Opened 3 years ago

Closed 3 years ago

#8896 closed defect (nonchimerax)

No space left on device

Reported by: nkkhandelwal@… Owned by: Eric Pettersen
Priority: normal Milestone:
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:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/niteshkhandelwal/Documents/UCSF_projects/EFPA/phenix-
> model/RealSpaceRefine_35/isolde33_real_space_refined_034_real_space_refined_035.pdb

Chain information for
isolde33_real_space_refined_034_real_space_refined_035.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/niteshkhandelwal/Documents/UCSF_projects/EFPA/pfinal_J164_fliped.mrc

Opened pfinal_J164_fliped.mrc as #2, grid size 392,392,392, pixel 0.834, shown
at level 0.125, step 2, values float32  

> set bgColor white

> open /Users/niteshkhandelwal/Documents/UCSF_projects/EFPA/phenix-
> model/RealSpaceRefine_35/isolde33_real_space_refined_034_real_space_refined_035.pdb

Chain information for
isolde33_real_space_refined_034_real_space_refined_035.pdb #3  
---  
Chain | Description  
A | No description available  
  

> volume #2 step 1

> volume #2 level 0.4169

> surface dust #2 size 8.34

> volume #2 level 0.4

> select add #3

7004 atoms, 7070 bonds, 467 residues, 1 model selected  

> hide #!2 models

> hide #1 models

> show #1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #1 models

> hide #!2 models

> show #1 models

> show #!2 models

> hide #1 models

> hide #!2 models

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,0.12459,0,1,0,-0.11498,0,0,1,-0.285

> view matrix models #3,1,0,0,0.12834,0,1,0,-0.095194,0,0,1,-0.30678

> view matrix models #3,1,0,0,0.1215,0,1,0,-0.05402,0,0,1,-0.31094

> view matrix models #3,1,0,0,-3.0171,0,1,0,7.007,0,0,1,4.4926

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.96247,0.251,-0.10321,294.01,0.085697,-0.079768,-0.99312,308.82,-0.2575,-0.9647,0.055264,337.28

> show #!2 models

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.96247,0.251,-0.10321,299.47,0.085697,-0.079768,-0.99312,322.96,-0.2575,-0.9647,0.055264,313.4

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.7422,0.064495,0.66706,-76.243,0.072871,-0.99722,0.015337,284.75,0.6662,0.037226,-0.74484,159.08

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.7422,0.064495,0.66706,-74.773,0.072871,-0.99722,0.015337,299.91,0.6662,0.037226,-0.74484,145.97

> view matrix models
> #3,0.7422,0.064495,0.66706,-73.187,0.072871,-0.99722,0.015337,300.01,0.6662,0.037226,-0.74484,147.82

> ui tool show "Fit in Map"

> fitmap #3 inMap #2

Fit molecule isolde33_real_space_refined_034_real_space_refined_035.pdb (#3)
to map pfinal_J164_fliped.mrc (#2) using 7004 atoms  
average map value = 0.1836, steps = 76  
shifted from previous position = 3.1  
rotated from previous position = 5.32 degrees  
atoms outside contour = 5565, contour level = 0.4  
  
Position of isolde33_real_space_refined_034_real_space_refined_035.pdb (#3)
relative to pfinal_J164_fliped.mrc (#2) coordinates:  
Matrix rotation and translation  
0.70632439 0.08197448 0.70312591 -75.53764581  
0.03357721 -0.99603408 0.08239345 293.04652431  
0.70709153 -0.03458750 -0.70627564 142.29630280  
Axis -0.92358793 -0.03130936 -0.38210608  
Axis point 0.00000000 150.28612014 81.74196507  
Rotation angle (degrees) 176.36905013  
Shift along axis 6.21827627  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.8334,0.40164,0.37965,-86.534,0.43598,-0.89994,-0.0049785,229.68,0.33967,0.16967,-0.92512,209.25

> fitmap #3 inMap #2

Fit molecule isolde33_real_space_refined_034_real_space_refined_035.pdb (#3)
to map pfinal_J164_fliped.mrc (#2) using 7004 atoms  
average map value = 0.3653, steps = 88  
shifted from previous position = 2.43  
rotated from previous position = 14.5 degrees  
atoms outside contour = 4056, contour level = 0.4  
  
Position of isolde33_real_space_refined_034_real_space_refined_035.pdb (#3)
relative to pfinal_J164_fliped.mrc (#2) coordinates:  
Matrix rotation and translation  
0.88071764 0.20338999 0.42774869 -76.15958255  
0.20574087 -0.97773504 0.04129038 270.00082718  
0.42662293 0.05164022 -0.90295413 205.99342443  
Axis 0.96972078 0.10547716 0.22026386  
Axis point 0.00000000 138.85897195 112.01768012  
Rotation angle (degrees) 179.69423916  
Shift along axis -0.00170356  
  

Populating font family aliases took 572 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

> save /Users/niteshkhandelwal/Desktop/efpa-update/part2.pdb models #3
> relModel #2

> show #1 models

> ui tool show "Color Zone"

> color zone #2 near #1 distance 5

> color single #2

> color sel bychain

> color zone #2 near #3 distance 5

> color zone #2 near #1 distance 5

> color single #2

> color zone #2 near #1 distance 5

> color zone #2 near #3 distance 5

> select add #1

14008 atoms, 14140 bonds, 934 residues, 2 models selected  

> select subtract #3

7004 atoms, 7070 bonds, 467 residues, 1 model selected  

> color sel bychain

[Repeated 2 time(s)]

> color #1 #f2765d transparency 0

> color zone #2 near #1 distance 5

> color zone #2 near #1 distance 4.9

> color zone #2 near #1 distance 4.8

> color zone #2 near #1 distance 4.7

> color zone #2 near #1 distance 4.6

> color zone #2 near #1 distance 4.7

> color zone #2 near #1 distance 4.8

> color zone #2 near #1 distance 4.9

> color zone #2 near #1 distance 5

[Repeated 1 time(s)]

> color zone #2 near #1 distance 4.9

> color zone #2 near #1 distance 4.8

[Repeated 1 time(s)]

> color #2 #5159bf models transparency 0

> color #2 #4556bf models transparency 0

> color #2 #8050bf models transparency 0

> color #2 #35afbf models transparency 0

> color #2 #31bfb0 models transparency 0

> color #2 #3f64bf models transparency 0

> color #2 #4d7ebf models transparency 0

> color #2 #5086bf models transparency 0

> color #2 #417bbf models transparency 0

> color #2 #3c7cbf models transparency 0

> color zone #2 near #1 distance 4.8

> volume #2 level -0.07911

> volume #2 level -0.05

> volume #2 level -0.5

> volume #2 level 0.5

> hide #!2 models

> hide #1 models

> show #!2 models

> hide #3 models

> volume #2 level 0.4428

> show #1 models

> show #3 models

> select subtract #1

Nothing selected  

> hide #1 models

> show #1 models

> volume #2 level 0.214

> volume #2 level 0.2604

> volume #2 level 4

> volume #2 level 0.4

> volume #2 level 0.35

> volume #2 level 0.45

> hide #1 models

> hide #3 models

> lighting soft

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/niteshkhandelwal/Desktop/movie12.mp4

Movie saved to /Users/niteshkhandelwal/Desktop/movie12.mp4  
  

> save /Users/niteshkhandelwal/Desktop/efpa-update/1.cxs includeMaps true

> show #1 models

> show #3 models

> volume #2 style mesh

> show atoms

> hide atoms

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/niteshkhandelwal/Desktop/movie12.mp4

Movie saved to /Users/niteshkhandelwal/Desktop/movie12.mp4  
  

> volume #2

> volume #2 style surface

> volume #2 color #3c7cbf00

> volume #2 color #3c7cbf25

> volume #2 color #3c7cbf80

> volume #2 color #3c7cbf

> volume #2 color #3c7cbfba

[Repeated 1 time(s)]

> ui tool show "Color Zone"

> color zone #2 near #1 distance 5

> hide #1 models

> hide #3 models

> color #2 #3c7cbf models transparency 0

> show #1 models

> show #3 models

> color #3 #3c7cbf models transparency 0

> save /Users/niteshkhandelwal/Desktop/efpa-update/2.cxs includeMaps true

> open /Users/niteshkhandelwal/Documents/UCSF_projects/EFPA/P135-sharp-
> flip.mrc

Opened P135-sharp-flip.mrc as #4, grid size 392,392,392, pixel 0.834, shown at
level 0.145, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.45

> volume #4 level 0.4

> hide #3 models

> hide #!2 models

> surface dust #4 size 8.34

> hide #1 models

> show #1 models

> show #3 models

> volume #4 level 0.2627

> select add #4

2 models selected  

> vop gaussian #4 sdev 2.5

Opened P135-sharp-flip.mrc gaussian as #5, grid size 392,392,392, pixel 0.834,
shown at step 1, values float32  

> color #5 #b2ffff19 models

> color #5 #b2ffff83 models

> color #5 #b2ffff84 models

> color #5 #b2ffff9f models

> color #5 #b2ffffae models

> color #5 #b2ffff4f models

> color #5 #b2ffff9c models

[Repeated 1 time(s)]

> hide #1 models

> hide #3 models

> show #!2 models

> hide #!5 models

> show #1 models

> show #3 models

> hide #3 models

> ui tool show "Color Zone"

> color zone #2 near #1 distance 5

> hide #1 models

> show #!4 models

> hide #!4 models

> show #!5 models

> color #5 #b2ffff2f models

> color #5 #b2ffff2e models

[Repeated 1 time(s)]

> show #!4 models

> hide #!4 models

> color #5 #b2ffff34 models

> color #5 #b2ffff33 models

> select add #5

4 models selected  

> volume #5 level 0.1447

> volume #5 level 0.1416

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/niteshkhandelwal/Desktop/movie12.mp4

Movie saved to /Users/niteshkhandelwal/Desktop/movie12.mp4  
  

> select subtract #4

2 models selected  

> save /Users/niteshkhandelwal/Desktop/efpa-update/3.cxs includeMaps true

> color #5 #bafff333 models

> color #5 #fff58533 models

> color #5 #00ff9b33 models

> color #5 #f6faff33 models

> color #5 #8df8ff33 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #1 models

> hide #1 models

> show #!4 models

> hide #!5 models

> select subtract #5

Nothing selected  

> hide #!2 models

> show #!2 models

> hide #!4 models

> show #!4 models

> hide #!2 models

> ui tool show "Map Eraser"

> volume erase #4 center 162.35,188.14,222.2 radius 54.851 outside true

Opened P135-sharp-flip.mrc copy as #7, grid size 392,392,392, pixel 0.834,
shown at step 1, values float32  

> surface dust #7 size 8.34

> volume erase #7 center 149.33,141.48,182.39 radius 22.068

> volume erase #7 center 172.49,152.98,168.41 radius 22.068

> show #!2 models

> show #3 models

> hide #3 models

> hide #!2 models

> show #3 models

> show #!4 models

> hide #3 models

> hide #!4 models

> show #!2 models

> show #!5 models

> hide #!5 models

> save /Users/niteshkhandelwal/Desktop/efpa-update/4.cxs includeMaps true

> color #4 #f5ffca models transparency 0

> color #4 #f5ffc7 models transparency 0

> color #4 #f7ffc5 models transparency 0

> select add #4

2 models selected  

> hide #!2 models

> color #4 #a5ffb8 models transparency 0

> show #!4 models

> hide #!4 models

> select subtract #4

Nothing selected  

> select add #7

2 models selected  

> color #4 #5efc8e models transparency 0

> color #7 #6cff70 models transparency 0

> show #3 models

> hide #3 models

> show #!2 models

> select subtract #7

Nothing selected  

> movie record

> turn y 2 180

> wait 180

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/movie/movie.py", line 172, in capture_image  
i.save(save_path, self.img_fmt)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/Image.py", line 2212, in save  
save_handler(self, fp, filename)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/PpmImagePlugin.py", line 149, in _save  
ImageFile._save(im, fp, [("raw", (0, 0) + im.size, 0, (rawmode, 0, 1))])  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/ImageFile.py", line 527, in _save  
s = e.encode_to_file(fh, bufsize)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "frame drawn":  
OSError: [Errno 28] No space left on device  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/ImageFile.py", line 527, in _save  
s = e.encode_to_file(fh, bufsize)  
  
See log for complete Python traceback.  
  

> movie encode /Users/niteshkhandelwal/Desktop/movie12.mp4

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
/Applications/ChimeraX-1.4.app/Contents/bin/ffmpeg -r 25 -i
/var/folders/bt/6vf3nw_n0gd1nlmwr7x2q9jm0000gn/T/chimovie_z3Qv-%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 /Users/niteshkhandelwal/Desktop/movie12.mp4  
stdout:  
  
stderr:  
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers  
built with Apple clang version 11.0.0 (clang-1100.0.33.16)  
configuration: --prefix=/private/var/tmp/chimerax_build/v1.1/chimerax/build
--enable-gpl --enable-version3 --disable-network --disable-doc --disable-
devices --disable-ffplay --disable-ffserver --disable-ffprobe --enable-
libtheora --enable-libvpx --enable-libx264
--yasmexe=/private/var/tmp/chimerax_build/v1.1/chimerax/build/bin/yasm
--optflags=-O --extra-
cflags=-I/private/var/tmp/chimerax_build/v1.1/chimerax/build/include --extra-
ldflags='-O3 -Wall -Wextra
-L/private/var/tmp/chimerax_build/v1.1/chimerax/build/lib' --extra-libs=-ldl  
libavutil 55. 34.101 / 55. 34.101  
libavcodec 57. 64.101 / 57. 64.101  
libavformat 57. 56.101 / 57. 56.101  
libavdevice 57. 1.100 / 57. 1.100  
libavfilter 6. 65.100 / 6. 65.100  
libswscale 4. 2.100 / 4. 2.100  
libswresample 2. 3.100 / 2. 3.100  
libpostproc 54. 1.100 / 54. 1.100  
Input #0, image2, from
'/var/folders/bt/6vf3nw_n0gd1nlmwr7x2q9jm0000gn/T/chimovie_z3Qv-%05d.ppm':  
Duration: 00:00:06.80, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1525x1102, 25 tbr, 25 tbn, 25 tbc  
[libx264 @ 0x7feccd80a600] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
AVX FMA3 AVX2 LZCNT BMI2  
[libx264 @ 0x7feccd80a600] profile High, level 4.0  
[libx264 @ 0x7feccd80a600] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft
2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3
deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00  
Output #0, mp4, to '/Users/niteshkhandelwal/Desktop/movie12.mp4':  
Metadata:  
encoder : Lavf57.56.101  
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1524x1102, q=-1--1, 25 fps, 12800 tbn, 25 tbc  
Metadata:  
encoder : Lavc57.64.101 libx264  
Side data:  
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1  
Stream mapping:  
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))  
Press [q] to stop, [?] for help  
frame= 32 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 51 fps= 50 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
av_interleaved_write_frame(): No space left on device  
Error writing trailer of /Users/niteshkhandelwal/Desktop/movie12.mp4: No space
left on deviceframe= 57 fps= 32 q=25.0 Lsize= 0kB time=-00:00:00.07
bitrate=N/A speed=N/A  
video:65kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing
overhead: unknown  
[libx264 @ 0x7feccd80a600] frame I:1 Avg QP:13.45 size: 66007  
[libx264 @ 0x7feccd80a600] frame P:14 Avg QP:21.09 size: 43323  
[libx264 @ 0x7feccd80a600] frame B:42 Avg QP:25.58 size: 18000  
[libx264 @ 0x7feccd80a600] consecutive B-frames: 1.8% 0.0% 0.0% 98.2%  
[libx264 @ 0x7feccd80a600] mb I I16..4: 52.5% 30.1% 17.4%  
[libx264 @ 0x7feccd80a600] mb P I16..4: 0.4% 0.9% 3.6% P16..4: 3.4% 6.4% 7.6%
0.0% 0.0% skip:77.7%  
[libx264 @ 0x7feccd80a600] mb B I16..4: 0.0% 0.1% 0.3% B16..8: 6.7% 5.9% 5.2%
direct: 1.9% skip:79.9% L0:34.2% L1:38.8% BI:27.0%  
[libx264 @ 0x7feccd80a600] 8x8 transform intra:25.0% inter:21.6%  
[libx264 @ 0x7feccd80a600] coded y,uvDC,uvAC intra: 44.3% 49.6% 48.2% inter:
7.4% 6.7% 3.8%  
[libx264 @ 0x7feccd80a600] i16 v,h,dc,p: 94% 3% 3% 0%  
[libx264 @ 0x7feccd80a600] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 43% 5% 37% 2% 2% 2%
2% 2% 3%  
[libx264 @ 0x7feccd80a600] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 17% 15% 14% 8% 9%
10% 9% 9% 8%  
[libx264 @ 0x7feccd80a600] i8c dc,h,v,p: 68% 11% 12% 9%  
[libx264 @ 0x7feccd80a600] Weighted P-Frames: Y:0.0% UV:0.0%  
[libx264 @ 0x7feccd80a600] ref P L0: 63.0% 20.1% 11.8% 5.1%  
[libx264 @ 0x7feccd80a600] ref B L0: 94.2% 4.8% 1.0%  
[libx264 @ 0x7feccd80a600] ref B L1: 97.9% 2.1%  
[libx264 @ 0x7feccd80a600] kb/s:5012.33  
Conversion failed!  
  
An error occurred during encoding. See Reply Log for details.  
  
Error during MPEG encoding:  
\-----------------------------  
Exit value: 1  
Error message:  
stdout:  
  
stderr:  
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers  
built with Apple clang version 11.0.0 (clang-1100.0.33.16)  
configuration: --prefix=/private/var/tmp/chimerax_build/v1.1/chimerax/build
--enable-gpl --enable-version3 --disable-network --disable-doc --disable-
devices --disable-ffplay --disable-ffserver --disable-ffprobe --enable-
libtheora --enable-libvpx --enable-libx264
--yasmexe=/private/var/tmp/chimerax_build/v1.1/chimerax/build/bin/yasm
--optflags=-O --extra-
cflags=-I/private/var/tmp/chimerax_build/v1.1/chimerax/build/include --extra-
ldflags='-O3 -Wall -Wextra
-L/private/var/tmp/chimerax_build/v1.1/chimerax/build/lib' --extra-libs=-ldl  
libavutil 55. 34.101 / 55. 34.101  
libavcodec 57. 64.101 / 57. 64.101  
libavformat 57. 56.101 / 57. 56.101  
libavdevice 57. 1.100 / 57. 1.100  
libavfilter 6. 65.100 / 6. 65.100  
libswscale 4. 2.100 / 4. 2.100  
libswresample 2. 3.100 / 2. 3.100  
libpostproc 54. 1.100 / 54. 1.100  
Input #0, image2, from
'/var/folders/bt/6vf3nw_n0gd1nlmwr7x2q9jm0000gn/T/chimovie_z3Qv-%05d.ppm':  
Duration: 00:00:06.80, start: 0.000000, bitrate: N/A  
Stream #0:0: Video: ppm, rgb24, 1525x1102, 25 tbr, 25 tbn, 25 tbc  
[libx264 @ 0x7feccd80a600] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
AVX FMA3 AVX2 LZCNT BMI2  
[libx264 @ 0x7feccd80a600] profile High, level 4.0  
[libx264 @ 0x7feccd80a600] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft
2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3
deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00  
Output #0, mp4, to '/Users/niteshkhandelwal/Desktop/movie12.mp4':  
Metadata:  
encoder : Lavf57.56.101  
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1524x1102, q=-1--1, 25 fps, 12800 tbn, 25 tbc  
Metadata:  
encoder : Lavc57.64.101 libx264  
Side data:  
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1  
Stream mapping:  
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))  
Press [q] to stop, [?] for help  
frame= 32 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 51 fps= 50 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
av_interleaved_write_frame(): No space left on device  
Error writing trailer of /Users/niteshkhandelwal/Desktop/movie12.mp4: No space
left on deviceframe= 57 fps= 32 q=25.0 Lsize= 0kB time=-00:00:00.07
bitrate=N/A speed=N/A  
video:65kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing
overhead: unknown  
[libx264 @ 0x7feccd80a600] frame I:1 Avg QP:13.45 size: 66007  
[libx264 @ 0x7feccd80a600] frame P:14 Avg QP:21.09 size: 43323  
[libx264 @ 0x7feccd80a600] frame B:42 Avg QP:25.58 size: 18000  
[libx264 @ 0x7feccd80a600] consecutive B-frames: 1.8% 0.0% 0.0% 98.2%  
[libx264 @ 0x7feccd80a600] mb I I16..4: 52.5% 30.1% 17.4%  
[libx264 @ 0x7feccd80a600] mb P I16..4: 0.4% 0.9% 3.6% P16..4: 3.4% 6.4% 7.6%
0.0% 0.0% skip:77.7%  
[libx264 @ 0x7feccd80a600] mb B I16..4: 0.0% 0.1% 0.3% B16..8: 6.7% 5.9% 5.2%
direct: 1.9% skip:79.9% L0:34.2% L1:38.8% BI:27.0%  
[libx264 @ 0x7feccd80a600] 8x8 transform intra:25.0% inter:21.6%  
[libx264 @ 0x7feccd80a600] coded y,uvDC,uvAC intra: 44.3% 49.6% 48.2% inter:
7.4% 6.7% 3.8%  
[libx264 @ 0x7feccd80a600] i16 v,h,dc,p: 94% 3% 3% 0%  
[libx264 @ 0x7feccd80a600] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 43% 5% 37% 2% 2% 2%
2% 2% 3%  
[libx264 @ 0x7feccd80a600] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 17% 15% 14% 8% 9%
10% 9% 9% 8%  
[libx264 @ 0x7feccd80a600] i8c dc,h,v,p: 68% 11% 12% 9%  
[libx264 @ 0x7feccd80a600] Weighted P-Frames: Y:0.0% UV:0.0%  
[libx264 @ 0x7feccd80a600] ref P L0: 63.0% 20.1% 11.8% 5.1%  
[libx264 @ 0x7feccd80a600] ref B L0: 94.2% 4.8% 1.0%  
[libx264 @ 0x7feccd80a600] ref B L1: 97.9% 2.1%  
[libx264 @ 0x7feccd80a600] kb/s:5012.33  
Conversion failed!  
  
\-----------------------------  
  

> save /Users/niteshkhandelwal/Desktop/efpa-update/5.cxs includeMaps true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
Cannot save '/Users/niteshkhandelwal/Desktop/efpa-update/5.cxs': [Errno 28] No
space left on device  

> save /Users/niteshkhandelwal/Desktop/image2.png supersample 3

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 350, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 452, in add  
self._history.enqueue((item, typed))  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
OSError: [Errno 28] No space left on device  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
Cannot save '/Users/niteshkhandelwal/Desktop/image2.png': [Errno 28] No space
left on device  




OpenGL version: 4.1 INTEL-16.1.7
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.7 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1554.60.15.0.0 (iBridge: 18.16.13030.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.1 (20C69)
      Kernel Version: Darwin 20.2.0
      Time since boot: 10 days 8:36

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        VX2768-2KP:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: WCZ220600583
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Input/Output
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → No space left on device

comment:2 by Eric Pettersen, 3 years ago

Resolution: → nonchimerax
Status: accepted → closed

Hi Nitesh,

Your disk drive ran out of space, so ChimeraX couldn't save images and movies. You would need to free up some space by removing files/folders in order to get things working again.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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