Merge branch 'feature/rename_atm' of https://github.com/NOAA-EMC/GDASApp

 into feature/rename_atm

* 'feature/rename_atm' of https://github.com/NOAA-EMC/GDASApp:
  Update wcoss2.intel.lua (#1142)
  Add yaml file for prepobsaero task (#1141)
  Diffusion parameter yaml template (#1140)
  Adjust absolute float tolerance for variational and ensemble DA jjob tests (#1136)
  Insitu temp and salt (#1135)
  Adds letkf.yaml(.j2)  (#1134)
  Add optional testing block to 3dvar and lgetkf input YAMLs for jjobs (#1129)
  updates to build and run some ctests on WCOSS2 (#1122)
  Addin a GFSv17 ctest (#1130)
  Feature/rtofs in situ (#1110)
  update jcb-gdas hash to bring in satwnd yaml changes (#1128)
  Optionally run specified rocoto task as part of the ctests  (#1121)
  Add build capability to Gaea-C5 (#1101)
  Python Converter and Json for the ADPUPA BUFR DUMP (#1115)
  Revert "Fix ice water FV3 increment variable name and add a few more … (#1125)
  Satwnd and variable name-convention updates for jcb implementation in GDASApp (#1119)
  Add inverse distance weighting option to superob function (#1116)
  Resume the Marine Vrfy Task on ctests (#1107)
  Replicate the creation of the gw-ci cycling test (#1114)
  Added YAML, JSON, python files for assimilating LEOGEO satwinds (#1099)
  Add an OOPS-based application to recenter snow analysis (#1102)
  Fix ice water FV3 increment variable name and add a few more (#1112)

build.sh

@@ -71,7 +71,7 @@ while getopts "p:t:c:hvdfa" opt; do
 done
 
 case ${BUILD_TARGET} in
- hera | orion | hercules | wcoss2 | noaacloud)
+ hera | orion | hercules | wcoss2 | noaacloud | gaea)
  echo "Building GDASApp on $BUILD_TARGET"
  source $dir_root/ush/module-setup.sh
  module use $dir_root/modulefiles

ci/run_ci.sh

@@ -61,7 +61,7 @@ module use $GDAS_MODULE_USE
 module load GDAS/$TARGET
 echo "---------------------------------------------------" >> $outfile
 rm -rf log.ctest
-ctest -R gdasapp --output-on-failure &>> log.ctest
+ctest -E "manual" -R gdasapp --output-on-failure &>> log.ctest
 ctest_status=$?
 npassed=$(cat log.ctest | grep "tests passed")
 if [ $ctest_status -eq 0 ]; then

modulefiles/EVA/wcoss2.lua

@@ -0,0 +1,25 @@
+help([[
+Load environment for running EVA.
+]])
+
+local pkgName = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+conflict(pkgName)
+
+load("PrgEnv-intel/8.2.0")
+load("craype")
+load("cray-pals")
+load("git/2.29.0")
+load("intel/19.1.3.304")
+load("python/3.10.4")
+load("ve/evs/1.0")
+
+append_path("PATH", "/lfs/h2/emc/da/noscrub/emc.da/eva/opt/bin")
+append_path("PYTHONPATH", "/lfs/h2/emc/da/noscrub/emc.da/eva/opt/")
+
+whatis("Name: ".. pkgName)
+whatis("Version: ".. pkgVersion)
+whatis("Category: EVA")
+whatis("Description: Load all libraries needed for EVA")

modulefiles/GDAS/gaea.intel.lua

@@ -0,0 +1,96 @@
+help([[
+Load environment for running the GDAS application with Intel compilers and MPI.
+]])
+
+local pkgName = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+prepend_path("MODULEPATH", '/ncrc/proj/epic/spack-stack/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core')
+prepend_path("MODULEPATH", '/ncrc/proj/epic/rocoto/modulefiles')
+
+-- below two lines get us access to the spack-stack modules
+load("stack-intel/2023.1.0")
+load("stack-cray-mpich/8.1.25")
+-- JCSDA has 'jedi-fv3-env/unified-dev', but we should load these manually as needed
+load("cmake/3.23.1")
+load("gettext/0.20.2")
+--load("libunistring/1.1")
+--load("libidn2/2.3.4")
+load("pcre2/10.42")
+load("curl/8.4.0")
+load("zlib/1.2.13")
+load("git/2.35.2")
+load("pkg-config/0.29.2")
+load("hdf5/1.14.0")
+load("parallel-netcdf/1.12.2")
+load("netcdf-c/4.9.2")
+load("nccmp/1.9.0.1")
+load("netcdf-fortran/4.6.1")
+load("nco/5.0.6")
+load("parallelio/2.5.10")
+load("wget/1.21.3")
+load("boost/1.83.0")
+load("bufr/12.0.1")
+load("git-lfs/2.11.0")
+load("ecbuild/3.7.2")
+load("openjpeg/2.3.1")
+load("eccodes/2.32.0")
+load("eigen/3.4.0")
+load("openblas/0.3.24")
+load("eckit/1.24.5")
+load("fftw/3.3.10")
+load("fckit/0.11.0")
+load("fiat/1.2.0")
+load("ectrans/1.2.0")
+load("atlas/0.35.1")
+load("sp/2.5.0")
+load("gsl-lite/0.37.0")
+load("libjpeg/2.1.0")
+load("krb5/1.16.3")
+load("libtirpc/1.3.3")
+load("hdf/4.2.15")
+load("jedi-cmake/1.4.0")
+load("libpng/1.6.37")
+--load("libxt/1.1.5")
+--load("libxmu/1.1.4")
+--load("libxpm/4.11.0")
+load("libxaw/1.10.13")
+load("udunits/2.2.28")
+load("ncview/2.1.9")
+load("netcdf-cxx4/4.3.1")
+load("json/3.10.5")
+load("crtm/2.4.0.1")
+load("rocoto/1.3.6")
+load("prod_util/2.1.1")
+
+load("py-jinja2/3.0.3")
+load("py-netcdf4/1.5.8")
+load("py-pybind11/2.11.0")
+load("py-pycodestyle/2.11.0")
+load("py-pyyaml/6.0")
+load("py-scipy/1.11.3")
+load("py-xarray/2023.7.0")
+load("py-f90nml/1.4.3")
+load("py-pip/23.1.2")
+
+-- hack for wxflow
+--prepend_path("PYTHONPATH", "/scratch1/NCEPDEV/da/python/gdasapp/wxflow/20240307/src")
+
+setenv("CC","cc")
+setenv("CXX","CC")
+setenv("FC","ftn")
+
+local mpiexec = '/usr/bin/srun'
+local mpinproc = '-n'
+setenv('MPIEXEC_EXEC', mpiexec)
+setenv('MPIEXEC_NPROC', mpinproc)
+
+setenv("CRTM_FIX","/gpfs/f5/ufs-ard/world-shared/GDASApp/fix/crtm/2.4.0")
+setenv("GDASAPP_TESTDATA","/gpfs/f5/ufs-ard/world-shared/GDASApp/CI/data")
+setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/gpfs/f5/ufs-ard/world-shared/GDASApp/CI/data/test")
+
+whatis("Name: ".. "pkgName")
+whatis("Version: ".. "pkgVersion")
+whatis("Category: GDASApp")
+whatis("Description: Load all libraries needed for GDASApp")

modulefiles/GDAS/wcoss2.intel.lua

@@ -29,12 +29,16 @@ load("eckit/1.24.4")
 load("fckit/0.11.0")
 load("atlas/0.35.0")
 load("nccmp")
+load("nco/5.0.6")
+load("gsl/2.7")
+load("prod_util/2.0.14")
+load("bufr/12.0.1")
 
 -- hack for pybind11
 setenv("pybind11_ROOT", "/apps/spack/python/3.8.6/intel/19.1.3.304/pjn2nzkjvqgmjw4hmyz43v5x4jbxjzpk/lib/python3.8/site-packages/pybind11/share/cmake/pybind11")
 
--- hack for wxflow
---prepend_path("PYTHONPATH", "/scratch1/NCEPDEV/da/python/gdasapp/wxflow/20240307/src")
+-- hack for git-lfs
+prepend_path("PATH", "/apps/spack/git-lfs/2.11.0/gcc/11.2.0/m6b6nl5kfqngfteqbggydc7kflxere3s/bin")
 
 local mpiexec = '/pe/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin/mpirun'
 local mpinproc = '-n'

parm/aero/berror/aero_diffparm.yaml.j2

@@ -0,0 +1,47 @@
+geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ npx: {{ npx_ges }}
+ npy: {{ npy_ges }}
+ npz: {{ npz_ges }}
+ field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
+date: '{{ current_cycle | to_isotime }}' 
+background:
+ datetime: '{{ current_cycle | to_isotime }}' 
+ filetype: fms restart
+ datapath: ./bkg
+ filename_core: '{{ current_cycle | to_fv3time }}.fv_core.res.nc'
+ filename_trcr: '{{ current_cycle | to_fv3time }}.fv_tracer.res.nc'
+ filename_cplr: '{{ current_cycle | to_fv3time }}.coupler.res'
+ state variables: [mass_fraction_of_sulfate_in_air,
+ mass_fraction_of_hydrophobic_black_carbon_in_air,
+ mass_fraction_of_hydrophilic_black_carbon_in_air,
+ mass_fraction_of_hydrophobic_organic_carbon_in_air,
+ mass_fraction_of_hydrophilic_organic_carbon_in_air,
+ mass_fraction_of_dust001_in_air, mass_fraction_of_dust002_in_air,
+ mass_fraction_of_dust003_in_air, mass_fraction_of_dust004_in_air,
+ mass_fraction_of_dust005_in_air, mass_fraction_of_sea_salt001_in_air,
+ mass_fraction_of_sea_salt002_in_air, mass_fraction_of_sea_salt003_in_air,
+ mass_fraction_of_sea_salt004_in_air]
+
+background error:
+ covariance model: SABER
+ saber central block: 
+ saber block name: diffusion
+ calibration:
+ normalization:
+ iterations: {{ diff_iter }} 
+ groups:
+ - horizontal:
+ fixed value: {{ horiz_len }} 
+ write:
+ filepath: ./diffusion_hz
+ - vertical:
+ levels: {{ npz_ges }} 
+ fixed value: {{ fixed_val }} 
+ as gaussian: true
+ write:
+ filepath: ./diffusion_vt
+

parm/aero/prep/prep_viirs.yaml.j2

@@ -0,0 +1,14 @@
+provider: VIIRSAOD
+window begin: {{ window_begin | to_isotime }}
+window end: {{ window_end | to_isotime }}
+binning:
+ cressman radius: 100
+ stride: 132
+ min number of obs: 500
+variable: aerosolOpticalDepth
+output file: {{ DATA }}/{{ OPREFIX }}viirs_{{sensor}}.{{ current_cycle | to_YMDH }}.nc4
+input files: {{ input_files }}
+thinning:
+ threshold: 0
+channel: 4
+preqc: 0

parm/ioda/bufr2ioda/bufr2ioda_adpupa.json

@@ -0,0 +1,12 @@
+{
+ "data_format": "bufr_d",
+ "data_type": "adpupa",
+ "cycle_type": "{{ RUN }}",
+ "cycle_datetime" : "{{ current_cycle | to_YMDH }}",
+ "dump_directory": "{{ DMPDIR }}",
+ "ioda_directory": "{{ COM_OBS }}",
+ "subsets": [ "NC002001, NC002002, NC002003, NC002004, NC002005" ],
+ "source": "NCEP data tank",
+ "data_provider": "U.S. NOAA",
+ "data_description": "UPPER-AIR (RAOB, PIBAL, RECCO, DROPS) REPORTS",
+}

parm/ioda/bufr2ioda/bufr2ioda_insitu_profile_marinemammals.json

@@ -2,7 +2,7 @@
  "data_format" : "tesac",
  "subsets" : "TESAC",
  "source" : "NCEP data tank",
- "data_type" : "marinemammals",
+ "data_type" : "marinemammal",
  "cycle_type" : "{{ RUN }}",
  "cycle_datetime" : "{{ current_cycle | to_YMDH }}",
  "dump_directory" : "{{ DMPDIR }}",

parm/ioda/bufr2ioda/bufr2ioda_satwnd_amv_leogeo.json

@@ -0,0 +1,15 @@
+{
+ "data_format" : "bufr_d",
+ "data_type" : "satwnd",
+ "cycle_type" : "{{ RUN }}",
+ "cycle_datetime" : "{{ current_cycle | to_YMDH }}",
+ "dump_directory" : "{{ DMPDIR }}",
+ "ioda_directory" : "{{ COM_OBS }}",
+ "subsets" : [ "NC005072" ],
+ "data_description" : "NC005072 LEOGEO SATWIND IR(LW)", 
+ "data_provider" : "U.S. NOAA/NESDIS",
+ "sensor_info" : { "sensor_name": "LEOGEO", "sensor_full_name": "Combined Platform LEO/GEO", "sensor_id": 999 },
+ "satellite_info" : [
+ { "satellite_name": "multi", "satellite_full_name": "MULTIPLE-SATS", "satellite_id": 854, "launch time": "YYYYMMDD" },
+ ]
+}

parm/soca/letkf/letkf.yaml.j2

@@ -0,0 +1,69 @@
+geometry:
+ geom_grid_file: soca_gridspec.nc
+ mom6_input_nml: mom_input.nml
+ fields metadata: fields_metadata.yaml
+
+time window:
+ begin: &date '{{ ATM_WINDOW_BEGIN }}'
+ length: PT6H 
+
+background:
+ members from template:
+ template:
+ date: '{{ ATM_WINDOW_MIDDLE }}'
+ ocn_filename: enkfgdas.ocean.t06z.inst.f009.nc
+ ice_filename: enkfgdas.ice.t06z.inst.f009.nc
+ read_from_file: 1
+ basename: ./ens/mem%mem%
+ state variables: [socn, tocn, ssh, uocn, vocn, cicen]
+ pattern: '%mem%'
+ nmembers: {{ NMEM_ENS }}
+
+observations:
+ observers:
+
+driver:
+ do posterior observer: true
+ save posterior mean increment: true
+ save posterior mean: true
+ save posterior variance: true
+ save prior mean: true
+ save prior variance: true
+
+local ensemble DA:
+ solver: LETKF
+ inflation:
+ rtps: 0.5
+ rtpp: 0.6
+ mult: 1.1
+
+output:
+ datadir: data_output/
+ date: *date
+ exp: letkf
+ type: ens
+
+output mean prior:
+ datadir: data_output/
+ date: *date
+ exp: letkf
+ type: fc
+
+output variance prior:
+ datadir: data_output/
+ date: *date
+ exp: letkf
+ type: fc
+
+output variance posterior:
+ datadir: data_output/
+ date: *date
+ exp: letkf
+ type: an
+
+output increment:
+ datadir: data_output/
+ date: *date
+ exp: letkf.inc
+ type: an
+