Bring in feature/hafs.v2.0.1 back to develop

jobs/JHAFS_ANALYSIS

@@ -36,20 +36,15 @@ if [ "${RUN_ENVIR^^}" != "NCO" ]; then
   if [ ${machine}  = "wcoss2" ]; then
     module reset
     module use $HOMEhafs/sorc/hafs_gsi.fd/modulefiles
-    module load gsi_${machine}
+    module load gsi_${machine}.intel
     module load cray-pals/1.2.2
     module load cfp/2.0.4
   fi
-  if [ ${machine}  = "hera" ]; then
+  if [[ ${machine}  = "jet" ]] || [[ ${machine}  = "orion" ]] || [[ ${machine}  = "hercules" ]] || [[ ${machine}  = "hera" ]]; then
     module purge
     module use $HOMEhafs/sorc/hafs_gsi.fd/modulefiles
     module load gsi_${machine}.intel
   fi
-  if [[ ${machine}  = "jet" ]] || [[ ${machine}  = "orion" ]] || [[ ${machine}  = "hercules" ]]; then
-    module purge
-    module use $HOMEhafs/sorc/hafs_gsi.fd/modulefiles
-    module load gsi_${machine}
-  fi
   module list
 else
   # Run by NCO on WCOSS2

jobs/JHAFS_ENKF

@@ -36,7 +36,7 @@ if [ "${RUN_ENVIR^^}" != "NCO" ]; then
   if [ ${machine}  = "wcoss2" ]; then
     module reset
     module use $HOMEhafs/sorc/hafs_gsi.fd/modulefiles
-    module load gsi_${machine}
+    module load gsi_${machine}.intel
     module load cray-pals/1.2.2
     module load cfp/2.0.4
   fi

jobs/JHAFS_ENKF_HX

@@ -36,7 +36,7 @@ if [ "${RUN_ENVIR^^}" != "NCO" ]; then
   if [ ${machine}  = "wcoss2" ]; then
     module reset
     module use $HOMEhafs/sorc/hafs_gsi.fd/modulefiles
-    module load gsi_${machine}
+    module load gsi_${machine}.intel
     module load cray-pals/1.2.2
     module load cfp/2.0.4
   fi

jobs/JHAFS_GRAPHICS

@@ -34,6 +34,9 @@ if [ "${RUN_ENVIR^^}" != "NCO" ]; then
   source ${USHhafs}/hafs_pre_job.sh.inc
   export machine=${WHERE_AM_I:-wcoss2}
   if [ "${GRAPH}" = "EMC" ]; then
+    if [ ${machine} = hera ]; then 
+       module purge
+    fi
     module use ${HOMEhafs}/sorc/hafs_graphics.fd/emc_graphics/modulefiles
     module load graphics.run.${machine}
   elif [ "${GRAPH}" = "HRD" ]; then

jobs/JHAFS_OCN_PREP

@@ -29,15 +29,21 @@ export FIXhafs=$HOMEhafs/fix
 
 export WORKhafs=${WORKhafs:-${DATAROOT:?}/${RUN:?}${storm_num:?}_${cyc:?}_${envir:?}_${hafs_ver:?}}
 
+export COMhafs=${COMhafs:-$(compath.py ${envir}/${NET}/${hafs_ver})/${RUN}.${PDY}/${cyc}}
+export CONFhafs=$COMhafs/$stormlabel.conf
+export HOLDVARS=${HOLDVARS:-$COMhafs/$stormlabel.holdvars.txt}
+
+source ${HOLDVARS}
+
 if [ "${RUN_ENVIR^^}" != "NCO" ]; then
   # Detect platform and load modules if not run by NCO
   source ${USHhafs}/hafs_pre_job.sh.inc
   export machine=${WHERE_AM_I:-wcoss2}
-  if [ "${machine}" != "wcoss2" ] ; then
+  if [[ "${machine}" != "wcoss2" ]] && [[ "${ocean_model}" == mom6 ]]; then
       module use ${HOMEhafs}/modulefile
       module load hafs_mom6_obc.${machine}  
+      module list
   fi
-  module list
 else
   # Run by NCO on WCOSS2
   export machine=${WHERE_AM_I:-wcoss2}
@@ -53,12 +59,6 @@ source ${USHhafs}/hafs_runcmd.sh.inc
 
 env
 
-export COMhafs=${COMhafs:-$(compath.py ${envir}/${NET}/${hafs_ver})/${RUN}.${PDY}/${cyc}}
-export CONFhafs=$COMhafs/$stormlabel.conf
-export HOLDVARS=${HOLDVARS:-$COMhafs/$stormlabel.holdvars.txt}
-
-source ${HOLDVARS}
-
 export PYTHONPATH=$PYTHONPATH:${HOMEhafs}/ush/mom6_obc
 
 export DATA=${WORKhafs}/ocn_prep

modulefiles/hafs.hera.lua

@@ -127,9 +127,6 @@ load(pathJoin("py-xarray", xarray_ver))
 scipy_ver=os.getenv("scipy_ver") or "1.11.3"
 load(pathJoin("py-scipy", scipy_ver))
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/hwrf/noscrub/local/modulefiles")
---load(pathJoin("python", "wcoss2_env"))
-
 setenv("CMAKE_C_COMPILER", "mpiicc")
 setenv("CMAKE_CXX_COMPILER", "mpiicpc")
 setenv("CMAKE_Fortran_COMPILER", "mpiifort")

modulefiles/hafs.hercules.lua

@@ -40,7 +40,7 @@ load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
 parallelio_ver=os.getenv("parallelio_ver") or "2.5.10"
 load(pathJoin("parallelio", parallelio_ver))
 
-esmf_ver=os.getenv("esmf_ver") or "8.5.0"
+esmf_ver=os.getenv("esmf_ver") or "8.6.0"
 load(pathJoin("esmf", esmf_ver))
 
 fms_ver=os.getenv("fms_ver") or "2023.04"
@@ -76,7 +76,7 @@ load(pathJoin("gftl-shared", gftl_shared_ver))
 yafyaml_ver=os.getenv("yafyaml_ver") or "0.2.5"
 load(pathJoin("libyaml", yafyaml_ver))
 
-mapl_ver=os.getenv("mapl_ver") or "2.40.3-esmf-8.5.0"
+mapl_ver=os.getenv("mapl_ver") or "2.40.3-esmf-8.6.0"
 load(pathJoin("mapl", mapl_ver))
 
 bufr_ver=os.getenv("bufr_ver") or "12.0.1"
@@ -118,10 +118,14 @@ load(pathJoin("tar", tar_ver))
 rocoto_ver=os.getenv("rocoto_ver") or "default"
 load(pathJoin("rocoto", rocoto_ver))
 
-unload("py-numpy/1.22.3")
+xarray_ver=os.getenv("xarray_ver") or "2023.7.0"
+load(pathJoin("py-xarray", xarray_ver))
 
-prepend_path("MODULEPATH", "/work/noaa/hwrf/noscrub/local/modulefiles")
-load(pathJoin("python", "wcoss2_env"))
+netcdf4_ver=os.getenv("netcdf4_ver") or "1.5.8"
+load(pathJoin("py-netcdf4", netcdf4_ver))
+
+scipy_ver=os.getenv("scipy_ver") or "1.11.3"
+load(pathJoin("py-scipy", scipy_ver)) 
 
 setenv("CMAKE_C_COMPILER", "mpiicc")
 setenv("CMAKE_CXX_COMPILER", "mpiicpc")

modulefiles/hafs.jet.lua

@@ -6,12 +6,12 @@ prepend_path("MODULEPATH", "/contrib/sutils/modulefiles")
 load("sutils")
 load("hpss")
 
-prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/contrib/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/modulefiles/Core")
 stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
 load(pathJoin("stack-intel", stack_intel_ver)) 
 
-stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1" 
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+stack_mpi_ver=os.getenv("stack_mpi_ver") or "2021.5.1" 
+load(pathJoin("stack-intel-oneapi-mpi", stack_mpi_ver))
 
 cmake_ver=os.getenv("cmake_ver") or "3.23.1"
 load(pathJoin("cmake", cmake_ver))
@@ -37,7 +37,7 @@ load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
 parallelio_ver=os.getenv("parallelio_ver") or "2.5.10"
 load(pathJoin("parallelio", parallelio_ver))
 
-esmf_ver=os.getenv("esmf_ver") or "8.5.0"
+esmf_ver=os.getenv("esmf_ver") or "8.6.0"
 load(pathJoin("esmf", esmf_ver))
 
 fms_ver=os.getenv("fms_ver") or "2023.04"
@@ -73,7 +73,7 @@ load(pathJoin("gftl-shared", gftl_shared_ver))
 yafyaml_ver=os.getenv("yafyaml_ver") or "0.2.5"
 load(pathJoin("libyaml", yafyaml_ver)) 
 
-mapl_ver=os.getenv("mapl_ver") or "2.40.3-esmf-8.5.0"
+mapl_ver=os.getenv("mapl_ver") or "2.40.3-esmf-8.6.0"
 load(pathJoin("mapl", mapl_ver))
 
 bufr_ver=os.getenv("bufr_ver") or "12.0.1"
@@ -114,8 +114,14 @@ load(pathJoin("cdo", cdo_ver))
 rocoto_ver=os.getenv("rocoto_ver") or "1.3.7"
 load("rocoto")
 
-prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hwrfv3/local/modulefiles")
-load(pathJoin("python", "wcoss2_env"))
+xarray_ver=os.getenv("xarray_ver") or "2023.7.0"
+load(pathJoin("py-xarray", xarray_ver))
+
+netcdf4_ver=os.getenv("netcdf4_ver") or "1.5.8"
+load(pathJoin("py-netcdf4", netcdf4_ver))
+
+scipy_ver=os.getenv("scipy_ver") or "1.11.3"
+load(pathJoin("py-scipy", scipy_ver))
 
 setenv("CMAKE_C_COMPILER", "mpiicc")
 setenv("CMAKE_CXX_COMPILER", "mpiicpc")

modulefiles/hafs.orion.lua

@@ -37,7 +37,7 @@ load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
 parallelio_ver=os.getenv("parallelio_ver") or "2.5.10"
 load(pathJoin("parallelio", parallelio_ver))
 
-esmf_ver=os.getenv("esmf_ver") or "8.5.0"
+esmf_ver=os.getenv("esmf_ver") or "8.6.0"
 load(pathJoin("esmf", esmf_ver))
 
 fms_ver=os.getenv("fms_ver") or "2023.04"
@@ -73,7 +73,7 @@ load(pathJoin("gftl-shared", gftl_shared_ver))
 yafyaml_ver=os.getenv("yafyaml_ver") or "0.2.5"
 load(pathJoin("libyaml", yafyaml_ver))
 
-mapl_ver=os.getenv("mapl_ver") or "2.40.3-esmf-8.5.0"
+mapl_ver=os.getenv("mapl_ver") or "2.40.3-esmf-8.6.0"
 load(pathJoin("mapl", mapl_ver))
 
 bufr_ver=os.getenv("bufr_ver") or "12.0.1"
@@ -112,12 +112,16 @@ load(pathJoin("intel-oneapi-mkl", mkl_ver))
 tar_ver=os.getenv("tar_ver") or "1.34"
 load(pathJoin("tar", tar_ver))
 
-prepend_path("PATH", "/apps/contrib/rocoto/1.3.7/bin")
+xarray_ver=os.getenv("xarray_ver") or "2023.7.0"
+load(pathJoin("py-xarray", xarray_ver))
+
+netcdf4_ver=os.getenv("netcdf4_ver") or "1.5.8"
+load(pathJoin("py-netcdf4", netcdf4_ver))
 
-unload("py-numpy/1.22.3")
+scipy_ver=os.getenv("scipy_ver") or "1.11.3"
+load(pathJoin("py-scipy", scipy_ver))
 
-prepend_path("MODULEPATH", "/work/noaa/hwrf/noscrub/local/modulefiles")
-load(pathJoin("python", "wcoss2_env"))
+prepend_path("PATH", "/apps/contrib/rocoto/1.3.7/bin")
 
 setenv("CMAKE_C_COMPILER", "mpiicc")
 setenv("CMAKE_CXX_COMPILER", "mpiicpc")

modulefiles/hafs.wcoss2.lua

@@ -36,13 +36,13 @@ libjpeg_ver=os.getenv("libjpeg_ver")
 load(pathJoin("libjpeg", libjpeg_ver))
 
 hdf5_ver=os.getenv("hdf5_ver")
-load(pathJoin("hdf5-A", hdf5_ver))
+load(pathJoin("hdf5-C", hdf5_ver))
 
 netcdf_ver=os.getenv("netcdf_ver")
-load(pathJoin("netcdf-A", netcdf_ver))
+load(pathJoin("netcdf-C", netcdf_ver))
 
 fms_ver=os.getenv("fms_ver")
-load(pathJoin("fms", fms_ver))
+load(pathJoin("fms-C", fms_ver))
 
 bacio_ver=os.getenv("bacio_ver")
 load(pathJoin("bacio", bacio_ver))
@@ -117,16 +117,16 @@ ncio_ver=os.getenv("ncio_ver")
 load(pathJoin("ncio-A", ncio_ver))
 
 pio_ver=os.getenv("pio_ver")
-load(pathJoin("pio-B", pio_ver))
+load(pathJoin("pio-C", pio_ver))
 
 esmf_ver=os.getenv("esmf_ver")
-load(pathJoin("esmf-B", esmf_ver))
+load(pathJoin("esmf-C", esmf_ver))
 
 gftl_shared_ver=os.getenv("gftl_shared_ver")
 --load(pathJoin("gftl-shared", gftl_shared_ver))
 
 mapl_ver=os.getenv("mapl_ver")
---load(pathJoin("mapl-B", mapl_ver))
+--load(pathJoin("mapl-C", mapl_ver))
 
 scotch_ver=os.getenv("scotch_ver")
 load(pathJoin("scotch", scotch_ver))

modulefiles/hafs_mom6_obc.hera.lua

@@ -2,8 +2,12 @@ help([[
 loads HAFS/MOM6 OBC modulefile on Hera
 ]])
 unload("esmf")
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/hwrf/save/Maria.Aristizabal/modulefiles")
-load("modulefile.OBC.run.hera")
-setenv("ESMFMKFILE", "/scratch1/NCEPDEV/hwrf/save/Maria.Aristizabal/miniconda3/envs/OBC_env/lib/esmf.mk")
+unload("py-numpy")
+unload("py-xarray")
+unload("py-scipy")
+unload("py-netcdf4")
+prepend_path("PATH", "/scratch2/NCEPDEV/hwrf/save/Maria.Aristizabal/miniconda3/envs/OBC_env/bin")
+prepend_path("PYTHONPATH", "/scratch2/NCEPDEV/hwrf/save/Maria.Aristizabal/miniconda3/envs/OBC_env")
+setenv("ESMFMKFILE", "/scratch2/NCEPDEV/hwrf/save/Maria.Aristizabal/miniconda3/envs/OBC_env/lib/esmf.mk")
 
 whatis("Description: HAFS/MOM6 OBC  environment")

modulefiles/hafs_mom6_obc.hercules.lua

@@ -2,8 +2,12 @@ help([[
 loads HAFS/MOM6 OBC modulefile on Hercules
 ]])
 unload("esmf")
-prepend_path("MODULEPATH", "/work/noaa/hwrf/save/maristiz/modulefiles")
-load("modulefile.OBC.run.orion")
-setenv("ESMFMKFILE", "/work/noaa/hwrf/save/maristiz/miniconda3/envs/OBC_env/lib/esmf.mk")
+unload("py-numpy")
+unload("py-xarray")
+unload("py-scipy")
+unload("py-netcdf4")
+prepend_path("PATH", "/work2/noaa/hwrf/maristiz/miniconda3/envs/OBC_env/bin")
+prepend_path("PYTHONPATH", "/work2/noaa/hwrf/maristiz/miniconda3/envs/OBC_env")
+setenv("ESMFMKFILE", "/work2/noaa/hwrf/maristiz/miniconda3/envs/OBC_env/lib/esmf.mk")
 
 whatis("Description: HAFS/MOM6 OBC  environment")

modulefiles/hafs_mom6_obc.jet.lua

@@ -2,8 +2,12 @@ help([[
 loads HAFS/MOM6 OBC modulefile on Jet
 ]])
 unload("esmf")
-prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hwrfv3/Maria.Aristizabal/modulefiles")
-load("modulefile.OBC.run.jet")
-setenv("ESMFMKFILE", "/mnt/lfs4/HFIP/hwrfv3/Maria.Aristizabal/miniconda3/envs/OBC_env/lib/esmf.mk")
+unload("py-numpy")
+unload("py-xarray")
+unload("py-scipy")
+unload("py-netcdf4")
+prepend_path("PATH", "/lfs5/HFIP/hwrfv3/Maria.Aristizabal/miniconda3/envs/OBC_env/bin")
+prepend_path("PYTHONPATH", "/lfs5/HFIP/hwrfv3/Maria.Aristizabal/miniconda3/envs/OBC_env")
+setenv("ESMFMKFILE", "/lfs5/HFIP/hwrfv3/Maria.Aristizabal/miniconda3/envs/OBC_env/lib/esmf.mk")
 
 whatis("Description: HAFS/MOM6 OBC  environment")

modulefiles/hafs_mom6_obc.orion.lua

@@ -2,8 +2,12 @@ help([[
 loads HAFS/MOM6 OBC modulefile on Orion
 ]])
 unload("esmf")
-prepend_path("MODULEPATH", "/work/noaa/hwrf/save/maristiz/modulefiles")
-load("modulefile.OBC.run.orion")
-setenv("ESMFMKFILE", "/work/noaa/hwrf/save/maristiz/miniconda3/envs/OBC_env/lib/esmf.mk")
+unload("py-numpy")
+unload("py-xarray")
+unload("py-scipy")
+unload("py-netcdf4")
+prepend_path("PATH", "/work2/noaa/hwrf/maristiz/miniconda3/envs/OBC_env/bin")
+prepend_path("PYTHONPATH", "/work2/noaa/hwrf/maristiz/miniconda3/envs/OBC_env")
+setenv("ESMFMKFILE", "/work2/noaa/hwrf/maristiz/miniconda3/envs/OBC_env/lib/esmf.mk")
 
 whatis("Description: HAFS/MOM6 OBC  environment")

parm/analysis/gsi/global_ozinfo.txt

@@ -163,6 +163,28 @@
  ompsnp_npp      20    1  631.000  3.000  2.198 10.000  0.000
  ompsnp_npp      21    1 1000.000  3.000  2.285 10.000  0.000
  ompsnp_npp      22   -1    0.000 12.000  7.236 10.000  0.000
+ ompsnp_n20       1    1    0.100  0.100  0.020 10.000  0.000
+ ompsnp_n20       2    1    0.158  0.100  0.020 10.000  0.000
+ ompsnp_n20       3    1    0.251  0.100  0.025 10.000  0.000
+ ompsnp_n20       4    1    0.398  0.200  0.040 10.000  0.000
+ ompsnp_n20       5    1    0.631  0.500  0.080 10.000  0.000
+ ompsnp_n20       6    1    1.000  1.000  0.156 10.000  0.000
+ ompsnp_n20       7    1    1.580  1.000  0.245 10.000  0.000
+ ompsnp_n20       8    1    2.510  1.282  0.510 10.000  0.000
+ ompsnp_n20       9    1    3.980  2.051  1.089 10.000  0.000
+ ompsnp_n20      10    1    6.310  2.641  3.917 10.000  0.000
+ ompsnp_n20      11    1   10.000  3.590  6.124 10.000  0.000
+ ompsnp_n20      12    1   15.800  5.052  6.347 10.000  0.000
+ ompsnp_n20      13    1   25.100  6.273  5.798 10.000  0.000
+ ompsnp_n20      14    1   39.800  7.000  6.843 10.000  0.000
+ ompsnp_n20      15    1   63.100  6.940  9.253 10.000  0.000
+ ompsnp_n20      16    1  100.000  5.752 10.091 10.000  0.000
+ ompsnp_n20      17    1  158.000  4.422 10.967 10.000  0.000
+ ompsnp_n20      18    1  251.000  4.000  8.478 10.000  0.000
+ ompsnp_n20      19    1  398.000  3.000  5.572 10.000  0.000
+ ompsnp_n20      20    1  631.000  3.000  2.638 10.000  0.000
+ ompsnp_n20      21    1 1000.000  3.000  3.525 10.000  0.000
+ ompsnp_n20      22   -1    0.000 12.000  7.236 10.000  0.000
  omi_aura         1    1    0.000  6.000  6.000 10.000  0.000
  gome_metop-a     1   -1    0.000 12.000  2.236 10.000  0.000
  gome_metop-b     1   -1    0.000 12.000  2.236 10.000  0.000
@@ -296,3 +318,4 @@
  mls30_aura      54   -1  999.999  9.999  9.999 10.000  0.000
  mls30_aura      55   -1  999.999  9.999  9.999 10.000  0.000
  ompstc8_npp      1    1    0.000  6.000  6.000 10.000  0.000
+ ompstc8_n20      1    1    0.000  6.000  6.000 10.000  0.000

parm/analysis/gsi/global_scaninfo.txt

@@ -13,6 +13,7 @@
  amsub_n17               -48.950      1.100        90    10    81
  atms_npp                -52.725      1.110        96     7    90
  atms_n20                -52.725      1.110        96     7    90
+ atms_n21                -52.725      1.110        96     7    90
  mhs_n18                 -49.444      1.111        90    10    81
  mhs_n19                 -49.444      1.111        90    10    81
  airs_aqua               -48.900      1.100        90    10    81
@@ -31,11 +32,19 @@
  msu_n14                 -47.370      9.474        90     2    10
  ssu                     -35.000     10.000        90     2     7
  hsb                     -48.950      1.100        90    10    81
+ seviri_m08                0.000      1.000        90    -1    -1
  seviri_m09                0.000      1.000        90    -1    -1
  seviri_m10                0.000      1.000        90    -1    -1
+ seviri_m11                0.000      1.000        90    -1    -1
+ abi_g16                   0.000      1.000        90    -1    -1
+ abi_g17                   0.000      1.000        90    -1    -1
+ abi_g18                   0.000      1.000        90    -1    -1
+ ahi_himawari8             0.000      1.000        90    -1    -1
+ ahi_himawari9             0.000      1.000        90    -1    -1
  cris_npp                -48.330     3.3331        30     1    30
  cris-fsr_npp            -48.330     3.3331        30     1    30
  cris-fsr_n20            -48.330     3.3331        30     1    30
+ cris-fsr_n21            -48.330     3.3331        30     1    30
  ssmis_f16                 0.000      1.000        60     1    60
  ssmis_f17                 0.000      1.000        60     1    60
  ssmis_f18                 0.000      1.000        60     1    60
@@ -45,4 +54,8 @@
  avhrr3_metop-b          -52.612      1.182        90     1    90
  avhrr3_metop-c          -52.612      1.182        90     1    90
  saphir_meghat           -42.960      0.666       130     1   130
+ viirs-m_npp             -56.280      1.265        90     1    90
+ viirs-m_j1              -56.280      1.265        90     1    90
+ viirs-m_j2              -56.280      1.265        90     1    90
+ gmi_gpm                   0.000      1.000       221    15   207
 !sat_sis                  start       step      nstep  edge1  edge2