[MacPorts] #56954: python: numpy.polyfit broken

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[MacPorts] #56954: python: numpy.polyfit broken

MacPorts
#56954: python: numpy.polyfit broken
--------------------+-------------------------------------------------
 Reporter:  mojca   |      Owner:  michaelld
     Type:  defect  |     Status:  assigned
 Priority:  Normal  |  Milestone:
Component:  ports   |    Version:
 Keywords:          |       Port:  py-numpy python27 python36 python37
--------------------+-------------------------------------------------
 There seems to be an issue with numpy.polyfit under various versions of
 python I tested (2.7, 3.6, 3.7).

 Running the following code under system python:
 {{{
 import numpy as np

 points = np.array([[0, -2.1108348e+04], [3.2768000e+04, -2.7959160e+03],
 [6.5534000e+04,  1.4279546e+04], [4.9151000e+04,  6.6721514e+03],
 [1.6384000e+04, -1.3232387e+04]], dtype=np.float32)

 koef1 = np.polyfit(points[:,0], points[:,1], 1)
 koef2 = np.polyfit(points[:,0], points[:,1], 2)
 }}}
 works and returns
 {{{
 >>> koef1
 array([  5.53485811e-01,  -2.13732832e+04], dtype=float32)
 >>> koef2
 array([ -4.00165135e-07,   5.79710186e-01,  -2.15881035e+04],
 dtype=float32)
 }}}

 However using python from MacPorts it looks much worse:
 {{{
 >>> koef1 = np.polyfit(points[:,0], points[:,1], 1)
 Python(83745,0x7fff9e546380) malloc: ***
 mach_vm_map(size=18446744072450498560) failed (error code=3)
 *** error: can't allocate region
 *** set a breakpoint in malloc_error_break to debug
 init_dgelsd failed init
 __main__:1: RankWarning: Polyfit may be poorly conditioned
 >>> koef2 = np.polyfit(points[:,0], points[:,1], 2)
 Python(83745,0x7fff9e546380) malloc: ***
 mach_vm_map(size=18446744072450498560) failed (error code=3)
 *** error: can't allocate region
 *** set a breakpoint in malloc_error_break to debug
 init_dgelsd failed init
 __main__:1: RankWarning: Polyfit may be poorly conditioned
 >>> koef1
 array([2.2937462e-317, 1.0438839e-312])
 >>> koef2
 array([5.05031302e+09, 8.97368555e+04, 2.23606798e+00])
 }}}

--
Ticket URL: <https://trac.macports.org/ticket/56954>
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Re: [MacPorts] #56954: python: numpy.polyfit broken

MacPorts
#56954: python: numpy.polyfit broken
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------

Comment (by mojca):

 The test suite for numpy can be run via
 {{{
 import numpy
 numpy.test('full')
 }}}
 and returns a number of errors:
 {{{
 20 failed, 4529 passed, 417 skipped, 7 xfailed, 17 warnings in 161.32
 seconds
 }}}

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Re: [MacPorts] #56954: python: numpy.polyfit broken

MacPorts
In reply to this post by MacPorts
#56954: python: numpy.polyfit broken
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------
Changes (by mojca):

 * Attachment "numpy-test-suite.txt" added.

 failed tests of numpy

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Re: [MacPorts] #56954: python: numpy.polyfit broken

MacPorts
In reply to this post by MacPorts
#56954: python: numpy.polyfit broken
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------

Comment (by mf2k):

 I cannot reproduce your polyfit error. It works fine for me with python36
 and ipython. Here are my test suite results:

 {{{
 NumPy version 1.15.0
 ...
 4946 passed, 20 skipped, 7 xfailed in 274.98 seconds
 }}}

 For reference, what are your installed versions of the relevant ports?

 {{{
 $ port installed python36 py36-numpy py36-ipython
 The following ports are currently installed:
   py36-ipython @6.4.0_0 (active)
   py36-numpy @1.15.0_0+gcc8 (active)
   python36 @3.6.6_0+optimizations (active)
 }}}

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Re: [MacPorts] #56954: python: numpy.polyfit broken

MacPorts
In reply to this post by MacPorts
#56954: python: numpy.polyfit broken
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------

Comment (by michaelld):

 The commands you list work for me using MacPorts' Python 2.7, 3.6, and 3.7
 && latest NumPy; all on 10.12 latest.

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Ticket URL: <https://trac.macports.org/ticket/56954#comment:3>
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Re: [MacPorts] #56954: python: numpy.polyfit broken

MacPorts
In reply to this post by MacPorts
#56954: python: numpy.polyfit broken
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------

Comment (by reneeotten):

 I am seeing the same errors as reported by mojca with Python 2.7, 3.6, and
 3.7. The only difference for me, compared to what Frank reports, is that
 all py-numpy ports were installed with the default +gfortran variant:

 {{{
   py36-numpy @1.15.0_0+gfortran (active)
 }}}

--
Ticket URL: <https://trac.macports.org/ticket/56954#comment:4>
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Re: [MacPorts] #56954: python: numpy.polyfit broken

MacPorts
In reply to this post by MacPorts
#56954: python: numpy.polyfit broken
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------

Comment (by mf2k):

 How about these ports? There was a problem with using llvm for them that
 surfaced recently.

 {{{
 $ port installed ld64 cctools
 The following ports are currently installed:
   cctools @895_6+xcode (active)
   ld64 @3_1+ld64_xcode (active)
 }}}

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Re: [MacPorts] #56954: python: numpy.polyfit broken

MacPorts
In reply to this post by MacPorts
#56954: python: numpy.polyfit broken
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------

Comment (by michaelld):

 All of my NumPy ports are installed using the default:
 {{{
   py27-numpy @1.15.0_0+gfortran (active)
   py36-numpy @1.15.0_0+gfortran (active)
   py37-numpy @1.15.0_0+gfortran (active)
 }}}
 my cctools & ld64 are up to date, but since these NumPy were installed way
 before these latest issues with cctools & ld64, I doubt that's what's
 causing the issue here (though one never knows ;)

--
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Re: [MacPorts] #56954: python: numpy.polyfit broken

MacPorts
In reply to this post by MacPorts
#56954: python: numpy.polyfit broken
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------

Comment (by reneeotten):

 Replying to [comment:5 mf2k]:
 > How about these ports? There was a problem with using llvm for them that
 surfaced recently.
 >
 > {{{
 > $ port installed ld64 cctools
 > The following ports are currently installed:
 >   cctools @895_6+xcode (active)
 >   ld64 @3_1+ld64_xcode (active)
 > }}}

 seem to be the latest as well:

 {{{
 ~> port installed ld64 cctools
 The following ports are currently installed:
   cctools @895_6+xcode (active)
   ld64 @3_1+ld64_xcode (active)
 }}}

 doing an uninstall and clean, followed by {{{ sudo port -vst install
 py37-numpy }}} didn't help either.

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Re: [MacPorts] #56954: python: numpy.polyfit broken

MacPorts
In reply to this post by MacPorts
#56954: python: numpy.polyfit broken
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------

Comment (by mf2k):

 I switched my py36-numpy to use {{{+gfortran}}} and I can confirm the
 error reported in this ticket. I installed with the binary from the
 buildbot and also built from source, and the same failed result occurs. So
 there is definitely something wrong with the {{{+gfortran}}} variant for
 py-numpy. I think it should switch to {{{+gcc8}}} as the default.

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Re: [MacPorts] #56954: python: numpy.polyfit broken

MacPorts
In reply to this post by MacPorts
#56954: python: numpy.polyfit broken
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------

Comment (by michaelld):

 What OSX version are folks having issues on?

 `py*-numpy +gfortran` built from source works for me on 10.12. Haven't
 tried this on other OSX versions, but I can easily do so; I do "import
 numpy; numpy.test()" on all OSX I have around &.it works about the same on
 all of them. All built from source.

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Re: [MacPorts] #56954: python: numpy.polyfit broken

MacPorts
In reply to this post by MacPorts
#56954: python: numpy.polyfit broken
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------

Comment (by michaelld):

 I have no objection to switching to `+gcc8`; just want to make sure that's
 the correct fix.

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Re: [MacPorts] #56954: python: numpy.polyfit broken

MacPorts
In reply to this post by MacPorts
#56954: python: numpy.polyfit broken
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------

Comment (by mf2k):

 I'm on High Sierra (10.13).

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Ticket URL: <https://trac.macports.org/ticket/56954#comment:11>
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Re: [MacPorts] #56954: python: numpy.polyfit broken

MacPorts
In reply to this post by MacPorts
#56954: python: numpy.polyfit broken
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------

Comment (by michaelld):

 Gotcha. I confirm the issue with 10.13. Doesn't happen with 10.12 or any
 prior (in my testing). So this bug is 10.13 only (in my testing).

 Thus, wondering if this is NumPy or something else. The routine
 "init_dgelsd" looks like it's from LAPACK(E).

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Re: [MacPorts] #56954: py-numpy: numpy.polyfit broken with +gfortran variant on High Sierra (was: python: numpy.polyfit broken)

MacPorts
In reply to this post by MacPorts
#56954: py-numpy: numpy.polyfit broken with +gfortran variant on High Sierra
--------------------------------------------------+-----------------------
  Reporter:  mojca                                |      Owner:  michaelld
      Type:  defect                               |     Status:  assigned
  Priority:  Normal                               |  Milestone:
 Component:  ports                                |    Version:
Resolution:                                       |   Keywords:
      Port:  py-numpy python27 python36 python37  |
--------------------------------------------------+-----------------------

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Re: [MacPorts] #56954: py-numpy: numpy.polyfit broken with +gfortran variant on High Sierra

MacPorts
In reply to this post by MacPorts
#56954: py-numpy: numpy.polyfit broken with +gfortran variant on High Sierra
-----------------------+-----------------------
  Reporter:  mojca     |      Owner:  michaelld
      Type:  defect    |     Status:  assigned
  Priority:  Normal    |  Milestone:
 Component:  ports     |    Version:
Resolution:            |   Keywords:
      Port:  py-numpy  |
-----------------------+-----------------------
Changes (by mf2k):

 * port:  py-numpy python27 python36 python37 => py-numpy


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Re: [MacPorts] #56954: py-numpy: numpy.polyfit broken with +gfortran variant on High Sierra

MacPorts
In reply to this post by MacPorts
#56954: py-numpy: numpy.polyfit broken with +gfortran variant on High Sierra
-----------------------+-----------------------
  Reporter:  mojca     |      Owner:  michaelld
      Type:  defect    |     Status:  assigned
  Priority:  Normal    |  Milestone:
 Component:  ports     |    Version:
Resolution:            |   Keywords:
      Port:  py-numpy  |
-----------------------+-----------------------

Comment (by michaelld):

 Following the instructions to set a breakpoint at `malloc_error_break`,
 here's the backtrace for Python 2.7:
 {{{
 % lldb /opt/local/bin/python2.7
 (lldb) target create "/opt/local/bin/python2.7"
 Current executable set to '/opt/local/bin/python2.7' (x86_64).
 (lldb) b malloc_error_break
 Breakpoint 1: where = libsystem_malloc.dylib`malloc_error_break, address =
 0x0000000000011962
 (lldb) r test_numpy_10_13.py
 Process 25452 launched: '/opt/local/bin/python2.7' (x86_64)
 Process 25452 stopped
 * thread #2, stop reason = exec
     frame #0: 0x000000010000519c dyld`_dyld_start
 dyld`_dyld_start:
 ->  0x10000519c <+0>: popq   %rdi
     0x10000519d <+1>: pushq  $0x0
     0x10000519f <+3>: movq   %rsp, %rbp
     0x1000051a2 <+6>: andq   $-0x10, %rsp
 Target 0: (Python) stopped.
 (lldb) c
 Process 25452 resuming
 Python(25452,0x7fff9cda4380) malloc: ***
 mach_vm_map(size=18446744072618995712) failed (error code=3)
 *** error: can't allocate region
 *** set a breakpoint in malloc_error_break to debug
 Process 25452 stopped
 * thread #2, queue = 'com.apple.main-thread', stop reason = breakpoint 1.1
     frame #0: 0x00007fff64772962 libsystem_malloc.dylib`malloc_error_break
 libsystem_malloc.dylib`malloc_error_break:
 ->  0x7fff64772962 <+0>: pushq  %rbp
     0x7fff64772963 <+1>: movq   %rsp, %rbp
     0x7fff64772966 <+4>: nop
     0x7fff64772967 <+5>: nopl   (%rax)
 Target 0: (Python) stopped.
 (lldb) bt
 * thread #2, queue = 'com.apple.main-thread', stop reason = breakpoint 1.1
   * frame #0: 0x00007fff64772962 libsystem_malloc.dylib`malloc_error_break
     frame #1: 0x00007fff6476fa08 libsystem_malloc.dylib`szone_error + 392
     frame #2: 0x00007fff64771ed6 libsystem_malloc.dylib`mvm_allocate_pages
 + 256
     frame #3: 0x00007fff64767475 libsystem_malloc.dylib`large_malloc + 464
     frame #4: 0x00007fff6476339d
 libsystem_malloc.dylib`szone_malloc_should_clear + 388
     frame #5: 0x00007fff647631bd libsystem_malloc.dylib`malloc_zone_malloc
 + 103
     frame #6: 0x00007fff647624c7 libsystem_malloc.dylib`malloc + 24
     frame #7: 0x0000000104fb5a2f _umath_linalg.so`DOUBLE_lstsq + 735
     frame #8: 0x0000000104934e27 umath.so`PyUFunc_GenericFunction + 19415
     frame #9: 0x00000001049378be umath.so`ufunc_generic_call + 174
     frame #10: 0x00000001000b0201 Python`PyObject_Call + 97
     frame #11: 0x000000010015b9aa Python`PyEval_EvalFrameEx + 9130
     frame #12: 0x00000001001593a4 Python`PyEval_EvalCodeEx + 2212
     frame #13: 0x0000000100163f0d Python`fast_function + 109
     frame #14: 0x000000010015b80c Python`PyEval_EvalFrameEx + 8716
     frame #15: 0x00000001001593a4 Python`PyEval_EvalCodeEx + 2212
     frame #16: 0x0000000100163f0d Python`fast_function + 109
     frame #17: 0x000000010015b80c Python`PyEval_EvalFrameEx + 8716
     frame #18: 0x00000001001593a4 Python`PyEval_EvalCodeEx + 2212
     frame #19: 0x0000000100158af2 Python`PyEval_EvalCode + 34
     frame #20: 0x0000000100186fed Python`PyRun_FileExFlags + 157
     frame #21: 0x0000000100186b24 Python`PyRun_SimpleFileExFlags + 740
     frame #22: 0x000000010019e71f Python`Py_Main + 3279
     frame #23: 0x00007fff645ba015 libdyld.dylib`start + 1
 (lldb)
 }}}

--
Ticket URL: <https://trac.macports.org/ticket/56954#comment:15>
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Re: [MacPorts] #56954: py-numpy: numpy.polyfit broken with +gfortran variant on High Sierra

MacPorts
In reply to this post by MacPorts
#56954: py-numpy: numpy.polyfit broken with +gfortran variant on High Sierra
-----------------------+-----------------------
  Reporter:  mojca     |      Owner:  michaelld
      Type:  defect    |     Status:  assigned
  Priority:  Normal    |  Milestone:
 Component:  ports     |    Version:
Resolution:            |   Keywords:
      Port:  py-numpy  |
-----------------------+-----------------------

Comment (by michaelld):

 and Python 3.6:
 {{{
 % lldb /opt/local/bin/python3.6
 (lldb) target create "/opt/local/bin/python3.6"
 Current executable set to '/opt/local/bin/python3.6' (x86_64).
 (lldb) b malloc_error_break
 Breakpoint 1: where = libsystem_malloc.dylib`malloc_error_break, address =
 0x00007fff64772962
 (lldb) r test_numpy_10_13.py
 Process 69019 launched:
 '/opt/local/Library/Frameworks/Python.framework/Versions/3.6/Resources/Python.app/Contents/MacOS/Python'
 (x86_64)
 python3.6(69019,0x7fff9cda4380) malloc: ***
 mach_vm_map(size=18446744072618991616) failed (error code=3)
 *** error: can't allocate region
 *** set a breakpoint in malloc_error_break to debug
 Process 69019 stopped
 * thread #1, queue = 'com.apple.main-thread', stop reason = breakpoint 1.1
     frame #0: 0x00007fff64772962 libsystem_malloc.dylib`malloc_error_break
 libsystem_malloc.dylib`malloc_error_break:
 ->  0x7fff64772962 <+0>: pushq  %rbp
     0x7fff64772963 <+1>: movq   %rsp, %rbp
     0x7fff64772966 <+4>: nop
     0x7fff64772967 <+5>: nopl   (%rax)
 Target 0: (Python) stopped.
 (lldb) bt
 * thread #1, queue = 'com.apple.main-thread', stop reason = breakpoint 1.1
   * frame #0: 0x00007fff64772962 libsystem_malloc.dylib`malloc_error_break
     frame #1: 0x00007fff6476fa08 libsystem_malloc.dylib`szone_error + 392
     frame #2: 0x00007fff64771ed6 libsystem_malloc.dylib`mvm_allocate_pages
 + 256
     frame #3: 0x00007fff64767475 libsystem_malloc.dylib`large_malloc + 464
     frame #4: 0x00007fff6476339d
 libsystem_malloc.dylib`szone_malloc_should_clear + 388
     frame #5: 0x00007fff647631bd libsystem_malloc.dylib`malloc_zone_malloc
 + 103
     frame #6: 0x00007fff647624c7 libsystem_malloc.dylib`malloc + 24
     frame #7: 0x0000000104ed4a2f _umath_linalg.cpython-36m-
 darwin.so`DOUBLE_lstsq + 735
     frame #8: 0x0000000104789267 umath.cpython-36m-
 darwin.so`PyUFunc_GenericFunction + 19415
     frame #9: 0x000000010478be3e umath.cpython-36m-
 darwin.so`ufunc_generic_call + 174
     frame #10: 0x00000001000ad243 Python`_PyObject_FastCallDict + 143
     frame #11: 0x00000001000ad5fc Python`_PyObject_FastCallKeywords + 97
     frame #12: 0x000000010014c356 Python`call_function + 443
     frame #13: 0x0000000100144c25 Python`_PyEval_EvalFrameDefault + 4479
     frame #14: 0x000000010014cb06 Python`_PyEval_EvalCodeWithName + 1747
     frame #15: 0x000000010014d1e9 Python`fast_function + 218
     frame #16: 0x000000010014c35d Python`call_function + 450
     frame #17: 0x0000000100144b8d Python`_PyEval_EvalFrameDefault + 4327
     frame #18: 0x000000010014cb06 Python`_PyEval_EvalCodeWithName + 1747
     frame #19: 0x000000010014d1e9 Python`fast_function + 218
     frame #20: 0x000000010014c35d Python`call_function + 450
     frame #21: 0x0000000100144b8d Python`_PyEval_EvalFrameDefault + 4327
     frame #22: 0x000000010014cb06 Python`_PyEval_EvalCodeWithName + 1747
     frame #23: 0x0000000100143a2c Python`PyEval_EvalCode + 42
     frame #24: 0x000000010016cd8f Python`run_mod + 54
     frame #25: 0x000000010016bd9e Python`PyRun_FileExFlags + 164
     frame #26: 0x000000010016b489 Python`PyRun_SimpleFileExFlags + 283
     frame #27: 0x000000010018026a Python`Py_Main + 3466
     frame #28: 0x0000000100001e1d Python`___lldb_unnamed_symbol1$$Python +
 227
     frame #29: 0x00007fff645ba015 libdyld.dylib`start + 1
 (lldb)
 }}}

--
Ticket URL: <https://trac.macports.org/ticket/56954#comment:16>
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Ports system for macOS
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Re: [MacPorts] #56954: py-numpy: numpy.polyfit broken with +gfortran variant on High Sierra

MacPorts
In reply to this post by MacPorts
#56954: py-numpy: numpy.polyfit broken with +gfortran variant on High Sierra
-----------------------+-----------------------
  Reporter:  mojca     |      Owner:  michaelld
      Type:  defect    |     Status:  assigned
  Priority:  Normal    |  Milestone:
 Component:  ports     |    Version:
Resolution:            |   Keywords:
      Port:  py-numpy  |
-----------------------+-----------------------

Comment (by michaelld):

 and Python 3.7:
 {{{
 % lldb /opt/local/bin/python3.7
 (lldb) target create "/opt/local/bin/python3.7"
 Current executable set to '/opt/local/bin/python3.7' (x86_64).
 (lldb) b malloc_error_break
 Breakpoint 1: where = libsystem_malloc.dylib`malloc_error_break, address =
 0x0000000000011962
 (lldb) r test_numpy_10_13.py
 Process 79296 launched: '/opt/local/bin/python3.7' (x86_64)
 Process 79296 stopped
 * thread #2, stop reason = exec
     frame #0: 0x000000010000519c dyld`_dyld_start
 dyld`_dyld_start:
 ->  0x10000519c <+0>: popq   %rdi
     0x10000519d <+1>: pushq  $0x0
     0x10000519f <+3>: movq   %rsp, %rbp
     0x1000051a2 <+6>: andq   $-0x10, %rsp
 Target 0: (Python) stopped.
 (lldb) c
 Process 79296 resuming
 Python(79296,0x7fff9cda4380) malloc: ***
 mach_vm_map(size=18446744072618991616) failed (error code=3)
 *** error: can't allocate region
 *** set a breakpoint in malloc_error_break to debug
 Process 79296 stopped
 * thread #2, queue = 'com.apple.main-thread', stop reason = breakpoint 1.1
     frame #0: 0x00007fff64772962 libsystem_malloc.dylib`malloc_error_break
 libsystem_malloc.dylib`malloc_error_break:
 ->  0x7fff64772962 <+0>: pushq  %rbp
     0x7fff64772963 <+1>: movq   %rsp, %rbp
     0x7fff64772966 <+4>: nop
     0x7fff64772967 <+5>: nopl   (%rax)
 Target 0: (Python) stopped.
 (lldb) bt
 * thread #2, queue = 'com.apple.main-thread', stop reason = breakpoint 1.1
   * frame #0: 0x00007fff64772962 libsystem_malloc.dylib`malloc_error_break
     frame #1: 0x00007fff6476fa08 libsystem_malloc.dylib`szone_error + 392
     frame #2: 0x00007fff64771ed6 libsystem_malloc.dylib`mvm_allocate_pages
 + 256
     frame #3: 0x00007fff64767475 libsystem_malloc.dylib`large_malloc + 464
     frame #4: 0x00007fff6476339d
 libsystem_malloc.dylib`szone_malloc_should_clear + 388
     frame #5: 0x00007fff647631bd libsystem_malloc.dylib`malloc_zone_malloc
 + 103
     frame #6: 0x00007fff647624c7 libsystem_malloc.dylib`malloc + 24
     frame #7: 0x0000000105256a2f _umath_linalg.cpython-37m-
 darwin.so`DOUBLE_lstsq + 735
     frame #8: 0x0000000104389267 umath.cpython-37m-
 darwin.so`PyUFunc_GenericFunction + 19415
     frame #9: 0x000000010438be3e umath.cpython-37m-
 darwin.so`ufunc_generic_call + 174
     frame #10: 0x00000001000bc6dd Python`_PyObject_FastCallKeywords + 359
     frame #11: 0x00000001001525d3 Python`call_function + 568
     frame #12: 0x000000010014a6ab Python`_PyEval_EvalFrameDefault + 2706
     frame #13: 0x0000000100152f31 Python`_PyEval_EvalCodeWithName + 1837
     frame #14: 0x00000001000bc83c Python`_PyFunction_FastCallKeywords +
 225
     frame #15: 0x00000001001525da Python`call_function + 575
     frame #16: 0x000000010014a617 Python`_PyEval_EvalFrameDefault + 2558
     frame #17: 0x0000000100152f31 Python`_PyEval_EvalCodeWithName + 1837
     frame #18: 0x00000001000bc83c Python`_PyFunction_FastCallKeywords +
 225
     frame #19: 0x00000001001525da Python`call_function + 575
     frame #20: 0x000000010014a586 Python`_PyEval_EvalFrameDefault + 2413
     frame #21: 0x0000000100152f31 Python`_PyEval_EvalCodeWithName + 1837
     frame #22: 0x0000000100149b91 Python`PyEval_EvalCode + 42
     frame #23: 0x0000000100177e7f Python`run_mod + 54
     frame #24: 0x0000000100176e9a Python`PyRun_FileExFlags + 164
     frame #25: 0x0000000100176579 Python`PyRun_SimpleFileExFlags + 283
     frame #26: 0x000000010018dc4e Python`pymain_main + 5114
     frame #27: 0x000000010018e3e0 Python`_Py_UnixMain + 104
     frame #28: 0x00007fff645ba015 libdyld.dylib`start + 1
     frame #29: 0x00007fff645ba015 libdyld.dylib`start + 1
 (lldb)
 }}}

--
Ticket URL: <https://trac.macports.org/ticket/56954#comment:17>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #56954: py-numpy: numpy.polyfit broken with +gfortran variant on High Sierra

MacPorts
In reply to this post by MacPorts
#56954: py-numpy: numpy.polyfit broken with +gfortran variant on High Sierra
-----------------------+-----------------------
  Reporter:  mojca     |      Owner:  michaelld
      Type:  defect    |     Status:  assigned
  Priority:  Normal    |  Milestone:
 Component:  ports     |    Version:
Resolution:            |   Keywords:
      Port:  py-numpy  |
-----------------------+-----------------------

Comment (by michaelld):

 So it seems like there's a memory allocation error in `umath_linalg`
 routine `DOUBLE_lstsq` ... or, something like that.

--
Ticket URL: <https://trac.macports.org/ticket/56954#comment:18>
MacPorts <https://www.macports.org/>
Ports system for macOS
12