Segfault in scraper while inspecting some pyx-produced libraries (pandas, sklearn)

[mikebz]

On my MacBook I continously get the crash below. I am not sure what causes. Seems like a background process.

Process:               Python [40993]
Path:                  /usr/local/Cellar/python/3.7.2_2/Frameworks/Python.framework/Versions/3.7/Resources/Python.app/Contents/MacOS/Python
Identifier:            Python
Version:               3.7.2 (3.7.2)
Code Type:             X86-64 (Native)
Parent Process:        Microsoft.Python.LanguageServer [40941]
Responsible:           Python [40993]
User ID:               41315233

Date/Time:             2019-03-12 15:36:10.899 -0700
OS Version:            Mac OS X 10.14.3 (18D109)
Report Version:        12
Bridge OS Version:     3.0 (14Y674)
Anonymous UUID:        1C1E39BC-AB50-7114-D6A6-FDABC423472D

Sleep/Wake UUID:       6DC543C8-505D-41EA-819B-CE369BF8254D

Time Awake Since Boot: 130000 seconds
Time Since Wake:       6900 seconds

System Integrity Protection: enabled

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

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000000000000
Exception Note:        EXC_CORPSE_NOTIFY

Termination Signal:    Segmentation fault: 11
Termination Reason:    Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [40993]

VM Regions Near 0:
--> 
    __TEXT                 00000001037a2000-00000001037a4000 [    8K] r-x/rwx SM=COW  /usr/local/Cellar/python/3.7.2_2/Frameworks/Python.framework/Versions/3.7/Resources/Python.app/Contents/MacOS/Python

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   algos.cpython-37m-darwin.so   	0x000000010f449520 __pyx_pf_6pandas_5_libs_5algos_600__defaults__ + 32
1   algos.cpython-37m-darwin.so   	0x000000010f599ed0 __Pyx_CyFunction_get_kwdefaults + 48
2   org.python.python             	0x00000001037c555c getset_get + 58
3   org.python.python             	0x00000001037ecb50 _PyObject_GenericGetAttrWithDict + 181
4   org.python.python             	0x00000001037eca40 _PyObject_LookupAttr + 166
5   org.python.python             	0x000000010384a1c4 builtin_getattr + 141
6   org.python.python             	0x00000001037c0637 _PyMethodDef_RawFastCallKeywords + 496
7   org.python.python             	0x00000001037bfbd3 _PyCFunction_FastCallKeywords + 44
8   org.python.python             	0x00000001038555f0 call_function + 636
9   org.python.python             	0x000000010384e2cf _PyEval_EvalFrameDefault + 7174
10  org.python.python             	0x00000001037bffae function_code_fastcall + 112
11  org.python.python             	0x0000000103855665 call_function + 753
12  org.python.python             	0x000000010384e2cf _PyEval_EvalFrameDefault + 7174
13  org.python.python             	0x0000000103855ef7 _PyEval_EvalCodeWithName + 1835
14  org.python.python             	0x00000001037bfb98 _PyFunction_FastCallKeywords + 225
15  org.python.python             	0x0000000103855665 call_function + 753
16  org.python.python             	0x000000010384e375 _PyEval_EvalFrameDefault + 7340
17  org.python.python             	0x00000001037bffae function_code_fastcall + 112
18  org.python.python             	0x0000000103855665 call_function + 753
19  org.python.python             	0x000000010384e2cf _PyEval_EvalFrameDefault + 7174
20  org.python.python             	0x0000000103855ef7 _PyEval_EvalCodeWithName + 1835
21  org.python.python             	0x00000001037bfb98 _PyFunction_FastCallKeywords + 225
22  org.python.python             	0x0000000103855665 call_function + 753
23  org.python.python             	0x000000010384e218 _PyEval_EvalFrameDefault + 6991
24  org.python.python             	0x0000000103855ef7 _PyEval_EvalCodeWithName + 1835
25  org.python.python             	0x00000001037bf801 _PyFunction_FastCallDict + 441
26  org.python.python             	0x00000001037c0931 _PyObject_Call_Prepend + 150
27  org.python.python             	0x00000001037fe05c slot_tp_init + 80
28  org.python.python             	0x00000001037fad28 type_call + 178
29  org.python.python             	0x00000001037bfa39 _PyObject_FastCallKeywords + 359
30  org.python.python             	0x000000010385565e call_function + 746
31  org.python.python             	0x000000010384e375 _PyEval_EvalFrameDefault + 7340
32  org.python.python             	0x0000000103855ef7 _PyEval_EvalCodeWithName + 1835
33  org.python.python             	0x00000001037bf801 _PyFunction_FastCallDict + 441
34  org.python.python             	0x00000001037c0931 _PyObject_Call_Prepend + 150
35  org.python.python             	0x00000001037fe05c slot_tp_init + 80
36  org.python.python             	0x00000001037fad28 type_call + 178
37  org.python.python             	0x00000001037bfa39 _PyObject_FastCallKeywords + 359
38  org.python.python             	0x000000010385565e call_function + 746
39  org.python.python             	0x000000010384e375 _PyEval_EvalFrameDefault + 7340
40  org.python.python             	0x00000001037bffae function_code_fastcall + 112
41  org.python.python             	0x0000000103855665 call_function + 753
42  org.python.python             	0x000000010384e218 _PyEval_EvalFrameDefault + 6991
43  org.python.python             	0x00000001037bffae function_code_fastcall + 112
44  org.python.python             	0x0000000103855665 call_function + 753
45  org.python.python             	0x000000010384e218 _PyEval_EvalFrameDefault + 6991
46  org.python.python             	0x0000000103855ef7 _PyEval_EvalCodeWithName + 1835
47  org.python.python             	0x000000010384c626 PyEval_EvalCode + 51
48  org.python.python             	0x000000010387b2a5 run_mod + 54
49  org.python.python             	0x000000010387a2c0 PyRun_FileExFlags + 164
50  org.python.python             	0x000000010387997a PyRun_SimpleFileExFlags + 266
51  org.python.python             	0x00000001038926a2 pymain_main + 5614
52  org.python.python             	0x0000000103892ca4 _Py_UnixMain + 56
53  libdyld.dylib                 	0x00007fff5bac0ed9 start + 1

Thread 1:
0   libsystem_kernel.dylib        	0x00007fff5bbfd7de __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff5bcb7593 _pthread_cond_wait + 724
2   libopenblasp-r0.3.5.dev.dylib 	0x00000001044f5a3b blas_thread_server + 619
3   libsystem_pthread.dylib       	0x00007fff5bcb4305 _pthread_body + 126
4   libsystem_pthread.dylib       	0x00007fff5bcb726f _pthread_start + 70
5   libsystem_pthread.dylib       	0x00007fff5bcb3415 thread_start + 13

Thread 2:
0   libsystem_kernel.dylib        	0x00007fff5bbfd7de __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff5bcb7593 _pthread_cond_wait + 724
2   libopenblasp-r0.3.5.dev.dylib 	0x00000001044f5a3b blas_thread_server + 619
3   libsystem_pthread.dylib       	0x00007fff5bcb4305 _pthread_body + 126
4   libsystem_pthread.dylib       	0x00007fff5bcb726f _pthread_start + 70
5   libsystem_pthread.dylib       	0x00007fff5bcb3415 thread_start + 13

Thread 3:
0   libsystem_kernel.dylib        	0x00007fff5bbfd7de __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff5bcb7593 _pthread_cond_wait + 724
2   libopenblasp-r0.3.5.dev.dylib 	0x00000001044f5a3b blas_thread_server + 619
3   libsystem_pthread.dylib       	0x00007fff5bcb4305 _pthread_body + 126
4   libsystem_pthread.dylib       	0x00007fff5bcb726f _pthread_start + 70
5   libsystem_pthread.dylib       	0x00007fff5bcb3415 thread_start + 13

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x0000000103e134a8  rcx: 0x0000000103e13490  rdx: 0x0000000110b4f780
  rdi: 0x0000000103e134c0  rsi: 0x0000000000000000  rbp: 0x00007ffeec45b350  rsp: 0x00007ffeec45b340
   r8: 0x0000000000000003   r9: 0x00007ffeec45b400  r10: 0x0000000000000002  r11: 0x00007ffeec45b458
  r12: 0x000000010f5f6ba8  r13: 0x000000010f5ac698  r14: 0x000000010f5f6ba8  r15: 0x0000000000000000
  rip: 0x000000010f449520  rfl: 0x0000000000010202  cr2: 0x000000010e4c7fc0
  
Logical CPU:     0
Error Code:      0x02000131
Trap Number:     133


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    0x7fff5b952000 -     0x7fff5b959fff  libcompiler_rt.dylib (63.4) <817772E3-E836-3FFD-A39B-BDCD1C357221> /usr/lib/system/libcompiler_rt.dylib
    0x7fff5b95a000 -     0x7fff5b963ff3  libcopyfile.dylib (146.200.3) <5C5C4F35-DAB7-3CF1-940F-F47192AB8289> /usr/lib/system/libcopyfile.dylib
    0x7fff5b964000 -     0x7fff5b9e8fdf  libcorecrypto.dylib (602.230.1) <C78D1A87-5543-3561-BEB4-3B480BA94ECB> /usr/lib/system/libcorecrypto.dylib
    0x7fff5ba6f000 -     0x7fff5baa9ff7  libdispatch.dylib (1008.220.2) <2FDB1401-5119-3DF0-91F5-F4E105F00CD7> /usr/lib/system/libdispatch.dylib
    0x7fff5baaa000 -     0x7fff5bad9ff3  libdyld.dylib (655.1) <90C801E7-5D05-37A8-810C-B58E8C53953A> /usr/lib/system/libdyld.dylib
    0x7fff5bada000 -     0x7fff5badaffb  libkeymgr.dylib (30) <A4EFD9A4-2EF3-3E18-B325-F527E3821939> /usr/lib/system/libkeymgr.dylib
    0x7fff5badb000 -     0x7fff5bae7ff7  libkxld.dylib (4903.241.1) <D039B38D-E8E6-3011-94F5-A21CD3D59526> /usr/lib/system/libkxld.dylib
    0x7fff5bae8000 -     0x7fff5bae8ff7  liblaunch.dylib (1336.240.2) <D5F0014D-CF46-3B04-9DE0-A1466DA14A2C> /usr/lib/system/liblaunch.dylib
    0x7fff5bae9000 -     0x7fff5baeefff  libmacho.dylib (921) <6ADB99F3-D142-3A0A-B3CE-031354766ACC> /usr/lib/system/libmacho.dylib
    0x7fff5baef000 -     0x7fff5baf1ffb  libquarantine.dylib (86.220.1) <58524FD7-63C5-38E0-9D90-845A79551C14> /usr/lib/system/libquarantine.dylib
    0x7fff5baf2000 -     0x7fff5baf3ff3  libremovefile.dylib (45.200.2) <BA53CA8A-9974-3A43-9265-B110B1AE470F> /usr/lib/system/libremovefile.dylib
    0x7fff5baf4000 -     0x7fff5bb0bff3  libsystem_asl.dylib (356.200.4) <33C62769-1242-3BC1-9459-13CBCDECC7FE> /usr/lib/system/libsystem_asl.dylib
    0x7fff5bb0c000 -     0x7fff5bb0cfff  libsystem_blocks.dylib (73) <152EDADF-7D94-35F2-89B7-E66DCD945BBA> /usr/lib/system/libsystem_blocks.dylib
    0x7fff5bb0d000 -     0x7fff5bb95fff  libsystem_c.dylib (1272.200.26) <D6C701A2-9F17-308D-B6AC-9E17EF31B7DF> /usr/lib/system/libsystem_c.dylib
    0x7fff5bb96000 -     0x7fff5bb99ff7  libsystem_configuration.dylib (963.200.27) <94898525-ECC8-3CC9-B312-CBEAAC305E32> /usr/lib/system/libsystem_configuration.dylib
    0x7fff5bb9a000 -     0x7fff5bb9dff7  libsystem_coreservices.dylib (66) <10818C17-70E1-328E-A3E3-C3EB81AEC590> /usr/lib/system/libsystem_coreservices.dylib
    0x7fff5bb9e000 -     0x7fff5bba4ffb  libsystem_darwin.dylib (1272.200.26) <07468CF7-982F-37C4-83D0-D5E602A683AA> /usr/lib/system/libsystem_darwin.dylib
    0x7fff5bba5000 -     0x7fff5bbabff7  libsystem_dnssd.dylib (878.240.1) <5FEA5E1E-E80F-3616-AD33-8E936D61F31A> /usr/lib/system/libsystem_dnssd.dylib
    0x7fff5bbac000 -     0x7fff5bbf8ff3  libsystem_info.dylib (517.200.9) <54B65F21-2E93-3579-9B72-6637A03245D9> /usr/lib/system/libsystem_info.dylib
    0x7fff5bbf9000 -     0x7fff5bc21ff7  libsystem_kernel.dylib (4903.241.1) <CA10BC3A-5B09-32CE-B74F-BAD01755AA37> /usr/lib/system/libsystem_kernel.dylib
    0x7fff5bc22000 -     0x7fff5bc6dff7  libsystem_m.dylib (3158.200.7) <AF25F8E8-194C-314F-A2D3-A424853EE796> /usr/lib/system/libsystem_m.dylib
    0x7fff5bc6e000 -     0x7fff5bc92ff7  libsystem_malloc.dylib (166.220.1) <4777DC06-F9C6-356E-82AB-86A1C6D62F3A> /usr/lib/system/libsystem_malloc.dylib
    0x7fff5bc93000 -     0x7fff5bc9eff3  libsystem_networkextension.dylib (767.240.1) <4DB0D4A2-83E7-3638-AAA0-39CECD5C25F8> /usr/lib/system/libsystem_networkextension.dylib
    0x7fff5bc9f000 -     0x7fff5bca6fff  libsystem_notify.dylib (172.200.21) <65B3061D-41D7-3485-B217-A861E05AD50B> /usr/lib/system/libsystem_notify.dylib
    0x7fff5bca7000 -     0x7fff5bcb0fef  libsystem_platform.dylib (177.200.16) <83DED753-51EC-3B8C-A98D-883A5184086B> /usr/lib/system/libsystem_platform.dylib
    0x7fff5bcb1000 -     0x7fff5bcbbfff  libsystem_pthread.dylib (330.230.1) <80CC5992-823E-327E-BB6E-9D4568B84161> /usr/lib/system/libsystem_pthread.dylib
    0x7fff5bcbc000 -     0x7fff5bcbfff7  libsystem_sandbox.dylib (851.230.3) <D6469A17-C13C-3538-A300-D6517BB7F249> /usr/lib/system/libsystem_sandbox.dylib
    0x7fff5bcc0000 -     0x7fff5bcc2ff3  libsystem_secinit.dylib (30.220.1) <5964B6D2-19D4-3CF9-BDBC-4EB1D42348F1> /usr/lib/system/libsystem_secinit.dylib
    0x7fff5bcc3000 -     0x7fff5bccaff7  libsystem_symptoms.dylib (820.237.2) <487E1794-4C6E-3B1B-9C55-95B1A5FF9B90> /usr/lib/system/libsystem_symptoms.dylib
    0x7fff5bccb000 -     0x7fff5bce0ff7  libsystem_trace.dylib (906.220.1) <4D4BA88A-FA32-379D-8860-33838723B35F> /usr/lib/system/libsystem_trace.dylib
    0x7fff5bce2000 -     0x7fff5bce7ffb  libunwind.dylib (35.4) <EF1A77FD-A86B-39F5-ABEA-6100AB23583A> /usr/lib/system/libunwind.dylib
    0x7fff5bce8000 -     0x7fff5bd18fff  libxpc.dylib (1336.240.2) <EE0CDA53-6FF9-3B4E-A571-335A5FF6B6F4> /usr/lib/system/libxpc.dylib

External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 0
    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: 91771
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=419.4M resident=0K(0%) swapped_out_or_unallocated=419.4M(100%)
Writable regions: Total=209.5M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=209.5M(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Kernel Alloc Once                    8K        2 
MALLOC                            76.0M       18 
MALLOC guard page                   16K        5 
MALLOC_LARGE (reserved)            128K        2         reserved VM address space (unallocated)
STACK GUARD                         16K        5 
Stack                             17.5M        5 
VM_ALLOCATE                       19.0M       47 
VM_ALLOCATE (reserved)            96.0M        2         reserved VM address space (unallocated)
__DATA                            18.4M      298 
__FONT_DATA                          4K        2 
__LINKEDIT                       224.4M       85 
__TEXT                           195.0M      268 
__UNICODE                          564K        2 
shared memory                       12K        4 
===========                     =======  ======= 
TOTAL                            647.1M      731 
TOTAL, minus reserved VM space   551.0M      731 

Model: MacBookPro14,3, BootROM 185.0.0.0.0, 4 processors, Intel Core i7, 2.8 GHz, 16 GB, SMC 2.45f0
Graphics: Intel HD Graphics 630, Intel HD Graphics 630, Built-In
Graphics: Radeon Pro 555, Radeon Pro 555, PCIe
Memory Module: BANK 0/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x80CE, 0x4B3445424533303445422D45474347202020
Memory Module: BANK 1/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x80CE, 0x4B3445424533303445422D45474347202020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x173), Broadcom BCM43xx 1.0 (7.77.61.1 AirPortDriverBrcmNIC-1305.2)
Bluetooth: Version 6.0.10f1, 3 services, 27 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
USB Device: USB 3.0 Bus
USB Device: iBridge
Thunderbolt Bus: MacBook Pro, Apple Inc., 39.2
Thunderbolt Bus: MacBook Pro, Apple Inc., 39.2

[MikhailArkhipov]

This is not LS, LS is .NET process, no native code. This looks like Python 3.7 itself.

Process:               Python [40993]
Path:                  /usr/local/Cellar/python/3.7.2_2/Frameworks/Python.framework/Versions/3.7/Resources/Python.app/Contents/MacOS/Python
Identifier:            Python
Version:               3.7.2 (3.7.2)
Code Type:             X86-64 (Native)

Would be useful to figure command line (i.e. which module we asked Python to introspect). However, no matter module, command like, script we passed Python should not be crashing. I'd recommend passing this to Python team as well. @brettcannon can suggest where to report.

[mikebz]

I see this as the parent process:
Parent Process: Microsoft.Python.LanguageServer [40941]

[MikhailArkhipov]

Yes, LS launched Python but it has no control of its behavior. We pass Python script and Python executable is crashing with segfault (aka null reference or buffer overflow) when executing it.

First, no script should be able to crash Python itself since it is, in fact, a security hole. Consider possibility of SQL query crashing SQL server.

Second, the script is unable to null ref itself as it is Python which is a managed environment and not down-to-metal C/C++.

[jakebailey]

This is what I described in #713.

[jakebailey]

#341 too, though we closed that without really solving it. A direct repro is there by executing scrape_module.py: #341 (comment)

[jakebailey]

https://bugs.python.org/issue36224 too (reported just last week), but was closed as not a Python problem. I have no idea what the solution to this would be; ignoring the root cause entirely, we can already technically catch crashes from the scraper, but the part where the OS (both macOS and Windows) show a visible message seems to be tied to the fact that those OSs know the processes are in a tree below a GUI application or similar.

[mikebz]

makes sense since I do use pandas and numpy in the project so I know there are some native libraries in there. Is it the case that maybe for libraries with native interfaces this doesn't work?

[MikhailArkhipov]

Catching native crashes is a security no-no

[jakebailey]

To be clear, by "catch" I meant "handle without crashing", i.e. we'd just get an incomplete result as the process ends early without writing all of the stub files.

[MikhailArkhipov]

Yes, handling segfaults without crashing in native code is a security hole.

[jakebailey]

Is it the case that maybe for libraries with native interfaces this doesn't work?

The Python script that is crashing is the thing we use specifically to inspect compiled libraries, which often includes functions in numpy/scikit/etc. In this script, we don't directly access anything, but use Python's built-in inspect library to read information. That's what's crashing; Python is going down into the compiled code and breaking.

Perhaps there's something in common with all of these functions which we could use to skip over them entirely. Since this is pyx, I looked around and found a potentially related issue: cython/cython#537

[brettcannon]

Chances are there is some extension module that isn't handling attribute access appropriately when the inspect module asks for something (which would explain why there's descriptor code in that traceback). I don't know what extension algos.cpython-37m-darwin.so 0x000000010f449520 __pyx_pf_6pandas_5_libs_5algos_600__defaults__ + 32 represents but that's what is doing the wrong thing triggering the segfault while getting/setting an attribute.

[jakebailey]

Unfortunately I've seen this in a wide range of libraries, numpy and scikit-learn included.

[gramster]

Related to this: https://bugs.python.org/issue36224. This is seemingly from a .pyx (Cython) file. I'd guess this one: https://github.com/pandas-dev/pandas/blob/master/pandas/_libs/algos.pyx.

@mikebz, I'd try update your brew packages first. If that doesn't help, try using Anaconda distribution instead; probably a much safer build of pandas than what you would get from Homebrew.