Merge branch 'develop' into feature/abi_sea_ice

build.sh

@@ -126,7 +126,7 @@ set -x
 if [[ $BUILD_JCSDA == 'YES' ]]; then
  make -j ${BUILD_JOBS:-6} VERBOSE=$BUILD_VERBOSE
 else
- builddirs="gdas iodaconv land-imsproc land-jediincr gdas-utils bufr-query"
+ builddirs="gdas iodaconv land-imsproc land-jediincr gdas-utils bufr-query da-utils"
  for b in $builddirs; do
  cd $b
  make -j ${BUILD_JOBS:-6} VERBOSE=$BUILD_VERBOSE

modulefiles/GDAS/hera.intel.lua

@@ -44,6 +44,7 @@ load("fckit/0.11.0")
 load("fiat/1.2.0")
 --load("ectrans/1.2.0")
 load("fms/2023.04")
+load("esmf/8.6.0")
 load("atlas/0.35.1")
 load("sp/2.5.0")
 load("gsl-lite/0.37.0")

modulefiles/GDAS/hercules.intel.lua

@@ -41,6 +41,7 @@ load("fckit/0.11.0")
 load("fiat/1.2.0")
 load("ectrans/1.2.0")
 load("fms/2023.04")
+load("esmf/8.6.0")
 load("atlas/0.35.1")
 load("sp/2.5.0")
 load("gsl-lite/0.37.0")

modulefiles/GDAS/orion.intel.lua

@@ -41,6 +41,7 @@ load("fckit/0.11.0")
 load("fiat/1.2.0")
 load("ectrans/1.2.0")
 load("fms/2023.04")
+load("esmf/8.6.0")
 load("atlas/0.35.1")
 load("sp/2.5.0")
 load("gsl-lite/0.37.0")

modulefiles/GDAS/wcoss2.intel.lua

@@ -34,6 +34,7 @@ load("gsl/2.7")
 load("prod_util/2.0.14")
 load("bufr/12.0.1")
 load("fms-C/2023.04")
+load("esmf-C/8.6.0")
 
 -- hack for pybind11
 setenv("pybind11_ROOT", "/apps/spack/python/3.8.6/intel/19.1.3.304/pjn2nzkjvqgmjw4hmyz43v5x4jbxjzpk/lib/python3.8/site-packages/pybind11/share/cmake/pybind11")

parm/soca/berror/obsolete/soca_parameters_diffusion_hz.yaml

@@ -13,7 +13,7 @@ background:
 background error:
  covariance model: SABER
  saber central block:
- saber block name: EXPLICIT_DIFFUSION
+ saber block name: diffusion
  geometry: *geom
  calibration:
  normalization:

parm/soca/berror/obsolete/soca_parameters_diffusion_vt.yaml

@@ -13,7 +13,7 @@ background:
 background error:
  covariance model: SABER
  saber central block:
- saber block name: EXPLICIT_DIFFUSION
+ saber block name: diffusion
  geometry: *geom
  calibration:
  normalization:

parm/soca/berror/soca_hybrid_bmat.yaml

@@ -3,7 +3,7 @@ components:
 - covariance:
  covariance model: SABER
  saber central block:
- saber block name: EXPLICIT_DIFFUSION
+ saber block name: diffusion
  active variables: [tocn, socn, ssh, cicen]
  geometry:
  mom6_input_nml: mom_input.nml
@@ -62,7 +62,7 @@ components:
  localization:
  localization method: SABER
  saber central block:
- saber block name: EXPLICIT_DIFFUSION
+ saber block name: diffusion
  active variables: [tocn, socn, ssh]
  geometry:
  mom6_input_nml: mom_input.nml

parm/soca/berror/soca_parameters_diffusion_hz.yaml.j2

@@ -8,30 +8,30 @@ background:
  ocn_filename: MOM.res.nc
  ice_filename: cice.res.nc
  date: '{{ MARINE_WINDOW_END | to_isotime }}'
- state variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
+ state variables: [ssh]
 
 background error:
  covariance model: SABER
  saber central block:
- saber block name: EXPLICIT_DIFFUSION
+ saber block name: diffusion
  geometry: *geom
  calibration:
  normalization:
  method: randomization
  iterations: 10000
 
  groups:
- - name: ocean
- horizontal:
- from file:
- filename: ocn.cor_rh.incr.0001-01-01T00:00:00Z.nc
- variable name: ave_ssh
+ - horizontal:
+ model file:
+ date: '{{ MARINE_WINDOW_END | to_isotime }}'
+ basename: ./
+ ocn_filename: ocn.cor_rh.incr.0001-01-01T00:00:00Z.nc
+ model variable: ssh
  write:
- filename: ./staticb/hz_ocean.nc
+ filepath: ./staticb/hz_ocean
 
- - name: ice
- horizontal:
+ - horizontal:
  as gaussian: true
  fixed value: 50000.0
  write:
- filename: ./staticb/hz_ice.nc
+ filepath: ./staticb/hz_ice

parm/soca/berror/soca_parameters_diffusion_vt.yaml.j2

@@ -8,12 +8,12 @@ background:
  ocn_filename: MOM.res.nc
  ice_filename: cice.res.nc
  date: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
- state variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
+ state variables: [tocn]
 
 background error:
  covariance model: SABER
  saber central block:
- saber block name: EXPLICIT_DIFFUSION
+ saber block name: diffusion
  geometry: *geom
  calibration:
  normalization:
@@ -22,11 +22,12 @@ background error:
  iterations: 1000 #< in the real world you'll want to use 1e4 or so
 
  groups:
- - name: vt_ocean
- vertical:
+ - vertical:
  as gaussian: true
- from file:
- filename: vt_scales.nc
- variable name: vt
+ model file:
+ date: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
+ basename: ./
+ ocn_filename: vt_scales.nc
+ model variable: tocn
  write:
- filename: ./staticb/vt_ocean.nc
+ filepath: ./staticb/vt_ocean

parm/soca/berror/soca_vtscales.yaml.j2

@@ -2,8 +2,8 @@ gridspec_filename: soca_gridspec.nc
 restart_filename: ./INPUT/MOM.res.nc
 mld_filename: './staticb/ocn.bkgerr_stddev.incr.{{ MARINE_WINDOW_END | to_isotime }}.nc'
 output_filename: ./vt_scales.nc
-output_variable_vt: vt
-output_variable_hz: hz
+output_variable_vt: Temp
+output_variable_hz: ave_ssh
 
 VT_MIN: 5
 VT_MAX: 15

parm/soca/marine-jcb-base.yaml

@@ -34,6 +34,7 @@ marine_window_middle: '{{MARINE_WINDOW_MIDDLE}}'
 
 # Geometry
 marine_soca_files_path: .
+marine_vt_levels: '{{MOM6_LEVS}}'
 
 # Initial conditions
 marine_background_path: ./INPUT/

test/atm/global-workflow/3dvar.ref

@@ -1,19 +1,19 @@
 CostJb : Nonlinear Jb = 0.0000000000000000e+00
-CostJo : Nonlinear Jo(AMSUA N19) = 3.9490015258335385e+04, nobs = 73667, Jo/n = 5.3606112992704180e-01, err = 6.2697697603632934e+00
+CostJo : Nonlinear Jo(AMSUA N19) = 3.9490015258335392e+04, nobs = 73667, Jo/n = 5.3606112992704180e-01, err = 6.2697697603632934e+00
 CostJo : Nonlinear Jo(sondes) = 1.0738590249678713e+04, nobs = 4255, Jo/n = 2.5237579905237868e+00, err = 1.0981123140127320e+01
-CostFunction: Nonlinear J = 5.0228605508014094e+04
-DRPCGMinimizer: reduction in residual norm = 9.6305250910880724e-01
+CostFunction: Nonlinear J = 5.0228605508014109e+04
+DRPCGMinimizer: reduction in residual norm = 1.2654930990384508e+00
 CostFunction::addIncrement: Analysis: 
 ----------------------------------------------------------------------------------------------------
 State print | number of fields = 22 | cube sphere face size: C48
-eastward_wind | Min:-5.5495644220059390e+01 Max:+8.4934651204487366e+01 RMS:+1.6388250288534095e+01
-northward_wind | Min:-7.3712421229093422e+01 Max:+7.6984825502186652e+01 RMS:+8.1424144891570869e+00
-air_temperature | Min:+1.7482158077318448e+02 Max:+3.1467235233685437e+02 RMS:+2.4978424883092669e+02
+eastward_wind | Min:-5.5495644220059390e+01 Max:+8.4934651204487366e+01 RMS:+1.6388250288535051e+01
+northward_wind | Min:-7.3712421229093422e+01 Max:+7.6984825502186652e+01 RMS:+8.1424144891572610e+00
+air_temperature | Min:+1.7482158077318425e+02 Max:+3.1467235233685437e+02 RMS:+2.4978424883106894e+02
 air_pressure_thickness | Min:+6.0599999874109178e-01 Max:+1.7760098554198755e+03 RMS:+9.5680601590204810e+02
 surface_pressure | Min:+5.3298485514404747e+04 Max:+1.0398027192902798e+05 RMS:+9.8897229693652524e+04
-specific_humidity | Min:+0.0000000000000000e+00 Max:+2.0041369334954085e-02 RMS:+4.7792636816418417e-03
-cloud_liquid_ice | Min:+0.0000000000000000e+00 Max:+1.2024392024662985e-03 RMS:+1.4396968866569995e-05
-cloud_liquid_water | Min:+0.0000000000000000e+00 Max:+1.5935686618789048e-03 RMS:+4.1931345590543333e-05
+specific_humidity | Min:+0.0000000000000000e+00 Max:+2.0041369334954085e-02 RMS:+4.7792637035328151e-03
+cloud_liquid_ice | Min:+0.0000000000000000e+00 Max:+1.2024285059501723e-03 RMS:+1.4396343608618137e-05
+cloud_liquid_water | Min:+0.0000000000000000e+00 Max:+1.5935686450466631e-03 RMS:+4.1864377574483124e-05
 ozone_mass_mixing_ratio | Min:+1.1998327271379204e-08 Max:+1.7808431790670831e-05 RMS:+4.4947917149861064e-06
 surface_geopotential_height | Min:-2.7018394470214844e+01 Max:+5.2697460937500000e+03 RMS:+6.3032575784066080e+02
 slmsk | Min:+0.0000000000000000e+00 Max:+2.0000000000000000e+00 RMS:+7.3450427349184144e-01
@@ -32,33 +32,33 @@ f10m | Min:+9.4613586695410434e-01 Max:+
 
 Obs bias coefficients: 
 ---------------------------------------------------------------
- constant: Min= -1.2424509525299072, Max= 1.6504349708035770, Norm= 3.1030146353133463
- lapseRate_order_2: Min= -7.0903420445872838, Max= 46.3166084284223771, Norm= 47.0185597979528609
- lapseRate: Min= -5.5814771650607220, Max= 1.2464430332789806, Norm= 5.7524772942406086
- emissivityJacobian: Min= -1.0039629936218262, Max= 10.5191706304246591, Norm= 10.5711704384468028
-sensorScanAngle_order_4: Min= -8.0552864073222832, Max= 2.4945130349138593, Norm= 13.5132453944315909
-sensorScanAngle_order_3: Min= -1.1528069971066446, Max= 2.1735479829142181, Norm= 3.0673534349517819
-sensorScanAngle_order_2: Min= -5.1097259521664853, Max= 2.8632600308292808, Norm= 7.2817410561999560
- sensorScanAngle: Min= -0.6898530126095289, Max= 0.0655509978252007, Norm= 1.1442823316972326
+ constant: Min= -1.2424509525299072, Max= 1.6504349707778374, Norm= 3.1030146350620180
+ lapseRate_order_2: Min= -7.0903420444281888, Max= 46.3166084283797588, Norm= 47.0185597978996128
+ lapseRate: Min= -5.5814771649382546, Max= 1.2464430333259036, Norm= 5.7524772941123183
+ emissivityJacobian: Min= -1.0039629936218262, Max= 10.5191705643602678, Norm= 10.5711703727068684
+sensorScanAngle_order_4: Min= -8.0552864072427965, Max= 2.4945130349633651, Norm= 13.5132453941396253
+sensorScanAngle_order_3: Min= -1.1528069970056642, Max= 2.1735479827935875, Norm= 3.0673534348153715
+sensorScanAngle_order_2: Min= -5.1097259521743421, Max= 2.8632600308748679, Norm= 7.2817410561387739
+ sensorScanAngle: Min= -0.6898530126324298, Max= 0.0655509978110177, Norm= 1.1442823317381461
 ---------------------------------------------------------------
 
 
-CostJb : Nonlinear Jb = 0.0000003247124839
-CostJo : Nonlinear Jo(AMSUA N19) = 39487.6033905210933881, nobs = 73667, Jo/n = 0.5360283897881154, err = 6.2697697603632934
-CostJo : Nonlinear Jo(sondes) = 10687.4014846169593511, nobs = 4255, Jo/n = 2.5117277284646202, err = 10.9811231401273197
-CostFunction: Nonlinear J = 50175.0048754627641756
-DRPCGMinimizer: reduction in residual norm = 1.0067413227974593
+CostJb : Nonlinear Jb = 0.0000014612994971
+CostJo : Nonlinear Jo(AMSUA N19) = 39390.2547489576390944, nobs = 73667, Jo/n = 0.5347069209952575, err = 6.2697697603632934
+CostJo : Nonlinear Jo(sondes) = 10684.1056534407689469, nobs = 4255, Jo/n = 2.5109531500448341, err = 10.9811231401273197
+CostFunction: Nonlinear J = 50074.3604038597040926
+DRPCGMinimizer: reduction in residual norm = 1.3784563235297740
 CostFunction::addIncrement: Analysis: 
 ----------------------------------------------------------------------------------------------------
 State print | number of fields = 22 | cube sphere face size: C48
-eastward_wind | Min:-5.5495644220059390e+01 Max:+8.4934651204487366e+01 RMS:+1.6388250288542654e+01
-northward_wind | Min:-7.3712421229093422e+01 Max:+7.6984825502186652e+01 RMS:+8.1424144891586234e+00
-air_temperature | Min:+1.7482158077318232e+02 Max:+3.1467235233685437e+02 RMS:+2.4978424883219918e+02
+eastward_wind | Min:-5.5495644220059390e+01 Max:+8.4934651204487366e+01 RMS:+1.6388250288545034e+01
+northward_wind | Min:-7.3712421229093422e+01 Max:+7.6984825502186652e+01 RMS:+8.1424144891590498e+00
+air_temperature | Min:+1.7482158077318175e+02 Max:+3.1467235233685437e+02 RMS:+2.4978424883255175e+02
 air_pressure_thickness | Min:+6.0599999874109178e-01 Max:+1.7760098554198755e+03 RMS:+9.5680601590204810e+02
 surface_pressure | Min:+5.3298485514404747e+04 Max:+1.0398027192902798e+05 RMS:+9.8897229693652524e+04
-specific_humidity | Min:+0.0000000000000000e+00 Max:+2.0041369334954085e-02 RMS:+4.7792637405692090e-03
-cloud_liquid_ice | Min:+0.0000000000000000e+00 Max:+1.2024392024662985e-03 RMS:+1.4396968866569995e-05
-cloud_liquid_water | Min:+0.0000000000000000e+00 Max:+1.5935686618789048e-03 RMS:+4.1931345590543333e-05
+specific_humidity | Min:+0.0000000000000000e+00 Max:+2.0041369334954085e-02 RMS:+4.7792636598075200e-03
+cloud_liquid_ice | Min:+0.0000000000000000e+00 Max:+1.2023914586805969e-03 RMS:+1.4394270245713929e-05
+cloud_liquid_water | Min:+0.0000000000000000e+00 Max:+1.5935685862194550e-03 RMS:+4.1737200829311335e-05
 ozone_mass_mixing_ratio | Min:+1.1998327271379204e-08 Max:+1.7808431790670831e-05 RMS:+4.4947917149861064e-06
 surface_geopotential_height | Min:-2.7018394470214844e+01 Max:+5.2697460937500000e+03 RMS:+6.3032575784066080e+02
 slmsk | Min:+0.0000000000000000e+00 Max:+2.0000000000000000e+00 RMS:+7.3450427349184144e-01
@@ -77,18 +77,18 @@ f10m | Min:+9.4613586695410434e-01 Max:+
 
 Obs bias coefficients: 
 ---------------------------------------------------------------
- constant: Min= -1.2424509525299072, Max= 1.6504349705701049, Norm= 3.1030146330531774
- lapseRate_order_2: Min= -7.0903420434846316, Max= 46.3166084260648887, Norm= 47.0185597955718677
- lapseRate: Min= -5.5814771643207211, Max= 1.2464430335558840, Norm= 5.7524772934110207
- emissivityJacobian: Min= -1.0039629936218262, Max= 10.5191700403026349, Norm= 10.5711698512230932
-sensorScanAngle_order_4: Min= -8.0552864066518524, Max= 2.4945130353434313, Norm= 13.5132453918536388
-sensorScanAngle_order_3: Min= -1.1528069962369289, Max= 2.1735479817619940, Norm= 3.0673534336938850
-sensorScanAngle_order_2: Min= -5.1097259522434877, Max= 2.8632600312042698, Norm= 7.2817410556587614
- sensorScanAngle: Min= -0.6898530128249588, Max= 0.0655509976984332, Norm= 1.1442823320888615
+ constant: Min= -1.2424509525299072, Max= 1.6504349705176715, Norm= 3.1030146324339514
+ lapseRate_order_2: Min= -7.0903420430554904, Max= 46.3166084270832954, Norm= 47.0185597965343405
+ lapseRate: Min= -5.5814771637081586, Max= 1.2464430337450372, Norm= 5.7524772928124595
+ emissivityJacobian: Min= -1.0039629936218262, Max= 10.5191698767122261, Norm= 10.5711696884361785
+sensorScanAngle_order_4: Min= -8.0552864064916889, Max= 2.4945130355171092, Norm= 13.5132453912586890
+sensorScanAngle_order_3: Min= -1.1528069959771197, Max= 2.1735479816041132, Norm= 3.0673534334487149
+sensorScanAngle_order_2: Min= -5.1097259522379295, Max= 2.8632600311870164, Norm= 7.2817410554387321
+ sensorScanAngle: Min= -0.6898530128687219, Max= 0.0655509976643010, Norm= 1.1442823321434776
 ---------------------------------------------------------------
 
 
-CostJb : Nonlinear Jb = 0.0000033199535370
-CostJo : Nonlinear Jo(AMSUA N19) = 39476.8510817764617968, nobs = 73667, Jo/n = 0.5358824315063252, err = 6.2697697603632934
-CostJo : Nonlinear Jo(sondes) = 10639.2476170353256748, nobs = 4255, Jo/n = 2.5004107208073623, err = 10.9811231401273197
-CostFunction: Nonlinear J = 50116.0987021317414474
+CostJb : Nonlinear Jb = 0.0000118072709876
+CostJo : Nonlinear Jo(AMSUA N19) = 39219.8814513386896579, nobs = 73667, Jo/n = 0.5323941717640014, err = 6.2697697603632934
+CostJo : Nonlinear Jo(sondes) = 10645.9197195859396743, nobs = 4255, Jo/n = 2.5019787825113844, err = 10.9811231401273197
+CostFunction: Nonlinear J = 49865.8011827318987343