Add sflux to post output

Adds the creation of surface flux files to the post job. Working
directories have 'atm' or 'sflux' added to the path so each has
its own for debugging purposes.

Copying of files into the working directory has been changed to
symlinks to prevent the increase in resources by multiple copies
of the model output.

Refs: NOAA-EMC#270

parm/post/atm_post.yaml

@@ -1,9 +1,9 @@
-work_dir: !ENV ${DATA}
+work_dir: !ENV ${DATA}/atm
 tmpl_file: !ENV ${PARMpost}/post.nml.j2
 mp_file: !ENV ${PARMpost}/nam_micro_lookup.dat
 grib_out: !ENV ${COMOUT}/${RUN}.${cycle}.master.grb2f${fhr}
 grib_idx_out: !ENV ${COMOUT}/${RUN}.${cycle}.master.grb2if${fhr}
-exe_log_file: !ENV ${pgmout}
+exe_log_file: !ENV ${DATA}/${pgmout}
 out_form: 'netcdfpara'
 cdate: !ENV ${CDATE}
 fhr: !ENV ${fhr}

parm/post/atm_post_gfs_anl.yaml → parm/post/atm_post_anl.yaml

@@ -7,7 +7,6 @@ trigger_file: !ENV ${COMIN}/${RUN}.${cycle}.atmanl.nc
 
 igen: anal_gfs
 flat_file: !ENV ${PARMpost}/postxconfig-NT-GFS-ANL.txt
-ctrl_file: !ENV ${PARMpost}/postcntrl_gfs_anl.xml
 grib2_table: !ENV ${g2tmpl_ROOT}/share/params_grib2_tbl_new
 
 dbn_signals:

parm/post/atm_post_gfs_f000.yaml → parm/post/atm_post_f000.yaml

@@ -7,9 +7,4 @@ trigger_file: !ENV ${COMIN}/${CDUMP}.t${cyc}z.logf000.txt
 
 igen: gfs_avn
 flat_file: !ENV ${PARMpost}/postxconfig-NT-GFS-F00.txt
-ctrl_file: !ENV ${PARMpost}/postcntrl_gfs_f00.xml
 grib2_table: !ENV ${g2tmpl_ROOT}/share/params_grib2_tbl_new
-
-dbn_signals:
-  GFS_SA: !ENV ${COMIN}/${RUN}.${cycle}.atmf000.nc
-  GFS_MSC_sfcanal: !ENV ${COMIN}/${RUN}.${cycle}.sfcf000.nc

parm/post/atm_post_gfs_fhr.yaml → parm/post/atm_post_fhr.yaml

@@ -7,5 +7,4 @@ trigger_file: !ENV ${COMIN}/${CDUMP}.t${cyc}z.logf${fhr}.txt
 
 igen: gfs_avn
 flat_file: !ENV ${PARMpost}/postxconfig-NT-GFS.txt
-ctrl_file: !ENV ${PARMpost}/postcntrl_gfs.xml
-grib2_table: !ENV ${g2tmpl_ROOT}/share/params_grib2_tbl_new
+grib2_table: !ENV ${g2tmpl_ROOT}/share/params_grib2_tbl_new

parm/post/sflux_post.yaml

@@ -0,0 +1,20 @@
+work_dir: !ENV ${DATA}/sflux
+tmpl_file: !ENV ${PARMpost}/post.nml.j2
+mp_file: !ENV ${PARMpost}/nam_micro_lookup.dat
+grib_out: !ENV ${COMOUT}/${RUN}.${cycle}.sfluxgrbf${fhr}.grb2
+grib_idx_out: !ENV ${COMOUT}/${RUN}.${cycle}.sfluxgrbf${fhr}.grb2.idx
+exe_log_file: !ENV ${pgmout}
+out_form: 'netcdfpara'
+cdate: !ENV ${CDATE}
+fhr: !ENV ${fhr}
+grib_version: 'grib2'
+grib_table: !ENV ${g2tmpl_ROOT}/share/params_grib2_tbl_new
+post_variables: 'KPO=57,PO=1000.,975.,950.,925.,900.,875.,850.,825.,800.,775.,750.,725.,700.,675.,650.,625.,600.,575.,550.,525.,500.,475.,450.,425.,400.,375.,350.,325.,300.,275.,250.,225.,200.,175.,150.,125.,100.,70.,50.,40.,30.,20.,15.,10.,7.,5.,3.,2.,1.,0.7,0.4,0.2,0.1,0.07,0.04,0.02,0.01,'
+post_exe: !ENV ${HOMEgfs}/exec/upp.x
+grib_idx_exe: !ENV ${GRB2INDEX}
+mpi_run: !ENV ${APRUNP}
+sleep_max: 900
+sleep_interval: 5
+send_com: !ENV ${SENDCOM}
+send_dbn: !ENV ${SENDDBN}
+dbn_alert: !ENV ${DBNROOT}/bin/dbn_alert

parm/post/sflux_post_anl.yaml

@@ -0,0 +1,10 @@
+include:
+  - !INC ${PARMpost}/sflux_post.yaml
+
+atm_file: !ENV ${COMIN}/${RUN}.${cycle}.atmanl.nc
+sfc_file: !ENV ${COMIN}/${RUN}.${cycle}.sfcanl.nc
+trigger_file: !ENV ${COMIN}/${RUN}.${cycle}.atmanl.nc
+
+igen: anal_gfs
+flat_file: !ENV ${PARMpost}/postxconfig-NT-GFS-FLUX-ANL.txt
+grib2_table: !ENV ${g2tmpl_ROOT}/share/params_grib2_tbl_new

parm/post/sflux_post_f000.yaml

@@ -0,0 +1,14 @@
+include:
+  - !INC ${PARMpost}/sflux_post.yaml
+
+atm_file: !ENV ${COMIN}/${RUN}.${cycle}.atmf000.nc
+sfc_file: !ENV ${COMIN}/${RUN}.${cycle}.sfcf000.nc
+trigger_file: !ENV ${COMIN}/${CDUMP}.t${cyc}z.logf000.txt
+
+igen: gfs_avn
+flat_file: !ENV ${PARMpost}/postxconfig-NT-GFS-FLUX-F00.txt
+grib2_table: !ENV ${g2tmpl_ROOT}/share/params_grib2_tbl_new
+
+dbn_signals:
+  GFS_SGB_GB2: $(include[0].grib_out)
+  GFS_SGB_GB2_WIDX: $(include[0].grib_idx_out)

parm/post/sflux_post_fhr.yaml

@@ -0,0 +1,14 @@
+include:
+  - !INC ${PARMpost}/sflux_post.yaml
+
+atm_file: !ENV ${COMIN}/${RUN}.${cycle}.atmf${fhr}.nc
+sfc_file: !ENV ${COMIN}/${RUN}.${cycle}.sfcf${fhr}.nc
+trigger_file: !ENV ${COMIN}/${CDUMP}.t${cyc}z.logf${fhr}.txt
+
+igen: gfs_avn
+flat_file: !ENV ${PARMpost}/postxconfig-NT-GFS-FLUX.txt
+grib2_table: !ENV ${g2tmpl_ROOT}/share/params_grib2_tbl_new
+
+dbn_signals:
+  GFS_SGB_GB2: !ENV ${COMOUT}/${RUN}.${cycle}.sfluxgrbf${fhr}.grb2
+  GFS_SGB_GB2_WIDX: !ENV ${COMOUT}/${RUN}.${cycle}.sfluxgrbf${fhr}.grb2.idx

scripts/exglobal_atmos_post.sh

@@ -2,16 +2,22 @@
 
 source "${HOMEgfs}/ush/preamble.sh"
 
-# Determine which yaml file to use
-case ${fhr} in
-	anl) yaml_cat='anl' ;;
-	000) yaml_cat='f000';;
-	*)   yaml_cat='fhr' ;;
-esac
-post_settings="${PARMpost}/atm_post_${CDUMP}_${yaml_cat}.yaml"
+for type in "atm" "sflux"; do
+	# Determine which yaml file to use
+	case ${fhr} in
+		anl) yaml_cat='anl' ;;
+		000) yaml_cat='f000';;
+		*)   yaml_cat='fhr' ;;
+	esac
+	post_settings="${PARMpost}/${type}_post_${yaml_cat}.yaml"
 
-# Run post
-"${HOMEgfs}/ush/atm_post.py" "${post_settings}"
-err=$?
+	# Run post
+	"${HOMEgfs}/ush/atm_post.py" "${post_settings}"
+	err=$?
 
-exit ${err}
+	if ((err > 0)); then
+		exit "${err}"
+	fi
+done
+
+exit

ush/atm_post.py

@@ -2,14 +2,13 @@
 
 import os
 import shutil
-import glob
 import subprocess
 import time
 from datetime import timedelta
 from argparse import ArgumentParser
 from python.pygw.src.pygw import timetools
 from python.pygw.src.pygw.template import Template, TemplateConstants
-from python.pygw.src.pygw.fsutils import mkdir, chdir, rm_p
+from python.pygw.src.pygw.fsutils import mkdir
 from python.pygw.src.pygw.yaml_file import YAMLFile
 from pprint import pprint
 from functools import partial
@@ -61,7 +60,7 @@ def run_post(settings: dict) -> None:
                 '''
               )
     os.environ['PGBOUT'] = 'pgbfile'
-    subprocess.run(f"{settings['mpi_run']} upp.x > {settings['exe_log_file']}", shell=True, check=True)
+    subprocess.run(f"{settings['mpi_run']} upp.x >> {settings['exe_log_file']}", shell=True, check=True)
     subprocess.run(f"{settings['grib_idx_exe']} pgbfile pgifile >> {settings['exe_log_file']}",
                    shell=True, check=True)
 
@@ -171,21 +170,21 @@ def stage_post(settings: dict, nml_filename: str = 'itag') -> None:
                        work_dir   : str
                                     The temporary working directory to use
                        atm_file   : str
-                                    Raw atmosphere model output in NetCDF format. Will be copied
+                                    Raw atmosphere model output in NetCDF format. Will be linked
                                     to work_dir as atm_file.
                        sfc_file   : str
-                                    Raw atmosphere flux output in NetCDF format. Will be copied
+                                    Raw atmosphere flux output in NetCDF format. Will be linked
                                     to work_dir as sfc_file.
                        flat_file  : str
-                                    Post 'flat' file. Will be copied to work_dir as
+                                    Post 'flat' file. Will be linked to work_dir as
                                     postxconfig-NT.txt.
                        grib_table : str
-                                    Grib2 table. Will be copied to work_dir.
+                                    Grib2 table. Will be linked to work_dir.
                        mp_file    : str
-                                    Microphysics .dat file. Will be copied to work_dir as
+                                    Microphysics .dat file. Will be linked to work_dir as
                                     eta_micro_lookup.dat.
                        post_exe   : str
-                                    Path to the post executable. Will be copied to work_dir as
+                                    Path to the post executable. Will be linked to work_dir as
                                     upp.x
 
                    Additionally, the following key/value pair may be defined:
@@ -199,18 +198,18 @@ def stage_post(settings: dict, nml_filename: str = 'itag') -> None:
     '''
     work_dir = settings['work_dir']
     mkdir(work_dir)
-    chdir(work_dir)
+    os.chdir(work_dir)
 
     namelist = make_namelist(settings)
     with open(nml_filename, 'w') as file:
         file.write(namelist)
 
-    shutil.copy(settings['flat_file'], 'postxconfig-NT.txt')
-    shutil.copy(settings['grib_table'], './')
-    shutil.copy(settings['mp_file'], 'eta_micro_lookup.dat')
-    shutil.copy(settings['atm_file'], 'atm_file')
-    shutil.copy(settings['sfc_file'], 'sfc_file')
-    shutil.copy(settings['post_exe'], 'upp.x')
+    os.symlink(settings['flat_file'], 'postxconfig-NT.txt')
+    os.symlink(settings['grib_table'], os.path.basename(settings['grib_table']))
+    os.symlink(settings['mp_file'], 'eta_micro_lookup.dat')
+    os.symlink(settings['atm_file'], 'atm_file')
+    os.symlink(settings['sfc_file'], 'sfc_file')
+    os.symlink(settings['post_exe'], 'upp.x')
 
     if settings.get('is_ens', False):
         # TODO replace negatively_post_fcst with ${ens_pert_type} in postxconfig-NT.txt
@@ -293,6 +292,7 @@ def send_dbn(settings: dict) -> None:
     stage_post(settings=settings)
     wait_for_model_output(settings=settings)
     run_post(settings=settings)
+
     if settings['send_com'] in ["YES"]:
         send_com(settings)