Merge branch 'develop' into feature/madis_ops

.github/workflows/unittests.yaml

@@ -15,15 +15,6 @@ jobs:
         pip install netCDF4
         pip install xarray
 
-    - name: Install other dependencies
-      run: |
-        wget https://ftp.emc.ncep.noaa.gov/static_files/public/GDASApp/r2d2-bb361c2.tar.gz
-        wget https://ftp.emc.ncep.noaa.gov/static_files/public/GDASApp/solo-877b414.tar.gz
-        tar -xvf r2d2-bb361c2.tar.gz
-        tar -xvf solo-877b414.tar.gz
-        cd solo && pip install . && cd ..
-        cd r2d2 && pip install . && cd ..
-
     - name: Checkout wxflow
       uses: actions/checkout@v3
       with:

build.sh

@@ -70,7 +70,7 @@ while getopts "p:t:c:hvdfa" opt; do
 done
 
 case ${BUILD_TARGET} in
-  hera | orion)
+  hera | orion | hercules)
     echo "Building GDASApp on $BUILD_TARGET"
     source $dir_root/ush/module-setup.sh
     module use $dir_root/modulefiles

modulefiles/GDAS/hera.lua

@@ -79,7 +79,6 @@ local mpinproc = '-n'
 setenv('MPIEXEC_EXEC', mpiexec)
 setenv('MPIEXEC_NPROC', mpinproc)
 
-setenv('R2D2_CONFIG', '/scratch1/NCEPDEV/stmp4/Cory.R.Martin/R2D2_SHARED/config_hera.yaml')
 setenv("CRTM_FIX","/scratch1/NCEPDEV/da/Cory.R.Martin/GDASApp/fix/crtm/2.4.0")
 setenv("GDASAPP_TESTDATA","/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/data")
 prepend_path("PATH","/scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/intel-18.0.5.274/prod_util/1.2.2/bin")

modulefiles/GDAS/hercules.lua

@@ -0,0 +1,98 @@
+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", '/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core')
+prepend_path("MODULEPATH", '/work2/noaa/da/python/opt/modulefiles/stack')
+
+-- below two lines get us access to the spack-stack modules
+load("stack-intel/2021.9.0")
+load("stack-intel-oneapi-mpi/2021.9.0")
+--load("stack-python/3.10.8")
+-- JCSDA has 'jedi-fv3-env/unified-dev', but we should load these manually as needed
+load("cmake/3.23.1")
+load("curl/8.1.2")
+load("zlib/1.2.13")
+load("git/2.40.0")
+--load("pkg-config/0.27.1")
+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/4.6.0")
+load("nco/5.0.6")
+load("parallelio/2.5.10")
+load("wget/1.21.1")
+load("boost/1.78")
+load("bufr/12.0.1")
+load("git-lfs/3.1.2")
+load("ecbuild/3.7.2")
+load("openjpeg/2.4.0")
+load("eccodes/2.27.0")
+load("eigen/3.4.0")
+load("openblas/0.3.19")
+load("eckit/1.24.4")
+load("fftw/3.3.10")
+load("fckit/0.11.0")
+load("fiat/1.2.0")
+load("ectrans/1.2.0")
+load("atlas/0.35.0")
+load("sp/2.3.3")
+load("gsl-lite/0.37.0")
+load("libjpeg/2.1.0")
+load("krb5/1.20.1")
+load("libtirpc/1.2.6")
+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/3.5.12")
+load("libxaw/1.0.13")
+load("udunits/2.2.28")
+load("ncview/2.1.8")
+load("netcdf-cxx4/4.3.1")
+load("py-pybind11/2.8.1")
+--load("crtm/v2.4_jedi")
+load("contrib/0.1")
+load("noaatools/3.1")
+load("rocoto/1.3.5")
+
+load("hpc/1.2.0")
+unload("python/3.10.8")
+unload("python/3.9.2")
+load("miniconda3/4.6.14")
+load("gdasapp/1.0.0")
+
+load("boost/1.78.0")
+load("bufr/12.0.1")
+load("fckit/0.11.0")
+load("atlas/0.35.0")
+load("py-pybind11/2.8.1")
+
+-- below is a hack because of cmake finding the wrong python...
+setenv("CONDA_PREFIX", "/work2/noaa/da/python/opt/core/miniconda3/4.6.14/envs/gdasapp/")
+
+setenv("CC","mpiicc")
+setenv("FC","mpiifort")
+setenv("CXX","mpiicpc")
+local mpiexec = '/opt/slurm/bin/srun'
+local mpinproc = '-n'
+setenv('MPIEXEC_EXEC', mpiexec)
+setenv('MPIEXEC_NPROC', mpinproc)
+
+setenv('R2D2_CONFIG', '/work2/noaa/da/cmartin/GDASApp/R2D2_SHARED/config_orion.yaml')
+setenv("CRTM_FIX","/work2/noaa/da/cmartin/GDASApp/fix/crtm/2.4.0")
+setenv("GDASAPP_TESTDATA","/work2/noaa/da/cmartin/CI/GDASApp/data")
+prepend_path("PATH","/apps/contrib/NCEP/libs/hpc-stack/intel-2018.4/prod_util/1.2.2/bin")
+
+execute{cmd="ulimit -s unlimited",modeA={"load"}}
+
+whatis("Name: ".. pkgName)
+whatis("Version: ".. pkgVersion)
+whatis("Category: GDASApp")
+whatis("Description: Load all libraries needed for GDASApp")

modulefiles/GDAS/orion.lua

@@ -78,7 +78,6 @@ local mpinproc = '-n'
 setenv('MPIEXEC_EXEC', mpiexec)
 setenv('MPIEXEC_NPROC', mpinproc)
 
-setenv('R2D2_CONFIG', '/work2/noaa/da/cmartin/GDASApp/R2D2_SHARED/config_orion.yaml')
 setenv("CRTM_FIX","/work2/noaa/da/cmartin/GDASApp/fix/crtm/2.4.0")
 setenv("GDASAPP_TESTDATA","/work2/noaa/da/cmartin/CI/GDASApp/data")
 prepend_path("PATH","/apps/contrib/NCEP/libs/hpc-stack/intel-2018.4/prod_util/1.2.2/bin")

parm/land/letkfoi/letkfoi.yaml

@@ -22,6 +22,7 @@ geometry:
 time window:
   begin: '{{ LAND_WINDOW_BEGIN | to_isotime }}'
   length: $(LAND_WINDOW_LENGTH)
+  bound to include: begin
 
 background:
    datetime: '{{ current_cycle | to_isotime }}'

parm/soca/obs/config/adt_all.yaml → parm/soca/obs/config/adt_rads_all.yaml

@@ -1,13 +1,13 @@
 obs space:
-  name: adt_all
+  name: adt_rads_all
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}adt_all.${PDY}${cyc}.nc4
+      obsfile: !ENV ${DATA}/obs/${OPREFIX}adt_rads_all.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/adt_all.${PDY}${cyc}.nc4
+      obsfile: !ENV ${DATA}/diags/adt_rads_all.${PDY}${cyc}.nc4
   simulated variables: [absoluteDynamicTopography]
   io pool:
     max pool size: 1

parm/soca/obs/config/sst_metopb_l3u_so025.yaml → parm/soca/obs/config/sst_metopb_l3u.yaml

@@ -1,13 +1,13 @@
 obs space:
-  name: sst_metopb_l3u_so025
+  name: sst_metopb_l3u
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}sst_metopb_l3u_so025.${PDY}${cyc}.nc4
+      obsfile: !ENV ${DATA}/obs/${OPREFIX}sst_metopb_l3u.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/sst_metopb_l3u_so025.${PDY}${cyc}.nc4
+      obsfile: !ENV ${DATA}/diags/sst_metopb_l3u.${PDY}${cyc}.nc4
   simulated variables: [seaSurfaceTemperature]
   io pool:
     max pool size: 1

parm/soca/obs/obs_list.yaml

@@ -1,22 +1,5 @@
 observers:
-- !INC ${OBS_YAML_DIR}/adt_all.yaml
-- !INC ${OBS_YAML_DIR}/adt_j3_egm2008.yaml
-- !INC ${OBS_YAML_DIR}/adt_3a_egm2008.yaml
-- !INC ${OBS_YAML_DIR}/adt_3b_egm2008.yaml
-- !INC ${OBS_YAML_DIR}/adt_c2_egm2008.yaml
-- !INC ${OBS_YAML_DIR}/adt_sa_egm2008.yaml
-- !INC ${OBS_YAML_DIR}/sst_viirs_npp_l3u_so025.yaml
-#- !INC ${OBS_YAML_DIR}/sst_metopa_l3u_so025.yaml
-#- !INC ${OBS_YAML_DIR}/sst_metopb_l3u_so025.yaml
-#- !INC ${OBS_YAML_DIR}/sst_metopc_l3u_so025.yaml
-- !INC ${OBS_YAML_DIR}/icec_ssmis_f17_north.yaml
-#- !INC ${OBS_YAML_DIR}/icec_ssmis_f17_south.yaml
-#- !INC ${OBS_YAML_DIR}/icec_ssmis_f18_north.yaml
-- !INC ${OBS_YAML_DIR}/icec_ssmis_f18_south.yaml
-#- !INC ${OBS_YAML_DIR}/temp_profile_argo.yaml
-#- !INC ${OBS_YAML_DIR}/temp_profile_bathy.yaml
-#- !INC ${OBS_YAML_DIR}/temp_profile_glider.yaml
-#- !INC ${OBS_YAML_DIR}/temp_profile_tesac.yaml
-#- !INC ${OBS_YAML_DIR}/salt_profile_argo.yaml
-#- !INC ${OBS_YAML_DIR}/salt_profile_glider.yaml
-#- !INC ${OBS_YAML_DIR}/salt_profile_tesac.yaml
+- !INC ${OBS_YAML_DIR}/adt_rads_all.yaml
+- !INC ${OBS_YAML_DIR}/sst_metopb_l3u.yaml
+- !INC ${OBS_YAML_DIR}/icec_amsr2_north.yaml
+- !INC ${OBS_YAML_DIR}/icec_amsr2_south.yaml

parm/soca/obsproc/obsproc_config.yaml

@@ -12,14 +12,30 @@ observations:
     output file: sss_smos.ioda.nc
     obsproc regex: SM_OPER_MIR_OSUDP2_????????T??????_????????T??????_700_001_1.nc
 - obs space:
-    name: adt_3b_egm2008
+    name: adt_rads_all
     obsproc subdir: ADT
-    obsproc regex: rads_adt_3b_???????.nc
+    obsproc regex: rads_adt_??_???????.nc
     provider: RADS
-    output file: adt_all.nc4
+    output file: adt_rads_all.nc4
 - obs space:
     name: icec_amsr2_north
     provider: AMSR2
     obsproc subdir: icec
-    output file: icec_amsr2_north_1.ioda.nc
+    output file: icec_amsr2_north.ioda.nc
     obsproc regex: AMSR2-SEAICE-NH_v2r2_GW1_s???????????????_e???????????????_c???????????????.nc
+- obs space:
+    name: icec_amsr2_south
+    provider: AMSR2
+    obsproc subdir: icec
+    output file: icec_amsr2_south.ioda.nc
+    obsproc regex: AMSR2-SEAICE-SH_v2r2_GW1_s???????????????_e???????????????_c???????????????.nc
+- obs space:
+    name: sst_metopb_l3u
+    provider: GHRSST
+    obsproc subdir: 'sst'
+    output file: sst_metopb_l3u.ioda.nc
+    obsproc regex: '??????????????-STAR-L3U_GHRSST-SSTsubskin-AVHRRF_MB-ACSPO_V2.80-v02.0-fv01.0.nc'
+    bounds:
+      units: C
+      min: -3.0
+      max: 50.0

parm/templates/stage.yaml

@@ -7,13 +7,6 @@ COMOUT: !ENV ${COMOUT}
 DATA: !ENV ${DATA}
 background_time: '{{background_time}}'
 dump: !ENV ${CDUMP}
-r2d2_obs_db: !ENV ${R2D2_OBS_DB}
-r2d2_obs_dump: !ENV ${R2D2_OBS_DUMP}
-r2d2_obs_src: !ENV ${R2D2_OBS_SRC}
-r2d2_bc_src: !ENV ${R2D2_BC_SRC}
-r2d2_bc_dump: !ENV ${R2D2_BC_DUMP}
-r2d2 window length: !ENV ${R2D2_OBS_WINDOW}
-r2d2 window begin: '{{r2d2_window_begin}}'
 fv3jedi_stage_files: !ENV ${FV3JEDI_STAGE_YAML}
 fv3jedi_stage: !ENV ${FV3JEDI_STAGE_YAML}
 stage_dir: !ENV ${DATA}

scripts/exgdas_global_marine_analysis_prep.py

@@ -45,7 +45,7 @@
 
 # import UFSDA utilities
 import ufsda
-from ufsda.stage import obs, soca_fix
+from ufsda.stage import soca_fix
 
 
 def agg_seaice(fname_in, fname_out):
@@ -225,7 +225,7 @@ def find_clim_ens(input_date):
 
 logging.info(f"---------------- Setup runtime environement")
 
-comin_obs = os.getenv('COMIN_OBS')  # R2D2 DB for now
+comin_obs = os.getenv('COMIN_OBS')
 anl_dir = os.getenv('DATA')
 staticsoca_dir = os.getenv('SOCA_INPUT_FIX_DIR')
 if os.getenv('DOHYBVAR') == "YES":
@@ -259,29 +259,14 @@ def find_clim_ens(input_date):
 
 logging.info(f"---------------- Stage observations")
 
-# setup the archive, local and shared R2D2 databases
-ufsda.r2d2.setup(r2d2_config_yaml=os.path.join(anl_dir, 'r2d2_config.yaml'), shared_root=comin_obs)
-
 # create config dict from runtime env
 envconfig = {'window_begin': f"{window_begin.strftime('%Y-%m-%dT%H:%M:%SZ')}",
-             'r2d2_obs_src': os.getenv('R2D2_OBS_SRC'),
-             'r2d2_obs_dump': os.getenv('R2D2_OBS_DUMP'),
-             'r2d2_obs_db': os.getenv('R2D2_OBS_DB'),
              'ATM_WINDOW_BEGIN': window_begin_iso,
              'ATM_WINDOW_MIDDLE': window_middle_iso,
              'ATM_WINDOW_LENGTH': f"PT{os.getenv('assim_freq')}H"}
 stage_cfg = YAMLFile(path=os.path.join(gdas_home, 'parm', 'templates', 'stage.yaml'))
 stage_cfg = Template.substitute_structure(stage_cfg, TemplateConstants.DOUBLE_CURLY_BRACES, envconfig.get)
 stage_cfg = Template.substitute_structure(stage_cfg, TemplateConstants.DOLLAR_PARENTHESES, envconfig.get)
-stage_cfg['r2d2_obs_out'] = os.getenv('COM_OBS')
-
-# stage observations from R2D2 COMIN_OBS to COM_OBS
-ufsda.stage.obs(stage_cfg)
-
-# concatenate altimeters into one obs space
-# TODO (SAMG)temporary, move this into the obs procecing eventually
-adt_obs = f"{os.getenv('COM_OBS')}/{RUN}.t{cyc}z.adt"
-ufsda.soca_utils.concatenate_ioda(adt_obs, wildcard="*.nc4", output_suffix=f"_all.{PDY}{cyc}.nc4", clean=True)
 
 # get the list of observations
 obs_files = []
@@ -294,6 +279,7 @@ def find_clim_ens(input_date):
     logging.info(f"******* {obs_file}")
     obs_src = os.path.join(os.getenv('COM_OBS'), obs_file)
     obs_dst = os.path.join(os.path.abspath(obs_in), obs_file)
+    logging.info(f"******* {obs_src}")
     if os.path.exists(obs_src):
         logging.info(f"******* fetching {obs_file}")
         obs_list.append([obs_src, obs_dst])

scripts/exglobal_prep_ocean_obs.py

@@ -85,4 +85,7 @@
     print("CRITICAL: Ill-formed OBS_YAML file, exiting")
     raise
 
+if not os.path.exists(COMOUT_OBS):
+    os.makedirs(COMOUT_OBS)
+
 FileHandler({'copy': filesToSave}).sync()