Crash in CP

Hi Everyone,

Has anyone seen this? It's reproducible every time with CP and a basic method.

15-10-22 17:08:42.252 CellProfiler[6257]: CellProfiler(6257,0xb27cb000) malloc: *** mach_vm_map(size=17403904) failed (error code=3)
*** error: can’t allocate region
*** set a breakpoint in malloc_error_break to debug

CP will just quit after clicking run.

-J

Hi J,

Hmm, not seen here. Can you give some more details:

  • Are you running the release version, or master branch, or?
  • Mac OS 10.?

Mac startup errors can often be fixed by (re)moving its config files here: ~/Library/Preferences/CellProfilerLocal.cfg (note the tilde)

You can also run CP from the command line, even the release build, and possibly get more feedback:
github.com/CellProfiler/CellPro … mmand-line

Let us know how it goes.
Thanks,
David

Deleting the prefs file didn’t help.

Updating to master didn’t help.

MacOS 10.11.1

running
| => pwd
/Applications/CellProfiler.app/Contents/Resources/

| => python CellProfiler.py
Traceback (most recent call last):
File “CellProfiler.py”, line 986, in
main(sys.argv)
File “CellProfiler.py”, line 75, in main
import cellprofiler.preferences as cpprefs
ImportError: No module named cellprofiler.preferences

Looks like the GUI crashing in wx? Error log:

Process: CellProfiler [55345]
Path: /Applications/CellProfiler.app/Contents/MacOS/CellProfiler
Identifier: org.cellprofiler.CellProfiler
Version: 2.1.2 (0.0.0)
Code Type: X86 (Native)
Parent Process: ??? [1]
Responsible: CellProfiler [55345]
User ID: 501

Date/Time: 2015-11-02 14:58:04.123 -0500
OS Version: Mac OS X 10.11.1 (15B42)
Report Version: 11
Anonymous UUID: 91D073F1-C990-B7CC-98B6-95F01432CAA5

Sleep/Wake UUID: D7F70A74-E4E0-4589-9ECA-97F160757583

Time Awake Since Boot: 600000 seconds

System Integrity Protection: enabled

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000060
Exception Note: EXC_CORPSE_NOTIFY

VM Regions Near 0x60:
–>
__TEXT 0000000000001000-0000000000008000 28K] r-x/rwx SM=COW /Applications/CellProfiler.app/Contents/MacOS/CellProfiler

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libwx_macud-2.8.0.8.0.dylib 0x07ac00d3 wxMacAppEventHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 25
1 com.apple.HIToolbox 0x91ebf68b _InvokeEventHandlerUPP(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*, long ()(OpaqueEventHandlerCallRef, OpaqueEventRef*, void*)) + 36
2 com.apple.HIToolbox 0x91e679a0 DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1832
3 com.apple.HIToolbox 0x91e66bb4 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 402
4 com.apple.HIToolbox 0x91e66a1a SendEventToEventTargetWithOptions + 40
5 com.apple.HIToolbox 0x91ea0212 ToolboxEventDispatcherHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 1994
6 com.apple.HIToolbox 0x91e67def DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 2935
7 com.apple.HIToolbox 0x91e66bb4 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 402
8 com.apple.HIToolbox 0x91e79f6d SendEventToEventTarget + 34
9 com.apple.HIToolbox 0x9201709e ToolboxEventDispatcher + 82
10 com.apple.HIToolbox 0x92016fdc HLTBEventDispatcher + 17
11 com.apple.HIToolbox 0x92018084 _RunAppModalLoop + 159
12 com.apple.HIToolbox 0x92017fa6 RunAppModalLoopForWindow + 120
13 com.apple.AppKit 0x9ab04e14 -[NSApplication _realDoModalLoop:peek:] + 440
14 com.apple.AppKit 0x9ab04c54 -[NSApplication _doModalLoop:peek:] + 207
15 com.apple.AppKit 0x9ab024f8 -[NSApplication runModalForWindow:] + 324
16 com.apple.AppKit 0x9aca03ee _NXDoLocalRunAlertPanel + 932
17 com.apple.AppKit 0x9aca0042 NSRunAlertPanel + 62
18 org.cellprofiler.CellProfiler 0x00005788 start + 13208
19 org.cellprofiler.CellProfiler 0x000069d8 start + 17896
20 org.cellprofiler.CellProfiler 0x00006fd9 main + 1481
21 org.cellprofiler.CellProfiler 0x00002426 start + 54

Thread 1:
0 libsystem_kernel.dylib 0x95d15e16 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x9509e35f _pthread_wqthread + 1289
2 libsystem_pthread.dylib 0x9509bf82 start_wqthread + 34

Thread 2:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x95d168b2 kevent_qos + 10
1 libdispatch.dylib 0x98b78792 _dispatch_mgr_invoke + 234
2 libdispatch.dylib 0x98b78366 _dispatch_mgr_thread + 52

Thread 3:
0 libsystem_kernel.dylib 0x95d15e16 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x9509e35f _pthread_wqthread + 1289
2 libsystem_pthread.dylib 0x9509bf82 start_wqthread + 34

Thread 4:
0 libsystem_kernel.dylib 0x95d15e16 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x9509e35f _pthread_wqthread + 1289
2 libsystem_pthread.dylib 0x9509bf82 start_wqthread + 34

Thread 5:
0 libsystem_kernel.dylib 0x95d15e16 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x9509e35f _pthread_wqthread + 1289
2 libsystem_pthread.dylib 0x9509bf82 start_wqthread + 34

Thread 6:
0 libsystem_kernel.dylib 0x95d15e16 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x9509e35f _pthread_wqthread + 1289
2 libsystem_pthread.dylib 0x9509bf82 start_wqthread + 34

Thread 7:
0 libsystem_kernel.dylib 0x95d15e16 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x9509e35f _pthread_wqthread + 1289
2 libsystem_pthread.dylib 0x9509bf82 start_wqthread + 34

Thread 8:
0 libsystem_kernel.dylib 0x95d15e16 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x9509e35f _pthread_wqthread + 1289
2 libsystem_pthread.dylib 0x9509bf82 start_wqthread + 34

Thread 9:
0 libsystem_kernel.dylib 0x95d15e16 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x9509e35f _pthread_wqthread + 1289
2 libsystem_pthread.dylib 0x9509bf82 start_wqthread + 34

Thread 10:
0 libsystem_kernel.dylib 0x95d15e16 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x9509e35f _pthread_wqthread + 1289
2 libsystem_pthread.dylib 0x9509bf82 start_wqthread + 34

Thread 11:
0 libsystem_kernel.dylib 0x95d15e16 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x9509e35f _pthread_wqthread + 1289
2 libsystem_pthread.dylib 0x9509bf82 start_wqthread + 34

Thread 12:
0 libsystem_kernel.dylib 0x95d15e16 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x9509e35f _pthread_wqthread + 1289
2 libsystem_pthread.dylib 0x9509bf82 start_wqthread + 34

Thread 13:
0 libsystem_kernel.dylib 0x95d15e16 __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x9509e35f _pthread_wqthread + 1289
2 libsystem_pthread.dylib 0x9509bf82 start_wqthread + 34

Thread 0 crashed with X86 Thread State (32-bit):
eax: 0x00000000 ebx: 0x07ac00c8 ecx: 0x0046ab20 edx: 0x005b0c60
edi: 0x0046ab20 esi: 0x080a8024 ebp: 0xbfffcf38 esp: 0xbfffced0
ss: 0x00000023 efl: 0x00010282 eip: 0x07ac00d3 cs: 0x0000001b
ds: 0x00000023 es: 0x00000023 fs: 0x00000000 gs: 0x0000000f
cr2: 0x00000060

Logical CPU: 10
Error Code: 0x00000004
Trap Number: 14

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0x977ee000 - 0x9783dfff libcurl.4.dylib (90) <14A1CC25-00E2-3FF8-AD2C-F29441EA7627> /usr/lib/libcurl.4.dylib
0x9783e000 - 0x9785aff7 com.apple.openscripting (1.7 - 169) <542F1C6C-CC7A-3961-ABC5-FA1CFFF9A8F8> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting
0x9785b000 - 0x97a3cfff com.apple.QuartzCore (1.11 - 410.9) /System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore
0x97a3d000 - 0x97a94ff7 com.apple.HIServices (1.22 - 548) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
0x97a95000 - 0x97a9bfff com.apple.IOAccelerator (203.10 - 203.10) <6E5CEC34-9027-353C-A89D-B40BBD023469> /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator
0x97a9c000 - 0x97ac2ffb com.apple.MultitouchSupport.framework (304.9 - 304.9) <8BDD42C8-3F40-332F-8E27-14B006E75446> /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
0x97ac3000 - 0x97acdffb com.apple.audio.SoundManager (4.2 - 4.2) <4DD24BFF-123C-3E9C-B255-1F85C4F81ADB> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CarbonSound.framework/Versions/A/CarbonSound
0x97ace000 - 0x97ad9ff7 libChineseTokenizer.dylib (16) /usr/lib/libChineseTokenizer.dylib
0x97ada000 - 0x97aeeff7 com.apple.CoreBluetooth (1.0 - 1) <303DDADD-C5CE-3AD7-BFEF-9FBD21544046> /System/Library/Frameworks/CoreBluetooth.framework/Versions/A/CoreBluetooth
0x97aef000 - 0x97b17ff7 com.apple.IconServices (68 - 68) /System/Library/PrivateFrameworks/IconServices.framework/Versions/A/IconServices
0x97b18000 - 0x97b83ff7 com.apple.framework.CoreWiFi (11.0 - 1101.20) /System/Library/PrivateFrameworks/CoreWiFi.framework/Versions/A/CoreWiFi
0x97b84000 - 0x97bf7ffb com.apple.datadetectorscore (7.0 - 460) <1F5138F5-F9DF-3802-B8E1-C63EBD24D16E> /System/Library/PrivateFrameworks/DataDetectorsCore.framework/Versions/A/DataDetectorsCore
0x97bf8000 - 0x97bfbff7 libdyld.dylib (360.17) /usr/lib/system/libdyld.dylib
0x97bfc000 - 0x97bfdfff com.apple.TrustEvaluationAgent (2.0 - 25) /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x97bfe000 - 0x97c06fff com.apple.CoreServices.FSEvents (1222.1.1 - 1222.1.1) <557E72FD-1EA6-373F-90BB-ECDE78885C59> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/FSEvents.framework/Versions/A/FSEvents
0x97c07000 - 0x97c0bfff libcache.dylib (75) /usr/lib/system/libcache.dylib
0x97c0c000 - 0x97ec4ffb com.apple.RawCamera.bundle (6.17 - 825) /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
0x97ec5000 - 0x97ee4fff com.apple.GenerationalStorage (2.0 - 239) <698BD3D0-84AC-39D4-8028-07FCB156C21C> /System/Library/PrivateFrameworks/GenerationalStorage.framework/Versions/A/GenerationalStorage
0x97ee5000 - 0x97ee7fff com.apple.securityhi (9.0 - 55006) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI
0x97ee8000 - 0x97ef3ff3 libcommonCrypto.dylib (60074) <448055DC-6EBC-3C23-ADBC-4C86ABC49A87> /usr/lib/system/libcommonCrypto.dylib
0x97ef4000 - 0x97fbdfff com.apple.DiscRecording (9.0.1 - 9010.4.3) /System/Library/Frameworks/DiscRecording.framework/Versions/A/DiscRecording
0x97fbe000 - 0x97fe1ffb com.apple.framework.Apple80211 (11.0 - 1102.32) /System/Library/PrivateFrameworks/Apple80211.framework/Versions/A/Apple80211
0x97fe2000 - 0x97fe6ffb com.apple.IOSurface (108.0.1 - 108.0.1) <77922C52-6101-3458-83A6-32F25CCD6850> /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface
0x97fe7000 - 0x97feafff libCoreVMClient.dylib (119.5) <4A09B0D8-F436-35D2-BFF8-BE67851B2DFE> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x97fec000 - 0x98047fff com.apple.print.framework.PrintCore (11.0 - 472) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
0x98048000 - 0x98048fff com.apple.ApplicationServices (48 - 48) <7173D2F6-1111-3DF5-AC2D-2AB27BC90B0B> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
0x98049000 - 0x98059fff libGL.dylib (12.0.34.12) <5A2608A3-328B-3FB3-A5C9-A93F4127571C> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib

External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 1
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 298879
thread_create: 0
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=226.7M resident=0K(0%) swapped_out_or_unallocated=226.7M(100%)
Writable regions: Total=186.1M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=186.1M(100%)

                            VIRTUAL   REGION 

REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
ATS (font support) 32.1M 6
ATS (font support) (reserved) 4K 2 reserved VM address space (unallocated)
Accelerate.framework 128K 2
Activity Tracing 2048K 2
CG backing stores 2776K 3
CG image 28K 4
CG shared images 240K 7
CoreAnimation 32K 6
CoreUI image data 228K 7
CoreUI image file 384K 6
Image IO 64K 2
Kernel Alloc Once 4K 2
MALLOC 115.9M 58
MALLOC guard page 48K 10
Memory Tag 242 12K 2
OpenCL 8K 2
Process Corpse Info 2048K 2
Stack 14.1M 15
Stack Guard 56.1M 15
VM_ALLOCATE 128K 17
__DATA 11.8M 321
__IMAGE 528K 2
__IMPORT 48K 11
__LINKEDIT 54.3M 92
__OBJC 2656K 64
__TEXT 172.4M 307
__UNICODE 552K 2
mapped file 154.6M 153
shared memory 16.3M 9
=========== ======= =======
TOTAL 639.2M 1102
TOTAL, minus reserved VM space 639.2M 1102

Model: MacPro6,1, BootROM MP61.0116.B16, 6 processors, 6-Core Intel Xeon E5, 3.5 GHz, 16 GB, SMC 2.20f18
Graphics: AMD FirePro D500, AMD FirePro D500, PCIe, 3072 MB
Graphics: AMD FirePro D500, AMD FirePro D500, PCIe, 3072 MB
Memory Module: DIMM1, 4 GB, DDR3 ECC, 1866 MHz, 0x802C, 0x394A53463531323732415A2D314739453220
Memory Module: DIMM2, 4 GB, DDR3 ECC, 1866 MHz, 0x802C, 0x394A53463531323732415A2D314739453220
Memory Module: DIMM3, 4 GB, DDR3 ECC, 1866 MHz, 0x802C, 0x394A53463531323732415A2D314739453220
Memory Module: DIMM4, 4 GB, DDR3 ECC, 1866 MHz, 0x802C, 0x394A53463531323732415A2D314739453220
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x135), Broadcom BCM43xx 1.0 (7.21.94.29.1a4)
Bluetooth: Version 4.4.2f1 16391, 3 services, 27 devices, 1 incoming serial ports
Network Service: Ethernet 1, Ethernet, en0
Network Service: Wi-Fi, AirPort, en2
PCI Card: AMD FirePro D500, Display Controller, Slot-1
PCI Card: AMD FirePro D500, Display Controller, Slot-2
Serial ATA Device: APPLE SSD SM0256F, 251 GB
USB Device: USB 2.0 Bus
USB Device: Hub
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
USB Device: USB 3.0 Bus
USB Device: Camera DK2
USB Device: Rift DK2
USB Device: Rift DK2
USB Device: Keyboard Hub
USB Device: Apple Optical USB Mouse
USB Device: Apple Keyboard
USB Device: Portable
Thunderbolt Bus: Mac Pro, Apple Inc., 19.2
Thunderbolt Bus: Mac Pro, Apple Inc., 19.2
Thunderbolt Bus: Mac Pro, Apple Inc., 19.2

Running the script from command line yields another bug. :confused:

Error detected during run of module TrackObjects
Traceback (most recent call last):
File “/usr/cellprofiler/src/CellProfiler/cellprofiler/pipeline.py”, line 1796, in run_with_yield
module.run(workspace)
File “/usr/cellprofiler/src/CellProfiler/cellprofiler/modules/trackobjects.py”, line 762, in run
image_pixels = figure_to_image(figure, dpi=figure.dpi)
File “/usr/cellprofiler/src/CellProfiler/cellprofiler/gui/cpfigure_tools.py”, line 32, in figure_to_image
return image:,:,:3]
IndexError: 0-d arrays can only use a single () or a list of newaxes (and a single …) as an index
Mon Nov 2 15:39:53 2015: Image # 1, module TrackObjects # 10: 32.76 sec

Hi,
When you say

[quote]Updating to master didn’t help.
[/quote]

do you mean you are running the trunk build from September, or are running the true, current master branch using a build yourself, via : github.com/CellProfiler/CellPro … stallation?

FYI, new Issue here: github.com/CellProfiler/CellPro … ssues/1680

Cheers,
David

Could you send us the pipeline that caused the crash in TrackObjects?

Thanks,
Lee

What version # or git hash are you trying to run? Lee’s response: github.com/CellProfiler/CellPro … -153461400

Cheers,
David