[MacPorts] #57251: py36-numpy crash on Mojave (workaround on #56954)

[MacPorts]

#57251: py36-numpy crash on Mojave (workaround on #56954)
--------------------+----------------------------------
Reporter: lfarv | Owner: (none)
Type: defect | Status: new
Priority: Normal | Milestone:
Component: ports | Version: 2.5.4
Keywords: mojave | Port: py27-numpy @1.15.2_0
--------------------+----------------------------------
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

[MacPorts]

#57251: py36-numpy crash on Mojave (workaround on #56954)
-----------------------------------+--------------------
Reporter: lfarv | Owner: (none)
Type: defect | Status: new
Priority: Normal | Milestone:
Component: ports | Version: 2.5.4
Resolution: | Keywords: mojave
Port: py27-numpy @1.15.2_0 |
-----------------------------------+--------------------

Comment (by mf2k):

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

[MacPorts]

#57251: py36-numpy crash on Mojave (workaround on #56954)
-----------------------+-----------------------
Reporter: lfarv | Owner: michaelld
Type: defect | Status: assigned
Priority: Normal | Milestone:
Component: ports | Version: 2.5.4
Resolution: | Keywords: mojave
Port: py-numpy |
-----------------------+-----------------------
Changes (by mf2k):

* owner: (none) => michaelld
* status: new => assigned

Post by MacPorts
The function "dgelsd" (among others) creates a memory allocation failure
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

New description:

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
}}}

--

[MacPorts]

#57251: py36-numpy crash on Mojave (workaround on #56954)
-----------------------+-----------------------
Reporter: lfarv | Owner: michaelld
Type: defect | Status: assigned
Priority: Normal | Milestone:
Component: ports | Version: 2.5.4
Resolution: | Keywords: mojave
Port: py-numpy |
-----------------------+-----------------------

Comment (by mf2k):

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

{{{
port installed py27-numpy
}}}

[MacPorts]

#57251: py36-numpy crash on Mojave (workaround on #56954)
-----------------------+-----------------------
Reporter: lfarv | Owner: michaelld
Type: defect | Status: assigned
Priority: Normal | Milestone:
Component: ports | Version: 2.5.4
Resolution: | Keywords: mojave
Port: py-numpy |
-----------------------+-----------------------

Comment (by lfarv):

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)

}}}

[MacPorts]

#57251: py36-numpy crash on Mojave (workaround on #56954)
-----------------------+-----------------------
Reporter: lfarv | Owner: michaelld
Type: defect | Status: assigned
Priority: Normal | Milestone:
Component: ports | Version: 2.5.4
Resolution: | Keywords: mojave
Port: py-numpy |
-----------------------+-----------------------

Comment (by mf2k):

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

[MacPorts]

#57251: py36-numpy crash on Mojave (workaround on #56954)
-----------------------+-----------------------
Reporter: lfarv | Owner: michaelld
Type: defect | Status: assigned
Priority: Normal | Milestone:
Component: ports | Version: 2.5.4
Resolution: | Keywords: mojave
Port: py-numpy |
-----------------------+-----------------------

Comment (by lfarv):

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).

[MacPorts]

#57251: py36-numpy crash on Mojave (workaround on #56954)
-----------------------+-----------------------
Reporter: lfarv | Owner: michaelld
Type: defect | Status: assigned
Priority: Normal | Milestone:
Component: ports | Version: 2.5.4
Resolution: | Keywords: mojave
Port: py-numpy |
-----------------------+-----------------------

Comment (by lpsinger):

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]
}}}

[MacPorts]

#57251: py36-numpy crash on Mojave (workaround on #56954)
-----------------------+-----------------------
Reporter: lfarv | Owner: michaelld
Type: defect | Status: assigned
Priority: Normal | Milestone:
Component: ports | Version: 2.5.4
Resolution: | Keywords: mojave
Port: py-numpy |
-----------------------+-----------------------
Changes (by lpsinger):

* cc: lpsinger (added)