Add GDASapp (first wave of JEDI changes)

.gitignore

@@ -82,6 +82,7 @@ sorc/gldas.fd
 sorc/gsi_enkf.fd
 sorc/gsi.fd
 sorc/enkf.fd
+sorc/gdas.cd
 sorc/gsi_utils.fd
 sorc/gsi_monitor.fd
 sorc/ufs_utils.fd
@@ -145,6 +146,12 @@ jobs/JGFS_ATMOS_WAFS_BLENDING_0P25
 jobs/JGFS_ATMOS_WAFS_GCIP
 jobs/JGFS_ATMOS_WAFS_GRIB2
 jobs/JGFS_ATMOS_WAFS_GRIB2_0P25
+jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST
+jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP
+jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN
+jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_POST
+jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_PREP
+jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_RUN
 # scripts symlinks
 scripts/exemcsfc_global_sfc_prep.sh
 scripts/exgdas_atmos_gldas.sh
@@ -188,6 +195,7 @@ ush/radmon_verf_angle.sh
 ush/radmon_verf_bcoef.sh
 ush/radmon_verf_bcor.sh
 ush/radmon_verf_time.sh
+ush/ufsda
 ush/wafs_blending.sh
 ush/wafs_grib2.regrid.sh
 ush/wafs_intdsk.sh

env/HERA.env

@@ -4,6 +4,7 @@ if [ $# -ne 1 ]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
+    echo "atmanalrun atmensanalrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -50,6 +51,30 @@ elif [ $step = "waveinit" -o $step = "waveprep" -o $step = "wavepostsbs" -o $ste
     export wavempexec=${launcher}
     export wave_mpmd=${mpmd}
 
+elif [ $step = "atmanalrun" ]; then
+
+    export CFP_MP=${CFP_MP:-"YES"}
+    export USE_CFP=${USE_CFP:-"YES"}
+    export APRUNCFP="$launcher -n \$ncmd --multi-prog"
+
+    nth_max=$(($npe_node_max / $npe_node_atmanalrun))
+
+    export NTHREADS_ATMANAL=${nth_atmanalrun:-$nth_max}
+    [[ $NTHREADS_ATMANAL -gt $nth_max ]] && export NTHREADS_ATMANAL=$nth_max
+    export APRUN_ATMANAL="$launcher -n $npe_atmanalrun"
+
+elif [ $step = "atmensanalrun" ]; then
+
+    export CFP_MP=${CFP_MP:-"YES"}
+    export USE_CFP=${USE_CFP:-"YES"}
+    export APRUNCFP="$launcher -n \$ncmd --multi-prog"
+
+    nth_max=$(($npe_node_max / $npe_node_atmensanalrun))
+
+    export NTHREADS_ATMENSANAL=${nth_atmensanalrun:-$nth_max}
+    [[ $NTHREADS_ATMENSANAL -gt $nth_max ]] && export NTHREADS_ATMENSANAL=$nth_max
+    export APRUN_ATMENSANAL="$launcher -n $npe_atmensanalrun"
+
 elif [ $step = "anal" ]; then
 
     export MKL_NUM_THREADS=4

env/JET.env

@@ -4,6 +4,7 @@ if [ $# -ne 1 ]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
+    echo "atmanalrun atmensanalrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -44,6 +45,22 @@ elif [ $step = "waveinit" -o $step = "waveprep" -o $step = "wavepostsbs" -o $ste
     export wavempexec=${launcher}
     export wave_mpmd=${mpmd}
 
+elif [ $step = "atmanalrun" ]; then
+
+    nth_max=$(($npe_node_max / $npe_node_atmanalrun))
+
+    export NTHREADS_ATMANAL=${nth_atmanalrun:-$nth_max}
+    [[ $NTHREADS_ATMANAL -gt $nth_max ]] && export NTHREADS_ATMANAL=$nth_max
+    export APRUN_ATMANAL="$launcher $npe_atmanalrun"
+
+elif [ $step = "atmensanalrun" ]; then
+
+    nth_max=$(($npe_node_max / $npe_node_atmensanalrun))
+
+    export NTHREADS_ATMENSANAL=${nth_atmensanalrun:-$nth_max}
+    [[ $NTHREADS_ATMENSANAL -gt $nth_max ]] && export NTHREADS_ATMENSANAL=$nth_max
+    export APRUN_ATMENSANAL="$launcher $npe_atmensanalrun"
+
 elif [ $step = "anal" ]; then
 
     nth_max=$(($npe_node_max / $npe_node_anal))

env/ORION.env

@@ -4,6 +4,7 @@ if [ $# -ne 1 ]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
+    echo "atmanalrun atmensanalrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -49,6 +50,30 @@ elif [ $step = "waveinit" -o $step = "waveprep" -o $step = "wavepostsbs" -o $ste
     export wavempexec=${launcher}
     export wave_mpmd=${mpmd}
 
+elif [ $step = "atmanalrun" ]; then
+
+    export CFP_MP=${CFP_MP:-"YES"}
+    export USE_CFP=${USE_CFP:-"YES"}
+    export APRUNCFP="$launcher -n \$ncmd --multi-prog"
+
+    nth_max=$(($npe_node_max / $npe_node_atmanalrun))
+
+    export NTHREADS_ATMANAL=${nth_atmanalrun:-$nth_max}
+    [[ $NTHREADS_ATMANAL -gt $nth_max ]] && export NTHREADS_ATMANAL=$nth_max
+    export APRUN_ATMANAL="$launcher -n $npe_atmanalrun"
+
+elif [ $step = "atmensanalrun" ]; then
+
+    export CFP_MP=${CFP_MP:-"YES"}
+    export USE_CFP=${USE_CFP:-"YES"}
+    export APRUNCFP="$launcher -n \$ncmd --multi-prog"
+
+    nth_max=$(($npe_node_max / $npe_node_atmensanalrun))
+
+    export NTHREADS_ATMENSANAL=${nth_atmensanalrun:-$nth_max}
+    [[ $NTHREADS_ATMENSANAL -gt $nth_max ]] && export NTHREADS_ATMENSANAL=$nth_max
+    export APRUN_ATMENSANAL="$launcher -n $npe_atmensanalrun"
+
 elif [ $step = "anal" ]; then
 
     export MKL_NUM_THREADS=4

jobs/rocoto/atmanalpost.sh

@@ -0,0 +1,13 @@
+#!/bin/bash -x
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# Execute the JJOB
+$HOMEgfs/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST
+status=$?
+exit $status

jobs/rocoto/atmanalprep.sh

@@ -0,0 +1,13 @@
+#!/bin/bash -x
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# Execute the JJOB
+$HOMEgfs/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP
+status=$?
+exit $status

jobs/rocoto/atmanalrun.sh

@@ -0,0 +1,13 @@
+#!/bin/bash -x
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# Execute the JJOB
+$HOMEgfs/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN
+status=$?
+exit $status

jobs/rocoto/atmensanalpost.sh

@@ -0,0 +1,13 @@
+#!/bin/bash -x
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# Execute the JJOB
+$HOMEgfs/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_POST
+status=$?
+exit $status

jobs/rocoto/atmensanalprep.sh

@@ -0,0 +1,13 @@
+#!/bin/bash -x
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# Execute the JJOB
+$HOMEgfs/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_PREP
+status=$?
+exit $status

jobs/rocoto/atmensanalrun.sh

@@ -0,0 +1,13 @@
+#!/bin/bash -x
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# Execute the JJOB
+$HOMEgfs/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_RUN
+status=$?
+exit $status

parm/config/config.atmanal

@@ -0,0 +1,24 @@
+#!/bin/bash -x
+
+########## config.atmanal ##########
+# configuration common to all atm analysis tasks
+
+echo "BEGIN: config.atmanal"
+
+export OBS_YAML_DIR=$HOMEgfs/sorc/gdas.cd/parm/atm/obs/config/
+export OBS_LIST=$HOMEgfs/sorc/gdas.cd/parm/atm/obs/lists/gdas_prototype.yaml
+export ATMVARYAML=$HOMEgfs/sorc/gdas.cd/parm/atm/variational/3dvar_dripcg.yaml
+export BERROR_YAML=$HOMEgfs/sorc/gdas.cd/parm/atm/berror/hybvar_bump.yaml
+export FV3JEDI_FIX=$HOMEgfs/fix/fix_jedi
+export R2D2_OBS_DB='ufsda_test'
+export R2D2_OBS_DUMP='oper_gdas'
+export R2D2_OBS_SRC='ncdiag'
+export R2D2_BC_SRC='gsi'
+export R2D2_BC_DUMP='oper_gdas'
+export R2D2_ARCH_DB='local'
+export INTERP_METHOD='barycentric'
+
+export io_layout_x=1
+export io_layout_y=1
+
+echo "END: config.atmanal"

parm/config/config.atmanalpost

@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+########## config.atmanalpost ##########
+# Post Atm Analysis specific
+
+echo "BEGIN: config.atmanalpost"
+
+# Get task specific resources
+. $EXPDIR/config.resources atmanalpost
+echo "END: config.atmanalpost"

parm/config/config.atmanalprep

@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+########## config.atmanalprep ##########
+# Pre Atm Analysis specific
+
+echo "BEGIN: config.atmanalprep"
+
+# Get task specific resources
+. $EXPDIR/config.resources atmanalprep
+echo "END: config.atmanalprep"

parm/config/config.atmanalrun

@@ -0,0 +1,14 @@
+#!/bin/bash -x
+
+########## config.atmanalrun ##########
+# Atm Analysis specific
+
+echo "BEGIN: config.atmanalrun"
+
+# Get task specific resources
+. $EXPDIR/config.resources atmanalrun
+
+# Task specific variables
+export JEDIVAREXE=$HOMEgfs/exec/fv3jedi_var.x
+
+echo "END: config.atmanalrun"

parm/config/config.atmensanal

@@ -0,0 +1,25 @@
+#!/bin/bash -x
+
+########## config.atmensanal ##########
+# configuration common to all atm atmensanal analysis tasks
+
+echo "BEGIN: config.atmensanal"
+
+export OBS_YAML_DIR=$HOMEgfs/sorc/gdas.cd/parm/atm/obs/config/
+export OBS_LIST=$HOMEgfs/sorc/gdas.cd/parm/atm/obs/lists/lgetkf_prototype.yaml
+export BERROR_YAML=$HOMEgfs/sorc/gdas.cd/parm/atm/berror/hybvar_bump.yaml
+export ATMENSYAML=$HOMEgfs/sorc/gdas.cd/parm/atm/lgetkf/lgetkf.yaml
+export FV3JEDI_FIX=$HOMEgfs/fix/fix_jedi
+export R2D2_OBS_DB='ufsda_test'
+export R2D2_OBS_DUMP='oper_gdas'
+export R2D2_OBS_SRC='ncdiag'
+export R2D2_BC_SRC='gsi'
+##export R2D2_BC_DUMP='oper_gdas'
+export R2D2_BC_DUMP='prgdasens'
+export R2D2_ARCH_DB='local'
+export INTERP_METHOD='barycentric'
+
+export io_layout_x=1  # hardwired to 1,1 in yamltools.py
+export io_layout_y=1
+
+echo "END: config.atmensanal"

parm/config/config.atmensanalpost

@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+########## config.atmensanalpost ##########
+# Post Atm Analysis specific
+
+echo "BEGIN: config.atmensanalpost"
+
+# Get task specific resources
+. $EXPDIR/config.resources atmensanalpost
+echo "END: config.atmensanalpost"

parm/config/config.atmensanalprep

@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+########## config.atmensanalprep ##########
+# Pre Atm Analysis specific
+
+echo "BEGIN: config.atmensanalprep"
+
+# Get task specific resources
+. $EXPDIR/config.resources atmensanalprep
+echo "END: config.atmensanalprep"

parm/config/config.atmensanalrun

@@ -0,0 +1,14 @@
+#!/bin/bash -x
+
+########## config.atmensanalrun ##########
+# Atm LETKFs specific
+
+echo "BEGIN: config.atmensanalrun"
+
+# Get task specific resources
+. $EXPDIR/config.resources atmensanalrun
+
+# Task specific variables
+export JEDIENSEXE=$HOMEgfs/exec/fv3jedi_letkf.x
+
+echo "END: config.atmensanalrun"

parm/config/config.base.emc.dyn

@@ -320,6 +320,10 @@ fi
 export imp_physics=8
 
 # Shared parameters
+# DA engine
+export DO_JEDIVAR="NO"
+export DO_JEDIENS="NO"
+
 # Hybrid related
 export DOHYBVAR="YES"
 export NMEM_ENKF=@NMEM_ENKF@

parm/config/config.base.nco.static

@@ -215,6 +215,9 @@ export DOBNDPNT_WAVE="YES"
 export imp_physics=8
 
 # Shared parameters
+# DA engine
+export DO_JEDIVAR="NO"
+
 # Hybrid related
 export DOHYBVAR="YES"
 export NMEM_ENKF="80"