atlas returns segmentation fault with macOS 10.15 and Xcode 11

[vdoublie]

building atlas to use with numpy parallelisation atlas + gcc9 returns segmentation fault

:info:build cd bin/ ; ./xatlas_build -1 0 -a 1 -l 1
:info:build /bin/sh: line 1:  8263 Segmentation fault: 11  ./xatlas_build -1 0 -a 1 -l 1
:info:build make[1]: *** [build] Error 139

and arch errors see log file attach config: MBP late 2015 13" 16Mb RAM 2,7 GHz Dual-Core Intel Core i5

maintainer: veence

[kencu (Ken)]

looks like yet another stack-protect segfault, as a starting thought.

<​https://github.com/macports/macports-ports/commit/a0be1d95abf6bf719c4f779a8d0701f535c9f00a>

[kuhnfe]

I have the very same problem and checked the portfile which already has included the edit described by kencu. Still got the syntax error.

Replying to kencu:

looks like yet another stack-protect segfault, as a starting thought.

<​https://github.com/macports/macports-ports/commit/a0be1d95abf6bf719c4f779a8d0701f535c9f00a>

[machielbos]

Same problem here. Updated to darwin19, tried to reinstall all ports and atlas build fails with

:info:build cd bin/ ; ./xatlas_build -1 0 -a 1 -l 1
:info:build /bin/sh: line 1: 29260 Segmentation fault: 11  ./xatlas_build -1 0 -a 1 -l 1
:info:build make[1]: *** [build] Error 139
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build'

Some info of my compiler

bash-3.2$ clang -v
Apple clang version 11.0.0 (clang-1100.0.33.8)
Target: x86_64-apple-darwin19.0.0
Thread model: posix

--->  Attempting to fetch atlas-3.10.2_2.darwin_19.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/atlas

[murrayE]

Any hope of getting this segmentation fault resolved in atlas? (Same problem here.)

[Veence (Vincent)]

Sorry guys I was really swamped lately.

I’m going to see what I can do with the latest unstable atlas release. But don’t expect miracles. The last unstable release of Atlas is more than one year old, so the project is more or less in a coma, if not dead. I’m gonna try it nonetheless.

Thanks for your patience.

[ryandesign (Ryan Schmidt)]

Has duplicate #59895.

[ccottap (Carlos Cotta)]

The compilation of atlas is now successful for me. Not sure about what exactly has changed (most likely some other compilation libraries/tools were updated) but it seems to be working on my machine now (OS 10.15.12, XCode 11A1027).

[Veence (Vincent)]

Ok, that’s a good thing. I think I’m going to give up on maintaining atlas, if only because my Mac is now more than six years old, and I’m unable to access new hardware, while Atlas has a lot of assembly routines that may, or may not, work on recent CPUs.

Besides, every compilation cycle takes more or less four hours, so Atlas is really a pain to test/debug on an old machine such as mine.

[pcapak]

I had the same problem on a macports install that was upgraded to Catalina from High-sierra but was able to install atlas on a new Catalina machine. I was able to clear up the issue on the upgraded machine by following the instructions here to re-install Xcode ​https://trac.macports.org/wiki/ProblemHotlist#reinstall-clt. I am using Xcode 11.3. When I followed the instructions it said it was installing updates for Xcode 11.0 and 11.3.

[Veence (Vincent)]

I’m closing all old tickets, since I’m not sure they’re relevant at all. Please reopen a new one in case the issue is still at hand.