1

I am trying to run some dimensionality reduction using UMAP. However, python keeps crashing. My hunch is that it has something to do with c compiler/cython, but I didn't succeed to re-install/fix this.

import pandas as pd
import umap

SIFdf = pd.read_csv("SIF2004and2005.csv") # large dataframe with sentence vectors

clusterable_embedding = umap.UMAP(
    metric='cosine',
    n_neighbors=5,
    min_dist=0.0,
    n_components=2, # 2 pro primou vizualizaci, protoze to chceme poslat dal tak bychom to meli nastavit tak na 50
    random_state=42,
).fit_transform(SIFdf)

This is followed by many numba warnings, which shouldn't be critical (according to this https://github.com/lmcinnes/umap/issues/252)

When checking the crash report, I can't seem to figure out, what exactly is causing the trouble.

Process:               Python [19906]
Path:                  /usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/Resources/Python.app/Contents/MacOS/Python
Identifier:            Python
Version:               3.7.4 (3.7.4)
Code Type:             X86-64 (Native)
Parent Process:        python3.6 [1328]
Responsible:           Python [19906]
User ID:               501

Date/Time:             2019-07-18 14:54:26.528 +0200
OS Version:            Mac OS X 10.13.6 (17G65)
Report Version:        12
Anonymous UUID:        60E722C2-5873-483E-7DC6-B76F77750C86

Sleep/Wake UUID:       7D8D6DEE-465E-4160-B665-753815757FE6

Time Awake Since Boot: 49000 seconds
Time Since Wake:       11000 seconds

System Integrity Protection: enabled

Crashed Thread:        0  ZMQbg/1  Dispatch queue: com.apple.main-thread

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

Termination Signal:    Segmentation fault: 11
Termination Reason:    Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [0]

VM Regions Near 0xfffffffffffffffa:
--> shared memory          00007ffffff7e000-00007ffffff7f000 [    4K] r-x/r-x SM=SHM  


Thread 0 Crashed:: ZMQbg/1  Dispatch queue: com.apple.main-thread
0   _dynfunc.cpython-37m-darwin.so  0x000000012d6c27cf closure_dealloc + 31
1   org.python.python               0x000000010d5fe4f3 meth_dealloc + 87
2   org.python.python               0x000000010d60bab3 tupledealloc + 94
3   org.python.python               0x000000010d60d72d subtype_dealloc + 892
4   org.python.python               0x000000010d5f43bf free_keys_object + 127
5   org.python.python               0x000000010d5f63d2 dict_dealloc + 187
6   org.python.python               0x000000010d5f8958 odict_dealloc + 124
7   org.python.python               0x000000010d5f43bf free_keys_object + 127
8   org.python.python               0x000000010d5f63d2 dict_dealloc + 187
9   org.python.python               0x000000010d60d7cd subtype_dealloc + 1052
10  org.python.python               0x000000010d5e53f7 frame_dealloc + 161
11  org.python.python               0x000000010d66a957 _PyEval_EvalCodeWithName + 1743
12  org.python.python               0x000000010d5d4100 _PyFunction_FastCallKeywords + 225
13  org.python.python               0x000000010d66a121 call_function + 753
14  org.python.python               0x000000010d662d9b _PyEval_EvalFrameDefault + 7174
15  org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
16  org.python.python               0x000000010d5d4100 _PyFunction_FastCallKeywords + 225
17  org.python.python               0x000000010d66a121 call_function + 753
18  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
19  org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
20  org.python.python               0x000000010d5d4100 _PyFunction_FastCallKeywords + 225
21  org.python.python               0x000000010d66a121 call_function + 753
22  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
23  org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
24  org.python.python               0x000000010d66110d PyEval_EvalCode + 42
25  org.python.python               0x000000010d65eb8c builtin_exec + 554
26  org.python.python               0x000000010d5d4bc0 _PyMethodDef_RawFastCallKeywords + 496
27  org.python.python               0x000000010d5d413b _PyCFunction_FastCallKeywords + 44
28  org.python.python               0x000000010d66a0ac call_function + 636
29  org.python.python               0x000000010d662d9b _PyEval_EvalFrameDefault + 7174
30  org.python.python               0x000000010d5dfd5a gen_send_ex + 242
31  org.python.python               0x000000010d66574a _PyEval_EvalFrameDefault + 17845
32  org.python.python               0x000000010d5dfd5a gen_send_ex + 242
33  org.python.python               0x000000010d66574a _PyEval_EvalFrameDefault + 17845
34  org.python.python               0x000000010d5dfd5a gen_send_ex + 242
35  org.python.python               0x000000010d5d4c1f _PyMethodDef_RawFastCallKeywords + 591
36  org.python.python               0x000000010d5d9556 _PyMethodDescr_FastCallKeywords + 82
37  org.python.python               0x000000010d66a151 call_function + 801
38  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
39  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
40  org.python.python               0x000000010d66a121 call_function + 753
41  org.python.python               0x000000010d662d9b _PyEval_EvalFrameDefault + 7174
42  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
43  org.python.python               0x000000010d66a121 call_function + 753
44  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
45  org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
46  org.python.python               0x000000010d5d3d69 _PyFunction_FastCallDict + 441
47  org.python.python               0x000000010d5d4ebd _PyObject_Call_Prepend + 150
48  org.python.python               0x000000010d5d4249 PyObject_Call + 136
49  org.python.python               0x000000010d663014 _PyEval_EvalFrameDefault + 7807
50  org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
51  org.python.python               0x000000010d5d4100 _PyFunction_FastCallKeywords + 225
52  org.python.python               0x000000010d66a121 call_function + 753
53  org.python.python               0x000000010d662e41 _PyEval_EvalFrameDefault + 7340
54  org.python.python               0x000000010d5dfd5a gen_send_ex + 242
55  org.python.python               0x000000010d65f66d builtin_next + 99
56  org.python.python               0x000000010d5d4bc0 _PyMethodDef_RawFastCallKeywords + 496
57  org.python.python               0x000000010d5d413b _PyCFunction_FastCallKeywords + 44
58  org.python.python               0x000000010d66a0ac call_function + 636
59  org.python.python               0x000000010d662d9b _PyEval_EvalFrameDefault + 7174
60  org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
61  org.python.python               0x000000010d5d4100 _PyFunction_FastCallKeywords + 225
62  org.python.python               0x000000010d66a121 call_function + 753
63  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
64  org.python.python               0x000000010d5dfd5a gen_send_ex + 242
65  org.python.python               0x000000010d65f66d builtin_next + 99
66  org.python.python               0x000000010d5d4bc0 _PyMethodDef_RawFastCallKeywords + 496
67  org.python.python               0x000000010d5d413b _PyCFunction_FastCallKeywords + 44
68  org.python.python               0x000000010d66a0ac call_function + 636
69  org.python.python               0x000000010d662d9b _PyEval_EvalFrameDefault + 7174
70  org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
71  org.python.python               0x000000010d5d4100 _PyFunction_FastCallKeywords + 225
72  org.python.python               0x000000010d66a121 call_function + 753
73  org.python.python               0x000000010d662d9b _PyEval_EvalFrameDefault + 7174
74  org.python.python               0x000000010d5dfd5a gen_send_ex + 242
75  org.python.python               0x000000010d65f66d builtin_next + 99
76  org.python.python               0x000000010d5d4bc0 _PyMethodDef_RawFastCallKeywords + 496
77  org.python.python               0x000000010d5d413b _PyCFunction_FastCallKeywords + 44
78  org.python.python               0x000000010d66a0ac call_function + 636
79  org.python.python               0x000000010d662d9b _PyEval_EvalFrameDefault + 7174
80  org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
81  org.python.python               0x000000010d5d3d69 _PyFunction_FastCallDict + 441
82  org.python.python               0x000000010d5d4ebd _PyObject_Call_Prepend + 150
83  org.python.python               0x000000010d5d4249 PyObject_Call + 136
84  org.python.python               0x000000010d663014 _PyEval_EvalFrameDefault + 7807
85  org.python.python               0x000000010d5dfd5a gen_send_ex + 242
86  org.python.python               0x000000010d5d4c1f _PyMethodDef_RawFastCallKeywords + 591
87  org.python.python               0x000000010d5d9556 _PyMethodDescr_FastCallKeywords + 82
88  org.python.python               0x000000010d66a151 call_function + 801
89  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
90  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
91  org.python.python               0x000000010d66a121 call_function + 753
92  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
93  org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
94  org.python.python               0x000000010d5d3d69 _PyFunction_FastCallDict + 441
95  org.python.python               0x000000010d6c1640 partial_call + 378
96  org.python.python               0x000000010d5d3fa1 _PyObject_FastCallKeywords + 359
97  org.python.python               0x000000010d66a11a call_function + 746
98  org.python.python               0x000000010d662d9b _PyEval_EvalFrameDefault + 7174
99  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
100 org.python.python               0x000000010d66a121 call_function + 753
101 org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
102 org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
103 org.python.python               0x000000010d5d4100 _PyFunction_FastCallKeywords + 225
104 org.python.python               0x000000010d68c1aa context_run + 65
105 org.python.python               0x000000010d5d46e0 _PyMethodDef_RawFastCallDict + 273
106 org.python.python               0x000000010d5d3de9 _PyCFunction_FastCallDict + 44
107 org.python.python               0x000000010d6630f1 _PyEval_EvalFrameDefault + 8028
108 org.python.python               0x000000010d5d4516 function_code_fastcall + 112
109 org.python.python               0x000000010d66a121 call_function + 753
110 org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
111 org.python.python               0x000000010d5d4516 function_code_fastcall + 112
112 org.python.python               0x000000010d66a121 call_function + 753
113 org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
114 org.python.python               0x000000010d5d4516 function_code_fastcall + 112
115 org.python.python               0x000000010d66a121 call_function + 753
116 org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
117 org.python.python               0x000000010d5d4516 function_code_fastcall + 112
118 org.python.python               0x000000010d66a121 call_function + 753
119 org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
120 org.python.python               0x000000010d5d4516 function_code_fastcall + 112
121 org.python.python               0x000000010d66a121 call_function + 753
122 org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
123 org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
124 org.python.python               0x000000010d5d4100 _PyFunction_FastCallKeywords + 225
125 org.python.python               0x000000010d66a121 call_function + 753
126 org.python.python               0x000000010d662cfd _PyEval_EvalFrameDefault + 7016
127 org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
128 org.python.python               0x000000010d66110d PyEval_EvalCode + 42
129 org.python.python               0x000000010d65eb8c builtin_exec + 554
130 org.python.python               0x000000010d5d4bc0 _PyMethodDef_RawFastCallKeywords + 496
131 org.python.python               0x000000010d5d413b _PyCFunction_FastCallKeywords + 44
132 org.python.python               0x000000010d66a0ac call_function + 636
133 org.python.python               0x000000010d662d9b _PyEval_EvalFrameDefault + 7174
134 org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
135 org.python.python               0x000000010d5d4100 _PyFunction_FastCallKeywords + 225
136 org.python.python               0x000000010d66a121 call_function + 753
137 org.python.python               0x000000010d662d9b _PyEval_EvalFrameDefault + 7174
138 org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
139 org.python.python               0x000000010d5d3d69 _PyFunction_FastCallDict + 441
140 org.python.python               0x000000010d6a7c87 pymain_run_module + 147
141 org.python.python               0x000000010d6a64d5 pymain_main + 2055
142 org.python.python               0x000000010d6a78a7 _Py_UnixMain + 75
143 libdyld.dylib                   0x00007fff6e9d2015 start + 1

Thread 1:
0   libsystem_kernel.dylib          0x00007fff6eb23bea kevent + 10
1   libzmq.cpython-37m-darwin.so    0x000000011067c5ab zmq::kqueue_t::loop() + 171
2   libzmq.cpython-37m-darwin.so    0x0000000110671fde thread_routine(void*) + 46
3   libsystem_pthread.dylib         0x00007fff6ecea661 _pthread_body + 340
4   libsystem_pthread.dylib         0x00007fff6ecea50d _pthread_start + 377
5   libsystem_pthread.dylib         0x00007fff6ece9bf9 thread_start + 13

Thread 2:
0   libsystem_kernel.dylib          0x00007fff6eb23bea kevent + 10
1   libzmq.cpython-37m-darwin.so    0x000000011067c5ab zmq::kqueue_t::loop() + 171
2   libzmq.cpython-37m-darwin.so    0x0000000110671fde thread_routine(void*) + 46
3   libsystem_pthread.dylib         0x00007fff6ecea661 _pthread_body + 340
4   libsystem_pthread.dylib         0x00007fff6ecea50d _pthread_start + 377
5   libsystem_pthread.dylib         0x00007fff6ece9bf9 thread_start + 13

Thread 3:
0   libsystem_kernel.dylib          0x00007fff6eb23bea kevent + 10
1   select.cpython-37m-darwin.so    0x000000010e392345 kqueue_queue_control + 826
2   org.python.python               0x000000010d5d4abc _PyMethodDef_RawFastCallKeywords + 236
3   org.python.python               0x000000010d5d9556 _PyMethodDescr_FastCallKeywords + 82
4   org.python.python               0x000000010d66a151 call_function + 801
5   org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
6   org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
7   org.python.python               0x000000010d5d4100 _PyFunction_FastCallKeywords + 225
8   org.python.python               0x000000010d66a121 call_function + 753
9   org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
10  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
11  org.python.python               0x000000010d66a121 call_function + 753
12  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
13  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
14  org.python.python               0x000000010d66a121 call_function + 753
15  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
16  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
17  org.python.python               0x000000010d66a121 call_function + 753
18  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
19  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
20  org.python.python               0x000000010d5d4ebd _PyObject_Call_Prepend + 150
21  org.python.python               0x000000010d5d4249 PyObject_Call + 136
22  org.python.python               0x000000010d663014 _PyEval_EvalFrameDefault + 7807
23  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
24  org.python.python               0x000000010d66a121 call_function + 753
25  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
26  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
27  org.python.python               0x000000010d66a121 call_function + 753
28  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
29  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
30  org.python.python               0x000000010d5d4ebd _PyObject_Call_Prepend + 150
31  org.python.python               0x000000010d5d4249 PyObject_Call + 136
32  org.python.python               0x000000010d6d1d80 t_bootstrap + 71
33  org.python.python               0x000000010d69859d pythread_wrapper + 25
34  libsystem_pthread.dylib         0x00007fff6ecea661 _pthread_body + 340
35  libsystem_pthread.dylib         0x00007fff6ecea50d _pthread_start + 377
36  libsystem_pthread.dylib         0x00007fff6ece9bf9 thread_start + 13

Thread 4:: ZMQbg/3
0   libsystem_kernel.dylib          0x00007fff6eb2409a poll + 10
1   libzmq.cpython-37m-darwin.so    0x000000011069cc96 zmq_poll + 422
2   libzmq.cpython-37m-darwin.so    0x000000011069f7ec zmq::proxy(zmq::socket_base_t*, zmq::socket_base_t*, zmq::socket_base_t*, zmq::socket_base_t*) + 284
3   _device.cpython-37m-darwin.so   0x000000011037a2aa __pyx_pw_3zmq_7backend_6cython_7_device_3proxy + 394
4   _device.cpython-37m-darwin.so   0x0000000110379c95 __Pyx_PyObject_Call + 85
5   _device.cpython-37m-darwin.so   0x0000000110378c11 __pyx_pw_3zmq_7backend_6cython_7_device_1device + 529
6   org.python.python               0x000000010d5d3fa1 _PyObject_FastCallKeywords + 359
7   org.python.python               0x000000010d66a11a call_function + 746
8   org.python.python               0x000000010d662cfd _PyEval_EvalFrameDefault + 7016
9   org.python.python               0x000000010d5d4516 function_code_fastcall + 112
10  org.python.python               0x000000010d66a121 call_function + 753
11  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
12  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
13  org.python.python               0x000000010d66a121 call_function + 753
14  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
15  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
16  org.python.python               0x000000010d5d4ebd _PyObject_Call_Prepend + 150
17  org.python.python               0x000000010d5d4249 PyObject_Call + 136
18  org.python.python               0x000000010d6d1d80 t_bootstrap + 71
19  org.python.python               0x000000010d69859d pythread_wrapper + 25
20  libsystem_pthread.dylib         0x00007fff6ecea661 _pthread_body + 340
21  libsystem_pthread.dylib         0x00007fff6ecea50d _pthread_start + 377
22  libsystem_pthread.dylib         0x00007fff6ece9bf9 thread_start + 13

Thread 5:
0   libsystem_kernel.dylib          0x00007fff6eb23bea kevent + 10
1   libzmq.cpython-37m-darwin.so    0x000000011067c5ab zmq::kqueue_t::loop() + 171
2   libzmq.cpython-37m-darwin.so    0x0000000110671fde thread_routine(void*) + 46
3   libsystem_pthread.dylib         0x00007fff6ecea661 _pthread_body + 340
4   libsystem_pthread.dylib         0x00007fff6ecea50d _pthread_start + 377
5   libsystem_pthread.dylib         0x00007fff6ece9bf9 thread_start + 13

Thread 6:
0   libsystem_kernel.dylib          0x00007fff6eb23bea kevent + 10
1   libzmq.cpython-37m-darwin.so    0x000000011067c5ab zmq::kqueue_t::loop() + 171
2   libzmq.cpython-37m-darwin.so    0x0000000110671fde thread_routine(void*) + 46
3   libsystem_pthread.dylib         0x00007fff6ecea661 _pthread_body + 340
4   libsystem_pthread.dylib         0x00007fff6ecea50d _pthread_start + 377
5   libsystem_pthread.dylib         0x00007fff6ece9bf9 thread_start + 13

Thread 7:
0   libsystem_kernel.dylib          0x00007fff6eb22a16 __psynch_cvwait + 10
1   libsystem_pthread.dylib         0x00007fff6eceb589 _pthread_cond_wait + 732
2   org.python.python               0x000000010d698914 PyThread_acquire_lock_timed + 401
3   org.python.python               0x000000010d6d164a acquire_timed + 104
4   org.python.python               0x000000010d6d140e lock_PyThread_acquire_lock + 44
5   org.python.python               0x000000010d5d4bf1 _PyMethodDef_RawFastCallKeywords + 545
6   org.python.python               0x000000010d5d9556 _PyMethodDescr_FastCallKeywords + 82
7   org.python.python               0x000000010d66a151 call_function + 801
8   org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
9   org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
10  org.python.python               0x000000010d5d4100 _PyFunction_FastCallKeywords + 225
11  org.python.python               0x000000010d66a121 call_function + 753
12  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
13  org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
14  org.python.python               0x000000010d5d4100 _PyFunction_FastCallKeywords + 225
15  org.python.python               0x000000010d66a121 call_function + 753
16  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
17  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
18  org.python.python               0x000000010d663014 _PyEval_EvalFrameDefault + 7807
19  org.python.python               0x000000010d66a9b6 _PyEval_EvalCodeWithName + 1838
20  org.python.python               0x000000010d5d4100 _PyFunction_FastCallKeywords + 225
21  org.python.python               0x000000010d66a121 call_function + 753
22  org.python.python               0x000000010d662d9b _PyEval_EvalFrameDefault + 7174
23  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
24  org.python.python               0x000000010d66a121 call_function + 753
25  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
26  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
27  org.python.python               0x000000010d66a121 call_function + 753
28  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
29  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
30  org.python.python               0x000000010d5d4ebd _PyObject_Call_Prepend + 150
31  org.python.python               0x000000010d5d4249 PyObject_Call + 136
32  org.python.python               0x000000010d6d1d80 t_bootstrap + 71
33  org.python.python               0x000000010d69859d pythread_wrapper + 25
34  libsystem_pthread.dylib         0x00007fff6ecea661 _pthread_body + 340
35  libsystem_pthread.dylib         0x00007fff6ecea50d _pthread_start + 377
36  libsystem_pthread.dylib         0x00007fff6ece9bf9 thread_start + 13

Thread 8:
0   libsystem_kernel.dylib          0x00007fff6eb22cf2 __select + 10
1   org.python.python               0x000000010d6cfaf8 time_sleep + 121
2   org.python.python               0x000000010d5d4c1f _PyMethodDef_RawFastCallKeywords + 591
3   org.python.python               0x000000010d5d413b _PyCFunction_FastCallKeywords + 44
4   org.python.python               0x000000010d66a0ac call_function + 636
5   org.python.python               0x000000010d662cfd _PyEval_EvalFrameDefault + 7016
6   org.python.python               0x000000010d5d4516 function_code_fastcall + 112
7   org.python.python               0x000000010d66a121 call_function + 753
8   org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
9   org.python.python               0x000000010d5d4516 function_code_fastcall + 112
10  org.python.python               0x000000010d66a121 call_function + 753
11  org.python.python               0x000000010d662ce4 _PyEval_EvalFrameDefault + 6991
12  org.python.python               0x000000010d5d4516 function_code_fastcall + 112
13  org.python.python               0x000000010d5d4ebd _PyObject_Call_Prepend + 150
14  org.python.python               0x000000010d5d4249 PyObject_Call + 136
15  org.python.python               0x000000010d6d1d80 t_bootstrap + 71
16  org.python.python               0x000000010d69859d pythread_wrapper + 25
17  libsystem_pthread.dylib         0x00007fff6ecea661 _pthread_body + 340
18  libsystem_pthread.dylib         0x00007fff6ecea50d _pthread_start + 377
19  libsystem_pthread.dylib         0x00007fff6ece9bf9 thread_start + 13

Thread 9:
0   libsystem_kernel.dylib          0x00007fff6eb22a16 __psynch_cvwait + 10
1   libsystem_pthread.dylib         0x00007fff6eceb589 _pthread_cond_wait + 732
2   libopenblasp-r0.3.7.dev.dylib   0x000000011d16fc0b blas_thread_server + 619
3   libsystem_pthread.dylib         0x00007fff6ecea661 _pthread_body + 340
4   libsystem_pthread.dylib         0x00007fff6ecea50d _pthread_start + 377
5   libsystem_pthread.dylib         0x00007fff6ece9bf9 thread_start + 13

Thread 10:
0   libsystem_kernel.dylib          0x00007fff6eb22a16 __psynch_cvwait + 10
1   libsystem_pthread.dylib         0x00007fff6eceb589 _pthread_cond_wait + 732
2   libopenblasp-r0.3.7.dev.dylib   0x000000011d16fc0b blas_thread_server + 619
3   libsystem_pthread.dylib         0x00007fff6ecea661 _pthread_body + 340
4   libsystem_pthread.dylib         0x00007fff6ecea50d _pthread_start + 377
5   libsystem_pthread.dylib         0x00007fff6ece9bf9 thread_start + 13

Thread 11:
0   libsystem_kernel.dylib          0x00007fff6eb22a16 __psynch_cvwait + 10
1   libsystem_pthread.dylib         0x00007fff6eceb589 _pthread_cond_wait + 732
2   libopenblasp-r0.3.7.dev.dylib   0x000000011d16fc0b blas_thread_server + 619
3   libsystem_pthread.dylib         0x00007fff6ecea661 _pthread_body + 340
4   libsystem_pthread.dylib         0x00007fff6ecea50d _pthread_start + 377
5   libsystem_pthread.dylib         0x00007fff6ece9bf9 thread_start + 13

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x000000010f830c30  rbx: 0x000000012eb03bb0  rcx: 0xfffffffffffffffa  rdx: 0x0000000131085470
  rdi: 0x000000012eb03bb0  rsi: 0x0000000131085bb0  rbp: 0x00007ffee2643c50  rsp: 0x00007ffee2643c40
   r8: 0x0000000000000000   r9: 0x0000000000008004  r10: 0x0000000000000000  r11: 0x0000000000003441
  r12: 0x00000001313c4940  r13: 0x000000010d60ba55  r14: 0x00007fc26340a230  r15: 0x000000000000000e
  rip: 0x000000012d6c27cf  rfl: 0x0000000000010282  cr2: 0xfffffffffffffffa

Logical CPU:     0
Error Code:      0x00000006
Trap Number:     14
  • I have figured out that this is only an issue in python 3.7.4. When using v.3.7.3, it does not crash. – Jan Pesl Jul 18 '19 at 16:57
0

I had this issue and solved it by upgrading my version of numba to the latest 0.45.1.

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