Merge branch 'feature/simplify_res' of github.com:davidhuber-noaa/glo…

…bal-workflow into feature/simplify_res

* 'feature/simplify_res' of github.com:davidhuber-noaa/global-workflow:
  Temporarily disable METplus jobs (#2796)
  Remove local declaration
  Remove unneeded _RUN_LIST
  Apply suggestions from code review
  Remove 'gefs' from default _RUN_LIST
  Replace CDUMP with RUN_local/RUN
  Require config.resources to be sourced for each job
  Remove unused ppn and nprocs from env files
  Refactoring of the marine B-matrix job (#2749)

ci/cases/gfsv17/ocnanal.yaml

@@ -14,17 +14,14 @@ base:
   DO_VERFRAD: "YES"
   DO_VRFY_OCEANDA: "NO"
   FHMAX_GFS: 240
+  ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
 
 ocnanal:
-  SOCA_INPUT_FIX_DIR: /scratch2/NCEPDEV/ocean/Guillaume.Vernieres/data/static/1440x1080x75/soca
-  CASE_ANL: 'C24'
+  SOCA_INPUT_FIX_DIR: {{ FIXgfs }}/gdas/soca/1440x1080x75/soca
   SOCA_OBS_LIST: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
   SOCA_NINNER: 100
-  SABER_BLOCKS_YAML: ''
-  NICAS_RESOL: 1
-  NICAS_GRID_SIZE: 15000
 
 prepoceanobs:
-  SOCA_OBS_LIST: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml 
+  SOCA_OBS_LIST: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
   OBSPREP_YAML: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obsprep/obsprep_config.yaml
   DMPDIR: /scratch1/NCEPDEV/da/common/

env/AWSPW.env

@@ -28,6 +28,9 @@ if [[ -n "${ntasks:-}" && -n "${max_tasks_per_node:-}" && -n "${tasks_per_node:-
     [[ ${NTHREADSmax} -gt ${max_threads_per_task} ]] && NTHREADSmax=${max_threads_per_task}
     [[ ${NTHREADS1} -gt ${max_threads_per_task} ]] && NTHREADS1=${max_threads_per_task}
     APRUN="${launcher} -n ${ntasks}"
+else
+    echo "ERROR config.resources must be sourced before sourcing AWSPW.env"
+    exit 2
 fi
 
 if [[ "${step}" = "fcst" ]] || [[ "${step}" = "efcs" ]]; then

env/GAEA.env

@@ -29,6 +29,9 @@ if [[ -n "${ntasks:-}" && -n "${max_tasks_per_node:-}" && -n "${tasks_per_node:-
     # This may be useful when Gaea is fully ported, so ignore SC warning
     # shellcheck disable=SC2034
     APRUN="${launcher} -n ${ntasks}"
+else
+    echo "ERROR config.resources must be sourced before sourcing GAEA.env"
+    exit 2
 fi
 
 if [[ "${step}" = "waveinit" ]]; then

env/HERA.env

@@ -40,6 +40,9 @@ if [[ -n "${ntasks:-}" && -n "${max_tasks_per_node:-}" && -n "${tasks_per_node:-
     [[ ${NTHREADSmax} -gt ${max_threads_per_task} ]] && NTHREADSmax=${max_threads_per_task}
     [[ ${NTHREADS1} -gt ${max_threads_per_task} ]] && NTHREADS1=${max_threads_per_task}
     APRUN="${launcher} -n ${ntasks}"
+else
+    echo "ERROR config.resources must be sourced before sourcing HERA.env"
+    exit 2
 fi
 
 if [[ "${step}" = "prep" ]] || [[ "${step}" = "prepbufr" ]]; then
@@ -103,11 +106,15 @@ elif [[ "${step}" = "snowanl" ]]; then
 
     export APRUN_APPLY_INCR="${launcher} -n 6"
 
-elif [[ "${step}" = "ocnanalbmat" ]]; then
+elif [[ "${step}" = "marinebmat" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
+    export APRUN_MARINEBMAT="${APRUN}"
 
-    export APRUN_OCNANAL="${APRUN}"
+elif [[ "${step}" = "marinebmat" ]]; then
+
+    export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
+    export APRUN_MARINEBMAT="${APRUN}"
 
 elif [[ "${step}" = "ocnanalrun" ]]; then
 
@@ -184,11 +191,6 @@ elif [[ "${step}" = "eupd" ]]; then
 
 elif [[ "${step}" = "fcst" ]] || [[ "${step}" = "efcs" ]]; then
 
-    ppn="tasks_per_node"
-    [[ -z "${!ppn+0}" ]] && ppn="tasks_per_node"
-    nprocs="ntasks"
-    [[ -z ${!nprocs+0} ]] && nprocs="ntasks"
-
     (( nnodes = (ntasks+tasks_per_node-1)/tasks_per_node ))
     (( ufs_ntasks = nnodes*tasks_per_node ))
     # With ESMF threading, the model wants to use the full node

env/HERCULES.env

@@ -37,6 +37,9 @@ if [[ -n "${ntasks:-}" && -n "${max_tasks_per_node:-}" && -n "${tasks_per_node:-
     [[ ${NTHREADSmax} -gt ${max_threads_per_task} ]] && NTHREADSmax=${max_threads_per_task}
     [[ ${NTHREADS1} -gt ${max_threads_per_task} ]] && NTHREADS1=${max_threads_per_task}
     APRUN="${launcher} -n ${ntasks}"
+else
+    echo "ERROR config.resources must be sourced before sourcing HERCULES.env"
+    exit 2
 fi
 
 case ${step} in
@@ -102,19 +105,15 @@ case ${step} in
 
     export APRUN_APPLY_INCR="${launcher} -n 6"
  ;;
- "ocnanalbmat")
+ "marinebmat")
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-
-    export NTHREADS_OCNANAL=${NTHREADSmax}
-    export APRUN_OCNANAL="${APRUN} --cpus-per-task=${NTHREADS_OCNANAL}"
+    export APRUN_MARINEBMAT="${APRUN}"
  ;;
  "ocnanalrun")
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-
-    export NTHREADS_OCNANAL=${NTHREADSmax}
-    export APRUN_OCNANAL="${APRUN} --cpus-per-task=${NTHREADS_OCNANAL}"
+    export APRUN_OCNANAL="${APRUN}"
  ;;
 "ocnanalecen")
 

env/JET.env

@@ -28,6 +28,9 @@ if [[ -n "${ntasks:-}" && -n "${max_tasks_per_node:-}" && -n "${tasks_per_node:-
     [[ ${NTHREADSmax} -gt ${max_threads_per_task} ]] && NTHREADSmax=${max_threads_per_task}
     [[ ${NTHREADS1} -gt ${max_threads_per_task} ]] && NTHREADS1=${max_threads_per_task}
     APRUN="${launcher} -n ${ntasks}"
+else
+    echo "ERROR config.resources must be sourced before sourcing JET.env"
+    exit 2
 fi
 
 if [[ "${step}" = "prep" ]] || [[ "${step}" = "prepbufr" ]]; then
@@ -91,18 +94,14 @@ elif [[ "${step}" = "atmanlfv3inc" ]]; then
     export NTHREADS_ATMANLFV3INC=${NTHREADSmax}
     export APRUN_ATMANLFV3INC="${APRUN}"
 
-elif [[ "${step}" = "ocnanalbmat" ]]; then
+elif [[ "${step}" = "marinebmat" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-
-    export NTHREADS_OCNANAL=${NTHREADSmax}
-    export APRUN_OCNANAL="${APRUN}"
+    export APRUN_MARINEBMAT="${APRUN}"
 
 elif [[ "${step}" = "ocnanalrun" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-
-    export NTHREADS_OCNANAL=${NTHREADSmax}
     export APRUN_OCNANAL="${APRUN}"
 
 elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then

env/ORION.env

@@ -35,6 +35,9 @@ if [[ -n "${ntasks:-}" && -n "${max_tasks_per_node:-}" && -n "${tasks_per_node:-
     [[ ${NTHREADSmax} -gt ${max_threads_per_task} ]] && NTHREADSmax=${max_threads_per_task}
     [[ ${NTHREADS1} -gt ${max_threads_per_task} ]] && NTHREADS1=${max_threads_per_task}
     APRUN="${launcher} -n ${ntasks}"
+else
+    echo "ERROR config.resources must be sourced before sourcing ORION.env"
+    exit 2
 fi
 
 if [[ "${step}" = "prep" ]] || [[ "${step}" = "prepbufr" ]]; then
@@ -99,19 +102,18 @@ elif [[ "${step}" = "atmanlfv3inc" ]]; then
     export NTHREADS_ATMANLFV3INC=${NTHREADSmax}
     export APRUN_ATMANLFV3INC="${APRUN} --cpus-per-task=${NTHREADS_ATMANLFV3INC}"
 
-elif [[ "${step}" = "ocnanalbmat" ]]; then
+elif [[ "${step}" = "marinebmat" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
-    export NTHREADS_OCNANAL=${NTHREADSmax}
-    export APRUN_OCNANAL="${APRUN} --cpus-per-task=${NTHREADS_OCNANAL}"
+    export NTHREADS_MARINEBMAT=${NTHREADSmax}
+    export APRUN_MARINEBMAT="${APRUN}"
 
 elif [[ "${step}" = "ocnanalrun" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
-    export NTHREADS_OCNANAL=${NTHREADSmax}
-    export APRUN_OCNANAL="${APRUN} --cpus-per-task=${NTHREADS_OCNANAL}"
+    export APRUN_OCNANAL="${APRUN}"
 
 elif [[ "${step}" = "ocnanalchkpt" ]]; then
 

env/S4.env

@@ -28,6 +28,9 @@ if [[ -n "${ntasks:-}" && -n "${max_tasks_per_node:-}" && -n "${tasks_per_node:-
     [[ ${NTHREADSmax} -gt ${max_threads_per_task} ]] && NTHREADSmax=${max_threads_per_task}
     [[ ${NTHREADS1} -gt ${max_threads_per_task} ]] && NTHREADS1=${max_threads_per_task}
     APRUN="${launcher} -n ${ntasks}"
+else
+    echo "ERROR config.resources must be sourced before sourcing S4.env"
+    exit 2
 fi
 
 if [[ "${step}" = "prep" ]] || [[ "${step}" = "prepbufr" ]]; then
@@ -91,10 +94,10 @@ elif [[ "${step}" = "atmanlfv3inc" ]]; then
     export NTHREADS_ATMANLFV3INC=${NTHREADSmax}
     export APRUN_ATMANLFV3INC="${APRUN}"
 
-elif [[ "${step}" = "ocnanalbmat" ]]; then
+elif [[ "${step}" = "marinebmat" ]]; then
      echo "WARNING: ${step} is not enabled on S4!"
 
-elif [[ "${step}" = "ocnanalrun" ]]; then
+elif [[ "${step}" = "marinerun" ]]; then
      echo "WARNING: ${step} is not enabled on S4!"
 
 elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then

env/WCOSS2.env

@@ -22,6 +22,9 @@ if [[ -n "${ntasks:-}" && -n "${max_tasks_per_node:-}" && -n "${tasks_per_node:-
     [[ ${NTHREADSmax} -gt ${max_threads_per_task} ]] && NTHREADSmax=${max_threads_per_task}
     [[ ${NTHREADS1} -gt ${max_threads_per_task} ]] && NTHREADS1=${max_threads_per_task}
     APRUN="${launcher} -n ${ntasks}"
+else
+    echo "ERROR config.resources must be sourced before sourcing WCOSS2.env"
+    exit 2
 fi
 
 if [[ "${step}" = "prep" ]] || [[ "${step}" = "prepbufr" ]]; then
@@ -153,11 +156,6 @@ elif [[ "${step}" = "eupd" ]]; then
 
 elif [[ "${step}" = "fcst" ]] || [[ "${step}" = "efcs" ]]; then
 
-    ppn="tasks_per_node"
-    [[ -z "${!ppn+0}" ]] && ppn="tasks_per_node"
-    nprocs="ntasks"
-    [[ -z ${!nprocs+0} ]] && nprocs="ntasks"
-
     (( nnodes = (ntasks+tasks_per_node-1)/tasks_per_node ))
     (( ufs_ntasks = nnodes*tasks_per_node ))
     # With ESMF threading, the model wants to use the full node

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP

@@ -27,6 +27,10 @@ RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
    COM_ICE_HISTORY_PREV:COM_ICE_HISTORY_TMPL \
    COM_ICE_RESTART_PREV:COM_ICE_RESTART_TMPL
 
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+   COMIN_OCEAN_BMATRIX:COM_OCEAN_BMATRIX_TMPL \
+   COMIN_ICE_BMATRIX:COM_ICE_BMATRIX_TMPL
+
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################

jobs/JGFS_ATMOS_GEMPAK_NCDC_UPAPGIF

@@ -4,7 +4,7 @@
 # GFS GEMPAK NCDC PRODUCT GENERATION
 ############################################
 source "${HOMEgfs}/ush/preamble.sh"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "gempak_gif" -c "base"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "gempak_gif" -c "base gempak"
 
 export MP_PULSE=0
 export MP_TIMEOUT=2000

jobs/JGFS_ATMOS_PGRB2_SPEC_NPOESS

@@ -6,7 +6,7 @@
 # GFS PGRB2_SPECIAL_POST PRODUCT GENERATION
 ############################################
 source "${HOMEgfs}/ush/preamble.sh"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "npoess" -c "base"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "npoess" -c "base npoess"
 
 export OMP_NUM_THREADS=${OMP_NUM_THREADS:-1}
 

jobs/JGLOBAL_ARCHIVE

@@ -33,6 +33,8 @@ YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
 	COMIN_OCEAN_GRIB:COM_OCEAN_GRIB_TMPL \
 	COMIN_OCEAN_NETCDF:COM_OCEAN_NETCDF_TMPL \
 	COMIN_OCEAN_ANALYSIS:COM_OCEAN_ANALYSIS_TMPL \
+        COMIN_OCEAN_BMATRIX:COM_OCEAN_BMATRIX_TMPL \
+        COMIN_ICE_BMATRIX:COM_ICE_BMATRIX_TMPL \
 	COMIN_WAVE_GRID:COM_WAVE_GRID_TMPL \
 	COMIN_WAVE_HISTORY:COM_WAVE_HISTORY_TMPL \
 	COMIN_WAVE_STATION:COM_WAVE_STATION_TMPL \