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Crash during groupby quantile #28882

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VelizarVESSELINOV opened this issue Oct 9, 2019 · 11 comments · Fixed by #29173
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@VelizarVESSELINOV
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@VelizarVESSELINOV VelizarVESSELINOV commented Oct 9, 2019

Code Sample, a copy-pastable example if possible

dtf = dtf.groupby(cut(dtf[X], rng)).quantile(.5)

Problem description

Process: Python [24642]
Path: /Library/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: Python [24593]
Responsible: iTerm2 [1703]
User ID: 501

Date/Time: 2019-10-09 17:11:04.949 -0500
OS Version: Mac OS X 10.15 (19A583)
Report Version: 12
Bridge OS Version: 3.0 (14Y904)
Anonymous UUID: F986CCB3-5DD1-9587-8492-6D8B8A43979D

Sleep/Wake UUID: 42F77302-9822-4979-89CB-7C39F3C0556A

Time Awake Since Boot: 67000 seconds
Time Since Wake: 1900 seconds

System Integrity Protection: enabled

Crashed Thread: 7

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x000000013a6dcff8
Exception Note: EXC_CORPSE_NOTIFY

Termination Signal: Segmentation fault: 11
Termination Reason: Namespace SIGNAL, Code 0xb
Terminating Process: exc handler [24642]

VM Regions Near 0x13a6dcff8:
MALLOC_LARGE 000000013a5ee000-000000013a633000 [ 276K] rw-/rwx SM=PRV
-->
MALLOC_LARGE 000000013a6dd000-000000013a74d000 [ 448K] rw-/rwx SM=PRV

0 groupby.cpython-37m-darwin.so 0x000000011b1596cf __pyx_fuse_9__pyx_pw_6pandas_5_libs_7groupby_125group_quantile + 6719
1 algos.cpython-37m-darwin.so 0x0000000119e8937c __pyx_FusedFunction_call + 812

Thread 0:: Dispatch queue: com.apple.main-thread 0 org.python.python 0x000000010d924bbf _PyEval_EvalFrameDefault + 1423 1 org.python.python 0x000000010d86ea10 function_code_fastcall + 128 2 org.python.python 0x000000010d92d8c2 call_function + 738 3 org.python.python 0x000000010d92a92e _PyEval_EvalFrameDefault + 25342 4 org.python.python 0x000000010d86ea10 function_code_fastcall + 128 5 org.python.python 0x000000010d92d8c2 call_function + 738 6 org.python.python 0x000000010d92a88d _PyEval_EvalFrameDefault + 25181 7 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467 8 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257 9 org.python.python 0x000000010d92d8c2 call_function + 738 10 org.python.python 0x000000010d92a92e _PyEval_EvalFrameDefault + 25342 11 org.python.python 0x000000010d86ea10 function_code_fastcall + 128 12 org.python.python 0x000000010d92d8c2 call_function + 738 13 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155 14 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467 15 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257 16 org.python.python 0x000000010d92d8c2 call_function + 738 17 org.python.python 0x000000010d92a92e _PyEval_EvalFrameDefault + 25342 18 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467 19 org.python.python 0x000000010d86e17b _PyFunction_FastCallDict + 523 20 org.python.python 0x000000010d92ab9e _PyEval_EvalFrameDefault + 25966 21 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467 22 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257 23 org.python.python 0x000000010d92d8c2 call_function + 738 24 org.python.python 0x000000010d92a9d4 _PyEval_EvalFrameDefault + 25508 25 org.python.python 0x000000010d86ea10 function_code_fastcall + 128 26 org.python.python 0x000000010d92d8c2 call_function + 738 27 org.python.python 0x000000010d92a92e _PyEval_EvalFrameDefault + 25342 28 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467 29 org.python.python 0x000000010d924554 PyEval_EvalCode + 100 30 org.python.python 0x000000010d961c31 PyRun_FileExFlags + 209 31 org.python.python 0x000000010d9614aa PyRun_SimpleFileExFlags + 890 32 org.python.python 0x000000010d980903 pymain_main + 6915 33 org.python.python 0x000000010d980e6a _Py_UnixMain + 58 34 libdyld.dylib 0x00007fff731e2405 start + 1

Thread 1:
0 libsystem_pthread.dylib 0x00007fff733eb5b4 start_wqthread + 0

Thread 2:
0 libsystem_kernel.dylib 0x00007fff7333359e poll + 10
1 select.cpython-37m-darwin.so 0x000000010e0c1982 poll_poll + 466
2 org.python.python 0x000000010d86f1cc _PyMethodDef_RawFastCallKeywords + 668
3 org.python.python 0x000000010d874d42 _PyMethodDescr_FastCallKeywords + 82
4 org.python.python 0x000000010d92d8ec call_function + 780
5 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
6 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
7 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
8 org.python.python 0x000000010d92d8c2 call_function + 738
9 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
10 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
11 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
12 org.python.python 0x000000010d92d8c2 call_function + 738
13 org.python.python 0x000000010d92a88d _PyEval_EvalFrameDefault + 25181
14 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
15 org.python.python 0x000000010d92d8c2 call_function + 738
16 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
17 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
18 org.python.python 0x000000010d86e17b _PyFunction_FastCallDict + 523
19 org.python.python 0x000000010d92ab9e _PyEval_EvalFrameDefault + 25966
20 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
21 org.python.python 0x000000010d92d8c2 call_function + 738
22 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
23 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
24 org.python.python 0x000000010d92d8c2 call_function + 738
25 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
26 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
27 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
28 org.python.python 0x000000010d86f4bf _PyObject_Call_Prepend + 143
29 org.python.python 0x000000010d86e707 PyObject_Call + 135
30 org.python.python 0x000000010d9b5b77 t_bootstrap + 71
31 org.python.python 0x000000010d96c939 pythread_wrapper + 25
32 libsystem_pthread.dylib 0x00007fff733eed76 _pthread_start + 125
33 libsystem_pthread.dylib 0x00007fff733eb5d7 thread_start + 15

Thread 3:
0 libsystem_kernel.dylib 0x00007fff7332e8f6 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff733ef082 _pthread_cond_wait + 701
2 org.python.python 0x000000010d96ce01 PyThread_acquire_lock_timed + 673
3 org.python.python 0x000000010d9b620f acquire_timed + 111
4 org.python.python 0x000000010d9b6320 lock_PyThread_acquire_lock + 48
5 org.python.python 0x000000010d86f1dd _PyMethodDef_RawFastCallKeywords + 685
6 org.python.python 0x000000010d874d42 _PyMethodDescr_FastCallKeywords + 82
7 org.python.python 0x000000010d92d8ec call_function + 780
8 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
9 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
10 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
11 org.python.python 0x000000010d92d8c2 call_function + 738
12 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
13 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
14 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
15 org.python.python 0x000000010d92d8c2 call_function + 738
16 org.python.python 0x000000010d92a9d4 _PyEval_EvalFrameDefault + 25508
17 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
18 org.python.python 0x000000010d92d8c2 call_function + 738
19 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
20 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
21 org.python.python 0x000000010d92d8c2 call_function + 738
22 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
23 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
24 org.python.python 0x000000010d92d8c2 call_function + 738
25 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
26 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
27 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
28 org.python.python 0x000000010d86f4bf _PyObject_Call_Prepend + 143
29 org.python.python 0x000000010d86e707 PyObject_Call + 135
30 org.python.python 0x000000010d9b5b77 t_bootstrap + 71
31 org.python.python 0x000000010d96c939 pythread_wrapper + 25
32 libsystem_pthread.dylib 0x00007fff733eed76 _pthread_start + 125
33 libsystem_pthread.dylib 0x00007fff733eb5d7 thread_start + 15

Thread 4:
0 libsystem_kernel.dylib 0x00007fff7332b146 mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff7332b6ac mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3bee419b __CFRunLoopServiceMachPort + 322
3 com.apple.CoreFoundation 0x00007fff3bee3737 __CFRunLoopRun + 1695
4 com.apple.CoreFoundation 0x00007fff3bee2e13 CFRunLoopRunSpecific + 499
5 com.apple.CoreFoundation 0x00007fff3bee2bea CFRunLoopRun + 40
6 _watchdog_fsevents.cpython-37m-darwin.so 0x00000001323a5915 watchdog_read_events + 149
7 org.python.python 0x000000010d86f1cc _PyMethodDef_RawFastCallKeywords + 668
8 org.python.python 0x000000010d86e5da _PyCFunction_FastCallKeywords + 42
9 org.python.python 0x000000010d92d8b4 call_function + 724
10 org.python.python 0x000000010d92a88d _PyEval_EvalFrameDefault + 25181
11 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
12 org.python.python 0x000000010d92d8c2 call_function + 738
13 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
14 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
15 org.python.python 0x000000010d92d8c2 call_function + 738
16 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
17 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
18 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
19 org.python.python 0x000000010d86f4bf _PyObject_Call_Prepend + 143
20 org.python.python 0x000000010d86e707 PyObject_Call + 135
21 org.python.python 0x000000010d9b5b77 t_bootstrap + 71
22 org.python.python 0x000000010d96c939 pythread_wrapper + 25
23 libsystem_pthread.dylib 0x00007fff733eed76 _pthread_start + 125
24 libsystem_pthread.dylib 0x00007fff733eb5d7 thread_start + 15

Thread 5:
0 libsystem_kernel.dylib 0x00007fff7332b146 mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff7332b6ac mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3bee419b __CFRunLoopServiceMachPort + 322
3 com.apple.CoreFoundation 0x00007fff3bee3737 __CFRunLoopRun + 1695
4 com.apple.CoreFoundation 0x00007fff3bee2e13 CFRunLoopRunSpecific + 499
5 com.apple.CoreFoundation 0x00007fff3bee2bea CFRunLoopRun + 40
6 _watchdog_fsevents.cpython-37m-darwin.so 0x00000001323a5915 watchdog_read_events + 149
7 org.python.python 0x000000010d86f1cc _PyMethodDef_RawFastCallKeywords + 668
8 org.python.python 0x000000010d86e5da _PyCFunction_FastCallKeywords + 42
9 org.python.python 0x000000010d92d8b4 call_function + 724
10 org.python.python 0x000000010d92a88d _PyEval_EvalFrameDefault + 25181
11 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
12 org.python.python 0x000000010d92d8c2 call_function + 738
13 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
14 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
15 org.python.python 0x000000010d92d8c2 call_function + 738
16 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
17 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
18 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
19 org.python.python 0x000000010d86f4bf _PyObject_Call_Prepend + 143
20 org.python.python 0x000000010d86e707 PyObject_Call + 135
21 org.python.python 0x000000010d9b5b77 t_bootstrap + 71
22 org.python.python 0x000000010d96c939 pythread_wrapper + 25
23 libsystem_pthread.dylib 0x00007fff733eed76 _pthread_start + 125
24 libsystem_pthread.dylib 0x00007fff733eb5d7 thread_start + 15

Thread 6:
0 libsystem_kernel.dylib 0x00007fff7332b146 mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff7332b6ac mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3bee419b __CFRunLoopServiceMachPort + 322
3 com.apple.CoreFoundation 0x00007fff3bee3737 __CFRunLoopRun + 1695
4 com.apple.CoreFoundation 0x00007fff3bee2e13 CFRunLoopRunSpecific + 499
5 com.apple.CoreFoundation 0x00007fff3bee2bea CFRunLoopRun + 40
6 _watchdog_fsevents.cpython-37m-darwin.so 0x00000001323a5915 watchdog_read_events + 149
7 org.python.python 0x000000010d86f1cc _PyMethodDef_RawFastCallKeywords + 668
8 org.python.python 0x000000010d86e5da _PyCFunction_FastCallKeywords + 42
9 org.python.python 0x000000010d92d8b4 call_function + 724
10 org.python.python 0x000000010d92a88d _PyEval_EvalFrameDefault + 25181
11 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
12 org.python.python 0x000000010d92d8c2 call_function + 738
13 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
14 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
15 org.python.python 0x000000010d92d8c2 call_function + 738
16 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
17 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
18 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
19 org.python.python 0x000000010d86f4bf _PyObject_Call_Prepend + 143
20 org.python.python 0x000000010d86e707 PyObject_Call + 135
21 org.python.python 0x000000010d9b5b77 t_bootstrap + 71
22 org.python.python 0x000000010d96c939 pythread_wrapper + 25
23 libsystem_pthread.dylib 0x00007fff733eed76 _pthread_start + 125
24 libsystem_pthread.dylib 0x00007fff733eb5d7 thread_start + 15

Thread 7 Crashed:
0 groupby.cpython-37m-darwin.so 0x000000011b1596cf __pyx_fuse_9__pyx_pw_6pandas_5_libs_7groupby_125group_quantile + 6719
1 algos.cpython-37m-darwin.so 0x0000000119e8937c __pyx_FusedFunction_call + 812
2 org.python.python 0x000000010d86e707 PyObject_Call + 135
3 org.python.python 0x000000010d9a45c0 partial_call + 256
4 org.python.python 0x000000010d86e707 PyObject_Call + 135
5 org.python.python 0x000000010d92ab9e _PyEval_EvalFrameDefault + 25966
6 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
7 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
8 org.python.python 0x000000010d92d8c2 call_function + 738
9 org.python.python 0x000000010d92a9d4 _PyEval_EvalFrameDefault + 25508
10 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
11 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
12 org.python.python 0x000000010d92d8c2 call_function + 738
13 org.python.python 0x000000010d92a88d _PyEval_EvalFrameDefault + 25181
14 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
15 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
16 org.python.python 0x000000010d92d8c2 call_function + 738
17 org.python.python 0x000000010d92a9d4 _PyEval_EvalFrameDefault + 25508
18 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
19 org.python.python 0x000000010d86e17b _PyFunction_FastCallDict + 523
20 org.python.python 0x000000010d92ab9e _PyEval_EvalFrameDefault + 25966
21 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
22 org.python.python 0x000000010d86e17b _PyFunction_FastCallDict + 523
23 org.python.python 0x000000010d92ab9e _PyEval_EvalFrameDefault + 25966
24 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
25 org.python.python 0x000000010d92d8c2 call_function + 738
26 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
27 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
28 org.python.python 0x000000010d92d8c2 call_function + 738
29 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
30 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
31 org.python.python 0x000000010d92d8c2 call_function + 738
32 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
33 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
34 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
35 org.python.python 0x000000010d86f4bf _PyObject_Call_Prepend + 143
36 org.python.python 0x000000010d8bc926 slot_tp_call + 150
37 org.python.python 0x000000010d86e3f1 _PyObject_FastCallKeywords + 433
38 org.python.python 0x000000010d92d784 call_function + 420
39 org.python.python 0x000000010d92a88d _PyEval_EvalFrameDefault + 25181
40 org.python.python 0x000000010d87ca5e gen_send_ex + 206
41 org.python.python 0x000000010d92a06f _PyEval_EvalFrameDefault + 23103
42 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
43 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
44 org.python.python 0x000000010d92d8c2 call_function + 738
45 org.python.python 0x000000010d92a92e _PyEval_EvalFrameDefault + 25342
46 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
47 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
48 org.python.python 0x000000010d92d8c2 call_function + 738
49 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
50 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
51 org.python.python 0x000000010d92d8c2 call_function + 738
52 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
53 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
54 org.python.python 0x000000010d92d8c2 call_function + 738
55 org.python.python 0x000000010d92a88d _PyEval_EvalFrameDefault + 25181
56 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
57 org.python.python 0x000000010d92d8c2 call_function + 738
58 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
59 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
60 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
61 org.python.python 0x000000010d86f4bf _PyObject_Call_Prepend + 143
62 org.python.python 0x000000010d8bdd61 slot_tp_init + 145
63 org.python.python 0x000000010d8b9749 type_call + 297
64 org.python.python 0x000000010d86e3f1 _PyObject_FastCallKeywords + 433
65 org.python.python 0x000000010d92d784 call_function + 420
66 org.python.python 0x000000010d92a88d _PyEval_EvalFrameDefault + 25181
67 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
68 org.python.python 0x000000010d92d8c2 call_function + 738
69 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
70 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
71 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
72 org.python.python 0x000000010d86f4bf _PyObject_Call_Prepend + 143
73 org.python.python 0x000000010d86e707 PyObject_Call + 135
74 org.python.python 0x000000010d92ab9e _PyEval_EvalFrameDefault + 25966
75 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
76 org.python.python 0x000000010d92d8c2 call_function + 738
77 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
78 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
79 org.python.python 0x000000010d92d8c2 call_function + 738
80 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
81 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
82 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
83 org.python.python 0x000000010d86f4bf _PyObject_Call_Prepend + 143
84 org.python.python 0x000000010d86e707 PyObject_Call + 135
85 org.python.python 0x000000010d9b5b77 t_bootstrap + 71
86 org.python.python 0x000000010d96c939 pythread_wrapper + 25
87 libsystem_pthread.dylib 0x00007fff733eed76 _pthread_start + 125
88 libsystem_pthread.dylib 0x00007fff733eb5d7 thread_start + 15

Thread 8:
0 _multiarray_umath.cpython-37m-darwin.so 0x000000010ea13664 BOOL_logical_not + 612
1 _multiarray_umath.cpython-37m-darwin.so 0x000000010eab05a1 trivial_two_operand_loop + 273
2 _multiarray_umath.cpython-37m-darwin.so 0x000000010eaa9140 PyUFunc_GenericFunction + 15792
3 _multiarray_umath.cpython-37m-darwin.so 0x000000010eaabc68 ufunc_generic_call + 136
4 org.python.python 0x000000010d86def9 _PyObject_FastCallDict + 297
5 org.python.python 0x000000010d87014c object_vacall + 316
6 org.python.python 0x000000010d870334 PyObject_CallFunctionObjArgs + 148
7 org.python.python 0x000000010d86f225 _PyMethodDef_RawFastCallKeywords + 757
8 org.python.python 0x000000010d86e5da _PyCFunction_FastCallKeywords + 42
9 org.python.python 0x000000010d92d8b4 call_function + 724
10 org.python.python 0x000000010d92a88d _PyEval_EvalFrameDefault + 25181
11 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
12 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
13 org.python.python 0x000000010d86f3df _PyObject_FastCall_Prepend + 127
14 org.python.python 0x000000010d8c0316 slot_nb_invert + 134
15 org.python.python 0x000000010d925152 _PyEval_EvalFrameDefault + 2850
16 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
17 org.python.python 0x000000010d92d8c2 call_function + 738
18 org.python.python 0x000000010d92a92e _PyEval_EvalFrameDefault + 25342
19 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
20 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
21 org.python.python 0x000000010d92d8c2 call_function + 738
22 org.python.python 0x000000010d92a9d4 _PyEval_EvalFrameDefault + 25508
23 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
24 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
25 org.python.python 0x000000010d92d8c2 call_function + 738
26 org.python.python 0x000000010d92a9d4 _PyEval_EvalFrameDefault + 25508
27 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
28 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
29 org.python.python 0x000000010d92d8c2 call_function + 738
30 org.python.python 0x000000010d92a9d4 _PyEval_EvalFrameDefault + 25508
31 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
32 org.python.python 0x000000010d86e17b _PyFunction_FastCallDict + 523
33 org.python.python 0x000000010d92ab9e _PyEval_EvalFrameDefault + 25966
34 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
35 org.python.python 0x000000010d86e17b _PyFunction_FastCallDict + 523
36 org.python.python 0x000000010d92ab9e _PyEval_EvalFrameDefault + 25966
37 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
38 org.python.python 0x000000010d92d8c2 call_function + 738
39 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
40 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
41 org.python.python 0x000000010d92d8c2 call_function + 738
42 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
43 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
44 org.python.python 0x000000010d92d8c2 call_function + 738
45 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
46 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
47 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
48 org.python.python 0x000000010d86f4bf _PyObject_Call_Prepend + 143
49 org.python.python 0x000000010d8bc926 slot_tp_call + 150
50 org.python.python 0x000000010d86e3f1 _PyObject_FastCallKeywords + 433
51 org.python.python 0x000000010d92d784 call_function + 420
52 org.python.python 0x000000010d92a88d _PyEval_EvalFrameDefault + 25181
53 org.python.python 0x000000010d87ca5e gen_send_ex + 206
54 org.python.python 0x000000010d92a06f _PyEval_EvalFrameDefault + 23103
55 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
56 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
57 org.python.python 0x000000010d92d8c2 call_function + 738
58 org.python.python 0x000000010d92a92e _PyEval_EvalFrameDefault + 25342
59 org.python.python 0x000000010d92e413 _PyEval_EvalCodeWithName + 2467
60 org.python.python 0x000000010d86e5a1 _PyFunction_FastCallKeywords + 257
61 org.python.python 0x000000010d92d8c2 call_function + 738
62 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
63 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
64 org.python.python 0x000000010d92d8c2 call_function + 738
65 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
66 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
67 org.python.python 0x000000010d92d8c2 call_function + 738
68 org.python.python 0x000000010d92a88d _PyEval_EvalFrameDefault + 25181
69 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
70 org.python.python 0x000000010d92d8c2 call_function + 738
71 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
72 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
73 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
74 org.python.python 0x000000010d86f4bf _PyObject_Call_Prepend + 143
75 org.python.python 0x000000010d8bdd61 slot_tp_init + 145
76 org.python.python 0x000000010d8b9749 type_call + 297
77 org.python.python 0x000000010d86e3f1 _PyObject_FastCallKeywords + 433
78 org.python.python 0x000000010d92d784 call_function + 420
79 org.python.python 0x000000010d92a88d _PyEval_EvalFrameDefault + 25181
80 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
81 org.python.python 0x000000010d92d8c2 call_function + 738
82 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
83 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
84 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
85 org.python.python 0x000000010d86f4bf _PyObject_Call_Prepend + 143
86 org.python.python 0x000000010d86e707 PyObject_Call + 135
87 org.python.python 0x000000010d92ab9e _PyEval_EvalFrameDefault + 25966
88 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
89 org.python.python 0x000000010d92d8c2 call_function + 738
90 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
91 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
92 org.python.python 0x000000010d92d8c2 call_function + 738
93 org.python.python 0x000000010d92a873 _PyEval_EvalFrameDefault + 25155
94 org.python.python 0x000000010d86ea10 function_code_fastcall + 128
95 org.python.python 0x000000010d86e004 _PyFunction_FastCallDict + 148
96 org.python.python 0x000000010d86f4bf _PyObject_Call_Prepend + 143
97 org.python.python 0x000000010d86e707 PyObject_Call + 135
98 org.python.python 0x000000010d9b5b77 t_bootstrap + 71
99 org.python.python 0x000000010d96c939 pythread_wrapper + 25
100 libsystem_pthread.dylib 0x00007fff733eed76 _pthread_start + 125
101 libsystem_pthread.dylib 0x00007fff733eb5d7 thread_start + 15

Thread 7 crashed with X86 Thread State (64-bit):
rax: 0x00007fc23e50d830 rbx: 0xffffffffffffffff rcx: 0x0000000148926000 rdx: 0x0000000131c66000
rdi: 0x000000000013dc10 rsi: 0xfffffffffffffff8 rbp: 0x0000700006b28490 rsp: 0x0000700006b27df0
r8: 0x0000000000000008 r9: 0x0000000000000008 r10: 0x0000000000000008 r11: 0x0000000000000001
r12: 0x000000013a6dd000 r13: 0x0000700006b282f8 r14: 0x00000001352d0760 r15: 0x000000000000880b
rip: 0x000000011b1596cf rfl: 0x0000000000010282 cr2: 0x000000013a6dcff8

Logical CPU: 4
Error Code: 0x00000006 (no mapping for user data read)
Trap Number: 14

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0x7fff72420000 - 0x7fff72423ffb libutil.dylib (57) <844B7887-09B3-3D12-ACDE-C4EB8F53DC62> /usr/lib/libutil.dylib
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0x7fff72fc3000 - 0x7fff72fceff7 libcommonCrypto.dylib (60165) <698BE754-137D-361D-B826-57B8DD969E4A> /usr/lib/system/libcommonCrypto.dylib
0x7fff72fcf000 - 0x7fff72fd6fff libcompiler_rt.dylib (101.2) <0BE7F119-C9C2-3612-A3F4-2336D4444476> /usr/lib/system/libcompiler_rt.dylib
0x7fff72fd7000 - 0x7fff72fe0ff7 libcopyfile.dylib (166) /usr/lib/system/libcopyfile.dylib
0x7fff72fe1000 - 0x7fff73078fc3 libcorecrypto.dylib (866.0.10) <58344B13-CD10-3697-A516-6F5B06DD1EB7> /usr/lib/system/libcorecrypto.dylib
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0x7fff731d1000 - 0x7fff73206fff libdyld.dylib (732.8) <98960E27-A08B-36DA-A5CB-8538B2D6757E> /usr/lib/system/libdyld.dylib
0x7fff73207000 - 0x7fff73207ffb libkeymgr.dylib (30) <682B41BC-BDC2-38D5-8820-87099606FA12> /usr/lib/system/libkeymgr.dylib
0x7fff73208000 - 0x7fff73214ff7 libkxld.dylib (6153.11.26) <53BE9630-BDC8-3649-8709-7A4F86777B1A> /usr/lib/system/libkxld.dylib
0x7fff73215000 - 0x7fff73215ff7 liblaunch.dylib (1738.11.1) <7FE11F0D-65BC-3726-B1DD-E84F329193E0> /usr/lib/system/liblaunch.dylib
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0x7fff7321c000 - 0x7fff7321eff3 libquarantine.dylib (110.0.4) /usr/lib/system/libquarantine.dylib
0x7fff7321f000 - 0x7fff73220ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff73221000 - 0x7fff73238fff libsystem_asl.dylib (377.0.1) <30CE9DAF-B1FA-3510-832B-F1CE19933ED7> /usr/lib/system/libsystem_asl.dylib
0x7fff73239000 - 0x7fff73239fff libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff7323a000 - 0x7fff732c1ff7 libsystem_c.dylib (1353.11.2) <2A5BFAFE-8214-3B35-AD46-C07A1A8B8941> /usr/lib/system/libsystem_c.dylib
0x7fff732c2000 - 0x7fff732c5fff libsystem_configuration.dylib (1061.0.2) <56174463-22ED-337F-B0D4-94995DCDB9B7> /usr/lib/system/libsystem_configuration.dylib
0x7fff732c6000 - 0x7fff732c9ff7 libsystem_coreservices.dylib (114) <01695913-028E-3AE1-8D4E-2B2769109811> /usr/lib/system/libsystem_coreservices.dylib
0x7fff732ca000 - 0x7fff732d1fff libsystem_darwin.dylib (1353.11.2) <4CE52C63-87AA-3C6D-899F-8C983E5FC061> /usr/lib/system/libsystem_darwin.dylib
0x7fff732d2000 - 0x7fff732d9ffb libsystem_dnssd.dylib (1096.0.2) /usr/lib/system/libsystem_dnssd.dylib
0x7fff732da000 - 0x7fff732dbffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff732dc000 - 0x7fff73329ff7 libsystem_info.dylib (538) <9F9D6368-A11E-32F1-9BB5-C153F42EFED8> /usr/lib/system/libsystem_info.dylib
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0x7fff733df000 - 0x7fff733e8fe7 libsystem_platform.dylib (220) <90E508E4-46D8-33FF-8552-DDAA079977A0> /usr/lib/system/libsystem_platform.dylib
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0x7fff733f4000 - 0x7fff733f8ffb libsystem_sandbox.dylib (1217.11.16) <51129CBB-BC46-37F1-A1B5-ECFA9530704D> /usr/lib/system/libsystem_sandbox.dylib
0x7fff733f9000 - 0x7fff733fbfff libsystem_secinit.dylib (62.0.4) /usr/lib/system/libsystem_secinit.dylib
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0x7fff73404000 - 0x7fff7341aff2 libsystem_trace.dylib (1147.0.3) <5836645E-9862-326D-AB3B-A19E76BE29B9> /usr/lib/system/libsystem_trace.dylib
0x7fff7341c000 - 0x7fff73421ffb libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff73422000 - 0x7fff73456ff6 libxpc.dylib (1738.11.1) <2E9076CD-6C0E-38B6-8403-B2DDCE125FBF> /usr/lib/system/libxpc.dylib

External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 32
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: 7803078
thread_create: 0
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=660.2M resident=0K(0%) swapped_out_or_unallocated=660.2M(100%)
Writable regions: Total=1.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.5G(100%)

                            VIRTUAL   REGION 

REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Activity Tracing 256K 1
Dispatch continuations 16.0M 1
Kernel Alloc Once 8K 1
MALLOC 1.1G 724
MALLOC guard page 16K 3
MALLOC_LARGE (reserved) 256K 2 reserved VM address space (unallocated)
STACK GUARD 36K 9
Stack 51.6M 9
VM_ALLOCATE 4K 1
VM_ALLOCATE (reserved) 192.0M 2 reserved VM address space (unallocated)
__DATA 62.5M 464
__DATA_CONST 20K 1
__LINKEDIT 380.1M 248
__OBJC_RO 31.8M 1
__OBJC_RW 1764K 2
__TEXT 280.2M 382
__UNICODE 564K 1
mapped file 28K 1
shared memory 44K 5
=========== ======= =======
TOTAL 2.1G 1858
TOTAL, minus reserved VM space 2.0G 1858

Model: MacBookPro13,3, BootROM 262.0.0.0.0, 4 processors, Quad-Core Intel Core i7, 2.9 GHz, 16 GB, SMC 2.38f8
Graphics: kHW_IntelHDGraphics530Item, Intel HD Graphics 530, spdisplays_builtin
Graphics: kHW_AMDRadeonPro460Item, AMD Radeon Pro 460, spdisplays_pcie_device, 4 GB
Memory Module: BANK 0/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C31473332443450472D30393320
Memory Module: BANK 1/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C31473332443450472D30393320
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x15A), Broadcom BCM43xx 1.0 (7.77.105.1 AirPortDriverBrcmNIC-1429)
Bluetooth: Version 7.0.0f8, 3 services, 27 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
USB Device: USB 3.0 Bus
USB Device: Apple T1 Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 41.2
Thunderbolt Bus: MacBook Pro, Apple Inc., 41.2

#### Expected Output

Output of pd.show_versions()

NSTALLED VERSIONS

commit : None
python : 3.7.4.final.0
python-bits : 64
OS : Darwin
OS-release : 19.0.0
machine : x86_64
processor : i386
byteorder : little
LC_ALL : None
LANG : en_US.UTF-8
LOCALE : en_US.UTF-8

pandas : 0.25.1
numpy : 1.17.2
pytz : 2019.2
dateutil : 2.8.0
pip : 19.2.3
setuptools : 40.8.0
Cython : None
pytest : None
hypothesis : None
sphinx : None
blosc : None
feather : None
xlsxwriter : None
lxml.etree : 4.4.1
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 2.10.1
IPython : None
pandas_datareader: 0.8.1
bs4 : None
bottleneck : None
fastparquet : None
gcsfs : None
lxml.etree : 4.4.1
matplotlib : None
numexpr : None
odfpy : None
openpyxl : None
pandas_gbq : None
pyarrow : None
pytables : None
s3fs : None
scipy : 1.3.1
sqlalchemy : 1.3.9
tables : None
xarray : None
xlrd : 1.2.0
xlwt : None
xlsxwriter : None

@WillAyd

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@WillAyd WillAyd commented Oct 10, 2019

Can you try on master? There were a few issues with quantile in 0.25.0 and 0.25.1 that will be fixed in the next minor release

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@dsaxton dsaxton commented Oct 10, 2019

Can you provide a reproducible example? Here is a good reference for making bug reports: https://blog.dask.org/2018/02/28/minimal-bug-reports

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@VelizarVESSELINOV VelizarVESSELINOV commented Oct 10, 2019

@WillAyd, when we switched from quantile to mean, is working much better, so suspect quantile issue. We will test with 0.25.2 when it is available to switch from mean to quantile and will let you know if there is still an issue. Thanks.

@dsaxton it is difficult to write "good" stable example reproducing MALLOC_LARGE issue :) it is not 100% reproducible even with the same datasets. The one that it is catching the most of malloc issues is with more than 4M rows and group by of ~30K intervals.

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@SeppMe SeppMe commented Oct 16, 2019

Ran into the same issue today. The problem is with None keys. Here is some C&P'able code:

import pandas

print(pandas.__version__)
df = pandas.DataFrame(data=[['A', 0], [None, 123], ['A', 0]], columns=['key', 'value'])
result = df.groupby('key').quantile()
print(result)

This works fine with pandas 0.24.2, but with 0.25.1 there are several issues:

  1. The result is wrong! It says 'A' -> 61.5. the correct result would be 'A' -> 0 and ignoring the None value. Having None as an additional category would also be acceptable. But mixing it into one of the other groups is just wrong. (If you have multiple different groups, it will get mixed into whatever group comes first in the result).
  2. This crashes frequently. The code above will crash when result is garbage collected. Other, slightly different variations may crash immediately. For example, adding as_index=False to the groupby will crash immediately.

Unfortunately, I cannot test this with the latest master branch, as I am on my business laptop where I cannot easily install the required C++ build tools. I will test this on another machine of mine but it may be several hours before I get around to that.

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@SeppMe SeppMe commented Oct 16, 2019

I got it installed. Here are results for pandas 0.26.0.dev0+583.g86e187f:

  1. The code above no longer crashes, but it still produces the wrong result of A->61.5
  2. The code starts crashing again when subject to slight modifications: Using as_index=False will crash immediately. Using a list of quantiles (p.e. df.groupby('key').quantile([0, 0.5, 1])) crashes immediately. Using the similar example from the other thread on this topic crashes immediately.
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@VelizarVESSELINOV VelizarVESSELINOV commented Oct 22, 2019

Confirm, the same crash with official 0.25.2 release

dtf = dtf.groupby(cut(dtf[col[0]], rng, duplicates='drop', precision=4)).quantile(.5)  # Crash
dtf = dtf.groupby(cut(dtf[col[0]], rng, duplicates='drop', precision=4)).mean()  # OK
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@TomAugspurger TomAugspurger commented Oct 22, 2019

This segfaults for me ~10% of the time on master

import pandas

print(pandas.__version__)
df = pandas.DataFrame(data=[['A', 0], [None, 123], ['A', 0]], columns=['key', 'value'])
result = df.groupby('key').quantile([0.25, 0.75])
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@WillAyd WillAyd commented Oct 22, 2019

If this was working on 0.24 but not 0.25 probably comes back to #20405

I'll see what I can find

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@TomAugspurger TomAugspurger commented Oct 22, 2019

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@WillAyd WillAyd commented Oct 22, 2019

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@WillAyd WillAyd commented Oct 22, 2019

Believe I have figured it out. The problem is on this line:

counts[lab] += 1

When NA values appear in the groupby they are indicated with a -1 label. However via decorators we disabled Cython.wraparound for negative indexing AND also Cython.boundscheck to detect index errors. The combination of all of those factors leads to a segfault

I'll push up a PR soon. Just thinking through test case(s)

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