Merge branch 'develop' into feature/calcanl-new

ci/run_ci.sh

@@ -91,6 +91,18 @@ if [[ $TEST_WORKFLOW == 1 ]]; then
 fi
 # ==============================================================================
 # run ctests
+
+# PATCH START
+# MSU role-da can not use /work/noaa/stmp at present. The logic below
+# modifies the stmp path used by g-w so that role-da can run g-w based
+# ctests. This logic will be removed after MSU role-da is added to the
+# stmp group.
+if [[ "${TARGET}" = "orion" || "${TARGET}" = "hercules" ]]; then
+    echo "***WARNING*** apply MSU stmp patch to $workflow_dir/workflow/hosts/${TARGET}.yaml"
+    sed -i "s|/noaa/stmp|/noaa/da|g" $workflow_dir/workflow/hosts/${TARGET}.yaml
+fi
+# PATCH END
+
 cd $gdasapp_dir/build
 module use $gdasapp_dir/modulefiles
 module load GDAS/$TARGET

ci/stable_driver.sh

@@ -73,7 +73,7 @@ $gdasdir/ush/submodules/update_develop.sh $gdasdir
 
 # ==============================================================================
 # email information
-PEOPLE="[email protected] Russ.Treadon@noaa.gov [email protected] David.New@noaa.gov"
+PEOPLE="[email protected] David.New@noaa.gov Russ.Treadon@noaa.gov"
 BODY=$stableroot/$datestr/stable_nightly  
 
 # ==============================================================================
@@ -84,41 +84,36 @@ total=0
 if [ $ci_status -eq 0 ]; then
   cd $gdasdir
   # checkout feature/stable-nightly
-  git stash
-  total=$(($total+$?))
-  if [ $total -ne 0 ]; then
-    echo "Unable to git stash" >> $stableroot/$datestr/output
-  fi
   git checkout feature/stable-nightly
-  total=$(($total+$?))
-  if [ $total -ne 0 ]; then
+  rc=$?
+  total=$(($total+$rc))
+  if [ $rc -ne 0 ]; then
     echo "Unable to checkout feature/stable-nightly" >> $stableroot/$datestr/output
   fi
   # merge in develop
   git merge develop
-  total=$(($total+$?))
-  if [ $total -ne 0 ]; then
+  rc=$?
+  total=$(($total+$rc))
+  if [ $rc -ne 0 ]; then
     echo "Unable to merge develop" >> $stableroot/$datestr/output
   fi
   # add in submodules
-  git stash pop
-  total=$(($total+$?))
-  if [ $total -ne 0 ]; then
-    echo "Unable to git stash pop" >> $stableroot/$datestr/output
-  fi
-  $my_dir/../ush/submodules/add_submodules.sh $gdasdir
-  total=$(($total+$?))
-  if [ $total -ne 0 ]; then
+  $gdasdir/ush/submodules/add_submodules.sh $gdasdir
+  rc=$?
+  total=$(($total+$rc))
+  if [ $rc -ne 0 ]; then
     echo "Unable to add updated submodules to commit" >> $stableroot/$datestr/output
   fi
   git diff-index --quiet HEAD || git commit -m "Update to new stable build on $datestr"
-  total=$(($total+$?))
-  if [ $total -ne 0 ]; then
+  rc=$?
+  total=$(($total+$rc))
+  if [ $rc -ne 0 ]; then
     echo "Unable to commit" >> $stableroot/$datestr/output
   fi
   git push --set-upstream origin feature/stable-nightly
-  total=$(($total+$?))
-  if [ $total -ne 0 ]; then
+  rc=$?
+  total=$(($total+$rc))
+  if [ $rc -ne 0 ]; then
     echo "Unable to push" >> $stableroot/$datestr/output
   fi
   if [ $total -ne 0 ]; then
@@ -152,4 +147,4 @@ mail -r "Darth Vader - NOAA Affiliate <[email protected]>" -s "$SUBJECT" "$PE
 
 # ==============================================================================
 # scrub working directory for older files
-find $stableroot/* -maxdepth 1 -mtime +3 -exec rm -rf {} \;
+find $stableroot/* -maxdepth 1 -mtime +1 -exec rm -rf {} \;

modulefiles/GDAS/wcoss2.intel.lua

@@ -3,49 +3,86 @@ Load environment for running the GDAS application with Intel compilers and MPI.
 ]])
 
 local pkgName    = myModuleName()
-local pkgVersion = myModuleVersion()
+local pkgVersion = myModuleVersion() or "1.0"
 local pkgNameVer = myModuleFullName()
 
-prepend_path("MODULEPATH", "/apps/dev/lmodules/core")
-
-load("PrgEnv-intel/8.2.0")
-load("cmake/3.20.2")
-load("craype")
-load("cray-pals")
-load("git/2.29.0")
-load("intel/19.1.3.304")
-load("cray-mpich/8.1.12")
-load("hdf5/1.12.2")
-load("netcdf/4.7.4")
-load("udunits/2.2.28")
+prepend_path("MODULEPATH", "/apps/ops/test/spack-stack-1.6.0-nco/envs/nco-intel-19.1.3.304/install/modulefiles/Core")
+
+load("PrgEnv-intel/8.3.3")
+load("stack-intel/19.1.3.304")
+load("stack-cray-mpich/8.1.9")
+load("stack-python/3.10.13")
+load("craype/2.7.17")
+load("cray-pals/1.3.2")
+load("cmake/3.23.1")
+load("gettext/0.19.7")
+load("pcre2/10.42")
+load("curl/8.4.0")
+load("zlib/1.2.13")
+load("git/2.35.3")
+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("boost/1.83.0")
+load("bufr/12.0.1")
+load("ecbuild/3.7.2")
+load("openjpeg/2.5.0")
 load("eigen/3.4.0")
-load("boost/1.79.0")
-load("gsl-lite/v0.40.0")
-load("sp/2.4.0")
-load("python/3.8.6")
-load("ecbuild/3.7.0")
-load("qhull/2020.2")
-load("eckit/1.24.4")
+load("openblas/0.3.24")
+load("eckit/1.24.5")
+load("fftw/3.3.10")
 load("fckit/0.11.0")
+load("fms/2023.04")
+load("esmf/8.5.0")
 load("atlas/0.35.0")
-load("nccmp")
-load("nco/5.0.6")
-load("gsl/2.7")
+load("sp/2.5.0")
+load("gsl-lite/0.37.0")
+load("libjpeg/2.1.0")
+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/2.1.9")
+load("netcdf-cxx4/4.3.1")
+load("core/rocoto/1.3.5")
 load("prod_util/2.0.14")
-load("bufr/12.0.1")
-load("fms-C/2023.04")
-load("esmf-C/8.6.0")
 
--- 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")
+load("py-setuptools/63.4.3")
+load("py-jinja2/3.1.2")
+load("py-netcdf4/1.5.8")
+load("py-pybind11/2.11.1")
+load("py-pycodestyle/2.11.0")
+load("py-pyyaml/5.4.1")
+load("py-scipy/1.10.1")
+load("py-xarray/2023.7.0")
+load("py-f90nml/1.4.3")
+load("py-pip/23.1.2")
+load("py-bottleneck/1.3.7")
+load("py-numexpr/2.8.4")
+load("py-six/1.16.0")
+load("py-python-dateutil/2.8.2")
+load("py-pytz/2023.3")
+load("py-pandas/1.5.3")
+load("py-numpy/1.24.4")
+load("py-markupsafe/2.1.3")
+load("py-cftime/1.0.3.4")
+load("py-packaging/23.1")
 
 -- hack for git-lfs
 prepend_path("PATH", "/apps/spack/git-lfs/2.11.0/gcc/11.2.0/m6b6nl5kfqngfteqbggydc7kflxere3s/bin")
 
--- hack for FMS
-setenv('fms_ROOT', '/apps/prod/hpc-stack/i-19.1.3.304__m-8.1.12__h-1.14.0__n-4.9.2__p-2.5.10__e-8.6.0pnetcdf/intel-19.1.3.304/cray-mpich-8.1.12/fms/2023.04')
+setenv("CC","cc")
+setenv("CXX","CC")
+setenv("FC","ftn")
 
-local mpiexec = '/pe/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin/mpirun'
+local mpiexec = '/opt/cray/pals/1.3.2/bin/mpirun'
 local mpinproc = '-n'
 setenv('MPIEXEC_EXEC', mpiexec)
 setenv('MPIEXEC_NPROC', mpinproc)

parm/aero/jcb-base.yaml.j2

@@ -128,12 +128,6 @@ aero_obsbiascovout_prefix: "{{APREFIX}}"
 aero_obsbiascovout_suffix: ".satbias_cov.nc"
 
 bias_files:
-  atms_n20: rad_varbc_params.tar
-  atms_npp: rad_varbc_params.tar
-  mtiasi_metop-a: rad_varbc_params.tar
-  mtiasi_metop-b: rad_varbc_params.tar
-  amsua_n19: rad_varbc_params.tar
-  ssmis_f17: rad_varbc_params.tar
-  ssmis_f18: rad_varbc_params.tar
-  cris-fsr_n20: rad_varbc_params.tar
-  cris-fsr_npp: rad_varbc_params.tar
+  viirs_npp_aod: aero_varbc_params.tar
+  viirs_n20_aod: aero_varbc_params.tar
+  viirs_n21_aod: aero_varbc_params.tar

parm/soca/obsprep/obsprep_config.yaml

@@ -244,6 +244,9 @@ observations:
     provider: GTS
     dmpdir subdir: atmos
     type: bufr
+    window:
+       back: 4
+       forward: 4
     dmpdir regex: 'gdas.*.subpfl.*.bufr_d'
 
 - obs space:

test/gw-ci/create_exp.sh

@@ -13,6 +13,9 @@ expyaml=${expyaml_ctest}
 export pslot=${pslot_ctest}
 export RUNTESTS=${exp_path}/${pslot}
 export HPC_ACCOUNT="da-cpu"
+if [[ $MACHINE_ID = wcoss2 ]]; then
+  export HPC_ACCOUNT="GFS-DEV"
+fi  
 
 # Source the gw environement
 source ${HOMEgfs}/workflow/gw_setup.sh

ush/module-setup.sh

@@ -38,6 +38,8 @@ elif [[ $MACHINE_ID = s4* ]] ; then
 
 elif [[ $MACHINE_ID = wcoss2 ]]; then
     # We are on WCOSS2
+    # Ignore default modules of the same version lower in the search path (req'd by spack-stack)
+    export LMOD_TMOD_FIND_FIRST=yes
     module reset
 
 elif [[ $MACHINE_ID = cheyenne* ]] ; then

ush/soca/prep_ocean_obs.py

@@ -138,39 +138,51 @@ def initialize(self):
                             interval = timedelta(hours=assim_freq * i)
                             window_cdates.append(cdate + interval)
 
-                        input_files = prep_ocean_obs_utils.obs_fetch(self.task_config,
-                                                                     self.task_config,
-                                                                     obsprep_space,
-                                                                     window_cdates)
+                        # fetch the obs files to DATA directory and get the list of files and cycles
+                        fetched_files = prep_ocean_obs_utils.obs_fetch(self.task_config,
+                                                                       self.task_config,
+                                                                       obsprep_space,
+                                                                       window_cdates)
 
-                        if not input_files:
+                        if not fetched_files:
                             logger.warning(f"No files found for obs source {obtype}, skipping")
                             break  # go to next observer in OBS_YAML
 
-                        obsprep_space['input files'] = input_files
                         obsprep_space['window begin'] = self.window_begin
                         obsprep_space['window end'] = self.window_end
-                        ioda_filename = f"{RUN}.t{cyc:02d}z.{obs_space_name}.{cdatestr}.nc4"
-                        obsprep_space['output file'] = ioda_filename
                         ioda_config_file = obtype + '2ioda.yaml'
+                        obsprep_space['conversion config file'] = ioda_config_file
 
                         # set up the config file for conversion to IODA for bufr and
                         # netcdf files respectively
                         if obsprep_space['type'] == 'bufr':
+                            # create a pre-filled template file for the bufr2ioda converter,
+                            # which will be overwritten for each input cycle
                             bufrconv_config = {
                                 'RUN': RUN,
                                 'current_cycle': cdate,
                                 'DMPDIR': COMIN_OBS,
                                 'COM_OBS': COMIN_OBS,
                                 'OCEAN_BASIN_FILE': OCEAN_BASIN_FILE}
-                            obsprep_space['conversion config file'] = ioda_config_file
-                            bufr2iodapy = BUFR2IODA_PY_DIR + '/bufr2ioda_' + obtype + '.py'
+                            bufr2iodapy = os.path.join(BUFR2IODA_PY_DIR, f'bufr2ioda_{obtype}.py')
                             obsprep_space['bufr2ioda converter'] = bufr2iodapy
-                            tmpl_filename = 'bufr2ioda_' + obtype + '.yaml'
+                            tmpl_filename = f"bufr2ioda_{obtype}.yaml"
                             bufrconv_template = os.path.join(BUFR2IODA_TMPL_DIR, tmpl_filename)
+                            output_files = []  # files to save to COM directory
+                            bufrconv_files = []  # files needed to populate the IODA converter config
+                            # for each cycle of the retrieved obs bufr files...
+                            for input_file, cycle in fetched_files:
+                                cycletime = cycle[8:10]
+                                ioda_filename = f"{RUN}.t{cycletime}z.{obs_space_name}.{cycle}.nc4"
+                                output_files.append(ioda_filename)
+                                bufrconv_files.append((cycle, input_file, ioda_filename))
+
+                            obsprep_space['output file'] = output_files
+                            obsprep_space['bufrconv files'] = bufrconv_files
 
                             try:
                                 bufrconv = parse_j2yaml(bufrconv_template, bufrconv_config)
+                                bufrconv.update(obsprep_space)
                                 bufrconv.save(ioda_config_file)
                             except Exception as e:
                                 logger.warning(f"An exeception {e} occured while trying to create BUFR2IODA config")
@@ -180,7 +192,10 @@ def initialize(self):
                             obsspaces_to_convert.append({"obs space": obsprep_space})
 
                         elif obsprep_space['type'] == 'nc':
-                            obsprep_space['conversion config file'] = ioda_config_file
+
+                            obsprep_space['input files'] = [f[0] for f in fetched_files]
+                            ioda_filename = f"{RUN}.t{cyc:02d}z.{obs_space_name}.{cdatestr}.nc4"
+                            obsprep_space['output file'] = [ioda_filename]
                             save_as_yaml(obsprep_space, ioda_config_file)
 
                             obsspaces_to_convert.append({"obs space": obsprep_space})
@@ -192,7 +207,7 @@ def initialize(self):
             logger.critical("Ill-formed OBS_YAML or OBSPREP_YAML file, exiting")
             raise
 
-        # yes, there is redundancy between the yamls fed to the ioda converter and here,
+        # yes, there is redundancy between the yamls fed to the ioda converters and here,
         # this seems safer and easier than being selective about the fields
         save_as_yaml({"observations": obsspaces_to_convert}, self.task_config.conversion_list_file)
 
@@ -258,16 +273,18 @@ def finalize(self):
 
         obsspaces_to_save = YAMLFile(self.task_config.save_list_file)
 
-        for obsspace_to_save in obsspaces_to_save['observations']:
-
-            output_file = os.path.basename(obsspace_to_save['output file'])
-            conv_config_file = os.path.basename(obsspace_to_save['conversion config file'])
-            output_file_dest = os.path.join(COMOUT_OBS, output_file)
+        for obs_space in obsspaces_to_save['observations']:
+            files_to_save = []
+            conv_config_file = os.path.basename(obs_space['conversion config file'])
             conv_config_file_dest = os.path.join(COMOUT_OBS, conv_config_file)
+            files_to_save.append([conv_config_file, conv_config_file_dest])
+
+            for output_file in obs_space['output file']:
+                output_file_dest = os.path.join(COMOUT_OBS, output_file)
+                files_to_save.append([output_file, output_file_dest])
 
             try:
-                FileHandler({'copy': [[output_file, output_file_dest]]}).sync()
-                FileHandler({'copy': [[conv_config_file, conv_config_file_dest]]}).sync()
+                FileHandler({'copy': files_to_save}).sync()
             except Exception as e:
                 logger.warning(f"An exeception {e} occured while trying to run gen_bufr_json")
             except OSError: