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* origin/develop:
  Update wcoss2.intel.lua (#1142)
  Add yaml file for prepobsaero task (#1141)
  Diffusion parameter yaml template (#1140)
  Adjust absolute float tolerance for variational and ensemble DA jjob tests (#1136)
  Insitu temp and salt (#1135)
  Adds letkf.yaml(.j2)  (#1134)
  Add optional testing block to 3dvar and lgetkf input YAMLs for jjobs (#1129)
  updates to build and run some ctests on WCOSS2 (#1122)
  Addin a GFSv17 ctest (#1130)
  Feature/rtofs in situ (#1110)
  update jcb-gdas hash to bring in satwnd yaml changes (#1128)
  Optionally run specified rocoto task as part of the ctests  (#1121)
  Add build capability to Gaea-C5 (#1101)
  Python Converter and Json for the ADPUPA BUFR DUMP (#1115)
  Revert "Fix ice water FV3 increment variable name and add a few more … (#1125)
  Satwnd and variable name-convention updates for jcb implementation in GDASApp (#1119)
  Add inverse distance weighting option to superob function (#1116)
  Resume the Marine Vrfy Task on ctests (#1107)
  Replicate the creation of the gw-ci cycling test (#1114)
  Added YAML, JSON, python files for assimilating LEOGEO satwinds (#1099)
  Add an OOPS-based application to recenter snow analysis (#1102)
  Fix ice water FV3 increment variable name and add a few more (#1112)
  Update hera.intel.lua (#1109)
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danholdaway committed Jun 4, 2024
2 parents cf4f3b5 + 3e50a8f commit 2ec1767
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Showing 77 changed files with 3,372 additions and 1,230 deletions.
2 changes: 1 addition & 1 deletion build.sh
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Expand Up @@ -71,7 +71,7 @@ while getopts "p:t:c:hvdfa" opt; do
done

case ${BUILD_TARGET} in
hera | orion | hercules | wcoss2 | noaacloud)
hera | orion | hercules | wcoss2 | noaacloud | gaea)
echo "Building GDASApp on $BUILD_TARGET"
source $dir_root/ush/module-setup.sh
module use $dir_root/modulefiles
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2 changes: 1 addition & 1 deletion ci/run_ci.sh
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Expand Up @@ -61,7 +61,7 @@ module use $GDAS_MODULE_USE
module load GDAS/$TARGET
echo "---------------------------------------------------" >> $outfile
rm -rf log.ctest
ctest -R gdasapp --output-on-failure &>> log.ctest
ctest -E "manual" -R gdasapp --output-on-failure &>> log.ctest
ctest_status=$?
npassed=$(cat log.ctest | grep "tests passed")
if [ $ctest_status -eq 0 ]; then
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25 changes: 25 additions & 0 deletions modulefiles/EVA/wcoss2.lua
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help([[
Load environment for running EVA.
]])

local pkgName = myModuleName()
local pkgVersion = myModuleVersion()
local pkgNameVer = myModuleFullName()

conflict(pkgName)

load("PrgEnv-intel/8.2.0")
load("craype")
load("cray-pals")
load("git/2.29.0")
load("intel/19.1.3.304")
load("python/3.10.4")
load("ve/evs/1.0")

append_path("PATH", "/lfs/h2/emc/da/noscrub/emc.da/eva/opt/bin")
append_path("PYTHONPATH", "/lfs/h2/emc/da/noscrub/emc.da/eva/opt/")

whatis("Name: ".. pkgName)
whatis("Version: ".. pkgVersion)
whatis("Category: EVA")
whatis("Description: Load all libraries needed for EVA")
96 changes: 96 additions & 0 deletions modulefiles/GDAS/gaea.intel.lua
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@@ -0,0 +1,96 @@
help([[
Load environment for running the GDAS application with Intel compilers and MPI.
]])

local pkgName = myModuleName()
local pkgVersion = myModuleVersion()
local pkgNameVer = myModuleFullName()

prepend_path("MODULEPATH", '/ncrc/proj/epic/spack-stack/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core')
prepend_path("MODULEPATH", '/ncrc/proj/epic/rocoto/modulefiles')

-- below two lines get us access to the spack-stack modules
load("stack-intel/2023.1.0")
load("stack-cray-mpich/8.1.25")
-- JCSDA has 'jedi-fv3-env/unified-dev', but we should load these manually as needed
load("cmake/3.23.1")
load("gettext/0.20.2")
--load("libunistring/1.1")
--load("libidn2/2.3.4")
load("pcre2/10.42")
load("curl/8.4.0")
load("zlib/1.2.13")
load("git/2.35.2")
load("pkg-config/0.29.2")
load("hdf5/1.14.0")
load("parallel-netcdf/1.12.2")
load("netcdf-c/4.9.2")
load("nccmp/1.9.0.1")
load("netcdf-fortran/4.6.1")
load("nco/5.0.6")
load("parallelio/2.5.10")
load("wget/1.21.3")
load("boost/1.83.0")
load("bufr/12.0.1")
load("git-lfs/2.11.0")
load("ecbuild/3.7.2")
load("openjpeg/2.3.1")
load("eccodes/2.32.0")
load("eigen/3.4.0")
load("openblas/0.3.24")
load("eckit/1.24.5")
load("fftw/3.3.10")
load("fckit/0.11.0")
load("fiat/1.2.0")
load("ectrans/1.2.0")
load("atlas/0.35.1")
load("sp/2.5.0")
load("gsl-lite/0.37.0")
load("libjpeg/2.1.0")
load("krb5/1.16.3")
load("libtirpc/1.3.3")
load("hdf/4.2.15")
load("jedi-cmake/1.4.0")
load("libpng/1.6.37")
--load("libxt/1.1.5")
--load("libxmu/1.1.4")
--load("libxpm/4.11.0")
load("libxaw/1.10.13")
load("udunits/2.2.28")
load("ncview/2.1.9")
load("netcdf-cxx4/4.3.1")
load("json/3.10.5")
load("crtm/2.4.0.1")
load("rocoto/1.3.6")
load("prod_util/2.1.1")

load("py-jinja2/3.0.3")
load("py-netcdf4/1.5.8")
load("py-pybind11/2.11.0")
load("py-pycodestyle/2.11.0")
load("py-pyyaml/6.0")
load("py-scipy/1.11.3")
load("py-xarray/2023.7.0")
load("py-f90nml/1.4.3")
load("py-pip/23.1.2")

-- hack for wxflow
--prepend_path("PYTHONPATH", "/scratch1/NCEPDEV/da/python/gdasapp/wxflow/20240307/src")

setenv("CC","cc")
setenv("CXX","CC")
setenv("FC","ftn")

local mpiexec = '/usr/bin/srun'
local mpinproc = '-n'
setenv('MPIEXEC_EXEC', mpiexec)
setenv('MPIEXEC_NPROC', mpinproc)

setenv("CRTM_FIX","/gpfs/f5/ufs-ard/world-shared/GDASApp/fix/crtm/2.4.0")
setenv("GDASAPP_TESTDATA","/gpfs/f5/ufs-ard/world-shared/GDASApp/CI/data")
setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/gpfs/f5/ufs-ard/world-shared/GDASApp/CI/data/test")

whatis("Name: ".. "pkgName")
whatis("Version: ".. "pkgVersion")
whatis("Category: GDASApp")
whatis("Description: Load all libraries needed for GDASApp")
2 changes: 1 addition & 1 deletion modulefiles/GDAS/hera.intel.lua
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Expand Up @@ -47,7 +47,7 @@ load("atlas/0.35.1")
load("sp/2.5.0")
load("gsl-lite/0.37.0")
load("libjpeg/2.1.0")
load("krb5/1.15.1")
load("krb5/1.20.1")
load("libtirpc/1.3.3")
load("hdf/4.2.15")
load("jedi-cmake/1.4.0")
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8 changes: 6 additions & 2 deletions modulefiles/GDAS/wcoss2.intel.lua
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Expand Up @@ -29,12 +29,16 @@ load("eckit/1.24.4")
load("fckit/0.11.0")
load("atlas/0.35.0")
load("nccmp")
load("nco/5.0.6")
load("gsl/2.7")
load("prod_util/2.0.14")
load("bufr/12.0.1")

-- 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")

-- hack for wxflow
--prepend_path("PYTHONPATH", "/scratch1/NCEPDEV/da/python/gdasapp/wxflow/20240307/src")
-- hack for git-lfs
prepend_path("PATH", "/apps/spack/git-lfs/2.11.0/gcc/11.2.0/m6b6nl5kfqngfteqbggydc7kflxere3s/bin")

local mpiexec = '/pe/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin/mpirun'
local mpinproc = '-n'
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47 changes: 47 additions & 0 deletions parm/aero/berror/aero_diffparm.yaml.j2
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geometry:
fms initialization:
namelist filename: ./fv3jedi/fmsmpp.nml
field table filename: ./fv3jedi/field_table
akbk: ./fv3jedi/akbk.nc4
npx: {{ npx_ges }}
npy: {{ npy_ges }}
npz: {{ npz_ges }}
field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
date: '{{ current_cycle | to_isotime }}'
background:
datetime: '{{ current_cycle | to_isotime }}'
filetype: fms restart
datapath: ./bkg
filename_core: '{{ current_cycle | to_fv3time }}.fv_core.res.nc'
filename_trcr: '{{ current_cycle | to_fv3time }}.fv_tracer.res.nc'
filename_cplr: '{{ current_cycle | to_fv3time }}.coupler.res'
state variables: [mass_fraction_of_sulfate_in_air,
mass_fraction_of_hydrophobic_black_carbon_in_air,
mass_fraction_of_hydrophilic_black_carbon_in_air,
mass_fraction_of_hydrophobic_organic_carbon_in_air,
mass_fraction_of_hydrophilic_organic_carbon_in_air,
mass_fraction_of_dust001_in_air, mass_fraction_of_dust002_in_air,
mass_fraction_of_dust003_in_air, mass_fraction_of_dust004_in_air,
mass_fraction_of_dust005_in_air, mass_fraction_of_sea_salt001_in_air,
mass_fraction_of_sea_salt002_in_air, mass_fraction_of_sea_salt003_in_air,
mass_fraction_of_sea_salt004_in_air]

background error:
covariance model: SABER
saber central block:
saber block name: diffusion
calibration:
normalization:
iterations: {{ diff_iter }}
groups:
- horizontal:
fixed value: {{ horiz_len }}
write:
filepath: ./diffusion_hz
- vertical:
levels: {{ npz_ges }}
fixed value: {{ fixed_val }}
as gaussian: true
write:
filepath: ./diffusion_vt

14 changes: 14 additions & 0 deletions parm/aero/prep/prep_viirs.yaml.j2
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provider: VIIRSAOD
window begin: {{ window_begin | to_isotime }}
window end: {{ window_end | to_isotime }}
binning:
cressman radius: 100
stride: 132
min number of obs: 500
variable: aerosolOpticalDepth
output file: {{ DATA }}/{{ OPREFIX }}viirs_{{sensor}}.{{ current_cycle | to_YMDH }}.nc4
input files: {{ input_files }}
thinning:
threshold: 0
channel: 4
preqc: 0
12 changes: 12 additions & 0 deletions parm/ioda/bufr2ioda/bufr2ioda_adpupa.json
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{
"data_format": "bufr_d",
"data_type": "adpupa",
"cycle_type": "{{ RUN }}",
"cycle_datetime" : "{{ current_cycle | to_YMDH }}",
"dump_directory": "{{ DMPDIR }}",
"ioda_directory": "{{ COM_OBS }}",
"subsets": [ "NC002001, NC002002, NC002003, NC002004, NC002005" ],
"source": "NCEP data tank",
"data_provider": "U.S. NOAA",
"data_description": "UPPER-AIR (RAOB, PIBAL, RECCO, DROPS) REPORTS",
}
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"data_format" : "tesac",
"subsets" : "TESAC",
"source" : "NCEP data tank",
"data_type" : "marinemammals",
"data_type" : "marinemammal",
"cycle_type" : "{{ RUN }}",
"cycle_datetime" : "{{ current_cycle | to_YMDH }}",
"dump_directory" : "{{ DMPDIR }}",
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15 changes: 15 additions & 0 deletions parm/ioda/bufr2ioda/bufr2ioda_satwnd_amv_leogeo.json
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{
"data_format" : "bufr_d",
"data_type" : "satwnd",
"cycle_type" : "{{ RUN }}",
"cycle_datetime" : "{{ current_cycle | to_YMDH }}",
"dump_directory" : "{{ DMPDIR }}",
"ioda_directory" : "{{ COM_OBS }}",
"subsets" : [ "NC005072" ],
"data_description" : "NC005072 LEOGEO SATWIND IR(LW)",
"data_provider" : "U.S. NOAA/NESDIS",
"sensor_info" : { "sensor_name": "LEOGEO", "sensor_full_name": "Combined Platform LEO/GEO", "sensor_id": 999 },
"satellite_info" : [
{ "satellite_name": "multi", "satellite_full_name": "MULTIPLE-SATS", "satellite_id": 854, "launch time": "YYYYMMDD" },
]
}
69 changes: 69 additions & 0 deletions parm/soca/letkf/letkf.yaml.j2
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geometry:
geom_grid_file: soca_gridspec.nc
mom6_input_nml: mom_input.nml
fields metadata: fields_metadata.yaml

time window:
begin: &date '{{ ATM_WINDOW_BEGIN }}'
length: PT6H

background:
members from template:
template:
date: '{{ ATM_WINDOW_MIDDLE }}'
ocn_filename: enkfgdas.ocean.t06z.inst.f009.nc
ice_filename: enkfgdas.ice.t06z.inst.f009.nc
read_from_file: 1
basename: ./ens/mem%mem%
state variables: [socn, tocn, ssh, uocn, vocn, cicen]
pattern: '%mem%'
nmembers: {{ NMEM_ENS }}

observations:
observers:

driver:
do posterior observer: true
save posterior mean increment: true
save posterior mean: true
save posterior variance: true
save prior mean: true
save prior variance: true

local ensemble DA:
solver: LETKF
inflation:
rtps: 0.5
rtpp: 0.6
mult: 1.1

output:
datadir: data_output/
date: *date
exp: letkf
type: ens

output mean prior:
datadir: data_output/
date: *date
exp: letkf
type: fc

output variance prior:
datadir: data_output/
date: *date
exp: letkf
type: fc

output variance posterior:
datadir: data_output/
date: *date
exp: letkf
type: an

output increment:
datadir: data_output/
date: *date
exp: letkf.inc
type: an

22 changes: 0 additions & 22 deletions parm/soca/obs/config/dev/insitu_profile_argo.yaml

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