gif,image_jpeg_pipe,image_png_pipe,image_webp_pipe,matroska,mjpeg,mov,mp3,mpegvideo,ogg,pcm_mulaw,pcm_alaw,pcm_s16be,pcm_s16le,rtp,wav,'
--enable-
filter='atempo,crop,scale,overlay,amix,amerge,aresample,format,aformat,fps,transpose,pad,'
--enable-indev='v4l2,xcbgrab,' --enable-
protocol='crypto,file,pipe,rtp,srtp,rtsp,tcp,udp,unix,' --arch=x86_64
--enable-libopenh264  
libavutil 57. 17.100 / 57. 17.100  
libavcodec 59. 18.100 / 59. 18.100  
libavformat 59. 16.100 / 59. 16.100  
libavdevice 59. 4.100 / 59. 4.100  
libavfilter 8. 24.100 / 8. 24.100  
libswscale 6. 4.100 / 6. 4.100  
libswresample 4. 3.100 / 4. 3.100  
/tmp/chimovie_Jjjo-%05d.ppm: No such file or directory  
  
\-----------------------------  
  




OpenGL version: 3.3.0 NVIDIA 520.61.05
OpenGL renderer: NVIDIA GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=/usr/share/xsessions/plasma5
XDG_SESSION_DESKTOP=KDE
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:1
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7B09
OS: Freedesktop SDK 22.08 Flatpak runtime
Architecture: 64bit ELF
Virtual Machine: detection failed
CPU: 32 AMD Ryzen Threadripper 1950X 16-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       6.9Gi       362Mi       903Mi        23Gi        22Gi
	Swap:          2.0Gi       878Mi       1.1Gi

Graphics:
	0a:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1080] [10de:1b80] (rev a1)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:3362]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.7.22
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.47.1
    ChimeraX-AtomicLibrary: 10.0.8
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.4
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202308212127
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.10
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.2
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.31.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.4
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7.post1
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.42.1
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.7.10
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.0
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.8
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.7
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.5
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 10.0.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.10.0
    prompt-toolkit: 3.0.39
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.2
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.3
    traitlets: 5.9.0
    typing-extensions: 4.7.1
    tzdata: 2023.3
    urllib3: 2.0.4
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.8

Change History (5)

comment:1 by Eric Pettersen, 2 years ago

Cc: Greg Couch added
Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ffmpeg failure

comment:2 by Tom Goddard, 2 years ago

The ffmpeg error encoding the movie suggests it didn't find the frame images

/tmp/chimovie_Jjjo-%05d.ppm: No such file or directory

One possibility is the files were written but your ffmpeg does not understand the "%05d" part of the file name which needs to be expanded to a sequence of files. Your version of ffmpeg is 5.0.3 in /usr/bin. The ChimeraX Ubuntu 22 distribution uses ffmpeg 4.4 which records spin movies fine.

Since I cannot reproduce your problem you will have to do further testing to figure out what is going wrong if you want a solution. I suggest checking whether ChimeraX writes the movie images. To do that try this command to create the image files

movie record ; turn y 1 15 ; wait 15 ; movie stop

Then look in the /tmp directory and see if ChimeraX created 15 ppm files. If it does show the files then try command

movie encode

and see if you get the encoding error. If so then I think we can conclude your installed ffmpeg cannot handle the "%05d.ppm" files.

Maybe your ffmpeg does not include the ppm decoder (although I think that is built into ffmpeg). You can tell ChimeraX to encode the movie frames as PNG images using

movie record format png ; turn y 1 15 ; wait 15 ; movie encode

See if that produces the same error.

comment:3 by Tom Goddard, 2 years ago

Cc: Tom Goddard added; Greg Couch removed
Milestone: → 1.7
Owner: changed from Tom Goddard to Greg Couch

Reassigning to Greg to debug flatpak-specific issue.

Greg tried flatpak ChimeraX spin movie and it failed with the same error. He did the tests I suggested in the previous comment and the image files were written to /tmp, and even if the format was png the same error occurred.

Greg also set ffmpeg 5.0.3 is part of the flatpak environment. I tried an ffmpeg 5.0.1 static build and 6.1 static build (from johnvansickle.com) on Ubuntu with ChimeraX and both worked fine.

So this looks like either a problem where the flatpak ffmpeg cannot see the image files in /tmp, or the flatpak ffmpeg is compiled in such a way that it does not handle %d file specifiers, or does not support ppm and png formats.

More testing in a flatpak environment will be needed to figure out the cause. If the flatpak ffmpeg is compiled without needed file support then we can include our own ffmpeg since we already build it for Redhat linux distributions.

Version 0, edited 2 years ago by Tom Goddard (next)

comment:4 by Greg Couch, 23 months ago

Resolution: → fixed
Status: assigned → closed

Had to compile ffmpeg from source to get a version that would encode files properly.

Make a flatpak available for download that corresponds to a recent 1.7 release candidate.

comment:5 by david.chalmers@…, 23 months ago 

Hi All,

Thanks very much for taking a look at this. I have downloaded version 1.7 and installed it, but movie generation still fails.

I have made a new submission using the bug-report button.

Cheers

David


________________________________________________________________________

  David Chalmers PhD BSc(Hons)
  Senior Lecturer

  Monash University
  Medicinal Chemistry. Monash Institute of Pharmaceutical Sciences (MIPS)
  Faculty of Pharmacy and Pharmaceutical Sciences

  Room 119. Level 1, Manning Building, Parkville Campus
  381 Royal Parade, Parkville, VIC 3052. Australia

  T:  +61 3 9903 9110
  E:  david.chalmers@monash.edu
  Twitter:  @davidkchalmers
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