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#4439 closed defect (fixed)

Large meeting session: msgpack.exceptions.BufferFull

Reported by:	goddard@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	VR	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description (last modified by pett)

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.dev202103310726 (2021-03-31 07:26:37 UTC)
Description
(Describe the actions that caused this problem to occur here)
Transfering 284 Mbyte apoferritin sessiion from Miike Schmid meeting got 35% of the way and then gave this error.

Log:
UCSF ChimeraX version: 1.2.dev202103310726 (2021-03-31)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Unable to load numpy_formathandler accelerator from OpenGL_accelerate  

> open C:\Users\goddard\Desktop\apoferritin.cxs format session

Opened emdb 22657 thresholded as #3, grid size 420,420,420, pixel 0.4, shown
at level 0.018, step 1, values float32  
Log from Tue Mar 30 18:57:35 2021UCSF ChimeraX version: 1.2.dev202103162155
(2021-03-16)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2gbp

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #1  
---  
Chain | Description  
A | D-galactose/D-glucose binding protein  
  
Non-standard residues in 2gbp #1  
---  
BGC — β-D-glucose  
CA — calcium ion  
  

> set bgColor white

> graphics silhouettes true

> molmap protein 8 gridSpacing 1

Opened 2gbp map 8 as #2, grid size 94,90,112, pixel 1, shown at level 0.0778,
step 1, values float32  

> transparency #2 70

> hide #!2 models

> save /Users/goddard/Desktop/image1.png supersample 3

> hide #!1 models

> show #!2 models

> graphics silhouettes false

> save /Users/goddard/Desktop/image2.png transparentBackground true

> close

> open 22658 fromDatabase emdb

Summary of feedback from opening 22658 fetched from emdb  
---  
note | Fetching compressed map 22658 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22658/map/emd_22658.map.gz  
  
Opened emdb 22658 as #1, grid size 330,330,330, pixel 0.502, shown at level
0.08, step 2, values float32  

> open 7k3v

Summary of feedback from opening 7k3v fetched from pdb  
---  
note | Fetching compressed mmCIF 7k3v from
http://files.rcsb.org/download/7k3v.cif  
  
7k3v title:  
Apoferritin structure at 1.34 angstrom resolution determined from a 300 kV
Titan Krios G3i electron microscope with K3 detector [more info...]  
  
Chain information for 7k3v #2  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain  
  
Non-standard residues in 7k3v #2  
---  
NA — sodium ion  
ZN — zinc ion  
  

> style stick

Changed 36918 atom styles  

> volume #1 level 0.03917

> ui tool show "Map Coordinates"

> volume #1 level 0.027

> style sphere

Changed 36918 atom styles  

> style stick

Changed 36918 atom styles  

> fitmap #2 inMap #1

Fit molecule 7k3v (#2) to map emdb 22658 (#1) using 36918 atoms  
average map value = 0.01362, steps = 68  
shifted from previous position = 0.0482  
rotated from previous position = 1.56 degrees  
atoms outside contour = 30977, contour level = 0.026997  
  
Position of 7k3v (#2) relative to emdb 22658 (#1) coordinates:  
Matrix rotation and translation  
0.99975395 -0.01556557 0.01580326 -0.02687632  
0.01581163 0.99975381 -0.01556648 -0.02836100  
-0.01555707 0.01581252 0.99975394 -0.02828319  
Axis 0.57747570 0.57713234 0.57744270  
Axis point 0.00000000 0.02720432 -0.03457098  
Rotation angle (degrees) 1.55686662  
Shift along axis -0.04822039  
  

> close #1

> close

> open 22657 fromDatabase emdb

Summary of feedback from opening 22657 fetched from emdb  
---  
note | Fetching compressed map 22657 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22657/map/emd_22657.map.gz  
  
Opened emdb 22657 as #1, grid size 420,420,420, pixel 0.4, shown at level
0.0273, step 2, values float32  

> open 7k3v format mmcif fromDatabase pdb

7k3v title:  
Apoferritin structure at 1.34 angstrom resolution determined from a 300 kV
Titan Krios G3i electron microscope with K3 detector [more info...]  
  
Chain information for 7k3v #2  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain  
  
Non-standard residues in 7k3v #2  
---  
NA — sodium ion  
ZN — zinc ion  
  

> style stick

Changed 36918 atom styles  

> volume #1 level 0.01701

> lighting soft

> volume #1 step 1

> volume #1 color #b2b2b2bf

> volume #1 color #b2b2b2e7

> volume #1 color #b2b2b2

> volume showOutlineBox true

> set bgColor black

> volume #1 color #b2b2b2d2

> uage material

Unknown command: uage material  

> usage material

material [preset] [reflectivity a number] [specularReflectivity a number]
[exponent a number] [ambientReflectivity a number] [transparentCastShadows
true or false] [meshesCastShadows true or false]  
— report or alter material parameters  
preset: one of default, dull, or shiny  

> material meshcast true

Expected one of 'default', 'dull', or 'shiny' or a keyword  

> material meshesCastShadows true

> material transparentCastShadows true

> volume #1 style mesh

> set bgColor white

> set bgColor black

> volume #1 style surface

> volume #1 step 2

> volume #1 level 0.01512

> volume #1 step 1

> close

> open 22658 format ccp4 fromDatabase emdb

Opened emdb 22658 as #1, grid size 330,330,330, pixel 0.502, shown at level
0.08, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.05226

> volume #1 level 0.0502

> volume showOutlineBox true

> open 7k3w

Summary of feedback from opening 7k3w fetched from pdb  
---  
note | Fetching compressed mmCIF 7k3w from
http://files.rcsb.org/download/7k3w.cif  
  
7k3w title:  
Apoferritin structure at 1.36 angstrom resolution determined from a 300 kV
Titan Krios G3i electron microscope with Falcon4 detector [more info...]  
  
Chain information for 7k3w #2  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain  
  
Non-standard residues in 7k3w #2  
---  
NA — sodium ion  
ZN — zinc ion  
  

> style stick

Changed 36974 atom styles  

> color byhetero

> volume #1 color #b2b2b2ae

> usage volume thresh

volume threshold volumes [minimum a number] [set a number] [maximum a number]
[setMaximum a number] [subregion map region] [step map step] [modelId modelId]  
— Set map values below a threshold to zero  
modelId: a model id  

> volume #1 level 0.0202

> volume #1 level 0.0502

> volume threshold #1 minimum 0.02

Opened emdb 22658 thresholded as #3, grid size 330,330,330, pixel 0.502, shown
at step 1, values float32  

> close #1

> save /Users/goddard/Desktop/test.cxs includeMaps true

> close

> open 22657 format ccp4 fromDatabase emdb

Opened emdb 22657 as #1, grid size 420,420,420, pixel 0.4, shown at level
0.0273, step 2, values float32  

> open 7k3v format mmcif fromDatabase pdb

7k3v title:  
Apoferritin structure at 1.34 angstrom resolution determined from a 300 kV
Titan Krios G3i electron microscope with K3 detector [more info...]  
  
Chain information for 7k3v #2  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain  
  
Non-standard residues in 7k3v #2  
---  
NA — sodium ion  
ZN — zinc ion  
  

> style stick

Changed 36918 atom styles  

> style stick

Changed 36918 atom styles  

> color byhetero

> volume #1 level 0.01

> volume #1 level 0.02

> volume #1 step 1

> volume #1 level 0.01

> volume #1 level 0.02

> volume #1 level 0.015

> volume threshold #1 minimum 0.01

Opened emdb 22657 thresholded as #3, grid size 420,420,420, pixel 0.4, shown
at step 1, values float32  

> close #1

> volume #3 level 0.018

> volume #3 color #b2b2b2c2

> volume #3 color #b2b2b2a9

> volume #3 color #b2b2b275

> volume #3 color #b2b2b290

> volume #3 color #b2b2b2c1

> save /Users/goddard/Desktop/apoferritin.cxs includeMaps true

——— End of log from Tue Mar 30 18:57:35 2021 ———

opened ChimeraX session  

> close

> ui tool show Meeting

> open C:\Users\goddard\Desktop\apoferritin.cxs format session

Opened emdb 22657 thresholded as #3, grid size 420,420,420, pixel 0.4, shown
at level 0.018, step 1, values float32  
Log from Tue Mar 30 18:57:35 2021UCSF ChimeraX version: 1.2.dev202103162155
(2021-03-16)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2gbp

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #1  
---  
Chain | Description  
A | D-galactose/D-glucose binding protein  
  
Non-standard residues in 2gbp #1  
---  
BGC — β-D-glucose  
CA — calcium ion  
  

> set bgColor white

> graphics silhouettes true

> molmap protein 8 gridSpacing 1

Opened 2gbp map 8 as #2, grid size 94,90,112, pixel 1, shown at level 0.0778,
step 1, values float32  

> transparency #2 70

> hide #!2 models

> save /Users/goddard/Desktop/image1.png supersample 3

> hide #!1 models

> show #!2 models

> graphics silhouettes false

> save /Users/goddard/Desktop/image2.png transparentBackground true

> close

> open 22658 fromDatabase emdb

Summary of feedback from opening 22658 fetched from emdb  
---  
note | Fetching compressed map 22658 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22658/map/emd_22658.map.gz  
  
Opened emdb 22658 as #1, grid size 330,330,330, pixel 0.502, shown at level
0.08, step 2, values float32  

> open 7k3v

Summary of feedback from opening 7k3v fetched from pdb  
---  
note | Fetching compressed mmCIF 7k3v from
http://files.rcsb.org/download/7k3v.cif  
  
7k3v title:  
Apoferritin structure at 1.34 angstrom resolution determined from a 300 kV
Titan Krios G3i electron microscope with K3 detector [more info...]  
  
Chain information for 7k3v #2  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain  
  
Non-standard residues in 7k3v #2  
---  
NA — sodium ion  
ZN — zinc ion  
  

> style stick

Changed 36918 atom styles  

> volume #1 level 0.03917

> ui tool show "Map Coordinates"

> volume #1 level 0.027

> style sphere

Changed 36918 atom styles  

> style stick

Changed 36918 atom styles  

> fitmap #2 inMap #1

Fit molecule 7k3v (#2) to map emdb 22658 (#1) using 36918 atoms  
average map value = 0.01362, steps = 68  
shifted from previous position = 0.0482  
rotated from previous position = 1.56 degrees  
atoms outside contour = 30977, contour level = 0.026997  
  
Position of 7k3v (#2) relative to emdb 22658 (#1) coordinates:  
Matrix rotation and translation  
0.99975395 -0.01556557 0.01580326 -0.02687632  
0.01581163 0.99975381 -0.01556648 -0.02836100  
-0.01555707 0.01581252 0.99975394 -0.02828319  
Axis 0.57747570 0.57713234 0.57744270  
Axis point 0.00000000 0.02720432 -0.03457098  
Rotation angle (degrees) 1.55686662  
Shift along axis -0.04822039  
  

> close #1

> close

> open 22657 fromDatabase emdb

Summary of feedback from opening 22657 fetched from emdb  
---  
note | Fetching compressed map 22657 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22657/map/emd_22657.map.gz  
  
Opened emdb 22657 as #1, grid size 420,420,420, pixel 0.4, shown at level
0.0273, step 2, values float32  

> open 7k3v format mmcif fromDatabase pdb

7k3v title:  
Apoferritin structure at 1.34 angstrom resolution determined from a 300 kV
Titan Krios G3i electron microscope with K3 detector [more info...]  
  
Chain information for 7k3v #2  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain  
  
Non-standard residues in 7k3v #2  
---  
NA — sodium ion  
ZN — zinc ion  
  

> style stick

Changed 36918 atom styles  

> volume #1 level 0.01701

> lighting soft

> volume #1 step 1

> volume #1 color #b2b2b2bf

> volume #1 color #b2b2b2e7

> volume #1 color #b2b2b2

> volume showOutlineBox true

> set bgColor black

> volume #1 color #b2b2b2d2

> uage material

Unknown command: uage material  

> usage material

material [preset] [reflectivity a number] [specularReflectivity a number]
[exponent a number] [ambientReflectivity a number] [transparentCastShadows
true or false] [meshesCastShadows true or false]  
— report or alter material parameters  
preset: one of default, dull, or shiny  

> material meshcast true

Expected one of 'default', 'dull', or 'shiny' or a keyword  

> material meshesCastShadows true

> material transparentCastShadows true

> volume #1 style mesh

> set bgColor white

> set bgColor black

> volume #1 style surface

> volume #1 step 2

> volume #1 level 0.01512

> volume #1 step 1

> close

> open 22658 format ccp4 fromDatabase emdb

Opened emdb 22658 as #1, grid size 330,330,330, pixel 0.502, shown at level
0.08, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.05226

> volume #1 level 0.0502

> volume showOutlineBox true

> open 7k3w

Summary of feedback from opening 7k3w fetched from pdb  
---  
note | Fetching compressed mmCIF 7k3w from
http://files.rcsb.org/download/7k3w.cif  
  
7k3w title:  
Apoferritin structure at 1.36 angstrom resolution determined from a 300 kV
Titan Krios G3i electron microscope with Falcon4 detector [more info...]  
  
Chain information for 7k3w #2  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain  
  
Non-standard residues in 7k3w #2  
---  
NA — sodium ion  
ZN — zinc ion  
  

> style stick

Changed 36974 atom styles  

> color byhetero

> volume #1 color #b2b2b2ae

> usage volume thresh

volume threshold volumes [minimum a number] [set a number] [maximum a number]
[setMaximum a number] [subregion map region] [step map step] [modelId modelId]  
— Set map values below a threshold to zero  
modelId: a model id  

> volume #1 level 0.0202

> volume #1 level 0.0502

> volume threshold #1 minimum 0.02

Opened emdb 22658 thresholded as #3, grid size 330,330,330, pixel 0.502, shown
at step 1, values float32  

> close #1

> save /Users/goddard/Desktop/test.cxs includeMaps true

> close

> open 22657 format ccp4 fromDatabase emdb

Opened emdb 22657 as #1, grid size 420,420,420, pixel 0.4, shown at level
0.0273, step 2, values float32  

> open 7k3v format mmcif fromDatabase pdb

7k3v title:  
Apoferritin structure at 1.34 angstrom resolution determined from a 300 kV
Titan Krios G3i electron microscope with K3 detector [more info...]  
  
Chain information for 7k3v #2  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X | Ferritin heavy chain  
  
Non-standard residues in 7k3v #2  
---  
NA — sodium ion  
ZN — zinc ion  
  

> style stick

Changed 36918 atom styles  

> style stick

Changed 36918 atom styles  

> color byhetero

> volume #1 level 0.01

> volume #1 level 0.02

> volume #1 step 1

> volume #1 level 0.01

> volume #1 level 0.02

> volume #1 level 0.015

> volume threshold #1 minimum 0.01

Opened emdb 22657 thresholded as #3, grid size 420,420,420, pixel 0.4, shown
at step 1, values float32  

> close #1

> volume #3 level 0.018

> volume #3 color #b2b2b2c2

> volume #3 color #b2b2b2a9

> volume #3 color #b2b2b275

> volume #3 color #b2b2b290

> volume #3 color #b2b2b2c1

> save /Users/goddard/Desktop/apoferritin.cxs includeMaps true

——— End of log from Tue Mar 30 18:57:35 2021 ———

opened ChimeraX session  

> close

> meeting mfs

Joining meeting"mfs" at chimeraxmeeting.net port 52203  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  

[deleted a ton of these]

See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1238, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Mar-31-2021\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1250, in _read_message  
unpacker.feed(rbytes)  
File "msgpack\\_unpacker.pyx", line 389, in msgpack._cmsgpack.Unpacker.feed  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
msgpack.exceptions.BufferFull  
  
msgpack.exceptions.BufferFull  
  
File "msgpack\\_unpacker.pyx", line 412, in
msgpack._cmsgpack.Unpacker.append_buffer  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z270X-Gaming K7
OS: Microsoft Windows 10 Home (Build 19041)
Memory: 17,129,693,184
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.4
    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: 1.12
    ChimeraX-AtomicLibrary: 3.0
    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: 2.5.1
    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: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202103310726
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 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
    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
    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: 1.1
    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
    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
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    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
    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: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.1
    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: 4.4.2
    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: 1.1.1
    matplotlib: 3.3.2
    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
    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
    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
    pywin32: 228
    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: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    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
    WMI: 1.5.1

Change History (3)

comment:1 by pett, 5 years ago

Component:	Unassigned → VR
Description:	modified (diff)
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Large meeting session: msgpack.exceptions.BufferFull

comment:2 by Tom Goddard, 5 years ago

Default msgpack unpacker buffer size is 100 Mbytes as described here

https://msgpack-python.readthedocs.io/en/latest/api.html

Maximum buffer size is 4 Gbytes and should set the limit to 4 Gbytes. Even that is going to cause future problems transmitting large image data sessions for meetings over fast network connections.

This msgpack unpacker is specific to the meeting code reading a session over a socket. I should look how the standard ChimeraX session restore from a file deals with the msgpack limit.

comment:3 by Tom Goddard, 5 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed.

I set the message pack object size limit in the meeting code to 2³² - 1 which is the maximum supported size. The code for restoring sessions from files already did this.

Last edited 5 years ago by Tom Goddard (previous) (diff)

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