Cell Profiler not starting increasing Java memory,MAC 10.10

Hello

During my analysis with huge images (4096x4096), I was running out of memory. So, I increased the memory to Java from default to 2000MB. Ever since, I can not start Cell Profiler anymore, the console never loads up. So I did following;

OS details: Mac OSX 10.10.2

  1. Uninstalled, reinstalled several times (Build 2.1.1), Did not work!!
  2. Installed 2.0, works!!
  3. Installed 2.1.1 candidate release build, did not work, same problem, console did not load.
  4. Installed 2.1.1 trunk build, did not work, but following error came up.
  5. Updated Java, reinstalled 2.1.1, same error.

At this point, I am not sure if this even was the problem. I would appreciate any thoughts, thanks!

Br, Vibhu

Process: CellProfiler [912]
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 [912]
User ID: 501

Date/Time: 2015-03-12 11:07:59.994 +0100
OS Version: Mac OS X 10.10.2 (14C109)
Report Version: 11
Anonymous UUID: A7BC0A29-D00B-C224-4FA1-C112ABB088AD

Time Awake Since Boot: 870 seconds

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

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

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 0x082930d3 wxMacAppEventHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 25
1 com.apple.HIToolbox 0x92de5624 _InvokeEventHandlerUPP(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*, long ()(OpaqueEventHandlerCallRef, OpaqueEventRef*, void*)) + 36
2 com.apple.HIToolbox 0x92c2f651 DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 2291
3 com.apple.HIToolbox 0x92c2e62c SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 402
4 com.apple.HIToolbox 0x92c2e493 SendEventToEventTargetWithOptions + 95
5 com.apple.HIToolbox 0x92c625ca ToolboxEventDispatcherHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 1912
6 com.apple.HIToolbox 0x92c2fa1b DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 3261
7 com.apple.HIToolbox 0x92c2e62c SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 402
8 com.apple.HIToolbox 0x92c41e65 SendEventToEventTarget + 88
9 com.apple.HIToolbox 0x92de4d05 ToolboxEventDispatcher + 82
10 com.apple.HIToolbox 0x92de4c46 HLTBEventDispatcher + 17
11 com.apple.HIToolbox 0x92de5e27 _RunAppModalLoop + 176
12 com.apple.HIToolbox 0x92de5d38 RunAppModalLoopForWindow + 120
13 com.apple.AppKit 0x9632bad9 -[NSApplication _realDoModalLoop:peek:] + 539
14 com.apple.AppKit 0x9632b8af -[NSApplication _doModalLoop:peek:] + 207
15 com.apple.AppKit 0x9632a165 -[NSApplication runModalForWindow:] + 246
16 com.apple.AppKit 0x963638e6 _NXDoLocalRunAlertPanel + 1000
17 com.apple.AppKit 0x963634f6 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:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x925f78ce kevent64 + 10
1 libdispatch.dylib 0x96db073f _dispatch_mgr_invoke + 245
2 libdispatch.dylib 0x96db03a2 _dispatch_mgr_thread + 52

Thread 2:
0 libsystem_kernel.dylib 0x925f6e6a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x98c622b1 _pthread_wqthread + 939
2 libsystem_pthread.dylib 0x98c5fe2e start_wqthread + 30

Thread 3:
0 libsystem_kernel.dylib 0x925f6e6a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x98c622b1 _pthread_wqthread + 939
2 libsystem_pthread.dylib 0x98c5fe2e start_wqthread + 30

Thread 4:
0 libsystem_kernel.dylib 0x925f6e6a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x98c622b1 _pthread_wqthread + 939
2 libsystem_pthread.dylib 0x98c5fe2e start_wqthread + 30

Thread 5:
0 libsystem_kernel.dylib 0x925f6e6a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x98c622b1 _pthread_wqthread + 939
2 libsystem_pthread.dylib 0x98c5fe2e start_wqthread + 30

Thread 6:: Java: Exception Handler Thread
0 libsystem_kernel.dylib 0x925f09ce mach_msg_trap + 10
1 libsystem_kernel.dylib 0x925efa70 mach_msg + 68
2 libsystem_kernel.dylib 0x925f03e2 mach_msg_server + 415
3 libjvm.dylib 0x0de5991a 0xde44000 + 88346
4 libjvm.dylib 0x0de597a3 0xde44000 + 87971
5 libjvm.dylib 0x0de5822c 0xde44000 + 82476
6 libsystem_pthread.dylib 0x98c61e13 _pthread_body + 138
7 libsystem_pthread.dylib 0x98c61d89 _pthread_start + 162
8 libsystem_pthread.dylib 0x98c5fe52 thread_start + 34

Thread 7:: Java: Gang worker#0 (Parallel GC Threads)
0 libsystem_kernel.dylib 0x925f09ce mach_msg_trap + 10
1 libsystem_kernel.dylib 0x925efa70 mach_msg + 68
2 libjvm.dylib 0x0de58986 0xde44000 + 84358
3 libjvm.dylib 0x0de588c2 0xde44000 + 84162
4 libjvm.dylib 0x0de58788 0xde44000 + 83848
5 libjvm.dylib 0x0de582cd 0xde44000 + 82637
6 libjvm.dylib 0x0de58157 0xde44000 + 82263
7 libjvm.dylib 0x0de6fbf9 0xde44000 + 179193
8 libjvm.dylib 0x0de6fae3 0xde44000 + 178915
9 libjvm.dylib 0x0de5822c 0xde44000 + 82476
10 libsystem_pthread.dylib 0x98c61e13 _pthread_body + 138
11 libsystem_pthread.dylib 0x98c61d89 _pthread_start + 162
12 libsystem_pthread.dylib 0x98c5fe52 thread_start + 34

Thread 8:: Java: Gang worker#1 (Parallel GC Threads)
0 libsystem_kernel.dylib 0x925f09ce mach_msg_trap + 10
1 libsystem_kernel.dylib 0x925efa70 mach_msg + 68
2 libjvm.dylib 0x0de58986 0xde44000 + 84358
3 libjvm.dylib 0x0de588c2 0xde44000 + 84162
4 libjvm.dylib 0x0de58788 0xde44000 + 83848
5 libjvm.dylib 0x0de582cd 0xde44000 + 82637
6 libjvm.dylib 0x0de58157 0xde44000 + 82263
7 libjvm.dylib 0x0de6fbf9 0xde44000 + 179193
8 libjvm.dylib 0x0de6fae3 0xde44000 + 178915
9 libjvm.dylib 0x0de5822c 0xde44000 + 82476
10 libsystem_pthread.dylib 0x98c61e13 _pthread_body + 138
11 libsystem_pthread.dylib 0x98c61d89 _pthread_start + 162
12 libsystem_pthread.dylib 0x98c5fe52 thread_start + 34

Thread 9:: Java: Gang worker#2 (Parallel GC Threads)
0 libsystem_kernel.dylib 0x925f09ce mach_msg_trap + 10
1 libsystem_kernel.dylib 0x925efa70 mach_msg + 68
2 libjvm.dylib 0x0de58986 0xde44000 + 84358
3 libjvm.dylib 0x0de588c2 0xde44000 + 84162
4 libjvm.dylib 0x0de58788 0xde44000 + 83848
5 libjvm.dylib 0x0de582cd 0xde44000 + 82637
6 libjvm.dylib 0x0de58157 0xde44000 + 82263
7 libjvm.dylib 0x0de6fbf9 0xde44000 + 179193
8 libjvm.dylib 0x0de6fae3 0xde44000 + 178915
9 libjvm.dylib 0x0de5822c 0xde44000 + 82476
10 libsystem_pthread.dylib 0x98c61e13 _pthread_body + 138
11 libsystem_pthread.dylib 0x98c61d89 _pthread_start + 162
12 libsystem_pthread.dylib 0x98c5fe52 thread_start + 34

Thread 10:: Java: Gang worker#3 (Parallel GC Threads)
0 libsystem_kernel.dylib 0x925f09ce mach_msg_trap + 10
1 libsystem_kernel.dylib 0x925efa70 mach_msg + 68
2 libjvm.dylib 0x0de58986 0xde44000 + 84358
3 libjvm.dylib 0x0de588c2 0xde44000 + 84162
4 libjvm.dylib 0x0de58788 0xde44000 + 83848
5 libjvm.dylib 0x0de582cd 0xde44000 + 82637
6 libjvm.dylib 0x0de58157 0xde44000 + 82263
7 libjvm.dylib 0x0de6fbf9 0xde44000 + 179193
8 libjvm.dylib 0x0de6fae3 0xde44000 + 178915
9 libjvm.dylib 0x0de5822c 0xde44000 + 82476
10 libsystem_pthread.dylib 0x98c61e13 _pthread_body + 138
11 libsystem_pthread.dylib 0x98c61d89 _pthread_start + 162
12 libsystem_pthread.dylib 0x98c5fe52 thread_start + 34

Thread 11:: Java: Gang worker#4 (Parallel GC Threads)
0 libsystem_kernel.dylib 0x925f09ce mach_msg_trap + 10
1 libsystem_kernel.dylib 0x925efa70 mach_msg + 68
2 libjvm.dylib 0x0de58986 0xde44000 + 84358
3 libjvm.dylib 0x0de588c2 0xde44000 + 84162
4 libjvm.dylib 0x0de58788 0xde44000 + 83848
5 libjvm.dylib 0x0de582cd 0xde44000 + 82637
6 libjvm.dylib 0x0de58157 0xde44000 + 82263
7 libjvm.dylib 0x0de6fbf9 0xde44000 + 179193
8 libjvm.dylib 0x0de6fae3 0xde44000 + 178915
9 libjvm.dylib 0x0de5822c 0xde44000 + 82476
10 libsystem_pthread.dylib 0x98c61e13 _pthread_body + 138
11 libsystem_pthread.dylib 0x98c61d89 _pthread_start + 162
12 libsystem_pthread.dylib 0x98c5fe52 thread_start + 34

Thread 12:: Java: Gang worker#5 (Parallel GC Threads)
0 libsystem_kernel.dylib 0x925f09ce mach_msg_trap + 10
1 libsystem_kernel.dylib 0x925efa70 mach_msg + 68
2 libjvm.dylib 0x0de58986 0xde44000 + 84358
3 libjvm.dylib 0x0de588c2 0xde44000 + 84162
4 libjvm.dylib 0x0de58788 0xde44000 + 83848
5 libjvm.dylib 0x0de582cd 0xde44000 + 82637
6 libjvm.dylib 0x0de58157 0xde44000 + 82263
7 libjvm.dylib 0x0de6fbf9 0xde44000 + 179193
8 libjvm.dylib 0x0de6fae3 0xde44000 + 178915
9 libjvm.dylib 0x0de5822c 0xde44000 + 82476
10 libsystem_pthread.dylib 0x98c61e13 _pthread_body + 138
11 libsystem_pthread.dylib 0x98c61d89 _pthread_start + 162
12 libsystem_pthread.dylib 0x98c5fe52 thread_start + 34

Thread 13:: Java: Gang worker#6 (Parallel GC Threads)
0 libsystem_kernel.dylib 0x925f09ce mach_msg_trap + 10
1 libsystem_kernel.dylib 0x925efa70 mach_msg + 68
2 libjvm.dylib 0x0de58986 0xde44000 + 84358
3 libjvm.dylib 0x0de588c2 0xde44000 + 84162
4 libjvm.dylib 0x0de58788 0xde44000 + 83848
5 libjvm.dylib 0x0de582cd 0xde44000 + 82637
6 libjvm.dylib 0x0de58157 0xde44000 + 82263
7 libjvm.dylib 0x0de6fbf9 0xde44000 + 179193
8 libjvm.dylib 0x0de6fae3 0xde44000 + 178915
9 libjvm.dylib 0x0de5822c 0xde44000 + 82476
10 libsystem_pthread.dylib 0x98c61e13 _pthread_body + 138
11 libsystem_pthread.dylib 0x98c61d89 _pthread_start + 162
12 libsystem_pthread.dylib 0x98c5fe52 thread_start + 34

Thread 14:: Java: Gang worker#7 (Parallel GC Threads)
0 libsystem_kernel.dylib 0x925f09ce mach_msg_trap + 10
1 libsystem_kernel.dylib 0x925efa70 mach_msg + 68
2 libjvm.dylib 0x0de58986 0xde44000 + 84358
3 libjvm.dylib 0x0de588c2 0xde44000 + 84162
4 libjvm.dylib 0x0de58788 0xde44000 + 83848
5 libjvm.dylib 0x0de582cd 0xde44000 + 82637
6 libjvm.dylib 0x0de58157 0xde44000 + 82263
7 libjvm.dylib 0x0de6fbf9 0xde44000 + 179193
8 libjvm.dylib 0x0de6fae3 0xde44000 + 178915
9 libjvm.dylib 0x0de5822c 0xde44000 + 82476
10 libsystem_pthread.dylib 0x98c61e13 _pthread_body + 138
11 libsystem_pthread.dylib 0x98c61d89 _pthread_start + 162
12 libsystem_pthread.dylib 0x98c5fe52 thread_start + 34

Thread 15:
0 libsystem_kernel.dylib 0x925f6e6a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x98c622b1 _pthread_wqthread + 939
2 libsystem_pthread.dylib 0x98c5fe2e start_wqthread + 30

Thread 16:
0 libsystem_kernel.dylib 0x925f6e6a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x98c622b1 _pthread_wqthread + 939
2 libsystem_pthread.dylib 0x98c5fe2e start_wqthread + 30

Thread 17:
0 libsystem_kernel.dylib 0x925f6e6a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x98c622b1 _pthread_wqthread + 939
2 libsystem_pthread.dylib 0x98c5fe2e start_wqthread + 30

Thread 18:
0 libsystem_kernel.dylib 0x925f6e6a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x98c622b1 _pthread_wqthread + 939
2 libsystem_pthread.dylib 0x98c5fe2e start_wqthread + 30

Thread 19:
0 libsystem_kernel.dylib 0x925f6e6a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x98c622b1 _pthread_wqthread + 939
2 libsystem_pthread.dylib 0x98c5fe2e start_wqthread + 30

Thread 0 crashed with X86 Thread State (32-bit):
eax: 0x00000000 ebx: 0x082930c8 ecx: 0x006b2970 edx: 0x001c6060
edi: 0x006b2970 esi: 0x0887b024 ebp: 0xbfffcc78 esp: 0xbfffcc10
ss: 0x00000023 efl: 0x00010282 eip: 0x082930d3 cs: 0x0000001b
ds: 0x00000023 es: 0x00000023 fs: 0x00000000 gs: 0x0000000f
cr2: 0x00000060

Logical CPU: 4
Error Code: 0x00000004
Trap Number: 14

Hi,

Hmm, something may have become corrupted in a configuration file. Would you please try the instructions here (viewtopic.php?f=14&t=3783&p=10952&hilit=CellProfilerLocal.cfg&sid=cf1cb618073133de168f562bc579d744#p10952) to clear your config files, and then try re-launching CellProfiler (2.1.1 release).

David

Hi,

Clearing the CellProfilerLocal.cfg and restarting has solved the problem, thanks!

Cheers,
Vibhu