[cmview-devel] Fwd: Bug report - PyMol frequently crashing when used by CMView
Jose Duarte
jose.duarte at psi.ch
Fri Nov 4 09:32:33 EDT 2011
Hi Thomas
Could you try something for us? Simply turn off the real time contact
mode by adding this to the cmview.cfg file:
SHOW_CONTACTS_IN_REALTIME=false
Then restart cmview and try a few selections and keep using it for a
couple of minutes as you say to see if it still crashes.
The real-time feature was introduced quite late and might have issues as
it produces a lot of pymol requests.
Cheers
Jose
PS: I'm copying to the list just to keep everyone informed
On 11/04/2011 01:50 PM, Thomas Hopf wrote:
> Hi Jose,
>
> yes, I tried it a couple of times and the bug was reproducible in a
> sense that it always happened after a couple of minutes, after
> performing the following actions for some time: I did nothing but
> select some of the contacts in CMView and rotate the protein in
> MacPymol. At some point, when selecting other contacts in CMView,
> Pymol crashes.
>
> Unfortunately, I can't link it to anything more specific like
> selecting a particular contact at the moment, but I will also try
> whether I can find out if there is a more specific pattern to it.
>
> Best,
> Thomas
>
> Am 04.11.11 12:40, schrieb Jose Duarte:
>> Hi Thomas
>>
>> Thanks a lot for the quick reply!
>>
>> Below is your email... I think the problem is that the mailing list
>> server we are using has some kind of misconfiguration issue at the
>> moment. It uses cmview-devel at www.bioinformatics.org rather than
>> cmview-devel at bioinformatics.org when you hit the "reply to" button
>> (it seems to depend on mail client anyway). We have reported the
>> problem and hope it will be solve soon. In the meantime please use
>> the address cmview-devel at bioinformatics.org
>>
>> Anyway thanks for the bug report, I'll try to have a look at it at
>> some point. Whenever you test from Linux it would be good to have the
>> outcome too. Also it would be good to know what exactly you were
>> doing to get the program to crash. You say it's reproducible isn't it?
>>
>> Cheers
>>
>> Jose
>>
>
Hi Jose and all,
here are both the console output and the crash log. I'll try and see
whether I can reproduce the bug in a Linux and Windows environment in
the next days.
Best,
Thomas
******************************
CMView console ouput
******************************
Starting CMView 1.1.1
Loading configuration file cmview.cfg
Using temporary directory
/var/folders/QW/QW00CdXLFnqZDuc5zJ5fBU+++TI/-Tmp-/
Connecting to PyMol...
Starting PyMol...
Connected.
Using DSSP executable ./DSSP_MAC.EXE
Mon Sep 26 12:15:20 Thomas-Hopfs-MacBook-Pro.local java[14704] <Error>:
kCGErrorIllegalArgument: CGSOrderWindowList
Mon Sep 26 12:15:20 Thomas-Hopfs-MacBook-Pro.local java[14704] <Error>:
kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors
as they are logged.
Loading from online PDB
PDB code: 1hzx
Model serial: 1
Chain code: A
Contact type: Ca
Dist. cutoff: 8.0
Min. Seq. Sep.: 6
Max. Seq. Sep.: none
(Re)assigning secondary structure using DSSP
Warning: 9 unobserved or non-standard residues
Contact map 1hzxA loaded.
Shutting down
******************************
Mac OS crash log
******************************
Process: MacPyMOL [14705]
Path: /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL
Identifier: com.schrodinger.macpymol
Version: 1.3 (1.3)
Code Type: X86 (Native)
Parent Process: java [14704]
Date/Time: 2011-09-26 12:18:35.517 -0400
OS Version: Mac OS X 10.6.8 (10K549)
Report Version: 6
Interval Since Last Report: 2118983 sec
Crashes Since Last Report: 30
Per-App Interval Since Last Report: 788771 sec
Per-App Crashes Since Last Report: 6
Anonymous UUID: 725F98BC-E768-4B0C-BD4C-88C9203C02CE
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000044656d3c
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Thread 0 Crashed: Dispatch queue: com.apple.main-thread
0 com.schrodinger.macpymol 0x000edfa6 SettingGet_i + 54
1 com.schrodinger.macpymol 0x0022f07e
ExecutiveUpdateSceneMembers + 718
2 com.schrodinger.macpymol 0x0022f347 ExecutiveDrawNow + 215
3 com.schrodinger.macpymol 0x002d21cd PyMOL_Draw + 573
4 com.schrodinger.macpymol 0x003ba204 -[PyMOLOpenGLView
drawRect:] + 148
5 com.apple.AppKit 0x9150e61e -[NSView
_drawRect:clip:] + 3510
6 com.apple.AppKit 0x9150d2bc -[NSView
_recursiveDisplayAllDirtyWithLockFocus:visRect:] + 1600
7 com.apple.AppKit 0x9150b7db -[NSView
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
+ 711
8 com.apple.AppKit 0x9150c750 -[NSView
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
+ 4668
9 com.apple.AppKit 0x9150c750 -[NSView
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
+ 4668
10 com.apple.AppKit 0x9150c750 -[NSView
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
+ 4668
11 com.apple.AppKit 0x9150b34f -[NSThemeFrame
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
+ 265
12 com.apple.AppKit 0x91507c96 -[NSView
_displayRectIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:] + 3309
13 com.apple.AppKit 0x9146884b -[NSView
displayIfNeeded] + 818
14 com.apple.AppKit 0x91431b64 -[NSWindow
displayIfNeeded] + 204
15 com.apple.AppKit 0x9146307e
_handleWindowNeedsDisplay + 696
16 com.apple.CoreFoundation 0x959f1e02 __CFRunLoopDoObservers
+ 1186
17 com.apple.CoreFoundation 0x959add1d __CFRunLoopRun + 557
18 com.apple.CoreFoundation 0x959ad3f4 CFRunLoopRunSpecific + 452
19 com.apple.CoreFoundation 0x959ad221 CFRunLoopRunInMode + 97
20 com.apple.HIToolbox 0x94551d60
RunCurrentEventLoopInMode + 392
21 com.apple.HIToolbox 0x94551b17 ReceiveNextEventCommon
+ 354
22 com.apple.HIToolbox 0x9455199c
BlockUntilNextEventMatchingListInMode + 81
23 com.apple.AppKit 0x91439595 _DPSNextEvent + 847
24 com.apple.AppKit 0x91438dd6 -[NSApplication
nextEventMatchingMask:untilDate:inMode:dequeue:] + 156
25 com.apple.AppKit 0x913fb1f3 -[NSApplication run] + 821
26 com.schrodinger.macpymol 0x003bbd7b main + 4139
27 com.schrodinger.macpymol 0x00002b72 start + 54
Thread 1: Dispatch queue: com.apple.libdispatch-manager
0 libSystem.B.dylib 0x90175382 kevent + 10
1 libSystem.B.dylib 0x90175a9c _dispatch_mgr_invoke + 215
2 libSystem.B.dylib 0x90174f59 _dispatch_queue_invoke
+ 163
3 libSystem.B.dylib 0x90174cfe
_dispatch_worker_thread2 + 240
4 libSystem.B.dylib 0x90174781 _pthread_wqthread + 390
5 libSystem.B.dylib 0x901745c6 start_wqthread + 30
Thread 2:
0 libSystem.B.dylib 0x9014ee26 read + 10
1 libSystem.B.dylib 0x901798fd _sread + 41
2 libSystem.B.dylib 0x9017977e __srefill + 48
3 libSystem.B.dylib 0x901802e0 __srget + 18
4 org.python.python 0x00a0a577 PyFile_AsFile + 407
5 org.python.python 0x00a0bd6a PyFile_SetBufSize + 2080
6 org.python.python 0x00a65d4d PyEval_EvalFrameEx + 16241
7 org.python.python 0x00a67ac6 PyEval_EvalCodeEx + 1734
8 org.python.python 0x00a12461 PyClassMethod_New + 2104
9 org.python.python 0x009f72a8 PyObject_Call + 50
10 org.python.python 0x00a67363 PyEval_EvalFrameEx + 21895
11 org.python.python 0x00a65edc PyEval_EvalFrameEx + 16640
12 org.python.python 0x00a65edc PyEval_EvalFrameEx + 16640
13 org.python.python 0x00a67ac6 PyEval_EvalCodeEx + 1734
14 org.python.python 0x00a124ce PyClassMethod_New + 2213
15 org.python.python 0x009f72a8 PyObject_Call + 50
16 org.python.python 0x00a00db7 PyClass_New + 1710
17 org.python.python 0x009f72a8 PyObject_Call + 50
18 org.python.python 0x00a61130
PyEval_CallObjectWithKeywords + 211
19 org.python.python 0x00a8eedf initthread + 1756
20 libSystem.B.dylib 0x9017c259 _pthread_start + 345
21 libSystem.B.dylib 0x9017c0de thread_start + 34
Thread 0 crashed with X86 Thread State (32-bit):
eax: 0x00002d3c ebx: 0x000edf84 ecx: 0x44656d3c edx: 0x01c27a50
edi: 0x00000243 esi: 0x00000000 ebp: 0xbfffb808 esp: 0xbfffb6d0
ss: 0x00000023 efl: 0x00010206 eip: 0x000edfa6 cs: 0x0000001b
ds: 0x00000023 es: 0x00000023 fs: 0x00000000 gs: 0x0000000f
cr2: 0x44656d3c
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com.apple.DirectoryService.PasswordServerFramework 6.1 (6.1)
<9E35835E-BC33-F8EC-8F3B-84D51DEBDB16>
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<579DC328-567D-A74C-4BCE-1D1C729E3F6D>
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(861.39) <5C59805C-AF39-9010-B8B5-D673C9C38538>
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/System/Library/PrivateFrameworks/FamilyControls.framework/Versions/A/FamilyControls
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<5920EB69-8D7F-5EFD-70AD-590FCB5C9E6C>
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib
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0x95b76000 - 0x95de7fef com.apple.Foundation 6.6.7 (751.62)
<5C995C7F-2EA9-50DC-9F2A-30237CDB31B1>
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/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
0x96b4c000 - 0x96c58ff7 libGLProgrammability.dylib ??? (???)
<04D7E5C3-B0C3-054B-DF49-3B333DCDEE22>
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
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<06484720-AB50-6FD9-B5BF-05F5A640C9E5>
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<25DF2360-BFD3-0165-51AC-0BDAF7899DEC>
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<873C8B8A-B563-50F7-7628-524EE9E8DF0F>
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
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/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x974bd000 - 0x974f0ff7 com.apple.AE 496.5 (496.5)
<BF9673D5-2419-7120-26A3-83D264C75222>
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
0x9770d000 - 0x97718ff7 libGL.dylib ??? (???)
<3E34468F-E9A7-8EFB-FF66-5204BD5B4E21>
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x978c2000 - 0x979c3fe7 libxml2.2.dylib 10.3.0 (compatibility 10.0.0)
<E1A44C67-FA6C-0188-F46F-EA14CEE557BB> /usr/lib/libxml2.2.dylib
0x979c4000 - 0x979d5ff7 com.apple.LangAnalysis 1.6.6 (1.6.6)
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/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
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/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
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/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
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0x99c62000 - 0x99c66ff7 libGIF.dylib ??? (???)
<2123645B-AC89-C4E2-8757-85834CAE3DD2>
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
0x99c67000 - 0x99c67ff7 com.apple.Cocoa 6.6 (???)
<5A785062-1ABB-2A54-BAAC-8FEF95275E05>
/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa
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(1.6.7) <2D31CC6F-32CC-72FF-34EC-AB40CEE496A7>
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<A5F4B929-AEDE-2DFB-E02F-89CEC0940023>
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0x9a2df000 - 0x9a312fff libTrueTypeScaler.dylib ??? (???)
<0F04DAC3-829A-FA1B-E9D0-1E9505713C5C>
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0x9a354000 - 0x9ab43557 com.apple.CoreGraphics 1.545.0 (???)
<1D9DC7A5-228B-42CB-7018-66F42C3A9BB3>
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
0x9ab4f000 - 0x9ab92ff7 libGLU.dylib ??? (???)
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/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0xffff0000 - 0xffff1fff libSystem.B.dylib ??? (???)
<2DCD13E3-1BD1-6F25-119A-3863A3848B90> /usr/lib/libSystem.B.dylib
Model: MacBookPro8,1, BootROM MBP81.0047.B1E, 2 processors, Intel Core
i5, 2.3 GHz, 4 GB, SMC 1.68f96
Graphics: Intel HD Graphics 3000, Intel HD Graphics 3000, Built-In, 384 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xD6),
Broadcom BCM43xx 1.0 5.100.198.104.5)
Bluetooth: Version 2.4.5f3, 2 service, 19 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Network Service: AirPort, AirPort, en1
Serial ATA Device: Hitachi HTS545032B9A302, 298.09 GB
Serial ATA Device: HL-DT-ST DVDRW GS31N
USB Device: FaceTime HD Camera (Built-in), 0x05ac (Apple Inc.), 0x8509,
0xfa200000 / 3
USB Device: Hub, 0x0424 (SMSC), 0x2513, 0xfa100000 / 2
USB Device: BRCM2070 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0xfa110000 / 5
USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x821a,
0xfa113000 / 8
USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.),
0x0246, 0xfa120000 / 4
USB Device: Hub, 0x0424 (SMSC), 0x2513, 0xfd100000 / 2
USB Device: Dell QuietKey Keyboard, 0x413c (Dell Inc.), 0x2106,
0xfd120000 / 4
USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8242, 0xfd110000 / 3
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