Merge branch 'NOAA-EMC:develop' into feature/stage_coldatm_warmocnice

ci/cases/pr/C96C48_ufs_hybatmDA.yaml

@@ -11,7 +11,7 @@ arguments:
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20240610
   idate: 2024022318
-  edate: 2024022400
+  edate: 2024022406
   nens: 2
   gfs_cyc: 1
   start: warm

docs/note_fixfield.txt

@@ -4,7 +4,7 @@ They are saved locally on all platforms
 
 Hera: /scratch1/NCEPDEV/global/glopara/fix
 Orion/Hercules: /work/noaa/global/glopara/fix
-Jet: /mnt/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix
+Jet: /mnt/lfs5/HFIP/hfv3gfs/glopara/FIX/fix
 S4: /data/prod/glopara/fix
 
 ------------------------------------------------------------------------------

docs/source/components.rst

@@ -59,7 +59,7 @@ Observation data, also known as dump data, is prepared in production and then ar
 
 * Hera: ``/scratch1/NCEPDEV/global/glopara/dump``
 * Orion/Hercules: ``/work/noaa/rstprod/dump``
-* Jet: ``/mnt/lfs4/HFIP/hfv3gfs/glopara/dump``
+* Jet: ``/mnt/lfs5/HFIP/hfv3gfs/glopara/dump``
 * WCOSS2: ``/lfs/h2/emc/global/noscrub/emc.global/dump``
 * S4: ``/data/prod/glopara/dump``
 

docs/source/init.rst

@@ -111,7 +111,7 @@ Warm-start cycled w/ coupled (S2S) model C48 atmosphere C48 enkf (80 members) 5
    Hera: /scratch1/NCEPDEV/global/glopara/data/ICSDIR/C48C48mx500
    Orion/Hercules: /work/noaa/global/glopara/data/ICSDIR/C48C48mx500
    WCOSS2: /lfs/h2/emc/global/noscrub/emc.global/data/ICSDIR/C48C48mx500
-   Jet: /lfs4/HFIP/hfv3gfs/glopara/data/ICSDIR/C48C48mx500
+   Jet: /lfs5/HFIP/hfv3gfs/glopara/data/ICSDIR/C48C48mx500
    AWS: https://noaa-nws-global-pds.s3.amazonaws.com/index.html#data/ICSDIR/C48C48mx500
 
 Start date = 2021032312
@@ -227,7 +227,7 @@ Forecast-only P8 prototype initial conditions are made available to users on sup
     WCOSS2: /lfs/h2/emc/global/noscrub/emc.global/IC/COUPLED
     HERA: /scratch1/NCEPDEV/climate/role.ufscpara/IC
     ORION/Hercules: /work/noaa/global/glopara/data/ICSDIR/prototype_ICs
-    JET: /mnt/lfs4/HFIP/hfv3gfs/glopara/data/ICSDIR/prototype_ICs
+    JET: /mnt/lfs5/HFIP/hfv3gfs/glopara/data/ICSDIR/prototype_ICs
     S4: /data/prod/glopara/coupled_ICs
 
 These locations are known within the workflow via paths set in ``parm/config/config.coupled_ic``.

env/ORION.env

@@ -142,7 +142,7 @@ elif [[ "${step}" = "marineanlchkpt" ]]; then
 
     export NTHREADS_OCNANAL=${NTHREADSmax}
 
-    export APRUN_MARINEANLCHKPT="${APRUN} --cpus-per-task=${NTHREADS_OCNANAL}"
+    export APRUN_MARINEANLCHKPT="${APRUN_default} --cpus-per-task=${NTHREADS_OCNANAL}"
 
 elif [[ "${step}" = "ocnanalecen" ]]; then
 

modulefiles/module_base.jet.lua

@@ -52,7 +52,7 @@ setenv("UTILROOT",(os.getenv("prod_util_ROOT") or "None"))
 prepend_path("MODULEPATH", pathJoin("/lfs5/HFIP/hfv3gfs/glopara/git/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles"))
 load(pathJoin("prepobs", (os.getenv("prepobs_run_ver") or "None")))
 
-prepend_path("MODULEPATH", pathJoin("/lfs4/HFIP/hfv3gfs/glopara/git/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))
+prepend_path("MODULEPATH", pathJoin("/lfs5/HFIP/hfv3gfs/glopara/git/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))
 load(pathJoin("fit2obs", (os.getenv("fit2obs_ver") or "None")))
 
 whatis("Description: GFS run environment")

modulefiles/module_gwsetup.jet.lua

@@ -4,7 +4,7 @@ Load environment to run GFS workflow setup scripts on Jet
 
 load(pathJoin("rocoto"))
 
-prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev-rocky8/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/contrib/spack-stack/spack-stack-1.6.0/envs/gsi-addon-intel/install/modulefiles/Core")
 
 local stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
 local python_ver=os.getenv("python_ver") or "3.11.6"

parm/archive/gdas_restarta.yaml.j2

@@ -32,6 +32,8 @@ gdas_restarta:
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}abias_int"
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}dtfanl.nc"
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}loginc.txt"
+        {% else %}
+        - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}rad_varbc_params.tar"
         {% endif %}
 
         # Snow surface data

parm/config/gfs/config.aero

@@ -24,7 +24,7 @@ case ${machine} in
     AERO_INPUTS_DIR="/gpfs/f5/epic/proj-shared/global/glopara/data/gocart_emissions"
     ;;
   "JET")
-    AERO_INPUTS_DIR="/lfs4/HFIP/hfv3gfs/glopara/data/gocart_emissions"
+    AERO_INPUTS_DIR="/lfs5/HFIP/hfv3gfs/glopara/data/gocart_emissions"
     ;;
   *)
     echo "FATAL ERROR: Machine ${machine} unsupported for aerosols"

parm/config/gfs/config.resources.ORION

@@ -23,6 +23,16 @@ case ${step} in
     # Remove this block once the GSI issue is resolved.
     export walltime="00:45:00"
   ;;
+  "atmanlvar")
+    # Run on 8 nodes for memory requirement
+    export tasks_per_node=8
+    export walltime="00:45:00"
+  ;;
+  "atmensanlobs")
+    # Run on 8 nodes for memory requirement
+    export tasks_per_node=8
+    export walltime="00:45:00"
+  ;;
   *)
   ;;
 esac

parm/stage/analysis.yaml.j2

@@ -10,17 +10,10 @@ analysis:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
-        {% for ftype in ["abias", "abias_air", "abias_int", "abias_pc", "atminc.nc", "atmi009.nc", "atmi003.nc", "radstat", "ratminc.nc", "ratmi009.nc", "ratmi003.nc"] %}
+        {% for ftype in ["abias", "abias_air", "abias_int", "abias_pc", "atminc.nc", "atmi009.nc", "atmi003.nc", "radstat", "ratminc.nc", "ratmi009.nc", "ratmi003.nc", "rad_varbc_params.tar"] %}
         {% if path_exists(ICSDIR ~ "/" ~ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) ~ "/" ~ RUN ~ ".t" ~ current_cycle_HH ~ "z." ~ ftype) %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ RUN }}.t{{ current_cycle_HH }}z.{{ ftype }}", "{{ COMOUT_ATMOS_ANALYSIS_MEM }}"]
         {% endif %}
         {% endfor %}
-        {% if DO_JEDIATMVAR %}
-        {% for ftype in ["satbias.nc", "satbias_cov.nc", "tlapse.txt"] %}
-        {% for file in glob(ICSDIR ~ "/" ~ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) ~ "/" ~ RUN ~ ".t" ~ current_cycle_HH ~ "z.atms_*." ~ ftype) %}
-        - ["{{ file }}", "{{ COMOUT_ATMOS_ANALYSIS_MEM }}"]
-        {% endfor %}
-        {% endfor %}
-        {% endif %}
         {% endfor %} # mem loop
 {% endif %}

sorc/link_workflow.sh

@@ -73,7 +73,7 @@ case "${machine}" in
   "hera")     FIX_DIR="/scratch1/NCEPDEV/global/glopara/fix" ;;
   "orion")    FIX_DIR="/work/noaa/global/glopara/fix" ;;
   "hercules") FIX_DIR="/work/noaa/global/glopara/fix" ;;
-  "jet")      FIX_DIR="/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix" ;;
+  "jet")      FIX_DIR="/lfs5/HFIP/hfv3gfs/glopara/FIX/fix" ;;
   "s4")       FIX_DIR="/data/prod/glopara/fix" ;;
   "gaea")     FIX_DIR="/gpfs/f5/ufs-ard/world-shared/global/glopara/data/fix" ;;
   "noaacloud") FIX_DIR="/contrib/global-workflow-shared-data/fix" ;;

ush/detect_machine.sh

@@ -67,7 +67,7 @@ if [[ -d /lfs/h3 ]]; then
 elif [[ -d /lfs/h1 && ! -d /lfs/h3 ]]; then
   # We are on NOAA TDS Acorn
   MACHINE_ID=acorn
-elif [[ -d /mnt/lfs1 ]]; then
+elif [[ -d /mnt/lfs5 ]]; then
   # We are on NOAA Jet
   MACHINE_ID=jet
 elif [[ -d /scratch1 ]]; then

ush/forecast_predet.sh

@@ -562,7 +562,6 @@ FV3_predet(){
       ${NCP} "${PARMgfs}/post/gefs/postxconfig-NT-gefs-f00.txt"   "${DATA}/postxconfig-NT_FH00.txt"
     fi
   fi
-
 }
 
 # Disable variable not used warnings

ush/python/pygfs/jedi/jedi.py

@@ -1,10 +1,12 @@
 #!/usr/bin/env python3
 
 import os
+import tarfile
 from logging import getLogger
 from typing import List, Dict, Any, Optional
 from jcb import render
 from wxflow import (AttrDict,
+                    FileHandler,
                     chdir, rm_p,
                     parse_j2yaml,
                     logit,
@@ -188,19 +190,19 @@ def get_obs_dict(self, task_config: AttrDict) -> Dict[str, Any]:
         return obs_dict
 
     @logit(logger)
-    def get_bias_dict(self, task_config: AttrDict) -> Dict[str, Any]:
+    def get_bias_dict(self, task_config: AttrDict, bias_file) -> Dict[str, Any]:
         """Compile a dictionary of observation files to copy
 
-        This method extracts 'observers' from the JEDI yaml and from that list, extracts a list of
-        observation bias correction files that are to be copied to the run directory
+        This method extracts 'observers' from the JEDI yaml and determines from that list
+        if bias correction tar files are to be copied to the run directory
         from the component directory.
-        TODO: COM_ATMOS_ANALYSIS_PREV is hardwired here and this method is not appropriate in
-        `analysis.py` and should be implemented in the component where this is applicable.
 
         Parameters
         ----------
         task_config: AttrDict
             Attribute-dictionary of all configuration variables associated with a GDAS task.
+        bias_file
+            name of bias correction tar file
 
         Returns
         ----------
@@ -216,18 +218,52 @@ def get_bias_dict(self, task_config: AttrDict) -> Dict[str, Any]:
                 obfile = ob['obs bias']['input file']
                 obdir = os.path.dirname(obfile)
                 basename = os.path.basename(obfile)
-                prefix = '.'.join(basename.split('.')[:-2])
-                for file in ['satbias.nc', 'satbias_cov.nc', 'tlapse.txt']:
-                    bfile = f"{prefix}.{file}"
-                    copylist.append([os.path.join(task_config.COM_ATMOS_ANALYSIS_PREV, bfile), os.path.join(obdir, bfile)])
-                    # TODO: Why is this specific to ATMOS?
+                prefix = '.'.join(basename.split('.')[:-3])
+                bfile = f"{prefix}.{bias_file}"
+                tar_file = os.path.join(obdir, bfile)
+                copylist.append([os.path.join(task_config.VarBcDir, bfile), tar_file])
+                break
 
         bias_dict = {
             'mkdir': [os.path.join(task_config.DATA, 'bc')],
             'copy': copylist
         }
+
         return bias_dict
 
+    @staticmethod
+    @logit(logger)
+    def extract_tar(tar_file: str) -> None:
+        """Extract files from a tarball
+
+        This method extract files from a tarball
+
+        Parameters
+        ----------
+        tar_file
+            path/name of tarball
+
+        Returns
+        ----------
+        None
+        """
+
+        # extract files from tar file
+        tar_path = os.path.dirname(tar_file)
+        try:
+            with tarfile.open(tar_file, "r") as tarball:
+                tarball.extractall(path=tar_path)
+                logger.info(f"Extract {tarball.getnames()}")
+        except tarfile.ReadError as err:
+            if tarfile.is_tarfile(tar_file):
+                logger.error(f"FATAL ERROR: {tar_file} could not be read")
+                raise tarfile.ReadError(f"FATAL ERROR: unable to read {tar_file}")
+            else:
+                logger.info()
+        except tarfile.ExtractError as err:
+            logger.exception(f"FATAL ERROR: unable to extract from {tar_file}")
+            raise tarfile.ExtractError("FATAL ERROR: unable to extract from {tar_file}")
+
 
 @logit(logger)
 def find_value_in_nested_dict(nested_dict: Dict, target_key: str) -> Any:

ush/python/pygfs/task/analysis.py

@@ -41,10 +41,6 @@ def initialize(self) -> None:
         obs_dict = self.get_obs_dict()
         FileHandler(obs_dict).sync()
 
-        # some analyses need to stage bias corrections
-        bias_dict = self.get_bias_dict()
-        FileHandler(bias_dict).sync()
-
         # link jedi executable to run directory
         self.link_jediexe()
 
@@ -127,47 +123,6 @@ def get_obs_dict(self) -> Dict[str, Any]:
         }
         return obs_dict
 
-    @logit(logger)
-    def get_bias_dict(self) -> Dict[str, Any]:
-        """Compile a dictionary of observation files to copy
-
-        This method extracts 'observers' from the JEDI yaml and from that list, extracts a list of
-        observation bias correction files that are to be copied to the run directory
-        from the component directory.
-        TODO: COM_ATMOS_ANALYSIS_PREV is hardwired here and this method is not appropriate in
-        `analysis.py` and should be implemented in the component where this is applicable.
-
-        Parameters
-        ----------
-
-        Returns
-        ----------
-        bias_dict: Dict
-            a dictionary containing the list of observation bias files to copy for FileHandler
-        """
-
-        logger.info(f"Extracting a list of bias correction files from Jedi config file")
-        observations = find_value_in_nested_dict(self.task_config.jedi_config, 'observations')
-        logger.debug(f"observations:\n{pformat(observations)}")
-
-        copylist = []
-        for ob in observations['observers']:
-            if 'obs bias' in ob.keys():
-                obfile = ob['obs bias']['input file']
-                obdir = os.path.dirname(obfile)
-                basename = os.path.basename(obfile)
-                prefix = '.'.join(basename.split('.')[:-2])
-                for file in ['satbias.nc', 'satbias_cov.nc', 'tlapse.txt']:
-                    bfile = f"{prefix}.{file}"
-                    copylist.append([os.path.join(self.task_config.COM_ATMOS_ANALYSIS_PREV, bfile), os.path.join(obdir, bfile)])
-                    # TODO: Why is this specific to ATMOS?
-
-        bias_dict = {
-            'mkdir': [os.path.join(self.task_config.DATA, 'bc')],
-            'copy': copylist
-        }
-        return bias_dict
-
     @logit(logger)
     def add_fv3_increments(self, inc_file_tmpl: str, bkg_file_tmpl: str, incvars: List) -> None:
         """Add cubed-sphere increments to cubed-sphere backgrounds