Refactor UFS-DA ATM var component to use python g-w (#1372)

This PR contains UFS-DA ATM var changes in PR #1354. Below is a list of changes in this PR - rename UFS-DA ATM var jobs `atmanalprep`, `atmanalrun`, and `atmanalpost` as `atmanlinit`, `atmanlrun`, and `atmanlfinal`, respectively - replace UFS-DA ATM var shell scripts with python scripts - rename UFS-DA ATM var j-jobs consistent with initialize, run, and finalize functions. Update j-jobs to execute python scripts instead of shell scripts - rename UFS-DA ATM var rocoto jobs to be consistent with initialize, run, and finalize functions. Update jobs to set python paths and execute renamed j-jobs - update rocoto workflow generation to new names for UFS-DA ATM var jobs - update UFS-DA ATM var job names in machine dependent `env` files to new job names - rename UFS-DA ATM var configuration files consistent with change in job names - add UFS-DA ATM yaml files for UFS-DA fix files, crtm files, and increments - add python class for UFS-DA ATM var analysis - link UFS-DA python increment conversion script from GDASApp to g-w `ush` directory The above changes are part of a larger g-w effort to transition from shell scripts to python. UFS-DA Aerosol was the first GDASApp system to be converted. This PR represents the second GDASApp system, UFS-DA atmospheric variational DA, to be converted. PR #1373 contains changes to convert the UFS-DA ensemble DA to a python based approach. Fixes (in part) #1313 Depends (in part) on PR #1370 and [GDASApp #388](NOAA-EMC/GDASApp#388)
NOAA-EMC · Apr 18, 2023 · b2ed864 · b2ed864
1 parent 70a7d99
commit b2ed864
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diff --git a/.gitignore b/.gitignore
@@ -129,6 +129,7 @@ ush/global_chgres.sh
 ush/global_chgres_driver.sh
 ush/global_cycle.sh
 ush/global_cycle_driver.sh
+ush/jediinc2fv3.py
 ush/mkwfsgbl.sh
 ush/ufsda
 ush/wafs_blending.sh

diff --git a/env/CONTAINER.env b/env/CONTAINER.env
@@ -4,8 +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 "aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"

diff --git a/env/HERA.env b/env/HERA.env
@@ -4,8 +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 "aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -49,22 +48,16 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
     export wavempexec=${launcher}
     export wave_mpmd=${mpmd_opt}
 
-elif [[ "${step}" = "atmanalrun" ]]; then
+elif [[ "${step}" = "atmanlrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
-    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
+    nth_max=$((npe_node_max / npe_node_atmanlrun))
 
-    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 ${npe_atmanalrun}"
+    export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
+    [[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
+    export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"
 
 elif [[ "${step}" = "atmensanalrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
     nth_max=$((npe_node_max / npe_node_atmensanalrun))

diff --git a/env/JET.env b/env/JET.env
@@ -4,7 +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 aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -47,17 +47,13 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
     export wavempexec=${launcher}
     export wave_mpmd=${mpmd_opt}
 
-elif [[ "${step}" = "atmanalrun" ]]; then
+elif [[ "${step}" = "atmanlrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
-    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-
-    nth_max=$((npe_node_max / npe_node_atmanalrun))
+    nth_max=$((npe_node_max / npe_node_atmanlrun))
 
-    export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
-    [[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
-    export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
+    export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
+    [[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
+    export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"
 
 elif [[ "${step}" = "atmensanalrun" ]]; then
 

diff --git a/env/ORION.env b/env/ORION.env
@@ -4,8 +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 "aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -49,17 +48,13 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
     export wavempexec=${launcher}
     export wave_mpmd=${mpmd_opt}
 
-elif [[ "${step}" = "atmanalrun" ]]; then
+elif [[ "${step}" = "atmanlrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
-    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-
-    nth_max=$((npe_node_max / npe_node_atmanalrun))
+    nth_max=$((npe_node_max / npe_node_atmanlrun))
 
-    export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
-    [[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
-    export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
+    export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
+    [[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
+    export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"
 
 elif [[ "${step}" = "atmensanalrun" ]]; then
 

diff --git a/env/S4.env b/env/S4.env
@@ -4,8 +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 "aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -47,17 +46,13 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
     export wavempexec=${launcher}
     export wave_mpmd=${mpmd_opt}
 
-elif [[ "${step}" = "atmanalrun" ]]; then
+elif [[ "${step}" = "atmanlrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
-    export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-
-    nth_max=$((npe_node_max / npe_node_atmanalrun))
+    nth_max=$((npe_node_max / npe_node_atmanlrun))
 
-    export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
-    [[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
-    export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
+    export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
+    [[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
+    export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"
 
 elif [[ "${step}" = "atmensanalrun" ]]; then
 

diff --git a/env/WCOSS2.env b/env/WCOSS2.env
@@ -4,8 +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 "aeroanlrun"
+    echo "atmanlrun atmensanalrun aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen esfc efcs epos"
     echo "postsnd awips gempak"
@@ -36,17 +35,13 @@ elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}
     export wavempexec="${launcher} -np"
     export wave_mpmd=${mpmd_opt}
 
-elif [[ "${step}" = "atmanalrun" ]]; then
+elif [[ "${step}" = "atmanlrun" ]]; then
 
-    export CFP_MP=${CFP_MP:-"YES"}
-    export USE_CFP=${USE_CFP:-"YES"}
-    export APRUNCFP="${launcher} -np \$ncmd ${mpmd_opt}"
-
-    nth_max=$((npe_node_max / npe_node_atmanalrun))
+    nth_max=$((npe_node_max / npe_node_atmanlrun))
 
-    export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
-    [[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
-    export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"
+    export NTHREADS_ATMANL=${nth_atmanlrun:-${nth_max}}
+    [[ ${NTHREADS_ATMANL} -gt ${nth_max} ]] && export NTHREADS_ATMANL=${nth_max}
+    export APRUN_ATMANL="${launcher} -n ${npe_atmanlrun}"
 
 elif [[ "${step}" = "atmensanalrun" ]]; then
 

diff --git a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST b/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST
diff --git a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP b/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP
diff --git a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN b/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN