Update JEDI components (branches) in ufs-bundle

[climbfuji]

Description

After #9 is merged let's update the JEDI components to more recent tags. Currently, they are as of Nov 22, 2022. The ufs-weather-model is as current as Jan 17, 2023.

[shlyaeva]

The update of JEDI components to develop as of today was straightforward; I have branches in ufs-bundle, fv3-jedi, fv3-jedi-data to update @climbfuji's branches. I seem to not have the rights to push to this repo (or assign estimates/sprints/etc); I'll push branches on Monday.

[climbfuji]

Excellent! Please ping me on Monday and we can get this merged. Thanks!

[climbfuji]

I created shlyaeva#1. You'll need to merge this into your branch to fix the netcdf-c linker errors that @cmgas and I were seeing.

[climbfuji]

First good news to report. I can build the atm-only config and run the UFS warmstart tests, they pass. The coldstart tests fail, but that's known and I am working on it.

[climbfuji]

On to the next app, NG-GODAS no longer compiles:

ce/soca_balance_mod.F90 -o CMakeFiles/soca.dir/LinearVariableChange/Balance/soca_balance_mod.F90.o
f951: Warning: Nonexistent include directory '/Users/heinzell/work/ufs-bundle/20230130/build-debug-ng-godas/Depends/include_r8' [-Wmissing-include-dirs]
/Users/heinzell/work/ufs-bundle/20230130/ufs-bundle/soca/src/soca/Covariance/soca_covariance_mod.F90:316:96:

  316 |   call horiz_convol%create(geom%f_comm,afunctionspace,afieldset,f_conf_bump,f_grid,universe_rad)
      |                                                                                                1
Error: Type mismatch in argument 'universe_radius' at (1); passed TYPE(fckit_configuration) to TYPE(fieldset_type)
make[2]: *** [soca/src/soca/CMakeFiles/soca.dir/Covariance/soca_covariance_mod.F90.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [soca/src/soca/CMakeFiles/soca.dir/all] Error 2
make: *** [all] Error 2

[climbfuji]

The third application, S2S, also doesn't compile:

[ 93%] Linking CXX shared library ../../../lib/libfv3jedi.dylib
cd /Users/heinzell/work/ufs-bundle/20230130/build-debug-s2s/fv3-jedi/src/fv3jedi && /usr/local/Cellar/cmake/3.23.1/bin/cmake -E remove /Users/heinzell/work/ufs-bundle/20230130/build-debug-s2s/lib/libfv3jedi.dylib
cd /Users/heinzell/work/ufs-bundle/20230130/build-debug-s2s/fv3-jedi/src/fv3jedi && /usr/local/Cellar/cmake/3.23.1/bin/cmake -E cmake_link_script CMakeFiles/fv3jedi.dir/link.txt --verbose=1
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++  -pipe -g -arch x86_64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -mmacosx-version-min=12.1 -dynamiclib -Wl,-headerpad_max_install_names -Wl,-commons,use_dylibs -Wl,-commons,use_dylibs -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/hwloc-2.8.0-bze24mn/lib -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/libevent-2.1.12-zi6rfeb/lib -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/pmix-4.1.2-n22o6fb/lib -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/hwloc-2.8.0-bze24mn/lib -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/libevent-2.1.12-zi6rfeb/lib -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/pmix-4.1.2-n22o6fb/lib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/llvm-openmp-14.0.6-4sjknt2/lib/libomp.dylib -o ../../../lib/libfv3jedi.dylib -install_name @rpath/libfv3jedi.dylib CMakeFiles/fv3jedi.dir/ErrorCovariance/ErrorCovariance.cc.o CMakeFiles/fv3jedi.dir/FieldMetadata/FieldsMetadata.cc.o CMakeFiles/fv3jedi.dir/FieldMetadata/FieldsMetadata.interface.cc.o CMakeFiles/fv3jedi.dir/FieldMetadata/fields_metadata_mod.f90.o CMakeFiles/fv3jedi.dir/Fields/fv3jedi_field_mod.f90.o CMakeFiles/fv3jedi.dir/Fields/fv3jedi_fields_mod.f90.o CMakeFiles/fv3jedi.dir/Geometry/Geometry.cc.o CMakeFiles/fv3jedi.dir/Geometry/fv3jedi_geom_interface_mod.F90.o CMakeFiles/fv3jedi.dir/Geometry/fv3jedi_geom_mod.f90.o CMakeFiles/fv3jedi.dir/Geometry/TimeInvariantFieldsHelpers.cc.o CMakeFiles/fv3jedi.dir/GeometryIterator/GeometryIterator.cc.o CMakeFiles/fv3jedi.dir/GeometryIterator/fv3jedi_geom_iter_interface.F90.o CMakeFiles/fv3jedi.dir/GeometryIterator/fv3jedi_geom_iter_mod.F90.o CMakeFiles/fv3jedi.dir/Increment/Increment.cc.o CMakeFiles/fv3jedi.dir/Increment/fv3jedi_increment_interface_mod.F90.o CMakeFiles/fv3jedi.dir/Increment/fv3jedi_increment_mod.F90.o CMakeFiles/fv3jedi.dir/IO/FV3Restart/fv3jedi_io_fms_mod.f90.o CMakeFiles/fv3jedi.dir/IO/FV3Restart/IOFms.cc.o CMakeFiles/fv3jedi.dir/IO/FV3Restart/IOFms.interface.F90.o CMakeFiles/fv3jedi.dir/IO/CubeSphereHistory/fv3jedi_io_cube_sphere_history_mod.f90.o CMakeFiles/fv3jedi.dir/IO/CubeSphereHistory/IOCubeSphereHistory.cc.o CMakeFiles/fv3jedi.dir/IO/CubeSphereHistory/IOCubeSphereHistory.interface.F90.o CMakeFiles/fv3jedi.dir/IO/AuxGrid/fv3jedi_io_auxgrid_mod.f90.o CMakeFiles/fv3jedi.dir/IO/AuxGrid/IOAuxGrid.cc.o CMakeFiles/fv3jedi.dir/IO/AuxGrid/IOAuxGrid.interface.F90.o CMakeFiles/fv3jedi.dir/IO/Utils/fv3jedi_io_utils_mod.f90.o CMakeFiles/fv3jedi.dir/IO/Utils/IOBase.cc.o CMakeFiles/fv3jedi.dir/LinearVariableChange/LinearVariableChange.cc.o CMakeFiles/fv3jedi.dir/LinearVariableChange/Analysis2Model/fv3jedi_linvarcha_a2m.interface.F90.o CMakeFiles/fv3jedi.dir/LinearVariableChange/Analysis2Model/fv3jedi_linvarcha_a2m_mod.f90.o CMakeFiles/fv3jedi.dir/LinearVariableChange/Analysis2Model/LinVarChaA2M.cc.o CMakeFiles/fv3jedi.dir/LinearVariableChange/Base/LinearVariableChangeBase.cc.o CMakeFiles/fv3jedi.dir/LinearVariableChange/Control2Analysis/fv3jedi_linvarcha_c2a.interface.F90.o CMakeFiles/fv3jedi.dir/LinearVariableChange/Control2Analysis/fv3jedi_linvarcha_c2a_mod.f90.o CMakeFiles/fv3jedi.dir/LinearVariableChange/Control2Analysis/LinVarChaC2A.cc.o CMakeFiles/fv3jedi.dir/LinearVariableChange/Model2GeoVaLs/fv3jedi_lvc_model2geovals.interface.F90.o CMakeFiles/fv3jedi.dir/LinearVariableChange/Model2GeoVaLs/fv3jedi_lvc_model2geovals_mod.f90.o CMakeFiles/fv3jedi.dir/LinearVariableChange/Model2GeoVaLs/LinVarChaModel2GeoVaLs.cc.o CMakeFiles/fv3jedi.dir/Model/fv3lm/fv3jedi_fv3lm_interface_mod.F90.o CMakeFiles/fv3jedi.dir/Model/fv3lm/fv3jedi_fv3lm_mod.f90.o CMakeFiles/fv3jedi.dir/Model/fv3lm/ModelFV3LM.cc.o CMakeFiles/fv3jedi.dir/Model/pseudo/ModelPseudo.cc.o CMakeFiles/fv3jedi.dir/State/State.cc.o CMakeFiles/fv3jedi.dir/State/fv3jedi_state_interface_mod.F90.o CMakeFiles/fv3jedi.dir/State/fv3jedi_state_mod.F90.o CMakeFiles/fv3jedi.dir/Utilities/fv3jedi_communication_mod.f90.o CMakeFiles/fv3jedi.dir/Utilities/fv3jedi_constants_mod.f90.o CMakeFiles/fv3jedi.dir/Utilities/fv3jedi_fmsnamelist_mod.f90.o CMakeFiles/fv3jedi.dir/Utilities/fv3jedi_interpolation_mod.f90.o CMakeFiles/fv3jedi.dir/Utilities/fv3jedi_kinds_mod.f90.o CMakeFiles/fv3jedi.dir/Utilities/fv3jedi_netcdf_utils_mod.F90.o CMakeFiles/fv3jedi.dir/Utilities/slow_unstructured_interpolation_mod.F90.o CMakeFiles/fv3jedi.dir/VariableChange/VariableChange.cc.o CMakeFiles/fv3jedi.dir/VariableChange/Analysis2Model/fv3jedi_varcha_a2m.interface.F90.o CMakeFiles/fv3jedi.dir/VariableChange/Analysis2Model/fv3jedi_varcha_a2m_mod.f90.o CMakeFiles/fv3jedi.dir/VariableChange/Analysis2Model/VarChaA2M.cc.o CMakeFiles/fv3jedi.dir/VariableChange/Base/VariableChangeBase.cc.o CMakeFiles/fv3jedi.dir/VariableChange/ColdStartWinds/fv3jedi_vc_coldstartwinds.interface.F90.o CMakeFiles/fv3jedi.dir/VariableChange/ColdStartWinds/fv3jedi_vc_coldstartwinds_mod.f90.o CMakeFiles/fv3jedi.dir/VariableChange/ColdStartWinds/VarChaColdStartWinds.cc.o CMakeFiles/fv3jedi.dir/VariableChange/Control2Analysis/fv3jedi_varcha_c2a.interface.F90.o CMakeFiles/fv3jedi.dir/VariableChange/Control2Analysis/fv3jedi_varcha_c2a_mod.f90.o CMakeFiles/fv3jedi.dir/VariableChange/Control2Analysis/VarChaC2A.cc.o CMakeFiles/fv3jedi.dir/VariableChange/GEOSRstToBkg/fv3jedi_vc_geosrst2bkg.interface.F90.o CMakeFiles/fv3jedi.dir/VariableChange/GEOSRstToBkg/fv3jedi_vc_geosrst2bkg_mod.f90.o CMakeFiles/fv3jedi.dir/VariableChange/GEOSRstToBkg/VarChaGeosRst2Bkg.cc.o CMakeFiles/fv3jedi.dir/VariableChange/Model2GeoVaLs/fv3jedi_vc_model2geovals.interface.F90.o CMakeFiles/fv3jedi.dir/VariableChange/Model2GeoVaLs/fv3jedi_vc_model2geovals_mod.f90.o CMakeFiles/fv3jedi.dir/VariableChange/Model2GeoVaLs/VarChaModel2GeoVaLs.cc.o CMakeFiles/fv3jedi.dir/VariableChange/Utils/fv3jedi_fieldfail_mod.f90.o CMakeFiles/fv3jedi.dir/VariableChange/Utils/height_variables_mod.f90.o CMakeFiles/fv3jedi.dir/VariableChange/Utils/moisture_variables_mod.f90.o CMakeFiles/fv3jedi.dir/VariableChange/Utils/pressure_variables_mod.f90.o CMakeFiles/fv3jedi.dir/VariableChange/Utils/surface_variables_mod.f90.o CMakeFiles/fv3jedi.dir/VariableChange/Utils/temperature_variables_mod.f90.o CMakeFiles/fv3jedi.dir/VariableChange/Utils/wind_variables_mod.f90.o CMakeFiles/fv3jedi.dir/VariableChange/VertRemap/fv3jedi_vc_vertremap.interface.F90.o CMakeFiles/fv3jedi.dir/VariableChange/VertRemap/fv3jedi_vc_vertremap_mod.f90.o CMakeFiles/fv3jedi.dir/VariableChange/VertRemap/VarChaVertRemap.cc.o CMakeFiles/fv3jedi.dir/Tlm/fv3jedi_tlm_mod.f90.o CMakeFiles/fv3jedi.dir/Tlm/fv3jedi_traj_mod.f90.o CMakeFiles/fv3jedi.dir/Tlm/Tlm.cc.o CMakeFiles/fv3jedi.dir/Tlm/Tlm.interface.F90.o CMakeFiles/fv3jedi.dir/Tlm/Traj.interface.F90.o CMakeFiles/fv3jedi.dir/Geometry/fv_prec_r8_mod.f90.o CMakeFiles/fv3jedi.dir/Geometry/fv_init_control_mod.F90.o CMakeFiles/fv3jedi.dir/Model/ufs/fv3jedi_ufs_interface_mod.F90.o CMakeFiles/fv3jedi.dir/Model/ufs/fv3jedi_ufs_mod.F90.o CMakeFiles/fv3jedi.dir/Model/ufs/ModelUFS.cc.o   -L/Users/heinzell/work/ufs-bundle/20230130/build-debug-s2s/Depends/lib  -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/esmf-8.3.0b09-yefmynv/lib  -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/netcdf-c-4.8.1-mozx6cv/lib  -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/netcdf-fortran-4.5.4-gorqimc/lib  -L/usr/local/Cellar/gcc/11.3.0/lib/gcc/11/gcc/x86_64-apple-darwin21/11  -L/usr/local/Cellar/gcc/11.3.0/lib/gcc/11/gcc  -L/usr/local/Cellar/gcc/11.3.0/lib/gcc/11  -Wl,-rpath,@loader_path/../lib -Wl,-rpath,/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/esmf-8.3.0b09-yefmynv/lib -Wl,-rpath,/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/netcdf-c-4.8.1-mozx6cv/lib -Wl,-rpath,/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/netcdf-fortran-4.5.4-gorqimc/lib -Wl,-rpath,/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/ecmwf-atlas-0.31.1-bxoewh4/lib -Wl,-rpath,/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/fckit-0.9.5-kshzgnu/lib -Wl,-rpath,/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/eckit-1.20.2-uyb5g7z/lib -Wl,-rpath,/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/gsibec-1.0.6-spanxse/lib -Wl,-rpath,/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/hdf5-1.12.1-52iyz6f/lib -Wl,-rpath,/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/odc-1.4.5-hb27ngr/lib -Wl,-rpath,/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/crtm-v2.4-jedi.2-bwoeec4/lib -Wl,-rpath,/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/llvm-openmp-14.0.6-4sjknt2/lib ../../../lib/libsaber.dylib ../../../lib/libufo.dylib ../../../lib/libvader.dylib ../../../lib/libfemps.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/ecmwf-atlas-0.31.1-bxoewh4/lib/libatlas_f.0.31.dylib ../../../lib/libfv3jedilm.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/openblas-0.3.19-k4scmn2/lib/libopenblas.dylib -lm -ldl /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/netcdf-c-4.8.1-mozx6cv/lib/libnetcdf.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/netcdf-fortran-4.5.4-gorqimc/lib/libnetcdff.dylib ../../../Depends/lib/libfv3atm.a -lfv3 -lccpp_physics -lfv3ccpp ../../../Depends/lib/libstochastic_physics.a ../../../Depends/lib/libccpp_framework.a -lpioc -lpiof ../../../Depends/lib/libcmeps.a -lcice ../../../Depends/lib/libmom6.a ../../../lib/libgsw.dylib ../../../Depends/lib/libufs.a /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/netcdf-fortran-4.5.4-gorqimc/lib/libnetcdff.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/nemsio-2.5.2-nu6njpz/lib/libnemsio.a /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/w3emc-2.9.2-2v3gen2/lib/libw3emc_d.a 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/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/gsibec-1.0.6-spanxse/lib/libgsibec.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/sp-2.3.3-x6l3hcu/lib/libsp_d.a /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/fckit-0.9.5-kshzgnu/lib/libfckit.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/eckit-1.20.2-uyb5g7z/lib/libeckit.dylib ../../../lib/libioda.dylib ../../../lib/libioda_engines.dylib ../../../lib/liboops.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/openblas-0.3.19-k4scmn2/lib/libopenblas.dylib -lm -ldl /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/netcdf-c-4.8.1-mozx6cv/lib/libnetcdf.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/ecmwf-atlas-0.31.1-bxoewh4/lib/libatlas_f.0.31.dylib 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/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/ecmwf-atlas-0.31.1-bxoewh4/lib/libatlas_io.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/eckit-1.20.2-uyb5g7z/lib/libeckit.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/udunits-2.2.28-4suhooj/lib/libudunits2.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/hdf5-1.12.1-52iyz6f/lib/libhdf5_hl.200.0.1.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/hdf5-1.12.1-52iyz6f/lib/libhdf5.200.1.0.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/odc-1.4.5-hb27ngr/lib/libodccore.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/eckit-1.20.2-uyb5g7z/lib/libeckit_sql.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/fckit-0.9.5-kshzgnu/lib/libfckit.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/eckit-1.20.2-uyb5g7z/lib/libeckit.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/crtm-v2.4-jedi.2-bwoeec4/lib/libcrtm.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/ecmwf-atlas-0.31.1-bxoewh4/lib/libatlas.0.31.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/eckit-1.20.2-uyb5g7z/lib/libeckit_geometry.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/eckit-1.20.2-uyb5g7z/lib/libeckit_linalg.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/eckit-1.20.2-uyb5g7z/lib/libeckit_maths.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/eckit-1.20.2-uyb5g7z/lib/libeckit_option.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/ecmwf-atlas-0.31.1-bxoewh4/lib/libatlas_io.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/llvm-openmp-14.0.6-4sjknt2/lib/libomp.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/fckit-0.9.5-kshzgnu/lib/libfckit.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/eckit-1.20.2-uyb5g7z/lib/libeckit_mpi.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/eckit-1.20.2-uyb5g7z/lib/libeckit.dylib /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/lib/libm.tbd /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/netcdf-fortran-4.5.4-gorqimc/lib/libnetcdff.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/openmpi-4.1.4-7lw72xe/lib/libmpi_usempif08.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/openmpi-4.1.4-7lw72xe/lib/libmpi_usempi_ignore_tkr.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/openmpi-4.1.4-7lw72xe/lib/libmpi_mpifh.dylib /Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/openmpi-4.1.4-7lw72xe/lib/libmpi.dylib /usr/local/Cellar/gcc/11.3.0/lib/gcc/11/libgomp.dylib -Wl,-rpath,/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/esmf-8.3.0b09-yefmynv/lib -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/esmf-8.3.0b09-yefmynv/lib -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/esmf-8.3.0b09-yefmynv/lib -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/netcdf-c-4.8.1-mozx6cv/lib -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-3.0.0/install/apple-clang/13.1.6/netcdf-fortran-4.5.4-gorqimc/lib -lstdc++ -lc++ -lnetcdf -lnetcdff -lnetcdf -lnetcdf -m64 -mcmodel=small -lgfortran -lemutls_w -lgcc -lquadmath -lm -lemutls_w -lgcc
ld: library not found for -lpioc
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [lib/libfv3jedi.dylib] Error 1
make[1]: *** [fv3-jedi/src/fv3jedi/CMakeFiles/fv3jedi.dir/all] Error 2
make: *** [all] Error 2

[shlyaeva]

I haven't looked into updating soca yet, this may be resolved by merging in develop (I think I remember this change in the covariances); I could look into it later this week (most likely Thursday pm)

[climbfuji]

Yes, thanks. I think we need to update all JEDI repos at once, or none. I can look into the PIO linker error, I thought I had seen that before and fixed it.

[climbfuji]

Closed via #20. Thanks very much, @shlyaeva and @cmgas for your help!