Bus error when running GDL on macOS Sonoma 14.2.1 #1728

spacemanjosh · 2024-01-18T01:39:09Z

spacemanjosh
Jan 18, 2024

First time building GDL, so I may be missing something. Any help is appreciated.
I've been able to build GDL with the steps outlined here: https://github.com/gnudatalanguage/gdl/wiki/GDL-on-OSX
I'm building in $HOME/gdl
But when I run even the simplest IDL commands I get a hard crash. The only information printed to the console indicates a bus error:

GDL> x = 42
GDL> print, x
zsh: bus error  ./install/bin/gdl

The build steps I took are:

cd $HOME
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
brew install cmake
brew install gcc
git clone https://github.com/gnudatalanguage/gdl.git
cd gdl
./scripts/build_gdl.sh prep
./scripts/build_gdl.sh configure
./scripts/build_gdl.sh build
./scripts/build_gdl.sh install

I've also tried building the app and dmg, which seems to work fine, and I'm able to launch GDL via the app icon as well. But I still get the crash either way.

I'm likely missing something

Answered by Barney-9000

Jan 29, 2024

Could #1675 be the solution? Worked for me (Sonoma 14.2.1) about six weeks ago.

View full answer

alaingdl · 2024-01-18T07:56:57Z

alaingdl
Jan 18, 2024
Maintainer

😞
Could you give more informations ? OS version (sw_vers), type of processor ...

On OSX I made frequent & extensive tests on x86 (intel) and also M1/M2 without any troubles
(except the specific performance issues #1498 especially
#1498 (comment)

1 reply

spacemanjosh Jan 18, 2024
Author

Sure, so I'm running on an M2 Max chip, macOS 14.2.1. It's entirely possible I'm just missing something in the build process, or something else in my environment.

I wonder if it's the version of gcc. I notice that although I'm putting the homebrew bin directory first on my path, a which gcc seems to still point to the system copy. How sensitive to the version of gcc is the build process?

alaingdl · 2024-01-18T19:16:14Z

alaingdl
Jan 18, 2024
Maintainer

I tested (two weeks ago) on M2 & macOS 14 (not sure on the details) and it was fine (including plot through network !)

1/ did you make : ./scripts/build_gdl.sh check (or test)
2/ do you have conda/miniconde/anaconda somewhere in the path ?

could you have a look to : otools -L /path/to/exe/gdl (maybe something is missing ?)
(sorry if a type, cannot check now)

1 reply

spacemanjosh Jan 19, 2024
Author

I had removed conda from my path prior to the build. I just double checked, and we're all good there.
As for the ./scripts/build_gdl.sh check, all of the tests return a Bus error.
otool -L ./install/bin/gdl doesn't seem to indicate anything missing.

As a test, I was able to run gdl on a Fedora instance, which works great there. I'm not sure what's wrong with my macOS build though.

alaingdl · 2024-01-19T10:10:45Z

alaingdl
Jan 19, 2024
Maintainer

@spacemanjosh Ha, I am not on 14.x, but only 13.y ... Maybe the main point ... No way to test that by myself

% sw_vers 
ProductName:		macOS
ProductVersion:		13.4.1
ProductVersionExtra:	(c)
BuildVersion:		22F770820d

(remotely on a laptop of one student here ... thanks !)

Whouaou, large update of the Brew when making ./scripts/build_gdl.sh prep, including LLVM ...
now compiling ! ... success ... all tests OK ...

Difficult to help more 😞

What I would do in your case : after carefully check that nothing related to Conda remains, compile again
(removing before the build path (rm -rf build) in order to clean the cache)

100% tests passed, 0 tests failed out of 205

Total Test time (real) = 113.82 sec

The following tests did not run:
	135 - test_mpi.pro (Skipped)
	154 - test_python.pro (Skipped)

(and plots are working remotely)

GDL> plot, findgen(10)
GDL> !gdl
{
    "RELEASE": "1.0.4 git",
    "BUILD_DATE": "Jan 19 2024",
    "EPOCH": 1705618800,
    "GDL_USE_DSFMT": 1,
    "GDL_USE_WX": 0,
    "GDL_POSIX": 1
}
GDL> !version
{
    "ARCH": "arm64",
    "OS": "darwin",
    "OS_FAMILY": "unix",
    "OS_NAME": "Mac OS X",
    "RELEASE": "8.2",
    "BUILD_DATE": "Jan 19 2024",
    "MEMORY_BITS": 64,
    "FILE_OFFSET_BITS": 64
}

alain@macm2 gdl-1.0.4git240119 % otool -L ./install/bin/gdl
./install/bin/gdl:
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1319.100.3)
	/usr/lib/libncurses.5.4.dylib (compatibility version 5.4.0, current version 5.4.0)
	/usr/lib/libform.5.4.dylib (compatibility version 5.4.0, current version 5.4.0)
	/opt/homebrew/opt/readline/lib/libreadline.8.dylib (compatibility version 8.2.0, current version 8.2.0)
	/opt/homebrew/opt/readline/lib/libhistory.8.dylib (compatibility version 8.2.0, current version 8.2.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/opt/homebrew/opt/gsl/lib/libgsl.27.dylib (compatibility version 28.0.0, current version 28.0.0)
	/opt/homebrew/opt/gsl/lib/libgslcblas.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	@rpath/libplplot.17.dylib (compatibility version 17.0.0, current version 17.0.0)
	@rpath/libplplotcxx.15.dylib (compatibility version 15.0.0, current version 15.0.0)
	/opt/homebrew/opt/libpng/lib/libpng16.16.dylib (compatibility version 57.0.0, current version 57.0.0)
	/System/Library/Frameworks/IOKit.framework/Versions/A/IOKit (compatibility version 1.0.0, current version 275.0.0)
	/System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 169.0.0)
	/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa (compatibility version 1.0.0, current version 23.0.0)
	/System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore (compatibility version 1.2.0, current version 1.11.0)
	/System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox (compatibility version 1.0.0, current version 1000.0.0)
	/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL (compatibility version 1.0.0, current version 1.0.0)
	/opt/homebrew/opt/wxwidgets/lib/libwx_baseu-3.2.dylib (compatibility version 3.0.0, current version 3.2.0)
	/opt/homebrew/opt/wxwidgets/lib/libwx_osx_cocoau_core-3.2.dylib (compatibility version 3.0.0, current version 3.2.0)
	/opt/homebrew/opt/libx11/lib/libX11.6.dylib (compatibility version 11.0.0, current version 11.0.0)
	/opt/X11/lib/libXext.6.dylib (compatibility version 11.0.0, current version 11.0.0)
	/opt/homebrew/opt/graphicsmagick/lib/libGraphicsMagick.3.dylib (compatibility version 28.0.0, current version 28.4.0)
	/opt/homebrew/opt/graphicsmagick/lib/libGraphicsMagick++.12.dylib (compatibility version 20.0.0, current version 20.0.0)
	/opt/homebrew/opt/libtiff/lib/libtiff.6.dylib (compatibility version 7.0.0, current version 7.2.0)
	/opt/homebrew/opt/libgeotiff/lib/libgeotiff.5.dylib (compatibility version 8.0.0, current version 8.0.0)
	/opt/homebrew/opt/netcdf/lib/libnetcdf.19.dylib (compatibility version 19.0.0, current version 19.0.0)
	/opt/homebrew/opt/hdf5/lib/libhdf5.310.dylib (compatibility version 314.0.0, current version 314.0.0)
	/opt/homebrew/opt/libaec/lib/libsz.2.dylib (compatibility version 2.0.0, current version 2.0.1)
	/opt/homebrew/opt/open-mpi/lib/libmpi.40.dylib (compatibility version 81.0.0, current version 81.1.0)
	/opt/homebrew/opt/fftw/lib/libfftw3.3.dylib (compatibility version 10.0.0, current version 10.10.0)
	/opt/homebrew/opt/fftw/lib/libfftw3f.3.dylib (compatibility version 10.0.0, current version 10.10.0)
	/opt/homebrew/opt/proj/lib/libproj.25.dylib (compatibility version 25.0.0, current version 25.9.3)
	/opt/homebrew/opt/udunits/lib/libudunits2.0.dylib (compatibility version 2.0.0, current version 2.0.0)
	/opt/homebrew/opt/eccodes/lib/libeccodes.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/homebrew/opt/glpk/lib/libglpk.40.dylib (compatibility version 44.0.0, current version 44.1.0)
	/opt/homebrew/opt/shapelib/lib/libshp.4.dylib (compatibility version 4.0.0, current version 1.6.0)
	/usr/lib/libexpat.1.dylib (compatibility version 7.0.0, current version 8.0.0)
	/opt/homebrew/opt/llvm/lib/libomp.dylib (compatibility version 5.0.0, current version 5.0.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 1500.65.0)
	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices (compatibility version 1.0.0, current version 61.0.0)
	/System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics (compatibility version 64.0.0, current version 1690.5.4)

1 reply

spacemanjosh Jan 24, 2024
Author

Still no luck here. Everything else looks ok. I even went so far as to completely remove miniconda from my system, but no luck. As a test, I tried building it in a container running Fedora, and that seems to work just fine. That should get me by for now, although it's a little less than ideal. If anyone else has tested on macOS 14.x I would be curious to see if they have the same problem. Again, this could all be something I'm doing incorrectly.

Barney-9000 · 2024-01-29T16:04:02Z

Barney-9000
Jan 29, 2024

Could #1675 be the solution? Worked for me (Sonoma 14.2.1) about six weeks ago.

3 replies

spacemanjosh Jan 30, 2024
Author

Thanks! That seems to have worked. I believe it was the openmp flag you mention. All I had to do was this from the gdl/build directory:
cmake -DOPENMP=OFF ..
And now the executable seems to work, without crashing.

I then ran ./scripts/build_gdl.sh check, which mostly worked, except for a single failure (and two skipped):

The following tests did not run:
	135 - test_mpi.pro (Skipped)
	154 - test_python.pro (Skipped)

The following tests FAILED:
	131 - test_matrix_multiply.pro (Failed)

The output from that test specifically is:

131/205 Test #131: test_matrix_multiply.pro ...........***Failed    0.67 sec
% Compiled module: TEST_MATRIX_MULTIPLY.
% TEST_MATRIX_MULTIPLY: Types 14 and 15 desactivated due to pbs in INVERT() in GDL for these 2 type
% Compiled module: DIAG_MATRIX.
size of matrix :        2
nb errors :        4
input type :        6
effective type :            6
size of matrix :        3
nb errors :        4
input type :        6
effective type :            6
size of matrix :        4
nb errors :        4
input type :        6
effective type :            6
% TEST_MATRIX_MULTIPLY: At least one error encountered, please rerun code with /verbose

So it's possible there still may be something not quite right, but this is definitely a step in the right direction.

GillesDuvert Jan 30, 2024
Maintainer

@spacemanjosh apparently there is a problem with complex (matrix) multiplication (type 6). As there are no other problems signaled, it would seem that only this type, on this architecture, and probably only with the Eigen:: library used behind the scene, will be affected.
This should be reported as an issue, but complementary tests will be needed.

spacemanjosh Jan 31, 2024
Author

That's certainly interesting @GillesDuvert, I'd be happy to file an issue. But first I'd be curious if others on macOS Sonoma also see that test failing. @Barney-9000, does test 131 fail for you as well?

Barney-9000 · 2024-02-02T18:23:48Z

Barney-9000
Feb 2, 2024

Actually, it passed -- note the test is numbered 130:

        Start 130: test_matrix_multiply.pro
130/202 Test #130: test_matrix_multiply.pro ...........   Passed    0.67 sec

However, test_systime.pro failed:

Total Test time (real) =  92.59 sec

The following tests did not run:
	134 - test_mpi.pro (Skipped)
	153 - test_python.pro (Skipped)

The following tests FAILED:
	182 - test_systime.pro (Failed)
Errors while running CTest
make: *** [test] Error 8

Here's the full listing of the error messages:

182/202 Test #182: test_systime.pro ...................***Failed    0.27 sec
% Compiled module: TEST_SYSTIME.
LC_ALL=C: Command not found.
% TEST_SYSTIME_LOCALE: Problem with LOCALE in GDL
% Compiled module: BANNER_FOR_TESTSUITE.
% Compiled module: GDL_IDL_FL.
% TEST_SYSTIME_LOCALE:   1 errors encountered during TEST_SYSTIME_LOCALE tests  
% Compiled module: ERRORS_CUMUL.
% TEST_SYSTIME_ZERO:   NO errors encountered during TEST_SYSTIME_ZERO tests  
% TEST_SYSTIME_EPOCH:   NO errors encountered during TEST_SYSTIME_EPOCH tests  
% TEST_SYSTIME_ELAPSED:   NO errors encountered during TEST_SYSTIME_ELAPSED tests  
% TEST_SYSTIME_JULIAN: Not finished
% TEST_SYSTIME_JULIAN: Not finished, please contributed !
% TEST_SYSTIME_JULIAN: Not finished
% TEST_SYSTIME_JULIAN:   NO errors encountered during TEST_SYSTIME_JULIAN tests  
% TEST_SYSTIME: ====================================================
% TEST_SYSTIME: =                                                  =
% TEST_SYSTIME: =  1 errors encountered during TEST_SYSTIME tests  =
% TEST_SYSTIME: =                                                  =
% TEST_SYSTIME: ====================================================

My version of gdl was compiled in December on an M2 Ultra Studio under (I think) Sonoma 14.1, however the test carried out just now was under 14.3.

GDL> !gdl
{
    "RELEASE": "1.0.4 git",
    "BUILD_DATE": "Dec 19 2023",
    "EPOCH": 1702944000,
    "GDL_USE_DSFMT": 1,
    "GDL_USE_WX": 1,
    "GDL_POSIX": 1

0 replies

GillesDuvert · 2024-02-02T20:46:29Z

GillesDuvert
Feb 2, 2024
Maintainer

I've access to an apple mini with Apple silicon M1, and it reports the same error as @spacemanjosh .
This really gonna be an issue.

0 replies

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Bus error when running GDL on macOS Sonoma 14.2.1 #1728

{{title}}

Replies: 6 comments 6 replies

{{title}}

{{title}}

{{editor}}'s edit

{{editor}}'s edit

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

Select a reply

Bus error when running GDL on macOS Sonoma 14.2.1 #1728

spacemanjosh Jan 18, 2024

Replies: 6 comments · 6 replies

alaingdl Jan 18, 2024 Maintainer

spacemanjosh Jan 18, 2024 Author

alaingdl Jan 18, 2024 Maintainer

spacemanjosh Jan 19, 2024 Author

alaingdl Jan 19, 2024 Maintainer

spacemanjosh Jan 24, 2024 Author

Barney-9000 Jan 29, 2024

spacemanjosh Jan 30, 2024 Author

GillesDuvert Jan 30, 2024 Maintainer

spacemanjosh Jan 31, 2024 Author

Barney-9000 Feb 2, 2024

GillesDuvert Feb 2, 2024 Maintainer

spacemanjosh
Jan 18, 2024

Replies: 6 comments 6 replies

alaingdl
Jan 18, 2024
Maintainer

spacemanjosh Jan 18, 2024
Author

alaingdl
Jan 18, 2024
Maintainer

spacemanjosh Jan 19, 2024
Author

alaingdl
Jan 19, 2024
Maintainer

spacemanjosh Jan 24, 2024
Author

Barney-9000
Jan 29, 2024

spacemanjosh Jan 30, 2024
Author

GillesDuvert Jan 30, 2024
Maintainer

spacemanjosh Jan 31, 2024
Author

Barney-9000
Feb 2, 2024

GillesDuvert
Feb 2, 2024
Maintainer