Closed asmagen closed 4 years ago
hmm... strange, i have never seen this error before and not sure how to even approach debugging as it looks like it is a very o/s or environment specific issue
i could make some suggestions
On Sat, Mar 21, 2020 at 4:00 PM Assaf Magen notifications@github.com wrote:
Process: Python [50597] Path: /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/Resources/Python.app/Contents/MacOS/Python Identifier: Python Version: 3.7.7 (3.7.7) Code Type: X86-64 (Native) Parent Process: Python [50593] Responsible: Terminal [485] User ID: 503
Date/Time: 2020-03-21 11:00:15.339 -0400 OS Version: Mac OS X 10.15 (19A603) Report Version: 12 Bridge OS Version: 4.0 (17P572) Anonymous UUID: 48FC0FFC-DDD2-B0DA-5458-CBFE8A108EDA
Sleep/Wake UUID: 26A63CDF-F5B3-47C0-9C66-C22D85CCB0E2
Time Awake Since Boot: 2500000 seconds Time Since Wake: 4500 seconds
System Integrity Protection: enabled
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY
Termination Reason: Namespace OBJC, Code 0x1
Application Specific Information: multi-threaded process forked objc[50597]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug. crashed on child side of fork pre-exec
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff655b9ade abort_with_payload + 10 1 libsystem_kernel.dylib 0x00007fff655bb4ef abort_with_payload_wrapper_internal + 80 2 libsystem_kernel.dylib 0x00007fff655bb49f abort_with_reason + 19 3 libobjc.A.dylib 0x00007fff64102c9a _objc_fatalv(unsigned long long, unsigned long long, char const*, va_list_tag) + 114 4 libobjc.A.dylib 0x00007fff64102c28 _objc_fatal(char const, ...) + 135 5 libobjc.A.dylib 0x00007fff640f4f8c performForkChildInitialize(objc_class, objc_class) + 318 6 libobjc.A.dylib 0x00007fff640f555f initializeNonMetaClass + 519 7 libobjc.A.dylib 0x00007fff640f53a4 initializeNonMetaClass + 76 8 libobjc.A.dylib 0x00007fff640f5b15 initializeAndMaybeRelock(objc_class, objc_object, mutex_tt&, bool) + 214 9 libobjc.A.dylib 0x00007fff640e7c5c lookUpImpOrForward + 969 10 libobjc.A.dylib 0x00007fff640e7419 _objc_msgSend_uncached + 73 11 com.apple.CoreFoundation 0x00007fff2e340332 -[NSDictionaryM setObject:forKey:] + 408 12 com.apple.CoreFoundation 0x00007fff2e2c57d2 parseXMLElement + 2740 13 com.apple.CoreFoundation 0x00007fff2e2c5151 parseXMLElement + 1075 14 com.apple.CoreFoundation 0x00007fff2e2c478e _CFPropertyListCreateFromUTF8Data + 1884 15 com.apple.CoreFoundation 0x00007fff2e3a987b _CFPropertyListCreateWithData + 600 16 com.apple.CoreFoundation 0x00007fff2e2c3aaf CFPropertyListCreateWithData + 51 17 com.apple.CoreFoundation 0x00007fff2e2d5efc _CFBundleCopyInfoDictionaryInDirectoryWithVersion + 814 18 com.apple.CoreFoundation 0x00007fff2e4599ed _CFBundleRefreshInfoDictionaryAlreadyLocked + 111 19 com.apple.CoreFoundation 0x00007fff2e2d5bbc CFBundleGetInfoDictionary + 33 20 com.apple.CoreFoundation 0x00007fff2e3a8fef _CFBundleCreate + 715 21 com.apple.CoreFoundation 0x00007fff2e2cee52 CFBundleGetMainBundle + 148 22 com.apple.CoreFoundation 0x00007fff2e2c95f9 _CFPrefsGetCacheStringForBundleID + 71 23 com.apple.CoreFoundation 0x00007fff2e2c945c -[_CFXPreferences(SearchListAdditions) withSearchListForIdentifier:container:cloudConfigurationURL:perform:] + 329 24 com.apple.CoreFoundation 0x00007fff2e2ef0ad -[_CFXPreferences copyDictionaryForApp:withContainer:] + 119 25 com.apple.CoreFoundation 0x00007fff2e2ef001 __CFXPreferencesCopyCurrentApplicationStateWithDeadlockAvoidance + 142 26 com.apple.CoreFoundation 0x00007fff2e2ee913 _CFLocaleCopyCurrentGuts + 321 27 Tcl 0x00007fff3bc26d6c 0x7fff3bb83000 + 671084 28 Tcl 0x00007fff3bb8e7c7 Tcl_CreateInterp + 1976 29 _tkinter.cpython-37m-darwin.so 0x0000000120fb6587 _tkinter_create + 344 30 org.python.python 0x000000010bd57ed0 _PyMethodDef_RawFastCallKeywords + 488 31 org.python.python 0x000000010bd5745c _PyCFunction_FastCallKeywords + 41 32 org.python.python 0x000000010bdeca6c call_function + 628 33 org.python.python 0x000000010bde5a47 _PyEval_EvalFrameDefault + 6767 34 org.python.python 0x000000010bded2cd _PyEval_EvalCodeWithName + 1698 35 org.python.python 0x000000010bd5709c _PyFunction_FastCallDict + 444 36 org.python.python 0x000000010bd581a3 _PyObject_Call_Prepend + 131 37 org.python.python 0x000000010bd95632 slot_tp_init + 80 38 org.python.python 0x000000010bd9235e type_call + 172 39 org.python.python 0x000000010bd572d2 _PyObject_FastCallKeywords + 358 40 org.python.python 0x000000010bdecad2 call_function + 730 41 org.python.python 0x000000010bde5b8a _PyEval_EvalFrameDefault + 7090 42 org.python.python 0x000000010bd57830 function_code_fastcall + 106 43 org.python.python 0x000000010bdecad9 call_function + 737 44 org.python.python 0x000000010bde5a47 _PyEval_EvalFrameDefault + 6767 45 org.python.python 0x000000010bded2cd _PyEval_EvalCodeWithName + 1698 46 org.python.python 0x000000010bd5709c _PyFunction_FastCallDict + 444 47 org.python.python 0x000000010bd581a3 _PyObject_Call_Prepend + 131 48 org.python.python 0x000000010bd57569 PyObject_Call + 136 49 org.python.python 0x000000010bde5d2b _PyEval_EvalFrameDefault + 7507 50 org.python.python 0x000000010bded2cd _PyEval_EvalCodeWithName + 1698 51 org.python.python 0x000000010bd57424 _PyFunction_FastCallKeywords + 212 52 org.python.python 0x000000010bdecad9 call_function + 737 53 org.python.python 0x000000010bde5ae2 _PyEval_EvalFrameDefault + 6922 54 org.python.python 0x000000010bd57830 function_code_fastcall + 106 55 org.python.python 0x000000010bdecad9 call_function + 737 56 org.python.python 0x000000010bde5ae2 _PyEval_EvalFrameDefault + 6922 57 org.python.python 0x000000010bded2cd _PyEval_EvalCodeWithName + 1698 58 org.python.python 0x000000010bd5709c _PyFunction_FastCallDict + 444 59 org.python.python 0x000000010bde5d2b _PyEval_EvalFrameDefault + 7507 60 org.python.python 0x000000010bded2cd _PyEval_EvalCodeWithName + 1698 61 org.python.python 0x000000010bd57424 _PyFunction_FastCallKeywords + 212 62 org.python.python 0x000000010bdecad9 call_function + 737 63 org.python.python 0x000000010bde5a47 _PyEval_EvalFrameDefault + 6767 64 org.python.python 0x000000010bd57830 function_code_fastcall + 106 65 org.python.python 0x000000010bdecad9 call_function + 737 66 org.python.python 0x000000010bde5ae2 _PyEval_EvalFrameDefault + 6922 67 org.python.python 0x000000010bd57830 function_code_fastcall + 106 68 org.python.python 0x000000010bde5d2b _PyEval_EvalFrameDefault + 7507 69 org.python.python 0x000000010bded2cd _PyEval_EvalCodeWithName + 1698 70 org.python.python 0x000000010bd5709c _PyFunction_FastCallDict + 444 71 org.python.python 0x000000010bde5d2b _PyEval_EvalFrameDefault + 7507 72 org.python.python 0x000000010bd57830 function_code_fastcall + 106 73 org.python.python 0x000000010bdecad9 call_function + 737 74 org.python.python 0x000000010bde5a2e _PyEval_EvalFrameDefault + 6742 75 org.python.python 0x000000010bd57830 function_code_fastcall + 106 76 org.python.python 0x000000010bdecad9 call_function + 737 77 org.python.python 0x000000010bde5a2e _PyEval_EvalFrameDefault + 6742 78 org.python.python 0x000000010bd57830 function_code_fastcall + 106 79 org.python.python 0x000000010bdecad9 call_function + 737 80 org.python.python 0x000000010bde5a2e _PyEval_EvalFrameDefault + 6742 81 org.python.python 0x000000010bd57830 function_code_fastcall + 106 82 org.python.python 0x000000010bd581a3 _PyObject_Call_Prepend + 131 83 org.python.python 0x000000010bd95632 slot_tp_init + 80 84 org.python.python 0x000000010bd9235e type_call + 172 85 org.python.python 0x000000010bd572d2 _PyObject_FastCallKeywords + 358 86 org.python.python 0x000000010bdecad2 call_function + 730 87 org.python.python 0x000000010bde5ae2 _PyEval_EvalFrameDefault + 6922 88 org.python.python 0x000000010bd57830 function_code_fastcall + 106 89 org.python.python 0x000000010bdecad9 call_function + 737 90 org.python.python 0x000000010bde5a47 _PyEval_EvalFrameDefault + 6767 91 org.python.python 0x000000010bd57830 function_code_fastcall + 106 92 org.python.python 0x000000010bdecad9 call_function + 737 93 org.python.python 0x000000010bde5a2e _PyEval_EvalFrameDefault + 6742 94 org.python.python 0x000000010bd57830 function_code_fastcall + 106 95 org.python.python 0x000000010bdecad9 call_function + 737 96 org.python.python 0x000000010bde5a2e _PyEval_EvalFrameDefault + 6742 97 org.python.python 0x000000010bded2cd _PyEval_EvalCodeWithName + 1698 98 org.python.python 0x000000010bd5709c _PyFunction_FastCallDict + 444 99 org.python.python 0x000000010bd581a3 _PyObject_Call_Prepend + 131 100 org.python.python 0x000000010bd95632 slot_tp_init + 80 101 org.python.python 0x000000010bd9235e type_call + 172 102 org.python.python 0x000000010bd572d2 _PyObject_FastCallKeywords + 358 103 org.python.python 0x000000010bdecad2 call_function + 730 104 org.python.python 0x000000010bde5b8a _PyEval_EvalFrameDefault + 7090 105 org.python.python 0x000000010bded2cd _PyEval_EvalCodeWithName + 1698 106 org.python.python 0x000000010bd57424 _PyFunction_FastCallKeywords + 212 107 org.python.python 0x000000010bdecad9 call_function + 737 108 org.python.python 0x000000010bde5b8a _PyEval_EvalFrameDefault + 7090 109 org.python.python 0x000000010bded2cd _PyEval_EvalCodeWithName + 1698 110 org.python.python 0x000000010bde3f35 PyEval_EvalCode + 51 111 org.python.python 0x000000010be1237c run_mod + 54 112 org.python.python 0x000000010be113af PyRun_FileExFlags + 160 113 org.python.python 0x000000010be10a66 PyRun_SimpleFileExFlags + 270 114 org.python.python 0x000000010be29276 pymain_main + 5445 115 org.python.python 0x000000010be298e4 _Py_UnixMain + 56 116 libdyld.dylib 0x00007fff65451405 start + 1
Thread 1: 0 libsystem_kernel.dylib 0x00007fff6559d8f6 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff6565e082 _pthread_cond_wait + 701 2 libopenblasp-r0.3.7.dylib 0x000000010d270c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff6565dd76 _pthread_start + 125 4 libsystem_pthread.dylib 0x00007fff6565a5d7 thread_start + 15
Thread 2: 0 libsystem_kernel.dylib 0x00007fff6559d8f6 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff6565e082 _pthread_cond_wait + 701 2 libopenblasp-r0.3.7.dylib 0x000000010d270c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff6565dd76 _pthread_start + 125 4 libsystem_pthread.dylib 0x00007fff6565a5d7 thread_start + 15
Thread 3: 0 libsystem_kernel.dylib 0x00007fff6559d8f6 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff6565e082 _pthread_cond_wait + 701 2 libopenblasp-r0.3.7.dylib 0x000000010d270c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff6565dd76 _pthread_start + 125 4 libsystem_pthread.dylib 0x00007fff6565a5d7 thread_start + 15
Thread 4: 0 libsystem_kernel.dylib 0x00007fff6559d8f6 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff6565e082 _pthread_cond_wait + 701 2 libopenblasp-r0.3.7.dylib 0x000000010d270c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff6565dd76 _pthread_start + 125 4 libsystem_pthread.dylib 0x00007fff6565a5d7 thread_start + 15
Thread 5: 0 libsystem_kernel.dylib 0x00007fff6559d8f6 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff6565e082 _pthread_cond_wait + 701 2 libopenblasp-r0.3.7.dylib 0x000000010d270c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff6565dd76 _pthread_start + 125 4 libsystem_pthread.dylib 0x00007fff6565a5d7 thread_start + 15
Thread 6: 0 libsystem_kernel.dylib 0x00007fff6559d8f6 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff6565e082 _pthread_cond_wait + 701 2 libopenblasp-r0.3.7.dylib 0x000000010d270c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff6565dd76 _pthread_start + 125 4 libsystem_pthread.dylib 0x00007fff6565a5d7 thread_start + 15
Thread 7: 0 libsystem_kernel.dylib 0x00007fff6559d8f6 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff6565e082 _pthread_cond_wait + 701 2 libopenblasp-r0.3.7.dylib 0x000000010d270c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff6565dd76 _pthread_start + 125 4 libsystem_pthread.dylib 0x00007fff6565a5d7 thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000002000209 rbx: 0x0000000000000080 rcx: 0x00007ffee3ec5c18 rdx: 0x0000000000000000 rdi: 0x0000000000000008 rsi: 0x0000000000000001 rbp: 0x00007ffee3ec5c60 rsp: 0x00007ffee3ec5c18 r8: 0x00007fc648cf6210 r9: 0x0000000000000080 r10: 0x0000000000000000 r11: 0x0000000000000246 r12: 0x0000000000000000 r13: 0x0000000000000000 r14: 0x0000000000000001 r15: 0x0000000000000008 rip: 0x00007fff655b9ade rfl: 0x0000000000000246 cr2: 0x00000001ce08a000
Logical CPU: 0 Error Code: 0x02000209 Trap Number: 133
Binary Images: 0x10bd34000 - 0x10bd35fff +org.python.python (3.7.7 - 3.7.7)
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It was the thread fault - requesting 4 threads for 1 image somehow crashed the system. I guess it's one thread per sample and running multiple made them run on the same image. I thought it would utilize multithreading for tasks per single image.
thanks for the feedback. we've not implemented multithreads per single image functionality. for most of our tests it takes < 1 minute per image, so hasnt been much demand
On Sat, Mar 21, 2020 at 4:15 PM Assaf Magen notifications@github.com wrote:
It was the thread fault - requesting 4 threads for 1 image somehow crashed the system. I guess it's one thread per sample and running multiple made them run on the same image. I thought it would utilize multithreading for tasks per single image.
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The pipeline works on NDPI partially but crashes before the end of the process after running
python3 qc_pipeline.py -c config.ini -n 4 /Users/Assaf/projects/imaging/Li63T_CD3.ndpi