Opened 4 years ago

Last modified 3 years ago

#6234 assigned defect

Cannot save session including volumes bigger than 4 Gbytes

Reported by: linda.franken@… Owned by: Tom Goddard
Priority: moderate Milestone:
Component: Sessions Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform: Linux-3.10.0-1160.36.2.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
I'm trying to save a session. The maps are really big, so it is giving a size error, but it is not my disc space that is limiting here... It would be nice if there isn't a size limit for saving sessions.

Best wishes,
Linda Franken

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX

open /beegfs/cssb/user/frankenl/ongoing/Kay_Gruenewald/SPA/ts1_vs_wt-
GFP/ts1_corrected_pixel/PostProcess/job084/postprocess.mrc

Opened postprocess.mrc as #1, grid size 350,350,350, pixel 2.66, shown at
level 0.0438, step 2, values float32
No atomic structure models chosen

rename #1 ts1

volume #1 step 1

volume #1 level 0.01675

rename #1 ts1_equalparticles

open /beegfs/cssb/user/frankenl/ongoing/Kay_Gruenewald/SPA/ts1_vs_wt-
GFP/Wildtype/PostProcess/exact_9000_high-quality/postprocess.mrc

Opened postprocess.mrc as #2, grid size 350,350,350, pixel 2.66, shown at
level 0.0436, step 2, values float32

rename #2 wt_equalparticles

volume #2 step 1

volume #2 level 0.0167

set bgColor white

select #1

2 models selected

undo

select #1

2 models selected

color #1.1 cyan

select #2

2 models selected

ui tool show "Color Actions"

color sel purple

color sel medium purple

color sel medium orchid

[Repeated 1 time(s)]

color sel slate blue

color sel thistle

color sel plum

select clear

ui tool show "Fit in Map"

Fit map ts1_equalparticles in map wt_equalparticles using 4347958 points
correlation = 0.9861, correlation about mean = 0.8794, overlap = 4125
steps = 24, shift = 0.00996, angle = 0.00027 degrees

Position of ts1_equalparticles (#1) relative to wt_equalparticles (#2)
coordinates:
Matrix rotation and translation
1.00000000 -0.00000006 0.00000005 -0.00050676
0.00000006 1.00000000 -0.00000471 -0.00777279
-0.00000005 0.00000471 1.00000000 -0.00169359
Axis 0.99984493 0.01125688 0.01354272
Axis point 0.00000000 357.82014136 -1648.91782432
Rotation angle (degrees) 0.00026989
Shift along axis -0.00061711

select #1

2 models selected

ui tool show "Color Actions"

color sel dark turquoise

color sel turquoise

select clear

lighting flat

[Repeated 1 time(s)]

lighting shadows true intensity 0.5

graphics silhouettes false

graphics silhouettes true

lighting full

graphics silhouettes false

graphics silhouettes true

graphics silhouettes false

graphics silhouettes true

graphics silhouettes false

graphics silhouettes true

graphics silhouettes false

volume #1 level 0.02

volume #2 level 0.02

open
/beegfs/cssb/user/frankenl/ongoing/Kay_Gruenewald/SPA/chimera_sessions/ts1_vs_wt_vs_empty/emd_7034.map

Opened emd_7034.map as #3, grid size 1280,1280,1280, pixel 0.85, shown at step
1, values float32

volume #3 region 0,0,0,1279,1279,1279 step 8

[Repeated 1 time(s)]

volume #3 step 1

QXcbConnection: XCB error: 8 (BadMatch), sequence: 8667, resource id:
35651594, major code: 42 (SetInputFocus), minor code: 0

select #3

3 models selected

ui mousemode right "translate selected models"

view matrix models #3,​1,​0,​0,​501.26,0,1,0,40.554,0,0,1,-37.342

view matrix models #3,​1,​0,​0,​586.61,0,1,0,442.84,0,0,1,479.8

view matrix models #3,​1,​0,​0,​619.15,0,1,0,619.86,0,0,1,755.53

view matrix models #3,​1,​0,​0,​718.43,0,1,0,424.73,0,0,1,492.18

view matrix models #3,​1,​0,​0,​468.07,0,1,0,399.97,0,0,1,369.25

view matrix models #3,​1,​0,​0,​531.59,0,1,0,414.24,0,0,1,394.26

view matrix models #3,​1,​0,​0,​297.69,0,1,0,576.8,0,0,1,553.15

view matrix models #3,​1,​0,​0,​380.18,0,1,0,505.72,0,0,1,499.9

view matrix models #3,​1,​0,​0,​460.34,0,1,0,432.62,0,0,1,448.97

ui mousemode right "rotate selected models"

view matrix models
#3,​0.38675,-0.8164,0.42886,460.32,0.92129,0.32154,-0.21873,432.66,0.04068,0.4797,0.87649,448.97

view matrix models
#3,-0.26739,-0.69237,0.67017,460.29,0.90948,-0.41112,-0.061862,432.66,0.31835,0.59297,0.73962,448.98

ui mousemode right "translate selected models"

view matrix models
#3,-0.26739,-0.69237,0.67017,494.55,0.90948,-0.41112,-0.061862,457.92,0.31835,0.59297,0.73962,467.48

view matrix models
#3,-0.26739,-0.69237,0.67017,470,0.90948,-0.41112,-0.061862,440.18,0.31835,0.59297,0.73962,450.97

ui mousemode right "rotate selected models"

view matrix models
#3,​0.38853,-0.91901,-0.066805,470.04,0.28954,0.052938,0.9557,440.13,-0.87476,-0.39066,0.28666,450.96

Fit map emd_7034.map in map wt_equalparticles using 20889339 points
correlation = 0.9292, correlation about mean = 0.08682, overlap = 3.822e+06
steps = 180, shift = 30.4, angle = 9.19 degrees

Position of emd_7034.map (#3) relative to wt_equalparticles (#2) coordinates:
Matrix rotation and translation
0.49998811 -0.86603227 -0.00008725 466.22115516
0.30900145 0.17830230 0.93419830 466.19252177
-0.80903030 -0.46711498 0.35675425 466.19205222
Axis -0.70076421 0.40453363 0.58760706
Axis point 0.00000000 648.22717595 129.94766006
Rotation angle (degrees) 88.99599295
Shift along axis 135.81719359

volume #3 change image level -0.5654,0 level 5.047,0.8 level 13.36,1

volume #3 level 2.146

select clear

open
/beegfs/cssb/user/frankenl/ongoing/Kay_Gruenewald/SPA/adeno_all_data_merged/PostProcess/CTF4-5_calibratedpixel_autobfactor/postprocess.mrc

Opened postprocess.mrc as #4, grid size 1280,1280,1280, pixel 1.05, shown at
step 1, values float32

volume #4 region 0,0,0,1279,1279,1279 step 8

[Repeated 1 time(s)]

volume #4 step 1

select #4

3 models selected

rename #4 ts1_highres

ui tool show "Color Actions"

color sel dark turquoise

rename #3

No name or id option specified for renaming

color sel medium slate blue

color sel dark turquoise

select #3

3 models selected

color sel medium purple

[Repeated 1 time(s)]

color #4 turquoise models transparency 0

color #3 #b2b2ff models transparency 0

hide #!1 models

select #4

3 models selected

ui mousemode right "translate selected models"

view matrix models #4,​1,​0,​0,-307.4,0,1,0,-216.47,0,0,1,-259.42

view matrix models #4,​1,​0,​0,-254.94,0,1,0,-180.4,0,0,1,-207.2

view matrix models #4,​1,​0,​0,-244.71,0,1,0,-172.22,0,0,1,-207.48

view matrix models #4,​1,​0,​0,-235.6,0,1,0,-165.62,0,0,1,-201.54

Fit map ts1_highres in map wt_equalparticles using 20480345 points
correlation = 0.9477, correlation about mean = 0.3258, overlap = 9664
steps = 128, shift = 49.9, angle = 0.00174 degrees

Position of ts1_highres (#4) relative to wt_equalparticles (#2) coordinates:
Matrix rotation and translation
1.00000000 -0.00000786 -0.00002089 -204.49115959
0.00000786 1.00000000 0.00002063 -204.54831261
0.00002089 -0.00002063 1.00000000 -204.52055094
Axis -0.67877313 -0.68729549 0.25863478
Axis point 12594222.77171497 -0.00000000 -2429688.62936232
Rotation angle (degrees) 0.00174152
Shift along axis 226.49210857

Fit map ts1_highres in map emd_7034.map using 20480345 points
correlation = 0.7329, correlation about mean = 0.3832, overlap = 7.975e+05
steps = 40, shift = 0.00712, angle = 0.00306 degrees

Position of ts1_highres (#4) relative to emd_7034.map (#3) coordinates:
Matrix rotation and translation
0.50001866 0.30900834 -0.80900875 -0.02150887
-0.86601462 0.17834599 -0.46713101 774.55398247
-0.00006390 0.93418761 0.35678207 -865.82885073
Axis 0.70076754 -0.40453490 -0.58760223
Axis point 0.00000000 932.61493878 186.92586541
Rotation angle (degrees) 88.99306898
Shift along axis 195.41377309

select clear

lighting full

lighting soft

[Repeated 1 time(s)]

lighting full

lighting simple

[Repeated 1 time(s)]

lighting full

lighting shadows false

lighting shadows true

graphics silhouettes true

graphics silhouettes false

ui tool show "Side View"

save
/beegfs/cssb/user/frankenl/ongoing/Kay_Gruenewald/SPA/chimera_sessions/chimerax_figures/wt_vs_ts1_maps.cxs

QXcbConnection: XCB error: 8 (BadMatch), sequence: 48073, resource id:
35651597, major code: 42 (SetInputFocus), minor code: 0

ui mousemode right zoom

close #1

close #2

transparency 50

transparency 0

select #4

5 models selected

transparency sel 50

select clear

volume #3 level 1.5

volume #4 level 0.009

volume #4 change image level 0.0005444,0 level 0.01237,0.8 level 0.02391,1

save
/beegfs/cssb/user/frankenl/ongoing/Kay_Gruenewald/SPA/chimera_sessions/chimerax_figures/wt_vs_ts1_maps.cxs
includeMaps true

Traceback (most recent call last):
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/session.py", line 890, in
save
session.save(output, version=version, include_maps=include_maps)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/session.py", line 624, in
save
fserialize(stream, data)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/serialize.py", line 65, in
msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 298, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 295, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack
ValueError: bytes object is too large

ValueError: bytes object is too large

File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack

See log for complete Python traceback.

Traceback (most recent call last):
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/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 "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line
127, in show_save_file_dialog
_dlg.display(session, kw)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line
51, in display
run(session, cmd)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36,
in run
results = command.run(text, log=log, return_json=return_json)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line
2856, in run
result = ci.function(session, kw_args)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 75,
in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line
2856, in run
result = ci.function(session, kw_args)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 89,
in provider_save
saver_info.save(session, path, provider_kw)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core_formats/init.py", line
84, in save
return cxs_save(session, path, kw)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/session.py", line 890, in
save
session.save(output, version=version, include_maps=include_maps)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/session.py", line 624, in
save
fserialize(stream, data)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/serialize.py", line 65, in
msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 298, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 295, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack
ValueError: bytes object is too large

ValueError: bytes object is too large

File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack

See log for complete Python traceback.

save
/beegfs/cssb/user/frankenl/ongoing/Kay_Gruenewald/SPA/chimera_sessions/chimerax_figures/wt_vs_ts1_maps.cxs

volume #4 level 0.01

ui tool show "Side View"

ui mousemode right zoom

volume gaussian #3 bfactor 50

Opened emd_7034.map gaussian as #1, grid size 1280,1280,1280, pixel 0.85,
shown at step 1, values float32

volume #1 level 1.5

volume #1 level 1

volume gaussian #3 bfactor 100

Opened emd_7034.map gaussian as #2, grid size 1280,1280,1280, pixel 0.85,
shown at step 1, values float32

volume #2 level 1.5

volume #2 level 1

close #1

close #2

volume gaussian #3 bfactor 100

Opened emd_7034.map gaussian as #1, grid size 1280,1280,1280, pixel 0.85,
shown at step 1, values float32

volume #1 level 1.4

volume #1 color #b2b2ff

volume #4 level 0.012

volume #4 level 0.011

save
/beegfs/cssb/user/frankenl/ongoing/Kay_Gruenewald/SPA/chimera_sessions/chimerax_figures/wt_vs_ts1_maps.cxs

Traceback (most recent call last):
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/session.py", line 890, in
save
session.save(output, version=version, include_maps=include_maps)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/session.py", line 624, in
save
fserialize(stream, data)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/serialize.py", line 65, in
msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 298, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 295, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack
ValueError: bytes object is too large

ValueError: bytes object is too large

File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack

See log for complete Python traceback.

Traceback (most recent call last):
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/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 "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line
127, in show_save_file_dialog
_dlg.display(session, kw)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line
51, in display
run(session, cmd)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36,
in run
results = command.run(text, log=log, return_json=return_json)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line
2856, in run
result = ci.function(session, kw_args)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 75,
in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line
2856, in run
result = ci.function(session, kw_args)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 89,
in provider_save
saver_info.save(session, path, provider_kw)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core_formats/init.py", line
84, in save
return cxs_save(session, path, kw)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/session.py", line 890, in
save
session.save(output, version=version, include_maps=include_maps)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/session.py", line 624, in
save
fserialize(stream, data)
File "/beegfs/cssb/software/em/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/serialize.py", line 65, in
msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 298, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 295, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack
ValueError: bytes object is too large

ValueError: bytes object is too large

File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack

See log for complete Python traceback.

OpenGL version: 3.3.0 NVIDIA 510.39.01
OpenGL renderer: NVIDIA GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-1029GQ-TRT
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 40 Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
Cache Size: 14080 KB
Memory:

total used free shared buff/cache available

Mem: 376G 164G 2.6G 230M 208G 210G
Swap: 4.0G 1.2G 2.8G

Graphics:

03:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)
Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]
Kernel driver in use: ast

Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:

alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
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: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
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: 1.0
ChimeraX-DistMonitor: 1.1.5
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: 1.1
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-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
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: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
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: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
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
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
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: 1.6.1
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: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
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: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
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: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0

Change History (5)

comment:1 by Eric Pettersen, 4 years ago

Another report of #5501

comment:2 by Tom Goddard, 4 years ago

Unfortunately ChimeraX uses the widely used msgpack library which is limited to containing objects smaller than 4 Gbytes (uses 32-bit integer object sizes). You must be including a map larger than 4 Gbytes. I made ChimeraX daily builds warn about this 4 months ago but that warning is not in ChimeraX 1.3 that you are using.

With more complex code we can have ChimeraX break up large maps into pieces smaller than 4 Gbytes in sessions and then reassemble them when the session is opened. I will look into adding that code in the future since I agree that the 4 Gbyte limit is unreasonable. But I don't know when I will have time to add that. I will reply when it has been added.

For now one way to handle this is not use the "includeMaps" option when saving a session. Then the session file will contain a path to the map file. If you want to make a self contained package, you could put the maps and .cxs file in a directory and zip that directory -- not a great solution I realize.

in reply to:  3 ; comment:3 by linda.franken@…, 4 years ago 

Hi Tom Goddard,
Thank you for looking into it. As a side node: The problem also arrised when saving a session without ticking the include maps, because I had an unsaved gaussian map open. After saving that map into a new file it I could at least save the session. I'm not sure if this problem/solution comes up in the warning in the daily built already, but it took me a while to figure out how to be able to save the session at all so it may be a nice interim solution to include this in the error message/warning message.

Best wishes,
Linda 

----- Original Message -----
From: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu, gregc@cgl.ucsf.edu, "Linda Franken" <linda.franken@cssb-hamburg.de>
Sent: Thursday, 24 February, 2022 23:39:55
Subject: Re: [ChimeraX] #6234: Cannot save session: bytes object is too large

#6234: Cannot save session: bytes object is too large
--------------------------------------+-------------------------
          Reporter:  linda.franken@…  |      Owner:  Tom Goddard
              Type:  defect           |     Status:  assigned
          Priority:  moderate         |  Milestone:
         Component:  Sessions         |    Version:
        Resolution:                   |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+-------------------------

Comment (by Tom Goddard):

 Unfortunately ChimeraX uses the widely used msgpack library which is
 limited to containing objects smaller than 4 Gbytes (uses 32-bit integer
 object sizes).  You must be including a map larger than 4 Gbytes.  I made
 ChimeraX daily builds warn about this 4 months ago but that warning is not
 in ChimeraX 1.3 that you are using.

 With more complex code we can have ChimeraX break up large maps into
 pieces smaller than 4 Gbytes in sessions and then reassemble them when the
 session is opened.  I will look into adding that code in the future since
 I agree that the 4 Gbyte limit is unreasonable.  But I don't know when I
 will have time to add that.  I will reply when it has been added.

 For now one way to handle this is not use the "includeMaps" option when
 saving a session.  Then the session file will contain a path to the map
 file.  If you want to make a self contained package, you could put the
 maps and .cxs file in a directory and zip that directory -- not a great
 solution I realize.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6234#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

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

Thanks for the explanation.  Yes, the warning message I put into ChimeraX 4 months ago for saving maps in sessions larger than 4 Gbytes does explain that you should save the map as a separate file.

Hopefully I can add support for larger maps in sessions before ChimeraX 1.4 comes out in a few months.

comment:5 by Tom Goddard, 3 years ago

Summary: Cannot save session: bytes object is too large → Cannot save session including volumes bigger than 4 Gbytes
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