8000 Bus Error 10 on Apple Silicon compiled for python 3.8 · Issue #19097 · scikit-learn/scikit-learn · GitHub
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iRonJ opened this issue Jan 3, 2021 · 9 comments
Closed

Bus Error 10 on Apple Silicon compiled for python 3.8 #19097

iRonJ opened this issue Jan 3, 2021 · 9 comments
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Bug Build / CI

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@iRonJ
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iRonJ commented Jan 3, 2021 •
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Describe the bug

When building from source for python3.8 on an Apple Silicon Mac, the build succeeds, but you can't import sklearn in python

Steps/Code to Reproduce

Follow directions here:
https://scikit-learn.org/stable/developers/advanced_installation.html

Install libomp via brew:
brew install libomp

Set libomp flags per openmp_helpers.py:

export LDFLAGS="$LDFLAGS -Wl,-rpath,/opt/homebrew/lib/ -L/usr/local/opt/libomp/lib -lomp"

export CPPFLAGS="$CPPFLAGS -Xpreprocessor -fopenmp"

Build succeeds but testing gives the error:

Successfully installed scikit-learn
Removed build tracker: '/private/var/folders/lp/ytqhb2lj0sxf89sdd16z61pc0000gn/T/pip-req-tracker-ja_3b66l'
(tfmac) bash-3.2$ python3 -c "import sklearn; sklearn.show_versions()"
Bus error: 10
(tfmac) bash-3.2$

Expected Results

python3 -c "import sklearn; sklearn.show_versions()" works correctly

Actual Results

Successfully installed scikit-learn
Removed build tracker: '/private/var/folders/lp/ytqhb2lj0sxf89sdd16z61pc0000gn/T/pip-req-tracker-ja_3b66l'
(tfmac) bash-3.2$ python3 -c "import sklearn; sklearn.show_versions()"
Bus error: 10
(tfmac) bash-3.2$

Versions

scipy.version.version
'1.7.0.dev0+9b9f2e8'
numpy.version.version
'1.18.5'
Full log of install process here:
https://pastebin.com/4yXK6KHS
@iRonJ
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iRonJ commented Jan 4, 2021

Here's part of the crash dump if this helps:

Path:                  /opt/homebrew/*/Python.framework/Versions/3.8/Resources/Python.app/Contents/MacOS/Python
Identifier:            Python
Version:               3.8.7 (3.8.7)
Code Type:             ARM-64 (Native)
Parent Process:        bash [27614]
Responsible:           Terminal [2051]
User ID:               501

Date/Time:             2021-01-03 23:20:35.237 -0500
OS Version:            macOS 11.1 (20C69)
Report Version:        12
Anonymous UUID:        81CDF7D7-A72E-587A-21C6-6F5C28028188

Sleep/Wake UUID:       D8EFD206-4AE2-4EA2-8FE1-2BFAC222C6AA

Time Awake Since Boot: 130000 seconds
Time Since Wake:       3600 seconds

System Integrity Protection: enabled

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

Exception Type:        EXC_BAD_ACCESS (SIGBUS)
Exception Codes:       EXC_ARM_DA_ALIGN at 0xf9000100d503201f
Exception Note:        EXC_CORPSE_NOTIFY

Termination Signal:    Bus error: 10
Termination Reason:    Namespace SIGNAL, Code 0xa
Terminating Process:   exc handler [88375]

VM Regions Near 0x100d503201f:
--> GPU Carveout (reserved)    1000000000-7000000000   [384.0G] ---/--- SM=NUL  reserved VM address space (unallocated)
    

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   ???                           	0x00000100d503201f 0 + 1103085379615
1   _arpack.cpython-38-darwin.so  	0x00000001173e2e0c PyFortranObject_New + 40 (fortranobject.c:43)
2   _arpack.cpython-38-darwin.so  	0x00000001173db8b0 PyInit__arpack + 1024 (_arpackmodule.c:4889)
3   org.python.python             	0x0000000103322424 _PyImport_LoadDynamicModuleWithSpec + 668
4   org.python.python             	0x0000000103321c90 _imp_create_dynamic + 328
5   org.python.python             	0x000000010329540c cfunction_vectorcall_FASTCALL + 220
6   org.python.python             	0x0000000103262c44 PyVectorcall_Call + 104
7   org.python.python             	0x0000000103305414 _PyEval_EvalFrameDefault + 25512
8   org.python.python             	0x00000001033082e8 _PyEval_EvalCodeWithName + 2040
9   org.python.python             	0x000000010326342c _PyFunction_Vectorcall + 228
10  org.python.python             	0x0000000103307760 call_function + 288
11  org.python.python             	0x0000000103305040 _PyEval_EvalFrameDefault + 24532
...
466 org.python.python             	0x0000000103307760 call_function + 288
467 org.python.python             	0x00000001033050c8 _PyEval_EvalFrameDefault + 24668
468 org.python.python             	0x00000001032632c0 function_code_fastcall + 120
469 org.python.python             	0x0000000103264458 object_vacall + 296
470 org.python.python             	0x000000010326453c _PyObject_CallMethodIdObjArgs + 96
471 org.python.python             	0x0000000103320c5c PyImport_ImportModuleLevelObject + 1496
472 org.python.python             	0x00000001033039a4 _PyEval_EvalFrameDefault + 18744
473 org.python.python             	0x00000001033082e8 _PyEval_EvalCodeWithName + 2040
474 org.python.python             	0x00000001032fefd8 PyEval_EvalCode + 60
475 org.python.python             	0x0000000103335940 run_eval_code_obj + 108
476 org.python.python             	0x00000001033349c4 run_mod + 96
477 org.python.python             	0x00000001033338fc PyRun_StringFlags + 128
478 org.python.python             	0x0000000103333838 PyRun_SimpleStringFlags + 64
479 org.python.python             	0x000000010334ad3c Py_RunMain + 408
480 org.python.python             	0x000000010334b57c pymain_main + 324
481 org.python.python             	0x000000010334b5f8 Py_BytesMain + 40
482 libdyld.dylib                 	0x0000000182d80f34 start + 4

Thread 0 crashed with ARM Thread State (64-bit):
    x0: 0x000000011744e950   x1: 0x000000011744e954   x2: 0x000000011744e958   x3: 0x000000011744e95c
    x4: 0x000000011744e960   x5: 0x000000011744e964   x6: 0x000000011744e968   x7: 0x000000011744e96c
    x8: 0xf9000100d503201f   x9: 0x000000011744e970  x10: 0x000000011744e9ac  x11: 0x000000011744e9a8
   x12: 0x000000011744e9a4  x13: 0x000000011744e9a0  x14: 0x000000011744e99c  x15: 0x000000011744e998
   x16: 0x10346ae8d65f03c0  x17: 0x000000011744e990  x18: 0x0000000000000000  x19: 0x0000000117358270
   x20: 0x0000000117359300  x21: 0x000000011744b8e0  x22: 0x0000000117354780  x23: 0x0000000117447ad0
   x24: 0x000000000000000d  x25: 0x0000000000000170  x26: 0x0000000117354440  x27: 0x0000000103484710
   x28: 0x0000000000000000   fp: 0x000000016cec71e0   lr: 0x00000001173e4d68
    sp: 0x000000016cec7120   pc: 0xf9000100d503201f cpsr: 0x20000000
   far: 0xf9000100d503201f  esr: 0x8a000000


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@glemaitre
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@ogrisel did you face any similar issue?

@iRonJ In the meanwhile, could you install the compilers and libopemp using conda-forge instead of brew?

@ogrisel
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ogrisel commented Jan 6, 2021

@iRonJ how did you install python3 with homebrew? With or without arch -x86_64?

Can you please report the output of the following command on your machine?

python3 -c "import platform; print(platform.platform())"

@ogrisel
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ogrisel commented Jan 6, 2021

From the dump I see Code Type: ARM-64 (Native) so you installed python3 from homebrew without the arch -x86_64 option I guess.

  • Did you do the same for libomp?
  • How did you install numpy? From source? If so how did you install openblas, using homebrew?

For reference, I installed my own dev env using the macos/aarch64 from miniforge https://github.com/conda-forge/miniforge to install a native ARM64 python + numpy + scipy + cython + "compilers" conda-forge package. Once I activate this env, I can build scikit-learn in native mode without any problem.

@iRonJ
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iRonJ commented Jan 7, 2021

@iRonJ how did you install python3 with homebrew? With or without arch -x86_64?

Can you please report the output of the following command on your machine?

python3 -c "import platform; print(platform.platform())"

(tfmac) bash-3.2$ python3 -c "import platform; print(platform.platform())"
macOS-11.1-arm64-arm-64bit

@iRonJ
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iRonJ commented Jan 7, 2021

From the dump I see Code Type: ARM-64 (Native) so you installed python3 from homebrew without the arch -x86_64 option I guess.

  • Did you do the same for libomp?
  • How did you install numpy? From source? If so how did you install openblas, using homebrew?

For reference, I installed my own dev env using the macos/aarch64 from miniforge https://github.com/conda-forge/miniforge to install a native ARM64 python + numpy + scipy + cython + "compilers" conda-forge package. Once I activate this env, I can build scikit-learn in native mode without any problem.

libomp was installed via brew

I think my NumPy install is broken, it was compiled from source, then I compiled scipy from source, but I think the NumPy compile actually had some failed components but they weren't detected as a failure, and the build process either linked corrupted files, or silently skipped some needed files.

I'll try Conda, I didn't think their repos were updated for AS yet though

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ogrisel commented Jan 8, 2021 •
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I'll try Conda, I didn't think their repos were updated for AS yet though

Note, that I used the conda-forge community distribution via the miniforge installer, not the default conda channel maintained by Anaconda Inc.

https://github.com/conda-forge/miniforge

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ogrisel commented Jan 8, 2021 •
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Also note that homebrew in arm64 native mode is still considered experimental by the homebrew developers. They recommend installing homebrew in x86_64 mode via Rosetta2 emulation for the time being (using the arch -x86_64 prefix on the brew install commands).

So maybe the arm64 native package package of openblas and libgfortran from homebrew are not fully stable either.

Related issues:

So as long as the above upstream issues are not solved, I would recommend scikit-learn users on M1 hardware to use the miniforge distribution.

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ogrisel commented Jan 8, 2021

I opened #19137 to track progress for this. Let's close this issue to keep things simple.

@ogrisel ogrisel closed this as completed Jan 8, 2021
@usr-ein usr-ein mentioned this issue Jan 31, 2021
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