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Fatal Python error: Bus error - when loading the SpatiaLite extension #3

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simonw opened this issue Jun 25, 2023 · 6 comments
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@simonw
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simonw commented Jun 25, 2023

I got this while running the test suite for my new sqlite-utils branch for sqlean:

https://github.com/simonw/sqlite-utils/tree/sqlean

I installed sqlean.py into the same environment and ran this:

pytest tests/test_gis.py

Here's the test failure:

============================================================================ test session starts =============================================================================
platform darwin -- Python 3.11.4, pytest-7.2.2, pluggy-1.0.0
rootdir: /Users/simon/Dropbox/Development/sqlite-utils
plugins: hypothesis-6.68.2
collected 12 items                                                                                                                                                           

tests/test_gis.py .Fatal Python error: Bus error

Current thread 0x00000001e5735b40 (most recent call first):
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/python.py", line 195 in pytest_pyfunc_call
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/python.py", line 1789 in runtest
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/runner.py", line 167 in pytest_runtest_call
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/runner.py", line 260 in <lambda>
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/runner.py", line 339 in from_call
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/runner.py", line 259 in call_runtest_hook
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/runner.py", line 220 in call_and_report
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/runner.py", line 131 in runtestprotocol
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/runner.py", line 112 in pytest_runtest_protocol
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/main.py", line 349 in pytest_runtestloop
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/main.py", line 324 in _main
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/main.py", line 270 in wrap_session
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/main.py", line 317 in pytest_cmdline_main
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/config/__init__.py", line 167 in main
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.11/site-packages/_pytest/config/__init__.py", line 190 in console_main
  File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/bin/pytest", line 8 in <module>

Extension modules: sqlean._sqlite3 (total: 1)
zsh: bus error  pytest tests/test_gis.py
@simonw
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simonw commented Jun 25, 2023

When I tried to run the whole pytest suite I got a macOS error box with the following error report (not sure why I get that for pytest but not for pytest tests/test_gis.py):

-------------------------------------
Translated Report (Full Report Below)
-------------------------------------

Process:               Python [91597]
Path:                  /opt/homebrew/*/Python.framework/Versions/3.11/Resources/Python.app/Contents/MacOS/Python
Identifier:            org.python.python
Version:               3.11.4 (3.11.4)
Code Type:             ARM-64 (Native)
Parent Process:        zsh [91496]
Responsible:           Terminal [483]
User ID:               501

Date/Time:             2023-06-25 14:33:50.4278 -0700
OS Version:            macOS 13.3 (22E252)
Report Version:        12
Anonymous UUID:        AA32BCEA-02C3-0406-C103-6C81844AE525

Sleep/Wake UUID:       A29C5D5F-11C7-4A88-8FAC-BE834A478139

Time Awake Since Boot: 780000 seconds
Time Since Wake:       2509 seconds

System Integrity Protection: enabled

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

Exception Type:        EXC_BAD_ACCESS (SIGBUS)
Exception Codes:       UNKNOWN_0x101 at 0x7369646565727472 -> 0x0000646565727472 (possible pointer authentication failure)
Exception Codes:       0x0000000000000101, 0x7369646565727472

VM Region Info: 0x646565727472 is not in any region.  Bytes after previous region: 4833003336819  
      REGION TYPE                    START - END         [ VSIZE] PRT/MAX SHRMOD  REGION DETAIL
      MALLOC_NANO              600018000000-600020000000 [128.0M] rw-/rwx SM=PRV  
--->  
      UNUSED SPACE AT END

Thread 0 Crashed::  Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib        	       0x18a2a4724 __pthread_kill + 8
1   libsystem_pthread.dylib       	       0x18a2dbc28 pthread_kill + 288
2   libsystem_c.dylib             	       0x18a1b246c raise + 32
3   Python                        	       0x10538d3c0 faulthandler_fatal_error + 440
4   libsystem_platform.dylib      	       0x18a30aa84 _sigtramp + 56
5   _sqlite3.cpython-311-darwin.so	       0x10664e0c8 sqlite3LeaveMutexAndCloseZombie + 544
6   _sqlite3.cpython-311-darwin.so	       0x1066553b8 sqlite3Close + 104
7   _sqlite3.cpython-311-darwin.so	       0x106655420 sqlite3_close_v2 + 16
8   _sqlite3.cpython-311-darwin.so	       0x106718654 pysqlite_connection_dealloc + 36
9   Python                        	       0x1052aef54 subtype_dealloc + 460
10  Python                        	       0x1053465e8 _PyFrame_Clear + 100
11  Python                        	       0x10532b484 _PyEval_Vector + 140
12  Python                        	       0x105328be4 _PyEval_EvalFrameDefault + 48380
13  Python                        	       0x10532b46c _PyEval_Vector + 116
14  Python                        	       0x105328be4 _PyEval_EvalFrameDefault + 48380
15  Python                        	       0x10532b46c _PyEval_Vector + 116
16  Python                        	       0x10524ee58 _PyObject_FastCallDictTstate + 208
17  Python                        	       0x1052b3758 slot_tp_call + 180
18  Python                        	       0x10524eb3c _PyObject_MakeTpCall + 128
19  Python                        	       0x105326dc0 _PyEval_EvalFrameDefault + 40664
20  Python                        	       0x10532b46c _PyEval_Vector + 116
21  Python                        	       0x105328be4 _PyEval_EvalFrameDefault + 48380
22  Python                        	       0x10532b46c _PyEval_Vector + 116
23  Python                        	       0x10524ee58 _PyObject_FastCallDictTstate + 208
24  Python                        	       0x1052b3758 slot_tp_call + 180
25  Python                        	       0x10524f9cc _PyObject_Call + 124
26  Python                        	       0x105328be4 _PyEval_EvalFrameDefault + 48380
27  Python                        	       0x10532b46c _PyEval_Vector + 116
28  Python                        	       0x105328be4 _PyEval_EvalFrameDefault + 48380
29  Python                        	       0x10532b46c _PyEval_Vector + 116
30  Python                        	       0x105328be4 _PyEval_EvalFrameDefault + 48380
31  Python                        	       0x10532b46c _PyEval_Vector + 116
32  Python                        	       0x10524ee58 _PyObject_FastCallDictTstate + 208
33  Python                        	       0x1052b3758 slot_tp_call + 180
34  Python                        	       0x10524eb3c _PyObject_MakeTpCall + 128
35  Python                        	       0x105326dc0 _PyEval_EvalFrameDefault + 40664
36  Python                        	       0x10532b46c _PyEval_Vector + 116
37  Python                        	       0x105328be4 _PyEval_EvalFrameDefault + 48380
38  Python                        	       0x10532b46c _PyEval_Vector + 116
39  Python                        	       0x10524ee58 _PyObject_FastCallDictTstate + 208
40  Python                        	       0x1052b3758 slot_tp_call + 180
41  Python                        	       0x10524eb3c _PyObject_MakeTpCall + 128
42  Python                        	       0x105326dc0 _PyEval_EvalFrameDefault + 40664
43  Python                        	       0x10532b46c _PyEval_Vector + 116
44  Python                        	       0x105328be4 _PyEval_EvalFrameDefault + 48380
45  Python                        	       0x10532b46c _PyEval_Vector + 116
46  Python                        	       0x10524ee58 _PyObject_FastCallDictTstate + 208
47  Python                        	       0x1052b3758 slot_tp_call + 180
48  Python                        	       0x10524eb3c _PyObject_MakeTpCall + 128
49  Python                        	       0x105326dc0 _PyEval_EvalFrameDefault + 40664
50  Python                        	       0x10531c3a4 PyEval_EvalCode + 168
51  Python                        	       0x10536dc64 run_eval_code_obj + 84
52  Python                        	       0x10536dbc8 run_mod + 112
53  Python                        	       0x10536da08 pyrun_file + 148
54  Python                        	       0x10536d45c _PyRun_SimpleFileObject + 268
55  Python                        	       0x10536cdec _PyRun_AnyFileObject + 216
56  Python                        	       0x105388c94 pymain_run_file_obj + 220
57  Python                        	       0x1053885d4 pymain_run_file + 72
58  Python                        	       0x105387eb4 Py_RunMain + 704
59  Python                        	       0x105388fec Py_BytesMain + 40
60  dyld                          	       0x189f83f28 start + 2236


Thread 0 crashed with ARM Thread State (64-bit):
    x0: 0x0000000000000000   x1: 0x0000000000000000   x2: 0x0000000000000001   x3: 0x0000000000000000
    x4: 0x0000000000000073   x5: 0x0000000000000073   x6: 0x0000000000000600   x7: 0x00000000fffffffe
    x8: 0x544bd3f08c3d920f   x9: 0x544bd3f1694ec94f  x10: 0xcccccccccccccccd  x11: 0x00000000000000f6
   x12: 0x000000012014fa63  x13: 0x0000000000000000  x14: 0x0000000000000031  x15: 0x00000000ffffffd1
   x16: 0x0000000000000148  x17: 0x00000001ea25cf20  x18: 0x0000000000000000  x19: 0x000000000000000a
   x20: 0x00000001e5735b40  x21: 0x0000000000000103  x22: 0x00000001e5735c20  x23: 0x0000000000000000
   x24: 0x0000000000000001  x25: 0x00000001054dfc78  x26: 0x00000001052ba790  x27: 0x0000000104ea5490
   x28: 0x0000000104ea54a0   fp: 0x000000012014fae0   lr: 0x000000018a2dbc28
    sp: 0x000000012014fac0   pc: 0x000000018a2a4724 cpsr: 0x40001000
   far: 0x0000000105f44098  esr: 0x56000080  Address size fault

Binary Images:
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External Modification Summary:
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    thread_create: 0
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  Calls made by this process:
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VM Region Summary:
ReadOnly portion of Libraries: Total=977.1M resident=0K(0%) swapped_out_or_unallocated=977.1M(100%)
Writable regions: Total=1.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.9G(100%)

                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
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Kernel Alloc Once                   32K        1 
MALLOC                           703.2M       49 
MALLOC guard page                   96K        5 
MALLOC_MEDIUM (reserved)           1.2G       10         reserved VM address space (unallocated)
SQLite page cache                  384K        3 
Stack                             16.0M        1 
Stack Guard                         16K        1 
VM_ALLOCATE                       39.0M       40 
__AUTH                             323K       66 
__AUTH_CONST                      3817K      154 
__DATA                            3892K      203 
__DATA_CONST                      5786K      210 
__DATA_DIRTY                       361K       58 
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__OBJC_RO                         66.2M        1 
__OBJC_RW                         2011K        1 
__TEXT                           169.1M      219 
dyld private memory                272K        2 
mapped file                         64K        1 
shared memory                       32K        2 
===========                     =======  ======= 
TOTAL                              2.9G     1085 
TOTAL, minus reserved VM space     1.8G     1085 



-----------
Full Report
-----------

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@simonw
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simonw commented Jun 25, 2023

I ran with -vv to try to isolate the test:

% pytest tests/test_gis.py -vv
============================================================================ test session starts =============================================================================
platform darwin -- Python 3.11.4, pytest-7.2.2, pluggy-1.0.0 -- /Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/bin/python
cachedir: .pytest_cache
hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase('/Users/simon/Dropbox/Development/sqlite-utils/.hypothesis/examples')
rootdir: /Users/simon/Dropbox/Development/sqlite-utils
plugins: hypothesis-6.68.2
collected 12 items                                                                                                                                                           

tests/test_gis.py::test_find_spatialite PASSED                                                                                                                         [  8%]
tests/test_gis.py::test_init_spatialite Fatal Python error: Bus error

Current thread 0x00000001e5735b40 (most recent call first):

It looks like it's test_init_spatialite that is crashing: https://github.com/simonw/sqlite-utils/blob/2747257a3334d55e890b40ec58fada57ae8cfbfd/tests/test_gis.py#L26-L30

def test_init_spatialite():
    db = Database(memory=True)
    spatialite = find_spatialite()
    db.init_spatialite(spatialite)
    assert "spatial_ref_sys" in db.table_names()

Here's the most interesting part of what init_spatialite() does: https://github.com/simonw/sqlite-utils/blob/2747257a3334d55e890b40ec58fada57ae8cfbfd/sqlite_utils/db.py#L1184-L1191

        self.conn.enable_load_extension(True)
        self.conn.load_extension(path)
        # Initialize SpatiaLite if not yet initialized
        if "spatial_ref_sys" in self.table_names():
            return False
        cursor = self.execute("select InitSpatialMetadata(1)")
        result = cursor.fetchone()
        return result and bool(result[0])

@simonw
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simonw commented Jun 25, 2023

So it looks like the problem here may be that sqlean.py doesn't play well with the SpatiaLite module, in particular the version that I have installed on my Mac (which I got via Homebrew, brew install spatialite-tools).

@simonw simonw changed the title Fatal Python error: Bus error Fatal Python error: Bus error - when loading the SpatiaLite extension Jun 25, 2023
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simonw commented Jun 25, 2023

I opened this in the wrong repo, it should be in https://github.com/nalgeon/sqlean.py

@nalgeon nalgeon transferred this issue from nalgeon/sqlean Jun 26, 2023
@nalgeon
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nalgeon commented Jun 26, 2023

I tried loading spatialite with pysqlite3 (python 3.11.2, pysqlite 0.5.1) and got exactly the same error:

import pysqlite3 as sqlite3
conn = sqlite3.connect(":memory:")
conn.enable_load_extension(True)
conn.load_extension("/opt/homebrew/lib/mod_spatialite.dylib")
conn.close()

Result:

Bus error: 10

So I don't think the problem is with sqlean.py per se. It probably "inherited" it from pysqlite3 (which in turn inherited it from Python's sqlite3).

@nalgeon
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nalgeon commented Jun 26, 2023

See this CPython issue python/cpython#101974:

Using mod_spatialite from conda instead of homebrew fixed the issue - no more bus errors! Are you happy to consider this fixed, or is the behaviour with the homebrew mod_spatialite still considered a bug?

Sounds to me that this is not an sqlite3 bug. The spatialite SQLite modules from Homebrew vs Conda may be compiled with different compilers, different compiler flags, and against different SQLite versions.

Closing as not-a-bug.

I'll probably do the same.

@nalgeon nalgeon closed this as not planned Won't fix, can't repro, duplicate, stale Jun 27, 2023
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