id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
3904	Input/output error reading session	chimerax-bug-report@…	Greg Couch	"{{{
The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.12.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 0.94 (2020-04-14)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.94.dev202004140658 (2020-04-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open2
> /run/media/tanjiaxing/JiaxingTan/1_1_Flagella_Figures/Figure0920new/Fig7-MSring/L1L2/L1L2.cxs

Traceback (most recent call last):  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/open_command/dialog.py"", line 146, in _qt_safe  
if data_format is None else "" format "" +
StringArg.unparse(data_format.nicknames[0])))  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py"", line 31, in run  
results = command.run(text, log=log)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py"", line 2848, in run  
result = ci.function(session, **kw_args)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/open_command/cmd.py"", line 86, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py"", line 2848, in run  
result = ci.function(session, **kw_args)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/open_command/cmd.py"", line 136, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/open_command/cmd.py"", line 349, in collated_open  
return func(*func_args, **func_kw)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py"", line 26, in open  
return cxs_open(session, data, **kw)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py"", line 913, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/session.py"", line 609, in restore  
metadata = fdeserialize(stream)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/serialize.py"", line 68, in msgpack_deserialize  
return next(stream)  
File ""msgpack/_unpacker.pyx"", line 562, in msgpack._cmsgpack.Unpacker.__next__  
File ""msgpack/_unpacker.pyx"", line 483, in msgpack._cmsgpack.Unpacker._unpack  
File ""msgpack/_unpacker.pyx"", line 468, in
msgpack._cmsgpack.Unpacker.read_from_file  
OSError: [Errno 5] Input/output error  
  
OSError: [Errno 5] Input/output error  
  
File ""msgpack/_unpacker.pyx"", line 468, in
msgpack._cmsgpack.Unpacker.read_from_file  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 418.43
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: C246-WU4
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
Cache Size: 12288 KB
Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P4000] [10de:1bb1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:11a3]
	Kernel driver in use: nvidia

}}}
"	defect	closed	normal		Sessions		can't reproduce						all	ChimeraX