Merge branch 'develop' into feature/build_jedi_exe

* develop:
  Using ioda util to convert the datetime in AMSR2 converter (#1077)
  Add modulefile for Dogwood/Cactus (#1073)
  Addition of a switch for the cycling type (#1072)

build.sh

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

modulefiles/GDAS/wcoss2.intel.lua

@@ -0,0 +1,51 @@
+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", "/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")
+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("fckit/0.11.0")
+load("atlas/0.35.0")
+load("nccmp")
+
+-- 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")
+
+local mpiexec = '/pe/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin/mpirun'
+local mpinproc = '-n'
+setenv('MPIEXEC_EXEC', mpiexec)
+setenv('MPIEXEC_NPROC', mpinproc)
+
+setenv("CRTM_FIX","/lfs/h2/emc/da/noscrub/emc.da/GDASApp/fix/crtm/2.4.0")
+setenv("GDASAPP_TESTDATA","/lfs/h2/emc/da/noscrub/emc.da/GDASApp/data")
+setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/lfs/h2/emc/da/noscrub/emc.da/GDASApp/data/test")
+
+whatis("Name: ".. pkgName)
+whatis("Version: ".. pkgVersion)
+whatis("Category: GDASApp")
+whatis("Description: Load all libraries needed for GDASApp")

scripts/exgdas_global_marine_analysis_post.py

@@ -50,6 +50,7 @@ def list_all_files(dir_in, dir_out, wc='*', fh_list=[]):
 cyc = str(os.getenv('cyc')).zfill(2)
 bcyc = str((int(cyc) - 3) % 24).zfill(2)
 gcyc = str((int(cyc) - 6) % 24).zfill(2)  # previous cycle
+cdatedt = datetime.strptime(cdate, '%Y%m%d%H')
 bdatedt = datetime.strptime(cdate, '%Y%m%d%H') - timedelta(hours=3)
 bdate = datetime.strftime(bdatedt, '%Y-%m-%dT%H:00:00Z')
 mdate = datetime.strftime(datetime.strptime(cdate, '%Y%m%d%H'), '%Y-%m-%dT%H:00:00Z')
@@ -93,8 +94,12 @@ def list_all_files(dir_in, dir_out, wc='*', fh_list=[]):
                        os.path.join(com_ocean_analysis, f'{RUN}.t{bcyc}z.ocngrid.nc')])
 
 # Copy the CICE analysis restart
-cdateice = pdy + '.' + cyc + '0000'
-post_file_list.append([os.path.join(anl_dir, 'Data', f'{cdateice}.cice_model.res.nc'),
+if os.getenv('DOIAU') == "YES":
+    cice_rst_date = bdatedt.strftime('%Y%m%d.%H%M%S')
+else:
+    cice_rst_date = cdatedt.strftime('%Y%m%d.%H%M%S')
+
+post_file_list.append([os.path.join(anl_dir, 'Data', f'{cice_rst_date}.cice_model.res.nc'),
                        os.path.join(com_ice_restart, f'{cdate}.cice_model_anl.res.nc')])
 
 FileHandler({'copy': post_file_list}).sync()

scripts/exgdas_global_marine_analysis_prep.py

@@ -70,10 +70,6 @@ def find_clim_ens(input_date):
 staticsoca_dir = os.getenv('SOCA_INPUT_FIX_DIR')
 nmem_ens = 0
 nmem_ens = int(os.getenv('NMEM_ENS'))
-if os.getenv('DOHYBVAR') == "YES":
-    dohybvar = True
-else:
-    dohybvar = False
 
 # create analysis directories
 diags = os.path.join(anl_dir, 'diags')            # output dir for soca DA obs space
@@ -89,12 +85,25 @@ def find_clim_ens(input_date):
 window_begin = datetime.strptime(os.getenv('PDY')+os.getenv('cyc'), '%Y%m%d%H') - half_assim_freq
 window_begin_iso = window_begin.strftime('%Y-%m-%dT%H:%M:%SZ')
 window_middle_iso = window_middle.strftime('%Y-%m-%dT%H:%M:%SZ')
-fcst_begin = datetime.strptime(os.getenv('PDY')+os.getenv('cyc'), '%Y%m%d%H')
 RUN = os.getenv('RUN')
 cyc = os.getenv('cyc')
 gcyc = os.getenv('gcyc')
 PDY = os.getenv('PDY')
 
+# hybrid-envar switch
+if os.getenv('DOHYBVAR') == "YES":
+    dohybvar = True
+else:
+    dohybvar = False
+
+# switch for the cycling type
+if os.getenv('DOIAU') == "YES":
+    # forecast initialized at the begining of the DA window
+    fcst_begin = window_begin
+else:
+    # forecast initialized at the middle of the DA window
+    fcst_begin = datetime.strptime(os.getenv('PDY')+os.getenv('cyc'), '%Y%m%d%H')
+
 ################################################################################
 # fetch observations
 

utils/obsproc/IcecAmsr2Ioda.h

@@ -13,8 +13,10 @@
 
 #include <Eigen/Dense>    // NOLINT
 
+#include "ioda/../../../../core/IodaUtils.h"
 #include "ioda/Group.h"
 #include "ioda/ObsGroup.h"
+
 #include "oops/util/dateFunctions.h"
 
 #include "NetCDFToIodaConverter.h"
@@ -83,30 +85,42 @@ namespace gdasapp {
         int minute =  oneTmpdateTimeVal[i+4];
         int second = static_cast<int>(oneTmpdateTimeVal[i+5]);
 
-        // Replace Fillvalue -9999 to 0 to avoid crash in dateToJulian
+        // Avoid crash util in ioda::convertDtimeToTimeOffsets
         if (year == -9999 || month == -9999 || day == -9999 ||
           hour == -9999 || minute == -9999 || second == -9999) {
           year = month = day = hour = minute = second = 0;
         }
 
-        // Convert a date to Julian date
-        uint64_t julianDate = util::datefunctions::dateToJulian(year, month, day);
-
-        // Subtract Julian day from January 1, 1970 (convert to epoch)
-        int daysSinceEpoch = julianDate - 2440588;
-
-        // Calculate seconds only from HHMMSS
-        int secondsOffset = util::datefunctions::hmsToSeconds(hour, minute, second);
-
-        iodaVars.datetime_(index) = static_cast<int64_t>(daysSinceEpoch*86400.0f) + secondsOffset;
+        // Construct iso8601 string format for each dateTime
+        std::stringstream ss;
+        ss << std::setfill('0')
+           << std::setw(4) << year << '-'
+           << std::setw(2) << month << '-'
+           << std::setw(2) << day << 'T'
+           << std::setw(2) << hour << ':'
+           << std::setw(2) << minute << ':'
+           << std::setw(2) << second << 'Z';
+        std::string formattedDateTime = ss.str();
+        util::DateTime dateTime(formattedDateTime);
+
+        // Set epoch time for AMSR2_ICEC
+        util::DateTime epochDtime("1970-01-01T00:00:00Z");
+
+        // Convert Obs DateTime objects to epoch time offsets in seconds
+        // 0000-00-00T00:00:00Z will be converterd to negative seconds
+        int64_t timeOffsets
+           = ioda::convertDtimeToTimeOffsets(epochDtime, {dateTime})[0];
+
+        // Update datetime Eigen Arrays
+        iodaVars.datetime_(index) = timeOffsets;
         index++;
       }
 
       // Update non-optional Eigen arrays
       for (int i = 0; i < iodaVars.location_; i++) {
         iodaVars.longitude_(i) = oneDimLonVal[i];
         iodaVars.latitude_(i) = oneDimLatVal[i];
-        iodaVars.obsVal_(i) = static_cast<float>(oneDimObsVal[i]*0.01f);
+        iodaVars.obsVal_(i) = static_cast<float>(oneDimObsVal[i]*0.01);
         iodaVars.obsError_(i) = 0.1;  // Do something for obs error
         iodaVars.preQc_(i) = oneDimFlagsVal[i];
         // Store optional metadata, set ocean basins to -999 for now