Orion's gsi-addon-env environment missing module files

[DavidHuber-NOAA]

Describe the bug
The official installation of spack-stack/1.6.0 on Orion is missing several modules that should be inherited from the unified-env environment.

To Reproduce
Steps to reproduce the behavior:

> module use /work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.6.0/envs/gsi-addon-env/install/modulefiles/Core
> module load stack-intel
> module load stack-intel-oneapi-mpi
> module avail
/work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.6.0/envs/gsi-addon-env/install/modulefiles/intel-oneapi-mpi/2021.5.1/intel/2022.0.2
   base-env/1.0.0               gsi-env/1.0.0                 met/9.1.3        py-netcdf4/1.5.8    ufs-weather-model-env/1.0.0
   global-workflow-env/1.0.0    mapl/2.40.3-esmf-8.6.0 (D)    metplus/3.1.1    ufs-pyenv/1.0.0

-------------------------------------------- /apps/modulefiles/mpi/intel-2022.1.2/impi-2022.1.2 ---------------------------------------------
   crtm/2.4.0    esmf/8.3.0 (D)    fms/2022.04        netcdf/4.7.4 (D)    pflogger/1.5.0    pnetcdf/1.12.1        (D)    su2/7.1.1
   esmf/8.1.1    fftw/3.3.8 (D)    hdf5/1.10.6 (D)    nwchem/7.0.0 (D)    pio/2.5.7         quantumespresso/6.6.0

------------ /work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.6.0/envs/gsi-addon-env/install/modulefiles/intel/2022.0.2 ------------
   bufr/11.7.0            py-numexpr/2.8.4            py-pyyaml/6.0                 py-xlrd/2.0.1
   py-bottleneck/1.3.7    py-numpy/1.23.4             py-setuptools-scm/7.1.0       py-xlsxwriter/3.1.7
   py-cftime/1.0.3.4      py-openpyxl/3.1.2           py-setuptools/63.4.3          py-xlwt/1.3.0
   py-cython/0.29.36      py-packaging/23.1           py-six/1.16.0                 python/3.11.6                   (D)
   py-et-xmlfile/1.0.1    py-pandas/1.5.3             py-tomli/2.0.1                stack-intel-oneapi-mpi/2021.5.1 (L)
   py-f90nml/1.4.3        py-pip/23.1.2               py-typing-extensions/4.8.0    stack-python/3.11.6
   py-flit-core/3.9.0     py-python-dateutil/2.8.2    py-versioneer/0.29
   py-jinja2/3.1.2        py-pytz/2023.3              py-wheel/0.41.2
   py-markupsafe/2.1.3    py-pyxlsb/1.0.10            py-xarray/2023.7.0

------------------------------------------------ /apps/modulefiles/compilers/intel-2022.1.2 -------------------------------------------------
   bacio/2.4.1           g2/3.4.5             impi/2022.1.2 (L)    mpich/3.3.2  (D)    openmpi/4.0.4 (D)    yafyaml/0.5.1
   cdo/1.9.10     (D)    g2tmpl/1.10.2        ip/3.3.3             nccmp/1.8.7  (D)    sp/2.3.3
   eccodes/2.22.1        gftl-shared/1.5.0    jasper/2.0.25 (D)    nco/4.9.3    (D)    w3emc/2.9.2
   flap/1.10.0           hdf5/1.10.6          libpng/1.6.37        netcdf/4.7.4        wgrib2/3.0.2  (D)

----------------- /work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.6.0/envs/gsi-addon-env/install/modulefiles/Core -----------------
   stack-gcc/10.2.0    stack-intel/2022.0.2 (L)

Compare this list against Hera:

---------------------------------------------- /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev/install/modulefiles/intel-oneapi-mpi/2021.5.1/intel/2021.5.0 -----------------------------------------------
   base-env/1.0.0        crtm/2.4.0.1    fms/2023.04                  gsi-ncdiag/1.1.2          met/9.1.3            ncio/1.1.2          nemsiogfs/2.5.3      netcdf-fortran/4.6.1      py-netcdf4/1.5.8    ufs-weather-model-env/1.0.0
   cdo/2.2.0      (D)    esmf/8.6.0      global-workflow-env/1.0.0    hdf5/1.14.0               metplus/3.1.1        nco/5.0.6    (D)    netcdf-c/4.9.2       parallel-netcdf/1.12.2    scotch/7.0.4        wrf-io/1.2.0
   cprnc/1.0.3           fftw/3.3.10     gsi-env/1.0.0                mapl/2.40.3-esmf-8.6.0    nccmp/1.9.0.1 (D)    nemsio/2.5.4        netcdf-cxx4/4.3.1    parallelio/2.5.10         ufs-pyenv/1.0.0

-------------------------------------------------------------------------------------------------- /apps/modules/modulefamilies/intel_impi --------------------------------------------------------------------------------------------------
   hdf5parallel/1.10.5    hdf5parallel/1.10.6 (D)    itac/latest    itac/2019 (D)    netcdf-hdf5parallel/4.7.0    netcdf-hdf5parallel/4.7.4 (D)    pnetcdf/1.7.0    pnetcdf/1.10.0    pnetcdf/1.11.2 (D)    tau/2.29

----------------------------------------------------------- /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev/install/modulefiles/intel/2021.5.0 ------------------------------------------------------------
   antlr/2.7.7                               g2/3.4.5             ip/4.3.0             openjpeg/2.3.1         py-markupsafe/2.1.3         py-setuptools-scm/7.1.0       python/3.11.6                          w3nco/2.4.1
   bacio/2.4.1                               g2c/1.6.4            jasper/2.0.32        pkg-config/0.27.1      py-numexpr/2.8.4            py-setuptools/63.4.3          sfcio/1.4.1                            wget/1.14
   bufr/11.7.0                               g2tmpl/1.10.2        landsfcutil/2.4.1    prod_util/2.1.1        py-numpy/1.23.4             py-six/1.16.0                 sigio/2.3.2                            wgrib2/2.0.8 (D)
   c-blosc/1.21.5                            gettext/0.19.8.1     libbsd/0.11.7        proj/9.2.1             py-openpyxl/3.1.2           py-tomli/2.0.1                snappy/1.1.10                          zlib/1.2.13
   ca-certificates-mozilla/2023-05-30        gftl-shared/1.6.1    libjpeg/2.1.0        py-bottleneck/1.3.7    py-packaging/23.1           py-typing-extensions/4.8.0    sp/2.5.0                               zstd/1.5.2
   cmake/3.23.1                              gftl/1.10.0          libmd/1.0.4          py-cftime/1.0.3.4      py-pandas/1.5.3             py-versioneer/0.29            sqlite/3.43.2
   crtm-fix/2.4.0.1_emc                      git-lfs/2.10.0       libpng/1.6.37        py-cython/0.29.36      py-pip/23.1.2               py-wheel/0.41.2               stack-intel-oneapi-mpi/2021.5.1 (L)
   curl/8.4.0                                git/2.18.0           libxcrypt/4.4.35     py-et-xmlfile/1.0.1    py-python-dateutil/2.8.2    py-xarray/2023.7.0            stack-python/3.11.6
   ecbuild/3.7.2                             gmake/3.82           libyaml/0.2.5        py-f90nml/1.4.3        py-pytz/2023.3              py-xlrd/2.0.1                 udunits/2.2.28                  (D)
   eccodes/2.32.0                     (D)    grib-util/1.3.0      nghttp2/1.57.0       py-flit-core/3.9.0     py-pyxlsb/1.0.10            py-xlsxwriter/3.1.7           util-linux-uuid/2.38.1
   fargparse/1.5.0                           gsl/2.7.1            openblas/0.3.24      py-jinja2/3.1.2        py-pyyaml/6.0               py-xlwt/1.3.0                 w3emc/2.10.0

Expected behavior
The available modules would be identical across systems.

System:
Orion

[climbfuji]

I wonder if the spack module lmod refresh command was run without --upstream-modules.

[ulmononian]

@RatkoVasic-NOAA can you please take a look at this?

[RatkoVasic-NOAA]

@DavidHuber-NOAA I just applied @climbfuji 's command addition. It looks like it is fixed. Can you please confirm? Orion is back online now.

[DavidHuber-NOAA]

It's working for me. Thank you @RatkoVasic-NOAA!!