Opened 4 months ago

Last modified 24 hours ago

#57251 assigned defect

py36-numpy crash on Mojave (workaround on #56954)

Reported by: lfarv (Laurent Farvacque) Owned by: michaelld (Michael Dickens)
Priority: Normal Milestone:
Component: ports Version: 2.5.4
Keywords: mojave Cc: rlhamil, lpsinger (Leo Singer)
Port: py-numpy

Description (last modified by mf2k (Frank Schima))

The function "dgelsd" (among others) creates a memory allocation failure on Mojave:

python(61682,0x1192915c0) malloc: can't allocate region
*** mach_vm_map(size=18446744071689490432) failed (error code=3)
python(61682,0x1192915c0) malloc: *** set a breakpoint in malloc_error_break to debug
init_dgelsd failed init

Change History (10)

comment:1 Changed 4 months ago by mf2k (Frank Schima)

In the future, please use WikiFormatting and add the port maintainer(s) to Cc (port info --maintainers py27-numpy), if any.

comment:2 Changed 4 months ago by mf2k (Frank Schima)

Description: modified (diff)
Owner: set to michaelld
Port: py-numpy added; py27-numpy @1.15.2_0 removed
Status: newassigned

comment:3 Changed 4 months ago by mf2k (Frank Schima)

Which compiler are you building with - i.e what is the output of following?

port installed py27-numpy

comment:4 Changed 4 months ago by lfarv (Laurent Farvacque)

compiler: standard Mojave installation, Xcode 10 installed

(test27) bijou:~ $ port installed py27-numpy
The following ports are currently installed:
  py27-numpy @1.15.2_0+gfortran (active)

comment:5 Changed 4 months ago by mf2k (Frank Schima)

How is this different than the issue reported in #56954?

comment:6 Changed 4 months ago by lfarv (Laurent Farvacque)

The behaviour changed with Mojave, and I wanted it to appear on the "Mojave" list for users experiencing a sudden crash after updating their system (as I did).

comment:7 Changed 4 months ago by rlhamil

Cc: rlhamil added

comment:8 Changed 2 months ago by lpsinger (Leo Singer)

I stumbled across this because np.polyfit was giving nonsense answers:

$ python -c 'import numpy as np; print(np.polyfit(np.arange(10), np.arange(10), 1))'
Python(94611,0x1125ca5c0) malloc: can't allocate region
*** mach_vm_map(size=18446744072329076736) failed (error code=3)
Python(94611,0x1125ca5c0) malloc: *** set a breakpoint in malloc_error_break to debug
init_dgelsd failed init
-c:1: RankWarning: Polyfit may be poorly conditioned
[1.21925297e-313 7.38137387e-313]

comment:9 Changed 2 months ago by lpsinger (Leo Singer)

Cc: lpsinger added

comment:10 Changed 24 hours ago by lpsinger (Leo Singer)

Could we please change the default variants so that this workaround is applied? It's very dangerous for us scientists working on macOS and using MacPorts that in some cases py37-numpy gives incorrect answers.

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