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jderrico-noaajderrico-noaa
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Merge branch 'NOAA-EMC:develop' into develop
2 parents 61975cf + d5bee38 commit f4c8e00

26 files changed

+115
-66
lines changed

‎ci/cases/pr/C48_ATM.yaml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,4 +10,4 @@ arguments:
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expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
1111
idate: 2021032312
1212
edate: 2021032312
13-
yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
13+
yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml

‎ci/cases/pr/C48_S2SW.yaml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,4 +11,4 @@ arguments:
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expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
1212
idate: 2021032312
1313
edate: 2021032312
14-
yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
14+
yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml

‎ci/cases/pr/C48_S2SWA_gefs.yaml

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Original file line numberDiff line numberDiff line change
@@ -15,4 +15,4 @@ arguments:
1515
expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
1616
idate: 2021032312
1717
edate: 2021032312
18-
yaml: {{ HOMEgfs }}/ci/platforms/gefs_ci_defaults.yaml
18+
yaml: {{ HOMEgfs }}/ci/cases/yamls/gefs_ci_defaults.yaml

‎ci/cases/pr/C96C48_hybatmDA.yaml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -16,4 +16,4 @@ arguments:
1616
nens: 2
1717
gfs_cyc: 1
1818
start: cold
19-
yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
19+
yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml

‎ci/cases/pr/C96_atm3DVar.yaml

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Original file line numberDiff line numberDiff line change
@@ -14,4 +14,4 @@ arguments:
1414
nens: 0
1515
gfs_cyc: 1
1616
start: cold
17-
yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
17+
yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml

‎ci/cases/pr/C96_atmsnowDA.yaml

Lines changed: 21 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,21 @@
1+
experiment:
2+
system: gfs
3+
mode: cycled
4+
5+
arguments:
6+
pslot: {{ 'pslot' | getenv }}
7+
app: ATM
8+
resdetatmos: 96
9+
comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
10+
expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
11+
icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
12+
idate: 2021122012
13+
edate: 2021122100
14+
nens: 0
15+
gfs_cyc: 1
16+
start: cold
17+
yaml: {{ HOMEgfs }}/ci/cases/yamls/atmsnowDA_defaults_ci.yaml
18+
19+
skip_ci_on_hosts:
20+
- orion
21+
- hercules

‎ci/cases/weekly/C384C192_hybatmda.yaml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -16,4 +16,4 @@ arguments:
1616
nens: 2
1717
gfs_cyc: 1
1818
start: cold
19-
yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
19+
yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml

‎ci/cases/weekly/C384_S2SWA.yaml

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Original file line numberDiff line numberDiff line change
@@ -11,4 +11,4 @@ arguments:
1111
expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
1212
idate: 2016070100
1313
edate: 2016070100
14-
yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
14+
yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml

‎ci/cases/weekly/C384_atm3DVar.yaml

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Original file line numberDiff line numberDiff line change
@@ -16,4 +16,4 @@ arguments:
1616
nens: 0
1717
gfs_cyc: 1
1818
start: cold
19-
yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
19+
yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml

‎ci/cases/yamls/atmsnowDA_defaults_ci.yaml

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
defaults:
2+
!INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
3+
base:
4+
DOIAU: "NO"
5+
DO_JEDILANDDA: "YES"
6+
ACCOUNT: {{ 'SLURM_ACCOUNT' | getenv }}

‎ci/platforms/gefs_ci_defaults.yaml renamed to ‎ci/cases/yamls/gefs_ci_defaults.yaml

File renamed without changes.

‎ci/platforms/gfs_defaults_ci.yaml renamed to ‎ci/cases/yamls/gfs_defaults_ci.yaml

File renamed without changes.

‎docs/source/index.rst

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Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ Status
1010
======
1111

1212
* State of develop (HEAD) branch: GFSv17+ development
13-
* State of operations (dev/gfs.v16 branch): GFS v16.3.12 `tag: [gfs.v16.3.12] <https://github.com/NOAA-EMC/global-workflow/releases/tag/gfs.v16.3.12>`_
13+
* State of operations (dev/gfs.v16 branch): GFS v16.3.13 `tag: [gfs.v16.3.13] <https://github.com/NOAA-EMC/global-workflow/releases/tag/gfs.v16.3.13>`_
1414

1515
=============
1616
Code managers

‎jobs/JGLOBAL_LAND_ANALYSIS

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
#! /usr/bin/env bash
22

33
source "${HOMEgfs}/ush/preamble.sh"
4+
export DATA=${DATA:-${DATAROOT}/${RUN}landanl_${cyc}}
45
source "${HOMEgfs}/ush/jjob_header.sh" -e "landanl" -c "base landanl"
56

67
##############################################

‎jobs/JGLOBAL_PREP_LAND_OBS

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
#! /usr/bin/env bash
22

33
source "${HOMEgfs}/ush/preamble.sh"
4+
export DATA=${DATA:-${DATAROOT}/${RUN}landanl_${cyc}}
45
source "${HOMEgfs}/ush/jjob_header.sh" -e "preplandobs" -c "base preplandobs"
56

67
##############################################

‎parm/config/gfs/config.prepoceanobs

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ echo "BEGIN: config.prepoceanobs"
77
export OCNOBS2IODAEXEC=${HOMEgfs}/sorc/gdas.cd/build/bin/gdas_obsprovider2ioda.x
88

99
export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config
10-
export OBSPROC_YAML=@OBSPROC_YAML@
10+
export OBSPREP_YAML=@OBSPREP_YAML@
1111
export OBS_LIST=@SOCA_OBS_LIST@
1212
[[ -n "${OBS_LIST}" ]] || export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
1313
export OBS_YAML=${OBS_LIST}

‎parm/config/gfs/config.resources

Lines changed: 19 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -60,6 +60,9 @@ case ${machine} in
6060
export PARTITION_BATCH="compute"
6161
npe_node_max=40
6262
;;
63+
"CONTAINER")
64+
npe_node_max=1
65+
;;
6366
*)
6467
echo "FATAL ERROR: Unknown machine encountered by ${BASH_SOURCE[0]}"
6568
exit 2
@@ -810,15 +813,15 @@ case ${step} in
810813
export npe_cleanup=1
811814
export npe_node_cleanup=1
812815
export nth_cleanup=1
813-
export memory_cleanu="4096M"
816+
export memory_cleanup="4096M"
814817
;;
815818

816819
"stage_ic")
817820
export wtime_stage_ic="00:15:00"
818821
export npe_stage_ic=1
819822
export npe_node_stage_ic=1
820823
export nth_stage_ic=1
821-
export is_exclusive=Tue
824+
export is_exclusive=True
822825
;;
823826

824827
"atmensanlinit")
@@ -953,7 +956,7 @@ case ${step} in
953956
export npe_node_esfc=$(( npe_node_max / nth_esfc ))
954957
export nth_cycle=${nth_esfc}
955958
export npe_node_cycle=$(( npe_node_max / nth_cycle ))
956-
export memory_esfc="8GB"
959+
export memory_esfc="80GB"
957960
;;
958961

959962
"epos")
@@ -983,15 +986,15 @@ case ${step} in
983986
export npe_awips=1
984987
export npe_node_awips=1
985988
export nth_awips=1
986-
export memory_awip="3GB"
989+
export memory_awips="3GB"
987990
;;
988991

989992
"npoess")
990993
export wtime_npoess="03:30:00"
991994
export npe_npoess=1
992995
export npe_node_npoess=1
993996
export nth_npoess=1
994-
export memory_npoes="3GB"
997+
export memory_npoess="3GB"
995998
;;
996999

9971000
"gempak")
@@ -1012,7 +1015,7 @@ case ${step} in
10121015
export nth_mos_stn_prep=1
10131016
export memory_mos_stn_prep="5GB"
10141017
export NTASK="${npe_mos_stn_prep}"
1015-
export PTILE="${npe_node_mos_stn_pep}"
1018+
export PTILE="${npe_node_mos_stn_prep}"
10161019
;;
10171020

10181021
"mos_grd_prep")
@@ -1022,7 +1025,7 @@ case ${step} in
10221025
export nth_mos_grd_prep=1
10231026
export memory_mos_grd_prep="16GB"
10241027
export NTASK="${npe_mos_grd_prep}"
1025-
export PTILE="${npe_node_mos_grd_pep}"
1028+
export PTILE="${npe_node_mos_grd_prep}"
10261029
;;
10271030

10281031
"mos_ext_stn_prep")
@@ -1032,7 +1035,7 @@ case ${step} in
10321035
export nth_mos_ext_stn_prep=1
10331036
export memory_mos_ext_stn_prep="5GB"
10341037
export NTASK="${npe_mos_ext_stn_prep}"
1035-
export PTILE="${npe_node_mos_ext_stn_pep}"
1038+
export PTILE="${npe_node_mos_ext_stn_prep}"
10361039
;;
10371040

10381041
"mos_ext_grd_prep")
@@ -1042,7 +1045,7 @@ case ${step} in
10421045
export nth_mos_ext_grd_prep=1
10431046
export memory_mos_ext_grd_prep="3GB"
10441047
export NTASK="${npe_mos_ext_grd_prep}"
1045-
export PTILE="${npe_node_mos_ext_grd_pep}"
1048+
export PTILE="${npe_node_mos_ext_grd_prep}"
10461049
;;
10471050

10481051
"mos_stn_fcst")
@@ -1052,7 +1055,7 @@ case ${step} in
10521055
export nth_mos_stn_fcst=1
10531056
export memory_mos_stn_fcst="40GB"
10541057
export NTASK="${npe_mos_stn_fcst}"
1055-
export PTILE="${npe_node_mos_stn_fst}"
1058+
export PTILE="${npe_node_mos_stn_fcst}"
10561059
;;
10571060

10581061
"mos_grd_fcst")
@@ -1062,7 +1065,7 @@ case ${step} in
10621065
export nth_mos_grd_fcst=1
10631066
export memory_mos_grd_fcst="50GB"
10641067
export NTASK="${npe_mos_grd_fcst}"
1065-
export PTILE="${npe_node_mos_grd_fst}"
1068+
export PTILE="${npe_node_mos_grd_fcst}"
10661069
;;
10671070

10681071
"mos_ext_stn_fcst")
@@ -1083,7 +1086,7 @@ case ${step} in
10831086
export nth_mos_ext_grd_fcst=1
10841087
export memory_mos_ext_grd_fcst="50GB"
10851088
export NTASK="${npe_mos_ext_grd_fcst}"
1086-
export PTILE="${npe_node_mos_ext_grd_fst}"
1089+
export PTILE="${npe_node_mos_ext_grd_fcst}"
10871090
;;
10881091

10891092
"mos_stn_prdgen")
@@ -1105,7 +1108,7 @@ case ${step} in
11051108
export memory_mos_grd_prdgen="20GB"
11061109
export NTASK="${npe_mos_grd_prdgen}"
11071110
export PTILE="${npe_node_mos_grd_prdgen}"
1108-
export OMP_NUM_THREADS="${nth_mos_grd_prden}"
1111+
export OMP_NUM_THREADS="${nth_mos_grd_prdgen}"
11091112
;;
11101113

11111114
"mos_ext_stn_prdgen")
@@ -1127,7 +1130,7 @@ case ${step} in
11271130
export memory_mos_ext_grd_prdgen="30GB"
11281131
export NTASK="${npe_mos_ext_grd_prdgen}"
11291132
export PTILE="${npe_node_mos_ext_grd_prdgen}"
1130-
export OMP_NUM_THREADS="${nth_mos_ext_grd_prden}"
1133+
export OMP_NUM_THREADS="${nth_mos_ext_grd_prdgen}"
11311134
;;
11321135

11331136
"mos_wx_prdgen")
@@ -1138,7 +1141,7 @@ case ${step} in
11381141
export memory_mos_wx_prdgen="10GB"
11391142
export NTASK="${npe_mos_wx_prdgen}"
11401143
export PTILE="${npe_node_mos_wx_prdgen}"
1141-
export OMP_NUM_THREADS="${nth_mos_wx_prden}"
1144+
export OMP_NUM_THREADS="${nth_mos_wx_prdgen}"
11421145
;;
11431146

11441147
"mos_wx_ext_prdgen")
@@ -1159,4 +1162,4 @@ case ${step} in
11591162

11601163
esac
11611164

1162-
echo "END: config.resources"
1165+
echo "END: config.resources"

‎parm/post/upp.yaml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,7 @@ analysis:
2828

2929
forecast:
3030
config:
31-
rdaod: False
31+
rdaod: True
3232
data_in:
3333
copy:
3434
{% if forecast_hour == 0 %}
@@ -47,7 +47,7 @@ forecast:
4747

4848
goes:
4949
config:
50-
rdaod: True
50+
rdaod: False
5151
data_in:
5252
copy:
5353
{% set crtm_coefficients = [

‎parm/ufs/gocart/ExtData.other

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -54,10 +54,10 @@ pSO2_OCS NA Y Y %y4-%m2-%d2t12:00:00 none none biofuel /dev/null
5454
# ---------------
5555

5656
# # VOCs - OFFLINE MEGAN BIOG
57-
OC_ISOPRENE NA N Y %y4-%m2-%d2t12:00:00 none none isoprene ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
58-
OC_LIMO NA N Y %y4-%m2-%d2t12:00:00 none none limo ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
59-
OC_MTPA NA N Y %y4-%m2-%d2t12:00:00 none none mtpa ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
60-
OC_MTPO NA N Y %y4-%m2-%d2t12:00:00 none none mtpo ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
57+
OC_ISOPRENE NA Y Y %y4-%m2-%d2t12:00:00 none none isoprene ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
58+
OC_LIMO NA Y Y %y4-%m2-%d2t12:00:00 none none limo ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
59+
OC_MTPA NA Y Y %y4-%m2-%d2t12:00:00 none none mtpa ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
60+
OC_MTPO NA Y Y %y4-%m2-%d2t12:00:00 none none mtpo ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
6161

6262
# Biofuel Source -- Included in AeroCom anthropogenic emissions
6363
OC_BIOFUEL NA Y Y %y4-%m2-%d2t12:00:00 none none biofuel /dev/null

‎sorc/gdas.cd

Submodule gdas.cd updated 40 files

‎sorc/link_workflow.sh

Lines changed: 12 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -130,15 +130,21 @@ cd "${HOMEgfs}/parm/ufs" || exit 1
130130
${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_model.fd/tests/parm/noahmptable.tbl" .
131131

132132
cd "${HOMEgfs}/parm/post" || exit 1
133-
for file in postxconfig-NT-GEFS-ANL.txt postxconfig-NT-GEFS-F00.txt postxconfig-NT-GEFS.txt postxconfig-NT-GFS-ANL.txt \
134-
postxconfig-NT-GFS-F00-TWO.txt postxconfig-NT-GFS-F00.txt postxconfig-NT-GFS-FLUX-F00.txt postxconfig-NT-GFS-FLUX.txt \
135-
postxconfig-NT-GFS-GOES.txt postxconfig-NT-GFS-TWO.txt \
136-
postxconfig-NT-GFS.txt postxconfig-NT-gefs-aerosol.txt postxconfig-NT-gefs-chem.txt params_grib2_tbl_new \
137-
post_tag_gfs128 post_tag_gfs65 nam_micro_lookup.dat \
138-
AEROSOL_LUTS.dat optics_luts_DUST.dat optics_luts_SALT.dat optics_luts_SOOT.dat optics_luts_SUSO.dat optics_luts_WASO.dat
133+
for file in postxconfig-NT-GEFS-F00.txt postxconfig-NT-GEFS.txt postxconfig-NT-GEFS-WAFS.txt \
134+
postxconfig-NT-GEFS-F00-aerosol.txt postxconfig-NT-GEFS-aerosol.txt \
135+
postxconfig-NT-GFS-ANL.txt postxconfig-NT-GFS-F00.txt postxconfig-NT-GFS-FLUX-F00.txt \
136+
postxconfig-NT-GFS.txt postxconfig-NT-GFS-FLUX.txt postxconfig-NT-GFS-GOES.txt \
137+
postxconfig-NT-GFS-F00-TWO.txt postxconfig-NT-GFS-TWO.txt \
138+
params_grib2_tbl_new post_tag_gfs128 post_tag_gfs65 nam_micro_lookup.dat
139139
do
140140
${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/${file}" .
141141
done
142+
for file in optics_luts_DUST.dat optics_luts_DUST_nasa.dat optics_luts_NITR_nasa.dat \
143+
optics_luts_SALT.dat optics_luts_SALT_nasa.dat optics_luts_SOOT.dat optics_luts_SOOT_nasa.dat \
144+
optics_luts_SUSO.dat optics_luts_SUSO_nasa.dat optics_luts_WASO.dat optics_luts_WASO_nasa.dat
145+
do
146+
${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/fix/chem/${file}" .
147+
done
142148

143149
cd "${HOMEgfs}/scripts" || exit 8
144150
${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_utils.fd/scripts/exemcsfc_global_sfc_prep.sh" .

‎ush/load_ufsda_modules.sh

Lines changed: 8 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -44,20 +44,15 @@ elif [[ -d /scratch1 ]] ; then
4444
# set NETCDF variable based on ncdump location
4545
NETCDF=$( which ncdump )
4646
export NETCDF
47-
# prod_util stuff, find a better solution later...
48-
module use /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/compiler/intel/2022.1.2/
49-
module load prod_util
5047
elif [[ -d /work ]] ; then
51-
# We are on MSU Orion
52-
# prod_util stuff, find a better solution later...
53-
#module use /apps/contrib/NCEP/hpc-stack/libs/hpc-stack/modulefiles/compiler/intel/2022.1.2/
54-
#module load prod_util
55-
export UTILROOT=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2
56-
export MDATE=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2/bin/mdate
57-
export NDATE=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2/bin/ndate
58-
export NHOUR=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2/bin/nhour
59-
export FSYNC=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2/bin/fsync_file
60-
module load "${MODS}/orion"
48+
# We are on MSU Orion or Hercules
49+
if [[ -d /apps/other ]] ; then
50+
# Hercules
51+
module load "${MODS}/hercules"
52+
else
53+
# Orion
54+
module load "${MODS}/orion"
55+
fi
6156
# set NETCDF variable based on ncdump location
6257
ncdump=$( which ncdump )
6358
NETCDF=$( echo "${ncdump}" | cut -d " " -f 3 )

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