Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5501 closed defect (fixed)

Cannot save session: bytes object is too large

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__actin_seg.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__F_prot_seg.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__Membrane_seg.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__mito_seg_2.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__ribosomes_seg.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__RSV_seg_2.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__vesicles_seg.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2.mrc

Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__actin_seg.hdf
as #1, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__F_prot_seg.hdf
as #2, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__Membrane_seg.hdf
as #3, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__mito_seg_2.hdf
as #4, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__ribosomes_seg.hdf
as #5, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__RSV_seg_2.hdf
as #6, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__vesicles_seg.hdf
as #7, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2.mrc as #8, grid
size 2046,2880,800, pixel 9.21,9.21,9.21, shown at step 1, values int16  

> volume #1 color #ff3300 color white color white

> volume #2 color #990099 color white color white

> volume #3 color #0033cc color white color white

> volume #4 color cyan color white color white

> volume #5 color #ffff33 color white color white

> volume #6 color magenta color white color white

> volume #7 color #3399ff color white color white

> volume #8 level -8.998,0 level 25.99,0.8 level 100,1

> volume #8 level -149,0 level 25.99,0.8 level 100,1

> volume #8 level -149,0 level -26.02,1 level 100,1

> volume #8 level -149,0 level -26.02,1 level 28.2,1

> volume #8 level -149,0 level 23.64,1 level 28.2,1

> volume #8 level -149,0 level 23.64,1 level 114.6,0.9706

> volume #8 level -66.42,0.01471 level 23.64,1 level 114.6,0.9706

> volume #8 level -66.42,0.01471 level 6.905,1 level 114.6,0.9706

> volume #8 level -74.52,0 level 6.905,1 level 114.6,0.9706

> volume #7 color black color white color white

> volume #7 color white color white color white

> volume #8 level -100.4,0 level 6.905,1 level 114.6,0.9706

> volume #8 level -100.4,0 level 27.41,1 level 114.6,0.9706

> volume #8 level -100.4,0 level 27.41,1 level 80.55,1

> volume #8 level -53.47,0 level 27.41,1 level 80.55,1

> volume #8 level -53.47,0 level 18.24,1 level 80.55,1

> volume #8 level -53.47,0 level 18.24,1 level 77.32,1

> volume #7 region 0,0,0,2047,2879,799 step 8

> volume #7 region 0,0,0,2047,2879,799 step 8

> volume #6 region 0,0,0,2047,2879,799 step 8

> volume #6 region 0,0,0,2047,2879,799 step 8

> volume #5 region 0,0,0,2047,2879,799 step 8

> volume #5 region 0,0,0,2047,2879,799 step 8

> volume #4 region 0,0,0,2047,2879,799 step 8

> volume #4 region 0,0,0,2047,2879,799 step 8

> ui tool show "Hide Dust"

> volume #3 region 0,0,0,2047,2879,799 step 8

> volume #3 region 0,0,0,2047,2879,799 step 8

> volume #2 region 0,0,0,2047,2879,799 step 8

> volume #2 region 0,0,0,2047,2879,799 step 8

> volume #1 region 0,0,0,2047,2879,799 step 8

> volume #1 region 0,0,0,2047,2879,799 step 8

> volume #1 step 4

> volume #2 step 4

> volume #3 step 4

> volume #4 step 4

> volume #5 step 4

> volume #6 step 4

> volume #1 color #ff6600

> volume #2 color #990099

> volume #3 color #3366ff

> volume #4 color cyan

> volume #5 color #ffcc00

> volume #1 color #33cc33

> volume #1 color #99ff99

> volume #6 color #ff33ff

> volume #7 color #3366cc

> volume #7 color #6699ff

> volume #7 step 4

> surface dust #3 size 809.79

> surface dust #6 size 1001.1

> surface dust #2 size 573.29

> surface dust #1 size 445.22

> surface dust #4 size 558.05

> surface dust #5 size 211.58

> surface dust #7 size 757.83

> volume #6 color #ff66cc

> volume #2 color #660066

> surface dust #2 size 588.53

> surface dust #2 size 311.08

> surface undust #2

> surface dust #2 size 311.08

> surface undust #1

> surface dust #1 size 831.33

> surface undust #4

> surface dust #4 size 1395.6

> surface undust #4

> surface dust #4 size 1945.7

> volume #7 color #3399ff

> volume #7 color #6699cc

> volume #7 color #3399cc

> volume #7 color #33ffff

> volume #7 color #00ffcc

> volume #7 color #669999

> volume #5 color #cc9900

> volume #5 color #ffcc33

> volume #5 color #cc9900

> volume #5 color #cc9933

> volume #5 color #ff9933

> volume #5 color #cc9933

> volume #6 step 2

> volume #2 step 2

> volume #6 color #990099

> volume #2 color #ff66ff

> volume #2 color #ff33cc

> volume #2 color #ff66cc

> surface undust #1

> surface dust #1 size 1945.7

> surface undust #3

> surface dust #3 size 1306.1

> surface dust #3 size 1359.5

> surface dust #3 size 488.73

> surface dust #3 size 495.19

> surface dust #3 size 411.22

> save /Users/dparrell/Desktop/Cimera_session/all_together.cxs

> surface dust #3 size 416.65

> surface dust #3 size 279.69

> surface dust #3 size 279.69

> surface undust #3

> surface dust #3 size 654.59

> open
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__RNP_seg.hdf

Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__RNP_seg.hdf
as #9, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  

> volume #9 region 0,0,0,2047,2879,799 step 8

> volume #9 region 0,0,0,2047,2879,799 step 8

> surface dust #9 size 355.2

> volume #9 step 2

> surface undust #9

> surface dust #9 size 1306.1

> volume #9 step 1

> volume #2 color #ffff33

> volume #5 color #ffcc66

> volume #5 color #996600

> volume #5 color #663300

> volume #5 color #cc9933

> volume #5 color #663300

> volume #5 color #996600

> volume #5 color #993300

> volume #5 color #996633

> volume #5 color #cc9966

> volume #5 color #996633

> volume #7 color #339999

> volume #7 color #3366ff

> save /Users/dparrell/Desktop/Cimera_session/all_together.cxs

> volume #9 change image level 0.001024,0 level 0.3416,0.8 level 5.121,1

> volume #6 level 0.06757

> volume #6 level 0.09577

> ui mousemode right "map eraser"

> volume erase #6 center 6212.1,15144,3786.2 radius 3139.8

Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__RSV_seg_2.hdf
copy as #11, grid size 2048,2880,800, pixel 9.21, shown at step 1, values
float32  
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py:2746: RuntimeWarning: invalid value
encountered in log  
h.show_data(log(counts + 1))  

> surface dust #11 size 881.6

> volume erase #11 center 3326.4,9530.3,3334.4 radius 6243.9

> volume erase #11 center 1409.6,17596,2895 radius 6243.9

> volume erase #11 center 4202.7,28267,1721.9 radius 6243.9

> volume erase #11 center 9729.6,23672,-2829.2 radius 6243.9

> volume erase #11 center 8636.4,26666,958.45 radius 6243.9

> volume erase #11 center 3077,4316,3490.6 radius 6243.9

> volume erase #11 center 13939,4017.2,-3371.2 radius 6243.9

> volume erase #11 center 12873,16895,-2776.1 radius 6243.9

> volume erase #11 center 11716,12726,-2098.6 radius 6243.9

> volume erase #11 center 10478,1740.8,-1711.7 radius 6243.9

> volume erase #11 center 9420.2,6733.4,-1046.6 radius 5514.8

> volume erase #11 center 12085,9343.6,-1188.3 radius 5514.8

> volume erase #11 center 16197,548.92,3457.6 radius 1895.7

> volume erase #11 center 11598,4213.1,4775.3 radius 596.55

> volume erase #11 center 11518,4117.8,5466.7 radius 636.32

> volume erase #11 center 11425,3928,5386.7 radius 636.32

> volume erase #11 center 12584,4354.6,5458 radius 477.24

> volume erase #11 center 10222,5066.8,5208 radius 596.55

> volume erase #11 center 11588,315.51,6818.3 radius 914.71

> volume erase #11 center 13368,539.76,6531.5 radius 914.71

> volume erase #11 center 11517,8218.9,7208.7 radius 1670.3

> volume erase #11 center 11223,11015,5278.5 radius 1445

> volume erase #11 center 9171.7,20186,4117.7 radius 2677.8

> surface undust #11

> surface dust #11 size 881.6

> volume erase #11 center 11140,25787,6577.3 radius 3155.1

> volume erase #11 center 12560,21685,9256.6 radius 3155.1

> volume erase #11 center 13039,21487,1294.8 radius 3155.1

> volume erase #11 center 9506,16183,1358.7 radius 3155.1

> save /Users/dparrell/Desktop/Cimera_session/all_together.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack/_packer.pyx", line 286, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 289, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 225, in msgpack._cmsgpack.Packer._pack  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
ValueError: bytes object is too large  
  
ValueError: bytes object is too large  
  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack/_packer.pyx", line 286, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 289, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 225, in msgpack._cmsgpack.Packer._pack  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
ValueError: bytes object is too large  
  
ValueError: bytes object is too large  
  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  

> volume erase #4 center 13068,19133,3729.4 radius 3155.1

Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__mito_seg_2.hdf
copy as #12, grid size 2048,2880,800, pixel 9.21, shown at step 1, values
float32  

> surface dust #12 size 1945.7

> surface dust #12 size 1975.5

> surface dust #12 size 2625.9

> volume erase #12 center 10906,2495.6,3867.8 radius 4586.8

> volume erase #12 center -790.17,13195,3067.3 radius 4586.8

> volume erase #12 center 2787.2,7535.9,4923.3 radius 4586.8

> volume erase #12 center 10599,18655,4194.2 radius 4586.8

> volume #12 level 0.2221

> volume #12 step 2

> surface dust #12 size 3270.9

> surface undust #12

> surface dust #12 size 3919.9

> volume erase #12 center 4903.7,21820,3696.3 radius 1060.5

> volume erase #12 center 5253.1,22175,3763.5 radius 1060.5

> volume erase #12 center 6611.3,14665,2814.6 radius 1060.5

> volume erase #12 center 7541.3,20717,3755.3 radius 1060.5

> volume erase #12 center 6678.8,19911,3583.8 radius 1060.5

> volume erase #12 center 7120.6,20292,3326.2 radius 1060.5

> volume erase #12 center 6106.1,19771,3044.1 radius 1060.5

> volume erase #12 center 2155.5,20228,3632.1 radius 1060.5

> volume erase #12 center 2639.5,20006,3685.5 radius 1060.5

> volume erase #12 center 2981.1,19839,3464.5 radius 1060.5

> volume erase #12 center 6117.8,24246,2221.5 radius 1060.5

> volume erase #12 center 5933.5,24412,2410.6 radius 1060.5

Can only have one displayed volume when erasing  

> volume erase #9 center 4679.8,23528,3625.6 radius 2134.3

Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__RNP_seg.hdf
copy as #13, grid size 2048,2880,800, pixel 9.21, shown at step 1, values
float32  

> surface dust #13 size 1305.2

> surface undust #13

> surface dust #13 size 1103.5

> surface undust #13

> surface dust #13 size 1008

> volume erase #13 center 2616.9,5089.2,2117.7 radius 6880.2

> volume erase #13 center 2616.9,5089.2,2117.7 radius 6880.2

> volume erase #13 center 2616.9,5089.2,2117.7 radius 6880.2

> volume erase #13 center 2561.5,14150,3378.7 radius 4653.1

> volume erase #13 center 13909,3411.8,-1672.6 radius 4653.1

> volume erase #13 center 14817,13419,-1362.8 radius 4653.1

> volume erase #13 center 12765,19995,-647.43 radius 4653.1

> volume erase #13 center 14997,23379,209.99 radius 4653.1

> surface dust #13 size 1020.6

> surface dust #13 size 146.61

> surface dust #13 size 12

> surface dust #13 size 120

> surface dust #13 size 1020

> volume erase #13 center 10046,4497.3,119.3 radius 4653.1

> volume erase #13 center 13169,20773,5542.5 radius 3407

> close #9

> close #4

> close #6

> save /Users/dparrell/Desktop/Cimera_session/all_together_clean.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack/_packer.pyx", line 286, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 289, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 225, in msgpack._cmsgpack.Packer._pack  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
ValueError: bytes object is too large  
  
ValueError: bytes object is too large  
  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack/_packer.pyx", line 286, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 289, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 225, in msgpack._cmsgpack.Packer._pack  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
ValueError: bytes object is too large  
  
ValueError: bytes object is too large  
  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.26
OpenGL renderer: AMD Radeon Pro Vega 64X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac Pro
      Model Identifier: iMacPro1,1
      Processor Name: Intel Xeon W
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 18
      L2 Cache (per Core): 1 MB
      L3 Cache: 24.8 MB
      Hyper-Threading Technology: Enabled
      Memory: 256 GB
      Boot ROM Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G9323)
      Kernel Version: Darwin 18.7.0
      Time since boot: 16 days 10:06

Graphics/Displays:

    Radeon Pro Vega 64X:

      Chipset Model: Radeon Pro Vega 64X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 16 GB
      Vendor: AMD (0x1002)
      Device ID: 0x686b
      Revision ID: 0x0000
      ROM Revision: 113-D0500D-114
      VBIOS Version: 113-D05001A1XX-021
      Option ROM Version: 113-D05001A1XX-021
      EFI Driver Version: 01.01.114
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
        LED Cinema Display:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 2A11515U6JL 
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (7)

comment:1 by pett, 4 years ago

Cc: chimera-programmers added
Component: Unassigned → Sessions
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Cannot save session: bytes object is too large

comment:2 by Greg Couch, 4 years ago

Owner: changed from Greg Couch to Tom Goddard

The maximum size of a binary object that can be serialized by msgpack is (232)-1 bytes. From the log it appears likely that the huge data object was from the volume code. So the easiest way to fix this if for the volume code to break the object into multiple parts.

comment:3 by Tom Goddard, 4 years ago

Yep the user opened a 2048,2880,800 map of float values (18 Gbytes), then erased part of it which made a copy, then tried to save a session.

It is a bit surprising that they tried to save this as a session since that is going to create unusably slow performance loading it later, while saving as a map file (.mrc, .cmap) would be able to load it quickly. Also after they save the map to a file, the session would just keep a path to that map so session save would work. So I think the user did not understand how to do this to get good performance.

That said, the session should save and this is an unfortunate limitation of msgpack. I can add some code to the map saving that breaks it into chunks less than 4 Gbytes in size and then reassembles them on restore. That adds complexity for a very rare case, and is probably not what the user wanted. So instead I should add an error message that explains they should save the map, then save the session.

comment:4 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Added error message that explain 4Gb limit and suggests saving map in separate map file. Might make sessions include larger maps if another user reports the need.

comment:5 by Tom Goddard, 4 years ago

Added error message only for ChimeraX 1.4, not 1.3.

comment:6 by Greg Couch, 4 years ago

Seems like it would be reasonable to add this to the 1.3 release as it should eliminate some future bug reports.

in reply to:  7 ; comment:7 by goddard@…, 4 years ago 

Don't want to add it to 1.3 because I had to change core/session.py to handle UserError specially when saving the session and that could have some unintended effects.
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