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Roll-out spack-stack-1.5.0 #765

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climbfuji opened this issue Sep 6, 2023 · 8 comments · Fixed by #787
Closed

Roll-out spack-stack-1.5.0 #765

climbfuji opened this issue Sep 6, 2023 · 8 comments · Fixed by #787
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@climbfuji @ulmononian @AlexanderRichert-NOAA
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INFRA JEDI Infrastructure

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@climbfuji
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climbfuji commented Sep 6, 2023 •
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Description

This PR captures the roll-out of spack-stack-1.5.0.

While we are at it, we should check and update thirdparty, install, and source-cache locations on preconfigured sites for spack-stack-1.5.0.

For example, gaea-c5 and hercules are following the new directory structure for sites that share a filesystem with another site, but their peers gaea-c4 and orion don't.

Important: check external packages for sites and remove any older, external bison to avoid duplicate packages

Latest release documentation: https://spack-stack.readthedocs.io/en/release-1.5.0/

Sites

Basic tests are: build jedi-bundle and run ctests AND/OR build ufs-weather-model and run regression tests AND/ORbuild ufs-srw-app and run tests (please denote in the list below). If someone wants to test an installation from a different installer with another set of tests, that is more than welcome (just note the github username when you add the test).

  • Orion (@climbfuji)
    • external bison removed
    • top-level directory structure
    • 3rdparty libraries and modules
    • source cache location
    • Installed in: /work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.5.0/envs/unified-env
    • basic tests performed for all supported compilers: jedi-bundle with GNU, only two ctests failed out of 1900
    • site/config and documentation updated: release/1.5.0: site updates part 1 (Orion, Hercules, Narwhal) #770
    • (re-)installed with ip@4.3.0
The following tests FAILED:
	405 - saber_test_dirac_gsi_gfs_global_1-1 (Failed)
	1627 - test_soca_sqrtvertloc (Failed)
  • Hercules (@climbfuji)
    • external bison removed
    • top-level directory structure
    • 3rdparty libraries and modules
    • source cache location
    • Installed in: /work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.5.0/envs/unified-env
    • basic tests performed for all supported compilers (jedi-bundle)
    • site/config and documentation updated: release/1.5.0: site updates part 1 (Orion, Hercules, Narwhal) #770
    • (re-)installed with ip@4.3.0
The following tests FAILED:
	405 - saber_test_dirac_gsi_gfs_global_1-1 (Failed)
	1532 - fv3jedi_test_tier1_dirac_gfs_gsi_global (Failed)
	1564 - fv3jedi_test_tier1_diffstates_gfs (Failed)
	1627 - test_soca_sqrtvertloc (Failed)
	1633 - test_soca_dirac_soca_mask (Failed)
	1642 - test_soca_3dvar_godas (Failed)

The following tests FAILED:
        408 - saber_test_dirac_gsi_gfs_global_1-1 (Failed)
        1541 - fv3jedi_test_tier1_dirac_geos_gsi_global (Failed)
        1542 - fv3jedi_test_tier1_3dvar_geos_sondes (Failed)
        1543 - fv3jedi_test_tier1_3dvar_geos_ozone (Failed)
        1544 - fv3jedi_test_tier1_dirac_gfs_gsi_global (Failed)
        1545 - fv3jedi_test_tier1_3dvar_gfs_sondes (Failed)
        1627 - test_soca_setcorscales (Failed)
        1629 - test_soca_parameters_bump_cor_nicas_scales (Failed)
        1632 - test_soca_enspert (Failed)
        1640 - test_soca_sqrtvertloc (Failed)
        1642 - test_soca_dirac_soca_cor_nicas_scales (Failed)
        1644 - test_soca_dirac_socahyb_cov (Failed)
        1646 - test_soca_dirac_soca_mask (Failed)
        1647 - test_soca_dirac_soca_nomask (Failed)
        1655 - test_soca_3dvar_godas (Failed)
  • Casper (@climbfuji)
  • Cheyenne (@climbfuji) - not making any changes unless necessary, since machine will be decommissioned at the end of this year
    • external bison removed
    • top-level directory structure
    • 3rdparty libraries and modules
    • source cache location
    • Installed in /glade/work/epicufsrt/contrib/spack-stack/cheyenne/spack-stack-1.5.0/envs/unified-env (gcc only) and /glade/work/epicufsrt/contrib/spack-stack/cheyenne/spack-stack-1.5.0/envs/ufs-env (intel only)
    • basic tests performed for all supported compilers:
      • jedi-bundle with gnu: all ctests pass
      • ufs-weather-model with intel: I compiled as follows after loading ufs-weather-model-env/1.0.0, and that worked (no more testing done)
git clone -b feature/spack_stack_150 --recurse-submodules https://github.com/climbfuji/ufs-weather-model
mkdir build; cd build
cmake -DAPP=S2SWA -DCCPP_SUITES=FV3_GFS_v17_coupled_p8 ../ufs-weather-model 2>&1 | tee log.cmake

- [x] site/config and documentation updated: https://github.com/JCSDA/spack-stack/pull/787
- [x] (re-)installed with ip@4.3.0

The following tests FAILED:
        412 - saber_test_dirac_gsi_gfs_global_1-1 (Failed)
        1403 - ufo_test_tier1_test_ufo_conventionalprofileprocessing_average_relativehumidity_obsfilter (Failed)
        1404 - ufo_test_tier1_test_ufo_conventionalprofileprocessing_average_relativehumidity_OPScomparison (Failed)
        1554 - fv3jedi_test_tier1_dirac_gfs_gsi_global (Failed)
        1576 - fv3jedi_test_tier1_4denvar_seq (Failed)
        1587 - fv3jedi_test_tier1_diffstates_gfs (Failed)
        1650 - test_soca_sqrtvertloc (Failed)

ctest.noget.timeout-0600.log

Many fv3-jedi and soca ctests fail when run consecutively, but when run individually they pass. Very weird.
  • [x Gaea C5 (@ulmononian, @climbfuji)
  • Hera (@ulmononian)
    • external bison removed
    • top-level directory structure
    • 3rdparty libraries and modules
    • source cache location
    • Install of unified-env for supported compilers (combined or separately) in /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env
    • basic tests performed for all supported compilers (ufs-weather-model)
    • site/config and documentation updated: Update Hera/Jet/Cheyenne site configs #779
    • (re-)installed with ip@4.3.0
  • Jet (@ulmononian)
    • external bison removed
    • top-level directory structure
    • 3rdparty libraries and modules
    • source cache location
    • Install of unified-env for supported compilers (combined or separately) in /mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env
    • basic tests performed for all supported compilers (ufs-weather-model)
    • site/config and documentation updated: Update Hera/Jet/Cheyenne site configs #779
    • (re-)installed with ip@4.3.0
  • Narwhal (@climbfuji)
    • external bison removed
    • top-level directory structure
    • 3rdparty libraries and modules
    • source cache location
    • Installed in: /p/app/projects/NEPTUNE/spack-stack/spack-stack-1.5.0/envs/unified-env-intel-2021.4.0 and /p/app/projects/NEPTUNE/spack-stack/spack-stack-1.5.0/envs/unified-env-gcc-10.3.0
    • basic tests performed for all supported compilers (jedi-bundle with Intel; basically all soca tests fail, the rest looks good)
    • site/config and documentation updated: release/1.5.0: site updates part 1 (Orion, Hercules, Narwhal) #770
    • (re-)installed with ip@4.3.0
         64 - test_l95_pseudomodel_state4d (Failed)
        403 - saber_test_dirac_gsi_gfs_global_1-1 (Failed)
        1021 - ufo_test_tier1_instrument_sonde_gfs_HofX (Failed)
        1022 - ufo_test_tier1_instrument_sonde_gfs_qc (Failed)
        1508 - fv3jedi_test_tier1_linearmodel_htlm_physics (Failed)
        1577 - fv3jedi_test_tier1_eda_3dvar (Failed)
        1581 - test_soca_gridgen (Failed)
        1582 - test_soca_geometry (Failed)
        1583 - test_soca_geometry_iterator_2d (Failed)
        1584 - test_soca_geometry_iterator_3d (Failed)
        1585 - test_soca_state (Failed)
        1586 - test_soca_increment (Failed)
        1587 - test_soca_model (Failed)
        1588 - test_soca_modelaux (Failed)
        1589 - test_soca_getvalues (Failed)
        1590 - test_soca_errorcovariance (Failed)
        1591 - test_soca_linearmodel (Failed)
        1592 - test_soca_varchange_ana2model (Failed)
        1593 - test_soca_varchange_balance (Failed)
        1594 - test_soca_varchange_balance_TSSSH (Failed)
        1597 - test_soca_varchange_bkgerrsoca (Failed)
        1598 - test_soca_varchange_bkgerrsoca_stddev (Failed)
        1599 - test_soca_varchange_bkgerrgodas (Failed)
        1600 - test_soca_varchange_vertconv (Failed)
        1601 - test_soca_obslocalization (Failed)
        1605 - test_soca_forecast_mom6 (Failed)
        1607 - test_soca_forecast_mom6_ens1 (Failed)
        1608 - test_soca_forecast_mom6_ens2 (Failed)
        1610 - test_soca_static_socaerror_init (Failed)
        1612 - test_soca_setcorscales (Failed)
        1614 - test_soca_parameters_bump_cor_nicas_scales (Failed)
        1615 - test_soca_parameters_bump_loc (Failed)
        1617 - test_soca_enspert (Failed)
        1618 - test_soca_convertstate (Failed)
        1619 - test_soca_convertstate_changevar (Failed)
        1620 - test_soca_ensvariance (Failed)
        1621 - test_soca_ensmeanandvariance (Failed)
        1622 - test_soca_parametric_stddev (Failed)
        1623 - test_soca_ensrecenter (Failed)
        1624 - test_soca_hybridgain (Failed)
        1625 - test_soca_sqrtvertloc (Failed)
        1626 - test_soca_diffstates (Failed)
        1627 - test_soca_dirac_soca_cor_nicas_scales (Failed)
        1628 - test_soca_dirac_soca_cov (Failed)
        1629 - test_soca_dirac_socahyb_cov (Failed)
        1630 - test_soca_dirac_horizfilt (Failed)
        1631 - test_soca_dirac_soca_mask (Failed)
        1633 - test_soca_makeobs (Failed)
        1634 - test_soca_hofx_3d (Failed)
        1635 - test_soca_hofx_4d (Failed)
        1636 - test_soca_hofx_4d_pseudo (Failed)
        1637 - test_soca_enshofx (Failed)
        1638 - test_soca_3dvar_soca (Failed)
        1640 - test_soca_3dvar_godas (Failed)
        1641 - test_soca_3dvarlowres_soca (Failed)
        1642 - test_soca_3dvarfgat (Failed)
        1643 - test_soca_3dvarfgat_pseudo (Failed)
        1644 - test_soca_3dhyb (Failed)
        1645 - test_soca_3dhybfgat (Failed)
        1646 - test_soca_4denvar (Failed)

The following tests FAILED:
        407 - saber_test_dirac_gsi_gfs_global_1-1 (Failed)
        1639 - test_soca_sqrtvertloc (Failed)
Errors while running CTest

The following tests FAILED:
        408 - saber_test_dirac_gsi_gfs_global_1-1 (Failed)
        1462 - test_femps_csgrid (Failed)
        1541 - fv3jedi_test_tier1_dirac_geos_gsi_global (Failed)
        1542 - fv3jedi_test_tier1_3dvar_geos_sondes (Failed)
        1543 - fv3jedi_test_tier1_3dvar_geos_ozone (Failed)
        1544 - fv3jedi_test_tier1_dirac_gfs_gsi_global (Failed)
        1545 - fv3jedi_test_tier1_3dvar_gfs_sondes (Failed)
        1627 - test_soca_setcorscales (Failed)
        1629 - test_soca_parameters_bump_cor_nicas_scales (Failed)
        1632 - test_soca_enspert (Failed)
        1640 - test_soca_sqrtvertloc (Failed)
        1642 - test_soca_dirac_soca_cor_nicas_scales (Failed)
        1644 - test_soca_dirac_socahyb_cov (Failed)
        1646 - test_soca_dirac_soca_mask (Failed)
        1647 - test_soca_dirac_soca_nomask (Failed)
        1655 - test_soca_3dvar_godas (Failed)

The following tests FAILED with Intel (two weeks ago, 20230910):
	406 - saber_test_dirac_gsi_gfs_global_1-1 (Failed)
	1636 - test_soca_sqrtvertloc (Failed)
Errors while running **CTest

The following tests FAILED with GNU (today, 20230922):
	408 - saber_test_dirac_gsi_gfs_global_1-1 (Failed)
	1493 - fv3jedi_test_tier1_convertstate_gfs (Timeout)
	1494 - fv3jedi_test_tier1_convertstate_geos (Timeout)
	1562 - fv3jedi_test_tier1_hyb-fgat_fv3lm (Timeout)
	1641 - test_soca_sqrtvertloc (Failed)

The following tests FAILED:
        407 - saber_test_dirac_gsi_gfs_global_1-1 (Failed)
        1140 - ufo_test_tier1_test_ufo_gmi_qc_filters (Failed)
        1141 - ufo_test_tier1_test_ufo_gmi_qc_filters_geos (Failed)
        1356 - ufo_test_tier1_test_ufo_opr_gmi_crtm (Failed)
        1541 - fv3jedi_test_tier1_dirac_geos_gsi_global (Failed)
        1542 - fv3jedi_test_tier1_3dvar_geos_sondes (Failed)
        1543 - fv3jedi_test_tier1_3dvar_geos_ozone (Failed)
        1544 - fv3jedi_test_tier1_dirac_gfs_gsi_global (Failed)
        1545 - fv3jedi_test_tier1_3dvar_gfs_sondes (Failed)
        1551 - fv3jedi_test_tier1_hyb-3dvar (Failed)
        1576 - fv3jedi_test_tier1_diffstates_gfs (Failed)
        1579 - fv3jedi_test_tier1_addincrement_gfs (Failed)
        1626 - test_soca_setcorscales (Failed)
        1628 - test_soca_parameters_bump_cor_nicas_scales (Failed)
        1631 - test_soca_enspert (Failed)
        1639 - test_soca_sqrtvertloc (Failed)
        1641 - test_soca_dirac_soca_cor_nicas_scales (Failed)
        1643 - test_soca_dirac_socahyb_cov (Failed)
        1645 - test_soca_dirac_soca_mask (Failed)
        1646 - test_soca_dirac_soca_nomask (Failed)
        1654 - test_soca_3dvar_godas (Failed)

The following tests FAILED:
        408 - saber_test_dirac_gsi_gfs_global_1-1 (Failed)
        808 - test_ioda_obsspace (Failed)
        809 - test_ioda_obsspace_reader_pool (Failed)
        811 - test_ioda_obsspace_out_odc (Failed)
        812 - test_ioda_obsspace_out_odc_mpi_2 (Failed)
        813 - test_ioda_obsspace_out_odc_compare_aircraft (Failed)
        814 - test_ioda_obsspace_out_odc_compare_atms (Failed)
        815 - test_ioda_obsspace_out_odc_compare_gmi (Failed)
        816 - test_ioda_obsspace_out_odc_compare_amsua (Failed)
        817 - test_ioda_obsspace_out_odc_compare_sonde (Failed)
        818 - test_ioda_obsspace_out_odc_compare_aod (Failed)
        819 - test_ioda_obsspace_out_odc_compare_iasi (Failed)
        820 - test_ioda_obsspace_out_odc_compare_aod_testdatsets_0000 (Failed)
        821 - test_ioda_obsspace_out_odc_compare_aod_testdatsets_0001 (Failed)
        1019 - ufo_test_tier1_instrument_aircraft_gfs_HofX (Failed)
        1325 - ufo_test_tier1_test_ufo_opr_sfcpcorrected (Failed)
        1541 - fv3jedi_test_tier1_dirac_geos_gsi_global (Failed)
        1542 - fv3jedi_test_tier1_3dvar_geos_sondes (Failed)
        1543 - fv3jedi_test_tier1_3dvar_geos_ozone (Failed)
        1544 - fv3jedi_test_tier1_dirac_gfs_gsi_global (Failed)
        1545 - fv3jedi_test_tier1_3dvar_gfs_sondes (Failed)
        1551 - fv3jedi_test_tier1_hyb-3dvar (Failed)
        1566 - fv3jedi_test_tier1_4denvar_seq (Failed)
        1577 - fv3jedi_test_tier1_diffstates_gfs (Failed)
        1580 - fv3jedi_test_tier1_addincrement_gfs (Failed)
        1627 - test_soca_setcorscales (Failed)
        1629 - test_soca_parameters_bump_cor_nicas_scales (Failed)
        1632 - test_soca_enspert (Failed)
        1640 - test_soca_sqrtvertloc (Failed)
        1642 - test_soca_dirac_soca_cor_nicas_scales (Failed)
        1644 - test_soca_dirac_socahyb_cov (Failed)
        1646 - test_soca_dirac_soca_mask (Failed)
        1647 - test_soca_dirac_soca_nomask (Failed)
        1655 - test_soca_3dvar_godas (Failed)

The following tests FAILED:
        407 - saber_test_dirac_gsi_gfs_global_1-1 (Failed)
        1541 - fv3jedi_test_tier1_dirac_geos_gsi_global (Failed)
        1542 - fv3jedi_test_tier1_3dvar_geos_sondes (Failed)
        1543 - fv3jedi_test_tier1_3dvar_geos_ozone (Failed)
        1544 - fv3jedi_test_tier1_dirac_gfs_gsi_global (Failed)
        1545 - fv3jedi_test_tier1_3dvar_gfs_sondes (Failed)
        1551 - fv3jedi_test_tier1_hyb-3dvar (Failed)
        1576 - fv3jedi_test_tier1_diffstates_gfs (Failed)
        1579 - fv3jedi_test_tier1_addincrement_gfs (Failed)
        1626 - test_soca_setcorscales (Failed)
        1628 - test_soca_parameters_bump_cor_nicas_scales (Failed)
        1631 - test_soca_enspert (Failed)
        1639 - test_soca_sqrtvertloc (Failed)
        1641 - test_soca_dirac_soca_cor_nicas_scales (Failed)
        1643 - test_soca_dirac_socahyb_cov (Failed)
        1645 - test_soca_dirac_soca_mask (Failed)
        1646 - test_soca_dirac_soca_nomask (Failed)
        1654 - test_soca_3dvar_godas (Failed)
  • JCSDA CI container gnu/openmpi, clang/mpich, intel/impi
    • external bison removed
    • top-level directory structure (n/a)
    • 3rdparty libraries and modules (n/a)
    • source cache location (n/a)
    • (re-)built with ip@4.3.0
    • basic tests performed (JCSDA CI)
    • Uploaded to JCSDA NOAA AWS ECR as "latest"
    • Uploaded to dockerhub as "latest" (not Intel due to licensing restrictions)
    • Converted to Singularity and signed
    • Singularity containers uploaded to JCSDA S3 and to sylabs.io (the latter not for Intel due to licensing restrictions)
    • site/config and documentation updated: release/1.5.0: site config and doc updates round 2 (S4, aws-pcluster, Discover, Nautilus, JCSDA CI containers) #775
The following tests FAILED:
        407 - saber_test_dirac_gsi_gfs_global_1-1 (Failed)
        520 - get_crtm_coeffs (Failed)
        1541 - fv3jedi_test_tier1_dirac_geos_gsi_global (Failed)
        1542 - fv3jedi_test_tier1_3dvar_geos_sondes (Failed)
        1543 - fv3jedi_test_tier1_3dvar_geos_ozone (Failed)
        1544 - fv3jedi_test_tier1_dirac_gfs_gsi_global (Failed)
        1545 - fv3jedi_test_tier1_3dvar_gfs_sondes (Failed)
        1626 - test_soca_setcorscales (Failed)
        1628 - test_soca_parameters_bump_cor_nicas_scales (Failed)
        1631 - test_soca_enspert (Failed)
        1639 - test_soca_sqrtvertloc (Failed)
        1641 - test_soca_dirac_soca_cor_nicas_scales (Failed)
        1643 - test_soca_dirac_socahyb_cov (Failed)
        1645 - test_soca_dirac_soca_mask (Failed)
        1646 - test_soca_dirac_soca_nomask (Failed)
        1654 - test_soca_3dvar_godas (Failed)
@climbfuji climbfuji added the INFRA JEDI Infrastructure label Sep 6, 2023
@climbfuji climbfuji moved this to In Progress in spack-stack-1.5.0 (2023 Q3) Sep 6, 2023
@climbfuji climbfuji moved this from In Progress to Todo in spack-stack-1.5.0 (2023 Q3) Sep 6, 2023
@climbfuji climbfuji changed the title Check and update thirdparty, install, and source-cache locations on preconfigured sites for spack-stack-1.5.0 Roll-out spack-stack-1.5.0 Sep 9, 2023
@climbfuji climbfuji moved this from Todo to In Progress in spack-stack-1.5.0 (2023 Q3) Sep 9, 2023
This was referenced Sep 9, 2023
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@ulmononian ulmononian mentioned this issue Sep 15, 2023
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@ulmononian
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on hera using spack-stack/1.5.0, the cmake step for the s2swa config of the ufs-wm fails:

-- Configuring done
CMake Error at /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env/install/intel/2021.5.0/mapl-2.35.2-rwaq27r/lib64/cmake/MAPL/MAPL-targets.cmake:158 (set_target_properties):
  The link interface of target "MAPL.gridcomps" contains:

    FARGPARSE::fargparse

  but the target was not found.  Possible reasons include:

    * There is a typo in the target name.
    * A find_package call is missing for an IMPORTED target.
    * An ALIAS target is missing.

Call Stack (most recent call first):
  /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env/install/intel/2021.5.0/mapl-2.35.2-rwaq27r/lib64/cmake/MAPL/mapl-config.cmake:74 (include)
  GOCART/CMakeLists.txt:64 (find_package)


CMake Error at /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env/install/intel/2021.5.0/mapl-2.35.2-rwaq27r/lib64/cmake/MAPL/MAPL-targets.cmake:166 (set_target_properties):
  The link interface of target "MAPL.cap" contains:

    FARGPARSE::fargparse

  but the target was not found.  Possible reasons include:

    * There is a typo in the target name.
    * A find_package call is missing for an IMPORTED target.
    * An ALIAS target is missing.

Call Stack (most recent call first):
  /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env/install/intel/2021.5.0/mapl-2.35.2-rwaq27r/lib64/cmake/MAPL/mapl-config.cmake:74 (include)
  GOCART/CMakeLists.txt:64 (find_package)


-- Generating done
CMake Generate step failed.  Build files cannot be regenerated correctly.

@AlexanderRichert-NOAA
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Blergh. Is there a reason we didn't go back to keep fargparse disabled for MAPL? In 1.4.1 the package default was for it to be off.

@climbfuji
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See the UFS weather model esmf 8.5.0 testing issue. I have branches that fix those problems.

@ulmononian
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this was w/ esmf 8.4.2, though...am i missing something?

@climbfuji
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The variants fargparse and pflogger being turned on by default in the new build recipes? Affects older mapl versions, too.

@ulmononian
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so without the fixes from the branches you alluded to, we should not expect the ufs wm to run with spack-stack/1.5.0?

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I think that is the case, yes. It's a tiny bug fix in GOCART, not more.

This was referenced Sep 25, 2023
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@climbfuji climbfuji linked a pull request Sep 28, 2023 that will close this issue
release/1.5.0: final site and documentation updates (Cheyenne, Casper, AWS single-node AMI) #787
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Closed via #787

@github-project-automation github-project-automation bot moved this from In Progress to Done in spack-stack-1.5.0 (2023 Q3) Sep 28, 2023
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@climbfuji climbfuji

@ulmononian ulmononian

@AlexanderRichert-NOAA AlexanderRichert-NOAA

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spack-stack-1.5.0 (2023 Q3)
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