Build error met-10.1.1.20220419 on macOS Monterey 12.1 / apple-clang 13.1.6 / homebrew Python 3.9 / spack #1762

climbfuji · 2022-08-23T21:55:35Z

climbfuji
Aug 23, 2022

Describe the Problem

Trying to build met-10.1.1.20220419 on macOS Monterey 12.1 with apple-clang 13.1.6, homebrew Python 3.9 using spack-stack (https://github.com/noaa-emc/spack-stack) in Rosetta2 emulator mode for x86_64. Build fails at the very end with a message that I can't make sense of:

/Users/heinzell/work/spack-stack/spack-stack-update-esmf-from-authoritative/spack/lib/spack/env/clang/clang++   -L../../../../src/basic/vx_cal -L../../../../src/basic/vx_config -L../../../../src/basic/vx_log -L../../../../src/basic/vx_math -L../../../../src/basic/vx_util -L../../../../src/libcode/vx_afm -L../../../../src/libcode/vx_analysis_util -L../../../../src/libcode/vx_color -L../../../../src/libcode/vx_data2d -L../../../../src/libcode/vx_data2d_factory -L../../../../src/libcode/vx_data2d_grib -L../../../../src/libcode/vx_data2d_grib2 -L../../../../src/libcode/vx_data2d_nccf -L../../../../src/libcode/vx_data2d_nc_met -L../../../../src/libcode/vx_data2d_nc_pinterp -L../../../../src/libcode/vx_data2d_python -L../../../../src/libcode/vx_python3_utils -L../../../../src/libcode/vx_geodesy -L../../../../src/libcode/vx_gis -L../../../../src/libcode/vx_gnomon -L../../../../src/libcode/vx_grid -L../../../../src/libcode/vx_gsl_prob -L../../../../src/libcode/vx_nav -L../../../../src/libcode/vx_nc_obs -L../../../../src/libcode/vx_nc_util -L../../../../src/libcode/vx_pb_util -L../../../../src/libcode/vx_plot_util -L../../../../src/libcode/vx_pointdata_python -L../../../../src/libcode/vx_ps -L../../../../src/libcode/vx_pxm -L../../../../src/libcode/vx_render -L../../../../src/libcode/vx_regrid -L../../../../src/libcode/vx_bool_calc -L../../../../src/libcode/vx_shapedata -L../../../../src/libcode/vx_solar -L../../../../src/libcode/vx_statistics -L../../../../src/libcode/vx_stat_out -L../../../../src/libcode/vx_summary -L../../../../src/libcode/vx_time_series -L../../../../src/libcode/vx_series_data -L../../../../src/libcode/vx_tc_util -L/Users/heinzell/work/spack-stack/spack-stack-update-esmf-from-authoritative/envs/met-test/install/apple-clang/13.1.6/netcdf-c-4.8.1-vzayhsp/lib -L/Users/heinzell/work/spack-stack/spack-stack-update-esmf-from-authoritative/envs/met-test/install/apple-clang/13.1.6/netcdf-cxx4-4.3.1-nvhg3ao/lib -L/Users/heinzell/work/spack-stack/spack-stack-update-esmf-from-authoritative/envs/met-test/install/apple-clang/13.1.6/zlib-1.2.12-e3supdv/lib  -L/Users/heinzell/work/spack-stack/spack-stack-update-esmf-from-authoritative/envs/met-test/install/apple-clang/13.1.6/g2c-1.6.4-4az7tn6/lib -L/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9 -lPython -L/Users/heinzell/work/spack-stack/spack-stack-update-esmf-from-authoritative/envs/met-test/install/apple-clang/13.1.6/gsl-2.7.1-lj7g63f/lib -L/Users/heinzell/work/spack-stack/spack-stack-update-esmf-from-authoritative/envs/met-test/install/apple-clang/13.1.6/bufr-11.7.0-772urso/lib -o ensemble_stat ensemble_stat-ensemble_stat.o ensemble_stat-ensemble_stat_conf_info.o -lvx_stat_out -lvx_statistics -lvx_shapedata -lvx_gsl_prob -lvx_analysis_util -lvx_data2d_factory -lvx_data2d_nc_met -lvx_data2d_grib -lvx_data2d_grib2 -lg2c -ljasper -lpng -lz -lvx_data2d_nc_pinterp -lvx_data2d_nccf -lvx_data2d_python -lvx_pointdata_python -lvx_python3_utils -L/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9 -lPython -lvx_data2d -lvx_nc_obs -lvx_nc_util -lvx_regrid -lvx_grid -lvx_config -lvx_color -lvx_util -lvx_math -lvx_cal -lvx_log -lvx_data2d_python -lvx_pointdata_python -lvx_python3_utils -L/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9 -lPython -lm -lnetcdf_c++4 -lnetcdf -lgsl -lgslcblas -lnetcdf -lnetcdf_c++4 -lz
ld: cannot link directly with dylib/framework, your binary is not an allowed client of /Library/Developer/CommandLineTools/SDKs/MacOSX12.1.sdk/usr/lib/libPython.tbd for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[5]: *** [ensemble_stat] Error 1

I don't see from that lengthy command where the macOS Python framework is coming in, all I see is multiple occurrences of -L/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9 -lPython. This should be fine, because that's homebrew's Python.

I searched for similar errors on the web, and noticed that there wasn't a lot of information out there, and what I could find didn't really explain why it's trying to use the Apple SDK when Python is actually coming from homebrew.

Just wondering if any of the MET developers have come across this issue by coincidence.

Note. MET builds fine in our GitHub actions CI tests, where we also have macOS builds.

Answered by climbfuji

Oct 19, 2022

@jprestop @JohnHalleyGotway I finally got to work on this and found the reason and a solution. It had to do with how spack defined the shared Python library. The issue and pull request for the authoritative spack repository are:

spack/spack#33409
spack/spack#33410

The same commits are used in our spack fork:

JCSDA/spack-stack#316
JCSDA/spack#185

View full answer

JohnHalleyGotway · 2022-08-25T16:42:20Z

JohnHalleyGotway
Aug 25, 2022
Maintainer

Hi @climbfuji! I see you created an issue in the MET repository about this compilation question. I transferred it over to the METplus repo and converted it to a discussion in the Installation category. We handle Q&A for all of the METplus components, including MET itself, in the single METplus discussions instance, rather than having separate discussion areas for each component.

I hope you're settling in well at JCSDA and hope there's some potential for the use of METplus there!

@jprestop is the person with the most experience compiling MET on a variety of platforms, so she's a great resource. Although I can confirm that I routinely compile MET during development on my own Mac laptop and don't experience this error. And I haven't heard of this issue from any other users or developers.

Some Googling led me to Stack Overflow and I thought this comment looked informative. There may be some system setting that's triggering this error.

Checking my own settings though, you'll see that I'm configured in a very similar way:

printenv | grep MET_PYTHON_
MET_PYTHON_CC=-I/opt/local/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8
MET_PYTHON_LD=-L/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/config-3.8-darwin -lpython3.8 -ldl -framework CoreFoundation

I believe I installed this using MacPorts rather than Homebrew. But one big difference is that I am NOT compiling with clang. Instead, I'm using GNU:

CXX=/opt/local/bin/g++
CC=/opt/local/bin/gcc
F77=/opt/local/bin/gfortran

And that was also installed via MacPorts (g++ (MacPorts gcc6 6.5.0_6) 6.5.0).

@jprestop I wonder if perhaps @prestopUCAR has compiled MET with python embedding support using clang via CLion?

7 replies

climbfuji Sep 1, 2022
Author

Apologies, I've been side tracked working on other issues. I'll try to do this as soon as I get the chance. FYI, I recorded an issue on our spack-stack repo as well - JCSDA/spack-stack#316. There is no more information in it for now, but it's good to have them linked.

jprestop Sep 1, 2022
Maintainer

Sounds good! Thank you!

jprestop Sep 20, 2022
Maintainer

Hi @climbfuji. I just wanted to check in again to see if you have been able to get back to this work?

jprestop Oct 4, 2022
Maintainer

Hi @climbfuji. Just following up on this Discussion. Have you been able to check on your MET_PYTHON_LD setting to check the python library you are linking with and retry the compilation?

jprestop Oct 4, 2022
Maintainer

Not yet, sorry. We have a release at the end of this week that has taken up all my time in the last month.

That's ok. I understand. I just didn't want to let this Discussion go unanswered for too long, so I thought I'd follow up. Good luck with the release!

prestopUCAR · 2022-08-25T20:33:19Z

prestopUCAR
Aug 25, 2022

@jprestop I wonder if perhaps @prestopUCAR has compiled MET with python embedding support using clang via CLion?

Sorry, no. I did not have my mac or CLion back when I was doing MET development.

1 reply

climbfuji Oct 4, 2022
Author

Not yet, sorry. We have a release at the end of this week that has taken up all my time in the last month.

climbfuji · 2022-10-19T14:33:13Z

climbfuji
Oct 19, 2022
Author

@jprestop @JohnHalleyGotway I finally got to work on this and found the reason and a solution. It had to do with how spack defined the shared Python library. The issue and pull request for the authoritative spack repository are:

spack/spack#33409
spack/spack#33410

The same commits are used in our spack fork:

JCSDA/spack-stack#316
JCSDA/spack#185

1 reply

jprestop Oct 19, 2022
Maintainer

That's great news, @climbfuji! Thank you so much for following up and letting us know. I'll go ahead and lock this Discussion. Please feel free to create a new discussion with any other issues that should arise.

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Build error met-10.1.1.20220419 on macOS Monterey 12.1 / apple-clang 13.1.6 / homebrew Python 3.9 / spack #1762

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Build error met-10.1.1.20220419 on macOS Monterey 12.1 / apple-clang 13.1.6 / homebrew Python 3.9 / spack #1762

climbfuji Aug 23, 2022

Describe the Problem

Replies: 3 comments · 9 replies

JohnHalleyGotway Aug 25, 2022 Maintainer

climbfuji Sep 1, 2022 Author

jprestop Sep 1, 2022 Maintainer

jprestop Sep 20, 2022 Maintainer

jprestop Oct 4, 2022 Maintainer

jprestop Oct 4, 2022 Maintainer

prestopUCAR Aug 25, 2022

climbfuji Oct 4, 2022 Author

climbfuji Oct 19, 2022 Author

jprestop Oct 19, 2022 Maintainer

climbfuji
Aug 23, 2022

Replies: 3 comments 9 replies

JohnHalleyGotway
Aug 25, 2022
Maintainer

climbfuji Sep 1, 2022
Author

jprestop Sep 1, 2022
Maintainer

jprestop Sep 20, 2022
Maintainer

jprestop Oct 4, 2022
Maintainer

jprestop Oct 4, 2022
Maintainer

prestopUCAR
Aug 25, 2022

climbfuji Oct 4, 2022
Author

climbfuji
Oct 19, 2022
Author

jprestop Oct 19, 2022
Maintainer