Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5770 closed defect (can't reproduce)

Crash in numpy, probably .any()

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimeraWindows fatal exception: code 0x8001010e

x\open_command\dialog.py"Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

, line 135 in show_openWindows fatal exception: code 0x_f8001010e

ile_diaWindows fatal exception: code 0x8001010e

log
  File "C:\Program Files Windows fatal exception: code 0x8001010e

(x86)\ChimeraX 1.3rWindows fatal exception: code 0xc28001010e0

211Windows fatal exception: 2code 0x08001010e4

04Windows fatal exception: 0code 0x78001010e\

biWindows fatal exception: ncode 0x\8001010el

ib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_Windows fatal exception: code 0xl8001010eo

op
Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e  File 

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

"C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

_Windows fatal exception: rcode 0xu8001010en

_coWindows fatal exception: dcode 0xe8001010e


  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-pacWindows fatal exception: code 0xk8001010ea

gesWindows fatal exception: \code 0xC8001010eh

imWindows fatal exception: ecode 0xr8001010ea

X_Windows fatal exception: mcode 0xa8001010ei

n.Windows fatal exception: pcode 0xy8001010e"

, line 1018Windows fatal exception:  in code 0x


  File Windows fatal exception: "code 0xC8001010e:

\ProWindows fatal exception: gcode 0xr8001010ea

m FWindows fatal exception: icode 0xl8001010ee

s (Windows fatal exception: xcode 0x88001010e6

)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_commWindows fatal exception: code 0xa8001010en

d\dWindows fatal exception: icode 0xa8001010el

og.Windows fatal exception: pcode 0xy8001010e"

, line 135 in Windows fatal exception: scode 0xh8001010e

owWindows fatal exception: _code 0xo8001010e

pWindows fatal exception: ecode 0xn8001010e_

fiWindows fatal exception: lcode 0xe8001010e_

dWindows fatal exception: iacode 0x8001010elo

g
  File Windows fatal exception: "code 0xC8001010e

:Windows fatal exception: \code 0xP8001010er

ogrWindows fatal exception: acode 0xm8001010e 

Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\Windows fatal exception: code 0x8001010eb

in\Windows fatal exception: lcode 0xib\8001010e

sitWindows fatal exception: ecode 0x-8001010ep

ackWindows fatal exception: acode 0xg8001010ee

s\Windows fatal exception: ccode 0xh8001010ei

merWindows fatal exception: acode 0xx8001010e\

uiWindows fatal exception: \code 0xg8001010eu

i.Windows fatal exception: pcode 0xy8001010e"

, line Windows fatal exception: Windows fatal exception: code 0x3018001010e in 

evcode 0xWindows fatal exception: ecode 0xn8001010et

_8001010eWindows fatal exception: lcode 0xo8001010eo

p

Windows fatal exception: 
code 0xWindows fatal exception: 8001010ecode 0x  File "

8001010eWindows fatal exception: C:

\Pcode 0xWindows fatal exception: 8001010ecode 0xr8001010eo

g

Windows fatal exception: code 0xra8001010em

 FiWindows fatal exception: lcode 0xe8001010es

 (xWindows fatal exception: 8code 0x68001010e)

\ChWindows fatal exception: icode 0xm8001010ee

Windows fatal exception: Windows fatal exception: rcode 0xa8001010eX

 1code 0x8001010e.

3Windows fatal exception: rcode 0xc8001010e2Windows fatal exception: 0code 0x28001010e1

1

Windows fatal exception: code 0x28001010e04

04Windows fatal exception: 0code 0x78001010e\

binWindows fatal exception: \code 0xl8001010ei

b\Windows fatal exception: scode 0xi8001010et

e-Windows fatal exception: pcode 0xa8001010ec

kWindows fatal exception: acode 0xg8001010ee

sWindows fatal exception: \code 0xC8001010eh

imeWindows fatal exception: rcode 0xa8001010eX

_mWindows fatal exception: acode 0xi8001010en

.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\sWindows fatal exception: code 0x8001010ei

te-Windows fatal exception: pcode 0xa8001010ec

kWindows fatal exception: acode 0xg8001010e

eWindows fatal exception: scode 0x\8001010ec

hiWindows fatal exception: mcode 0xe8001010er

axWindows fatal exception: \code 0xu8001010ei

\gWindows fatal exception: ucode 0xi8001010e.

pWindows fatal exception: ycode 0x"8001010e, line 

301Windows fatal exception:  in code 0xe8001010ev

enWindows fatal exception: tcode 0x_lo8001010eo

p
  File Windows fatal exception: "code 0xC8001010e:

\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\liWindows fatal exception: code 0xb8001010e\

siteWindows fatal exception: -code 0xp8001010ea

ckagWindows fatal exception: ecode 0xs8001010e\

ChimWindows fatal exception: ecode 0xr8001010ea

X_mWindows fatal exception: acode 0xi8001010en

.pWindows fatal exception: ycode 0x"8001010e, line 

1018Windows fatal exception:  in code 0xWindows fatal exception: 
code 0x  File 8001010e"

CWindows fatal exception: :code 0x\8001010eP

rWindows fatal exception: ocode 0xg8001010er

am Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _rWindows fatal exception: code 0x8001010e

uWindows fatal exception: ncode 0x_8001010ec

oWindows fatal exception: dcode 0xe
  File "8001010eC

:\Windows fatal exception: Pcode 0xr8001010eo

gWindows fatal exception: rcode 0xa8001010em

 Windows fatal exception: Fcode 0xi8001010el

eWindows fatal exception: scode 0x 8001010e(

xWindows fatal exception: 8code 0x68001010e)

\Windows fatal exception: Ccode 0xh8001010ei

mWindows fatal exception: ecode 0xr8001010e

Windows fatal exception: code 0x8001010eaX

 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
Windows fatal exception: code 0x8001010e

  File Windows fatal exception: "code 0xC8001010e:

\ProWindows fatal exception: code 0xg8001010er

am Windows fatal exception: Fcode 0xi8001010el

esWindows fatal exception:  code 0x(8001010ex

86)Windows fatal exception: \code 0xC8001010eh

imeWindows fatal exception: rcode 0xa8001010eX

 1.Windows fatal exception: 3rcode 0x8001010ec

202Windows fatal exception: 1code 0x18001010e2

040Windows fatal exception: 4code 0xWindows fatal exception: code 0x08001010e7

\8001010eWindows fatal exception: 

code 0x8001010ebWindows fatal exception: 

iWindows fatal exception: ncode 0x8001010ecode 0x

8001010e\

libWindows fatal exception: \code 0xs8001010ei

te-Windows fatal exception: pcode 0xa8001010ec

kaWindows fatal exception: gcode 0xe8001010es

\cWindows fatal exception: hcode 0xi8001010em

erWindows fatal exception: acode 0xx8001010e\o

penWindows fatal exception: _code 0xc8001010eo

mmaWindows fatal exception: code 0xn8001010ed

\diWindows fatal exception: acode 0xl8001010eo

g.py", line 135 in show_oWindows fatal exception: code 0xp8001010ee

n_fWindows fatal exception: icode 0xl8001010ee

_dWindows fatal exception: icode 0xa8001010el

ogWindows fatal exception: 
code 0x  File 8001010e"

C:Windows fatal exception: \code 0xP8001010er

ogWindows fatal exception: rcode 0xa8001010em

 FWindows fatal exception: icode 0xl8001010ee

s (xWindows fatal exception: code 0x88001010e6

)\CWindows fatal exception: hcode 0xi8001010em

eraXWindows fatal exception:  code 0x18001010e.

3rcWindows fatal exception: 2code 0x08001010e2

112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\siteWindows fatal exception: code 0x-p8001010e

acWindows fatal exception: kcode 0xa8001010eg

esWindows fatal exception: \ccode 0xhi8001010em

erWindows fatal exception: acode 0xx8001010e\

uWindows fatal exception: icode 0x\8001010eg

uiWindows fatal exception: .code 0xp8001010ey

"Windows fatal exception: , line code 0x3018001010e in 

Windows fatal exception: code 0x8001010eev

entWindows fatal exception: _code 0xl8001010eo

opWindows fatal exception: 
code 0x  File 8001010e"

C:Windows fatal exception: code 0x8001010e\

Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimerWindows fatal exception: code 0x8001010e

aXWindows fatal exception:  code 0x18001010e.

3rc20Windows fatal exception: 2code 0x18001010e1

2040Windows fatal exception: 4code 0x08001010e7

\biWindows fatal exception: ncode 0x\8001010el

ib\Windows fatal exception: scode 0xi8001010et

e-paWindows fatal exception: ccode 0xk8001010ea

gesWindows fatal exception: \code 0xC8001010eh

imeWindows fatal exception: rcode 0xa8001010eX

_mWindows fatal exception: acode 0xi8001010en

.pWindows fatal exception: ycode 0x"8001010e, line 

1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraXWindows fatal exception:  code 0x18001010e.

3rWindows fatal exception: code 0xc8001010e2

02Windows fatal exception: 1code 0x18001010e2

040Windows fatal exception: 40code 0x78001010e\

bWindows fatal exception: icode 0xn8001010e\

lWindows fatal exception: icode 0xb8001010e\

rWindows fatal exception: ucode 0xn8001010ep

yWindows fatal exception: .code 0xp8001010ey

"Windows fatal exception: , line code 0x1978001010e in 

_Windows fatal exception: rcode 0xu8001010en

_Windows fatal exception: mcode 0xo8001010ed

ule_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000033d8 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3rc202112040407\bin\lib\site-packages\numpy\core\_methods.py", line 57 in _any
Windows fatal exception: access violation



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  




OpenGL version: 3.3.0 - Build 24.20.100.6292
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: FUJITSU
Model: FMVU7C3RDA
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 8,325,218,304
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz
OSLanguage: ja-JP
Locale: ('ja_JP', 'cp932')
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: 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
    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: 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
    WMI: 1.5.1

Change History (3)

comment:1 by pett, 4 years ago

Component: Unassigned → Core
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in numpy, probably .any()

comment:2 by pett, 4 years ago

Resolution: → can't reproduce
Status: assigned → closed

comment:3 by Tom Goddard, 4 years ago

We see many crashes in basic numpy operations. My theory was that these often result in garbage collection and the crash is not related to numpy. But maybe it is related to numpy. We do a pretty dangerous hack in the atomic collection numpy array when an object is deleted. Our C++ resizes the array smaller in place, and maybe this somehow leads to crashes. Just a theory.

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