py-scipy does not build on Mac using apple-clang@15.0.0

[srherbener]

Describe the bug

When building py-scipy, the build fails with this message:

meson.build:1:0: ERROR: Unable to detect linker for compiler `/Users/steveherbener/spack-stack/spack/lib/spack/env/clang/clang -Wl,--version`
stdout: 
stderr: ld: unknown options: --version 
clang: error: linker command failed with exit code 1 (use -v to see invocation)

The issue appears to be in the meson package and it looks like this issue was fixed, and will be available in the upcoming meson 1.3.0 release: mesonbuild/meson#12419. The fix is currently available in the release candidate: 1.3.0rc3 if we want to test now. (We are currently using meson version 1.1.0).

To Reproduce
Steps to reproduce the behavior:

Update command lines tools to latest version which installs apple-clang%15.0.0.
Build the unified-env

Expected behavior
Build succeeds

System:
mac0S 13.6 (Ventura)

Additional context
Add any other context about the problem here.

[srherbener]

When I tried to build the entire spack-stack, using the prior fixes for boost and ecflow, I got the following messages at the end of the build.

==> Error: Installation request failed.  Refer to reported errors for failing package(s).
==> Removing failure mark on py-scipy-1.9.3-zdschxduujbomzbeiwpgepy7hgschki3
==> Removing failure mark on py-cartopy-0.21.1-4n2t3bvyr6spqwnsasablb24t3qymwbp
==> Removing failure mark on gmao-swell-env-1.0.0-d4fruiuualecesvmsor5edpqjofr6ryx
==> Removing failure mark on ewok-env-1.0.0-ivjqzxy4sjzmgdec5nikkhosjtyvmlme
==> Removing failure mark on jedi-tools-env-1.0.0-vs2kuhnphzr264lbfu6u5gvzgvo6iawd
==> Removing failure mark on jedi-base-env-1.0.0-j5l4b3esr4oip7uokdckpncwvaedbu37
==> Removing failure mark on jedi-fv3-env-1.0.0-chhxd3f7sqvkxxypc3v2ce6lkjz6w5x6
==> Removing failure mark on jedi-ufs-env-1.0.0-4e2q4aeww6ljnljcnc5yet7g2p33ha5f
==> Removing failure mark on jedi-um-env-1.0.0-l2l4f5g2r4sidktiw3r3zthf6r62wwft
==> Removing failure mark on jedi-neptune-env-1.0.0-ejeldscgs3gjhofj2lz3vj3if3va3at3
==> Removing failure mark on jedi-mpas-env-1.0.0-uec34zh7ufospflou7lvi4txqjh6oe6f
==> Removing failure mark on soca-env-1.0.0-66vuqpxwi6xtsfnfe327ozyassydzkz7

I'm guessing that means that there are two packages left to debug: py-scipy and py-cartopy.

I tried building py-cartopy by itself (spack install -v py-cartopy) and it suffered the exact same error from meson. It appears that updating meson may enable the whole spack-stack build to complete successfully.

[srherbener]

I tried building py-cartopy by itself (spack install -v py-cartopy) and it suffered the exact same error from meson. It appears that updating meson may enable the whole spack-stack build to complete successfully.

Scratch this part in my prior comment. I misread the log and it turns out that py-scipy is a dependency for py-cartopy (makes sense) and the build failed when trying to build py-scipy. So, we don't know about py-cartopy yet.

[climbfuji]

We will want to wait until we have an official release of meson available. Until then there will simply not be support for clang@15 ...

[srherbener]

I tested a build using my Mac with apple-clang@15.0.0 using the Nov 23 spack merge PR (JCSDA/spack#371) after it was merged, and the corresponding spack-stack updates (#884). The spack-stack build (unified-env) successfully completed, and I was able to successfully build jedi-bundle from scratch.

I see 37 ctest failures which appear to be similar to when building with apple-clang@14.0.3 on the Mac:

98% tests passed, 37 tests failed out of 2416



Label Time Summary:

CRTM_Tests            = 169.56 sec*proc (160 tests)

GEOS                  =   6.98 sec*proc (3 tests)

HofX                  =   3.72 sec*proc (10 tests)

QC                    =  21.83 sec*proc (16 tests)

UV                    =   3.97 sec*proc (2 tests)

actions               =   8.11 sec*proc (4 tests)

aircraft              =   2.42 sec*proc (3 tests)

compo                 =   0.77 sec*proc (2 tests)

coupling              =  13.75 sec*proc (9 tests)

crtm                  =  56.98 sec*proc (56 tests)

crtm_tests            = 169.56 sec*proc (160 tests)

download_data         =  59.26 sec*proc (1 test)

errors                =   2.47 sec*proc (8 tests)

executable            = 107.43 sec*proc (236 tests)

femps                 =   5.60 sec*proc (1 test)

filters               = 155.51 sec*proc (179 tests)

fortran               =   0.95 sec*proc (3 tests)

fov                   =   0.47 sec*proc (2 tests)

fv3-jedi              = 229.90 sec*proc (125 tests)

fv3jedi               = 231.41 sec*proc (126 tests)

gnssro                =   0.93 sec*proc (1 test)

gsw                   =   1.32 sec*proc (6 tests)

instrument            =  26.32 sec*proc (28 tests)

ioda                  =  68.26 sec*proc (315 tests)

iodaconv              = 138.33 sec*proc (330 tests)

iodaconv_validate     =  29.47 sec*proc (176 tests)

metoffice             =   0.51 sec*proc (2 tests)

mpasjedi              = 161.55 sec*proc (51 tests)

mpi                   = 1023.18 sec*proc (976 tests)

obsfunctions          =  41.39 sec*proc (80 tests)

oops                  =  96.49 sec*proc (295 tests)

openmp                = 204.38 sec*proc (270 tests)

operators             =  84.17 sec*proc (146 tests)

ozone                 =   1.09 sec*proc (2 tests)

pibal                 =   0.97 sec*proc (1 test)

predictors            =   8.80 sec*proc (20 tests)

profile               =  28.89 sec*proc (41 tests)

radarVAD              =   1.28 sec*proc (2 tests)

rass                  =   1.21 sec*proc (2 tests)

saber                 = 176.13 sec*proc (219 tests)

satwinds              =   2.26 sec*proc (3 tests)

scatwinds             =   2.21 sec*proc (3 tests)

script                = 1381.38 sec*proc (2070 tests)

sfcLand               =   4.39 sec*proc (3 tests)

sfcMarine             =   4.38 sec*proc (3 tests)

soca                  =  88.72 sec*proc (75 tests)

sonde                 =   4.40 sec*proc (3 tests)

ufo                   = 355.47 sec*proc (485 tests)

ufo_data              =  52.57 sec*proc (315 tests)

ufo_data_validate     =  52.57 sec*proc (315 tests)

unit_tests            =  65.87 sec*proc (90 tests)

utils                 =   0.52 sec*proc (2 tests)

vader                 =   6.79 sec*proc (33 tests)

variablenamemap       =   0.27 sec*proc (1 test)

variabletransforms    =  27.72 sec*proc (27 tests)



Total Test time (real) = 1569.37 sec



The following tests FAILED:

	339 - saber_test_randomization_bump_nicas_UL2_1-1 (Failed)

	359 - saber_test_error_covariance_training_bump_hdiag-nicas_2_1-1 (Failed)

	362 - saber_test_error_covariance_training_bump_hdiag-nicas_5_1-1 (Failed)

	407 - saber_test_dirac_fastlam_1_1-1 (Failed)

	409 - saber_test_dirac_fastlam_3_1-1 (Failed)

	447 - saber_test_randomization_bump_nicas_UL2_2-1 (Failed)

	467 - saber_test_error_covariance_training_bump_hdiag-nicas_2_2-1 (Failed)

	470 - saber_test_error_covariance_training_bump_hdiag-nicas_5_2-1 (Failed)

	518 - saber_test_dirac_fastlam_1_2-1 (Failed)

	1390 - ufo_test_tier1_instrument_sonde_geos_qc (Failed)

	1393 - ufo_test_tier1_instrument_sfcLand_geos_qc (Failed)

	1396 - ufo_test_tier1_instrument_sfcMarine_geos_qc (Failed)

	1464 - ufo_test_tier1_test_ufo_qc_average_obs_to_mod_levels (Failed)

	1480 - ufo_test_tier1_test_ufo_qc_variableassignment (Failed)

	1500 - ufo_test_tier1_test_ufo_mhs_qc_filters_geos (Failed)

	1542 - ufo_test_tier1_test_ufo_function_metoffice_rh_corr (Failed)

	1809 - ufo_test_tier1_test_ufo_variabletransforms_rhumidity_part2 (Failed)

	1825 - iodaconv_compo_coding_norms (Failed)

	1826 - iodaconv_gsi_ncdiag_coding_norms (Failed)

	1829 - iodaconv_land_coding_norms (Failed)

	1830 - iodaconv_lib-python_coding_norms (Failed)

	1831 - iodaconv_marine_coding_norms (Failed)

	1838 - iodaconv_gnssro_coding_norms (Failed)

	2182 - fv3jedi_test_tier1_increment_geos (Failed)

	2183 - fv3jedi_test_tier1_errorcovariance (Failed)

	2230 - fv3jedi_test_tier1_errorcovariance_bump (Failed)

	2293 - test_soca_errorcovariance (Failed)

	2328 - test_soca_sqrtvertloc (Failed)

	2336 - test_soca_dirac_diffusion (Failed)

	2356 - test_soca_convertincrement (Failed)

	2363 - test_mpasjedi_errorcovariance (Failed)

	2375 - test_mpasjedi_hofx4d (Failed)

	2391 - test_mpasjedi_3denvar_amsua_bc (Failed)

	2393 - test_mpasjedi_3dfgat (Failed)

	2399 - test_mpasjedi_4dfgat (Failed)

	2415 - test_coupled_hofx3d_fv3_mom6 (Failed)

	2416 - test_coupled_hofx3d_fv3_mom6_dontusemom6 (Failed)

Errors while running CTest

[climbfuji]

Great, thanks! Then we can close this issue.