Merge HAFSv0.2 configuration into develop and sync HAFS submodules as of 202107

.gitmodules

@@ -30,3 +30,7 @@
 	path = sorc/hafs_graphics.fd/emc_graphics
 	url = https://github.com/hafs-community/hafs_graphics.git
 	branch = support/HAFS
+[submodule "obs_preproc"]
+	path = sorc/hafs_tools.fd/sorc/hafs_obs_preproc/obs_preproc
+	url = https://github.com/hafs-community/obs-preproc.git
+	branch = support/HAFS

jobs/JHAFS_FORECAST

@@ -17,6 +17,9 @@ export machine=${WHERE_AM_I:-wcoss_cray}
 export envir=${envir:-prod} # prod, para, test
 export RUN_ENVIR=${RUN_ENVIR:-dev} # nco or dev
 if [ "${RUN_ENVIR^^}" != NCO ]; then
+  if [ "${machine}" = "hera" ]; then 
+    module unload intelpython 
+  fi
   module use ${HOMEhafs}/sorc/hafs_forecast.fd/modulefiles
   module load ufs_${machine}
   module list

jobs/JHAFS_HRDGRAPHICS

@@ -10,6 +10,9 @@ export EXEChafs=${EXEChafs:-${HOMEhafs}/exec}
 export PARMhafs=${PARMhafs:-${HOMEhafs}/parm}
 export FIXhafs=${FIXhafs:-${HOMEhafs}/fix}
 
+export GPLOThafs=${GPLOThafs:-${HOMEhafs}/sorc/hafs_graphics.fd/hrd_gplot}
+export GPLOT_DIR=${GPLOThafs}
+
 source ${USHhafs}/hafs_pre_job.sh.inc
 source ${HOLDVARS:-storm1.holdvars.txt}
 
@@ -33,9 +36,6 @@ export COMIN=${COMIN:?}
 export COMOUT=${COMOUT:?}
 export COMhafs=${COMhafs:-${COMOUT}}
 
-export GPLOThafs=${GPLOThafs:-${HOMEhafs}/sorc/hafs_graphics.fd/hrd_gplot}
-export GPLOT_DIR=${GPLOThafs}
-
 export ADECKgraph=${ADECKhafs:?}
 export BDECKgraph=${BDECKhafs:?}
 export SYNDAThafs=${SYNDAThafs:?}

jobs/JHAFS_OBS_PROC

@@ -0,0 +1,62 @@
+#!/bin/sh
+
+date
+export PS4='+ $SECONDS + '
+set -xue
+
+export HOMEhafs=${HOMEhafs:?}
+export USHhafs=${USHhafs:-${HOMEhafs}/ush}
+export EXEChafs=${EXEChafs:-${HOMEhafs}/exec}
+export PARMhafs=${PARMhafs:-${HOMEhafs}/parm}
+export FIXhafs=${FIXhafs:-${HOMEhafs}/fix}
+
+source ${USHhafs}/hafs_pre_job.sh.inc
+source ${HOLDVARS:-storm1.holdvars.txt}
+
+export machine=${WHERE_AM_I:-wcoss_cray}
+export envir=${envir:-prod} # prod, para, test
+export RUN_ENVIR=${RUN_ENVIR:-dev} # nco or dev
+if [ "${RUN_ENVIR^^}" != NCO ]; then
+  module use ${HOMEhafs}/modulefiles
+  module load modulefile.hafs.${machine}
+  module list
+fi
+
+source ${USHhafs}/hafs_runcmd.sh.inc
+
+# Run setpdy and initialize PDY variables
+#setpdy.sh
+#. ./PDY
+export PDY=${PDY:-$(echo ${YMDH} | cut -c 1-8 )}
+
+export WORKhafs=${WORKhafs:?}
+export COMIN=${COMIN:?}
+export COMOUT=${COMOUT:?}
+export COMhafs=${COMhafs:-${COMOUT}}
+
+export CDATE=${CDATE:-${YMDH}}
+export cyc=${cyc:?}
+export STORM=${STORM:-FAKE}
+export STORMID=${STORMID:-00L}
+
+export DATA=${WORKhafs}/obs_proc
+
+export SCRUBDATA=${SCRUBDATA:-YES}
+if [ "${SCRUBDATA}" = YES ]; then
+  rm -rf $DATA
+fi
+
+mkdir -p $DATA
+cd $DATA
+
+# Execute ex-script
+${HOMEhafs}/scripts/exhafs_obs_proc.sh
+export err=$?
+exit $err
+
+export KEEPDATA=${KEEPDATA:-YES}
+if [ "${KEEPDATA^^}" != YES ]; then
+  rm -rf $DATA
+fi
+
+date

modulefiles/modulefile.hafs.hera

@@ -10,7 +10,7 @@ module use /contrib/sutils/modulefiles
 module load sutils
 module load hpss
 
-module load cmake/3.16.1
+module load cmake/3.20.1
 setenv CMAKE_C_COMPILER mpiicc
 setenv CMAKE_CXX_COMPILER mpiicpc
 setenv CMAKE_Fortran_COMPILER mpiifort
@@ -29,17 +29,25 @@ module load hdf5/1.10.6
 module load netcdf/4.7.4
 module load pio/2.5.2
 module load esmf/8_1_1
+module load fms/2020.04.03
 
 module load bacio/2.4.1
 module load crtm/2.3.0
-module load g2/3.4.1
-module load g2tmpl/1.9.1
+module load g2/3.4.2
+module load g2tmpl/1.10.0
 module load ip/3.3.3
 module load nemsio/2.5.2
 module load sp/2.3.3
 module load w3emc/2.7.3
 module load w3nco/2.4.1
-module load upp/10.0.4
+module load upp/10.0.8
+
+module load gftl-shared/v1.3.0
+module load yafyaml/v0.5.1
+module load mapl/v2.7.3
+
+# a temporary workaround, since hafs_gfs2ofs2.x needs g2/3.4.1.
+module load g2/3.4.1
 
 module load bufr/11.4.0
 module load gfsio/1.4.1

modulefiles/modulefile.hafs.jet

@@ -10,7 +10,7 @@ module use /contrib/sutils/modulefiles
 module load sutils
 module load hpss
 
-module load cmake/3.16.1
+module load cmake/3.20.1
 setenv CMAKE_C_COMPILER mpiicc
 setenv CMAKE_CXX_COMPILER mpiicpc
 setenv CMAKE_Fortran_COMPILER mpiifort
@@ -29,17 +29,25 @@ module load hdf5/1.10.6
 module load netcdf/4.7.4
 module load pio/2.5.2
 module load esmf/8_1_1
+module load fms/2020.04.03
 
 module load bacio/2.4.1
 module load crtm/2.3.0
-module load g2/3.4.1
-module load g2tmpl/1.9.1
+module load g2/3.4.2
+module load g2tmpl/1.10.0
 module load ip/3.3.3
 module load nemsio/2.5.2
 module load sp/2.3.3
 module load w3emc/2.7.3
 module load w3nco/2.4.1
-module load upp/10.0.4
+module load upp/10.0.8
+
+module load gftl-shared/v1.3.0
+module load yafyaml/v0.5.1
+module load mapl/v2.7.3
+
+# a temporary workaround, since hafs_gfs2ofs2.x needs g2/3.4.1.
+module load g2/3.4.1
 
 module load bufr/11.4.0
 module load gfsio/1.4.1

modulefiles/modulefile.hafs.orion

@@ -27,17 +27,25 @@ module load hdf5/1.10.6
 module load netcdf/4.7.4
 module load pio/2.5.2
 module load esmf/8_1_1
+module load fms/2020.04.03
 
 module load bacio/2.4.1
 module load crtm/2.3.0
-module load g2/3.4.1
-module load g2tmpl/1.9.1
+module load g2/3.4.2
+module load g2tmpl/1.10.0
 module load ip/3.3.3
 module load nemsio/2.5.2
 module load sp/2.3.3
 module load w3emc/2.7.3
 module load w3nco/2.4.1
-module load upp/10.0.4
+module load upp/10.0.8
+
+module load gftl-shared/v1.3.0
+module load yafyaml/v0.5.1
+module load mapl/v2.7.3
+
+# a temporary workaround, since hafs_gfs2ofs2.x needs g2/3.4.1.
+module load g2/3.4.1
 
 module load bufr/11.4.0
 module load gfsio/1.4.1

modulefiles/modulefile.hafs.wcoss_cray

@@ -36,13 +36,16 @@ module load pio/2.5.2
 module load bacio/2.4.1
 module load crtm/2.3.0
 module load g2/3.4.1
-module load g2tmpl/1.9.1
+module load g2tmpl/1.10.0
 module load ip/3.3.3
 module load nemsio/2.5.2
 module load sp/2.3.3
 module load w3emc/2.7.3
 module load w3nco/2.4.1
-module load upp/10.0.4
+module load upp/10.0.8
+
+# a temporary workaround, since hafs_gfs2ofs2.x needs g2/3.4.1.
+module load g2/3.4.1
 
 module load bufr/11.4.0
 module load gfsio/1.4.1
@@ -60,6 +63,7 @@ module load wgrib2/2.0.8
 #doesn't work setenv WGRIB2 /usrx/local/nceplibs/NCEPLIBS/cmake/install/NCEPLIBS-v1.3.0/wgrib2/wgrib2-2.0.8/bin/wgrib2
 
 module load esmf/811
+module load fms/2020.04.03
 
 ## WCOSS Cray execution prereqs:
 module load rca

modulefiles/modulefile.hafs.wcoss_dell_p3

@@ -10,11 +10,11 @@ module load ips/18.0.1.163
 module load impi/18.0.1
 module load lsf/10.1
 module load python/3.6.3
-module load cmake/3.16.2
 
 module use /usrx/local/nceplibs/dev/hpc-stack/libs/hpc-stack/modulefiles/stack
 
 module load hpc/1.1.0
+module load cmake/3.20.0
 module load hpc-ips/18.0.1.163
 module load hpc-impi/18.0.1
 
@@ -26,17 +26,25 @@ module load hdf5/1.10.6
 module load netcdf/4.7.4
 module load pio/2.5.2
 module load esmf/8_1_1
+module load fms/2020.04.03
 
 module load bacio/2.4.1
 module load crtm/2.3.0
-module load g2/3.4.1
-module load g2tmpl/1.9.1
+module load g2/3.4.2
+module load g2tmpl/1.10.0
 module load ip/3.3.3
 module load nemsio/2.5.2
 module load sp/2.3.3
 module load w3emc/2.7.3
 module load w3nco/2.4.1
-module load upp/10.0.4
+module load upp/10.0.8
+
+module load gftl-shared/v1.3.0
+module load yafyaml/v0.5.1
+module load mapl/v2.7.3
+
+# a temporary workaround, since hafs_gfs2ofs2.x needs g2/3.4.1. 
+module load g2/3.4.1
 
 module load bufr/11.4.0
 module load gfsio/1.4.1

parm/analysis/gsi/bufrinfo.json.tempdrop

@@ -0,0 +1,7 @@
+[
+    {
+        "obs_type_mass": 137,
+        "obs_type_wind": 237,
+        "subset": "ADPUPA"
+    }
+]

parm/analysis/gsi/enkf.nml.tmp

@@ -2,10 +2,10 @@
    datestring="_datestring_",datapath="./",
    analpertwtnh=0.85,analpertwtsh=0.85,analpertwttr=0.85,
    covinflatemax=1.e2,covinflatemin=1,pseudo_rh=.true.,iassim_order=0,
-   corrlengthnh=400,corrlengthsh=400,corrlengthtr=400,
-   lnsigcutoffnh=0.5,lnsigcutoffsh=0.5,lnsigcutofftr=0.5,
-   lnsigcutoffpsnh=0.5,lnsigcutoffpssh=0.5,lnsigcutoffpstr=0.5,
-   lnsigcutoffsatnh=0.5,lnsigcutoffsatsh=0.5,lnsigcutoffsattr=0.5,
+   corrlengthnh=_corrlength_,corrlengthsh=_corrlength_,corrlengthtr=_corrlength_,
+   lnsigcutoffnh=_lnsigcutoff_,lnsigcutoffsh=_lnsigcutoff_,lnsigcutofftr=_lnsigcutoff_,
+   lnsigcutoffpsnh=_lnsigcutoff_,lnsigcutoffpssh=_lnsigcutoff_,lnsigcutoffpstr=_lnsigcutoff_,
+   lnsigcutoffsatnh=_lnsigcutoff_,lnsigcutoffsatsh=_lnsigcutoff_,lnsigcutoffsattr=_lnsigcutoff_,
    obtimelnh=1.e30,obtimelsh=1.e30,obtimeltr=1.e30,
    saterrfact=1.0,numiter=1,
    sprd_tol=1.e30,paoverpb_thresh=0.98,

parm/analysis/gsi/gsiparm.anl.tmp

@@ -229,8 +229,8 @@ SUPEROB_RADAR::
   n_ens=_N_ENS_,
   uv_hyb_ens=T,
   beta_s0=_BETA_S0_,
-  s_ens_h=300,
-  s_ens_v=-0.5,
+  s_ens_h=_S_ENS_H_,
+  s_ens_v=_S_ENS_V_,
   readin_localization=F,
   generate_ens=F,
   regional_ensemble_option=_REGIONAL_ENSEMBLE_OPTION_,

parm/analysis/gsi/hafs_convinfo.txt

@@ -30,30 +30,30 @@
  t        126    0   -1     3.0      0      0      0   8.0   5.6   1.3   8.0  0.001000     0    0.     0.      0    0.     0.
  t        130    0    1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.001000     0    0.     0.      0    0.     0.
  t        131    0    1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.001000     0    0.     0.      0    0.     0.
- t        132    0    1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.001000     0    0.     0.      0    0.     0.
+ t        132    0   -1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.001000     0    0.     0.      0    0.     0.
  t        133    0    1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.004000     0    0.     0.      0    0.     0.
  t        134    0   -1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.004000     0    0.     0.      0    0.     0.
  t        135    0   -1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.004000     0    0.     0.      0    0.     0.
  t        136    0    1     3.0      0      0      0   2.0   5.6   1.3  10.0  0.000000     0    0.     0.      0    0.     0.
  t        137    0    1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.001000     0    0.     0.      0    0.     0.
  t        180    0    1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.004000     0    0.     0.      0    0.     0.
  t        180    01   1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.004000     0    0.     0.      0    0.     0.
- t        181    0   -1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.004000     0    0.     0.      0    0.     0.
+ t        181    0    1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.004000     0    0.     0.      0    0.     0.
  t        182    0    1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.004000     0    0.     0.      0    0.     0.
  t        183    0   -1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.004000     0    0.     0.      0    0.     0.
  t        187    0   -1     3.0      0      0      0   7.0   5.6   1.3   7.0  0.004000     0    0.     0.      0    0.     0.
  q        120    0    1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000500     0    0.     0.      0    0.     0.
  q        130    0   -1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000600     0    0.     0.      0    0.     0.
  q        131    0   -1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000600     0    0.     0.      0    0.     0.
- q        132    0    1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000600     0    0.     0.      0    0.     0.
+ q        132    0   -1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000600     0    0.     0.      0    0.     0.
  q        133    0    1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000600     0    0.     0.      0    0.     0.
  q        134    0   -1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000600     0    0.     0.      0    0.     0.
  q        135    0   -1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000600     0    0.     0.      0    0.     0.
  q        136    0    1     3.0      0      0      0   2.0  50.0   5.0  10.0  0.000000     0    0.     0.      0    0.     0.
  q        137    0    1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000600     0    0.     0.      0    0.     0.
  q        180    0    1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000500     0    0.     0.      0    0.     0.
  q        180    01   1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000500     0    0.     0.      0    0.     0.
- q        181    0   -1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000500     0    0.     0.      0    0.     0.
+ q        181    0    1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000500     0    0.     0.      0    0.     0.
  q        182    0    1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000600     0    0.     0.      0    0.     0.
  q        183    0   -1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000600     0    0.     0.      0    0.     0.
  q        187    0   -1     3.0      0      0      0   8.0 100.0  10.0   8.0  0.000600     0    0.     0.      0    0.     0.
@@ -94,7 +94,7 @@
  uv       229    0    1     3.0      0      0      0   6.5   6.1   1.4   6.5  0.000001     0    0.     0.      0    0.     0.
  uv       230    0    1     3.0      0      0      0   6.0   6.1   1.4   6.0  0.000100     0    0.     0.      0    0.     0.
  uv       231    0    1     3.0      0      0      0   6.5   6.1   1.4   6.5  0.000100     0    0.     0.      0    0.     0.
- uv       232    0    1     3.0      0      0      0   7.0   6.1   1.4   7.0  0.000100     0    0.     0.      0    0.     0.
+ uv       232    0   -1     3.0      0      0      0   7.0   6.1   1.4   7.0  0.000100     0    0.     0.      0    0.     0.
  uv       233    0    1     3.0      0      0      0   7.5   6.1   1.4   7.5  0.000100     0    0.     0.      0    0.     0.
  uv       234    0    1     3.0      0      0      0   7.5   6.1   1.4   7.5  0.000100     0    0.     0.      0    0.     0.
  uv       235    0    1     3.0      0      0      0   7.5   6.1   1.4   7.5  0.000100     0    0.     0.      0    0.     0.