Merge branch 'develop' into feature/abi_sea_ice

NOAA-EMC · Oct 15, 2024 · ee45e80 · ee45e80
2 parents 843bb6c + e44d21e
commit ee45e80
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diff --git a/.github/workflows/hera.yaml b/.github/workflows/hera.yaml
@@ -5,7 +5,7 @@ on:
 
 jobs:
  test:
- runs-on: ubuntu-latest
+ runs-on: ubuntu-22.04
  name: Passes on Hera 
 
  steps:

diff --git a/.github/workflows/norms.yaml b/.github/workflows/norms.yaml
@@ -3,7 +3,7 @@ on: [push]
 
 jobs:
  check_pynorms:
- runs-on: ubuntu-latest
+ runs-on: ubuntu-22.04
  name: Check coding norms with pycodestyle and cpplint
 
  steps:

diff --git a/.github/workflows/orion.yaml b/.github/workflows/orion.yaml
@@ -5,7 +5,7 @@ on:
 
 jobs:
  test:
- runs-on: ubuntu-latest
+ runs-on: ubuntu-22.04
  name: Passes on Orion
 
  steps:

diff --git a/.github/workflows/unittests.yaml b/.github/workflows/unittests.yaml
@@ -3,7 +3,7 @@ on: [push, pull_request]
 
 jobs:
  ctests:
- runs-on: ubuntu-latest
+ runs-on: ubuntu-22.04
  name: Run Unit Tests with ctest
 
  steps:

diff --git a/.github/workflows/unittests_g-w.yaml b/.github/workflows/unittests_g-w.yaml
@@ -3,7 +3,7 @@ on: [push, pull_request]
 
 jobs:
  ctests:
- runs-on: ubuntu-latest
+ runs-on: ubuntu-22.04
  name: Run Unit Tests inside global-workflow with ctest
 
  steps:

diff --git a/build.sh b/build.sh
@@ -71,7 +71,7 @@ while getopts "p:t:c:hvdfa" opt; do
 done
 
 case ${BUILD_TARGET} in
- hera | orion | hercules | wcoss2 | noaacloud | gaea)
+ hera | orion | hercules | wcoss2 | noaacloud | gaea | gaeac6 )
  echo "Building GDASApp on $BUILD_TARGET"
  source $dir_root/ush/module-setup.sh
  module use $dir_root/modulefiles

diff --git a/modulefiles/GDAS/gaeac6.intel.lua b/modulefiles/GDAS/gaeac6.intel.lua
@@ -0,0 +1,95 @@
+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/c6/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/2023.2.0")
+load("stack-cray-mpich/8.1.29")
+-- 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/2.42.0")
+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("fms/2023.04")
+load("esmf/8.6.0")
+load("atlas/0.35.1")
+load("sp/2.5.0")
+load("gsl-lite/0.37.0")
+load("libjpeg/2.1.0")
+load("krb5/1.20.1")
+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")
+
+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/f6/ira-sti/world-shared/GDASApp/fix/crtm/2.4.0")
+setenv("GDASAPP_TESTDATA","/gpfs/f6/ira-sti/world-shared/GDASApp/testdata")
+setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/gpfs/f6/ira-sti/world-shared/GDASApp/unittestdata")
+
+whatis("Name: ".. "pkgName")
+whatis("Version: ".. "pkgVersion")
+whatis("Category: GDASApp")
+whatis("Description: Load all libraries needed for GDASApp")
diff --git a/parm/atm/jcb-base.yaml.j2 b/parm/atm/jcb-base.yaml.j2
@@ -71,6 +71,8 @@ observations: all_observations
 crtm_coefficient_path: "{{ DATA }}/crtm/"
 
 # Naming conventions for observational files
+atmosphere_obsdataroot_path: "{{COM_OBS}}"
+
 atmosphere_obsdatain_path: "{{atm_obsdatain_path}}"
 atmosphere_obsdatain_prefix: "{{OPREFIX}}"
 atmosphere_obsdatain_suffix: ".tm00.nc"
@@ -80,6 +82,8 @@ atmosphere_obsdataout_prefix: diag_
 atmosphere_obsdataout_suffix: "_{{ current_cycle | to_YMDH }}.nc"
 
 # Naming conventions for bias correction files
+atmosphere_obsbiasroot_path: "{{COM_ATMOS_ANALYSIS_PREV}}"
+
 atmosphere_obsbiasin_path: "{{DATA}}/obs/"
 atmosphere_obsbiasin_prefix: "{{GPREFIX}}"
 atmosphere_obsbiasin_suffix: ".satbias.nc"
@@ -94,6 +98,16 @@ atmosphere_obsbiasout_suffix: ".satbias.nc"
 atmosphere_obsbiascovout_prefix: "{{APREFIX}}"
 atmosphere_obsbiascovout_suffix: ".satbias_cov.nc"
 
+bias_files:
+ atms_n20: rad_varbc_params.tar
+ atms_npp: rad_varbc_params.tar
+ mtiasi_metop-a: rad_varbc_params.tar
+ mtiasi_metop-b: rad_varbc_params.tar
+ amsua_n19: rad_varbc_params.tar
+ ssmis_f17: rad_varbc_params.tar
+ ssmis_f18: rad_varbc_params.tar
+ cris-fsr_n20: rad_varbc_params.tar
+ cris-fsr_npp: rad_varbc_params.tar
 
 # Local Ensemble DA (LETKF)
 # -------------------------

diff --git a/parm/jcb-gdas b/parm/jcb-gdas
diff --git a/sorc/oops b/sorc/oops
diff --git a/sorc/saber b/sorc/saber
diff --git a/test/atm/global-workflow/config.yaml b/test/atm/global-workflow/config.yaml
@@ -10,7 +10,7 @@ base:
  PTMP: "@bindir@/test/atm/global-workflow/testrun"
 
 atmanl:
- JCB_ALGO_YAML: "@srcdir@/test/atm/global-workflow/jcb-prototype_3dvar.yaml.j2"
+ JCB_ALGO_YAML_VAR: "@srcdir@/test/atm/global-workflow/jcb-prototype_3dvar.yaml.j2"
  STATICB_TYPE: "identity"
  ATMRES_ANL: "C48"
  LAYOUT_X_ATMANL: 1
@@ -19,11 +19,6 @@ atmanl:
 atmensanl:
  JCB_ALGO_YAML_LETKF: "@srcdir@/test/atm/global-workflow/jcb-prototype_lgetkf.yaml.j2"
  JCB_ALGO_YAML_OBS: "@srcdir@/test/atm/global-workflow/jcb-prototype_lgetkf_observer.yaml.j2"
+ JCB_ALGO_YAML_SOL: "@srcdir@/test/atm/global-workflow/jcb-prototype_lgetkf_solver.yaml.j2"
  LAYOUT_X_ATMENSANL: 1
  LAYOUT_Y_ATMENSANL: 1
-
-atmensanlobs:
- JCB_ALGO_YAML: "@srcdir@/test/atm/global-workflow/jcb-prototype_lgetkf_observer.yaml.j2"
-
-atmensanlsol:
- JCB_ALGO_YAML: "@srcdir@/test/atm/global-workflow/jcb-prototype_lgetkf_solver.yaml.j2"
diff --git a/test/gw-ci/CMakeLists.txt b/test/gw-ci/CMakeLists.txt
@@ -20,17 +20,17 @@ function(add_cycling_tests pslot YAML_PATH HOMEgfs RUNTESTS PROJECT_SOURCE_DIR T
 
  # stage IC's
  message(STATUS "staging the 1/2 cycle IC's for ${test_name} ctest")
- add_test(NAME ${test_name}_gdasstage_ic_${HALF_CYCLE}
- COMMAND /bin/bash -c "${PROJECT_SOURCE_DIR}/test/gw-ci/run_exp.sh ${pslot} gdasstage_ic ${HALF_CYCLE}"
+ add_test(NAME ${test_name}_gdas_stage_ic_${HALF_CYCLE}
+ COMMAND /bin/bash -c "${PROJECT_SOURCE_DIR}/test/gw-ci/run_exp.sh ${pslot} gdas_stage_ic ${HALF_CYCLE}"
  WORKING_DIRECTORY ${RUNTESTS})
- set_tests_properties(${test_name}_gdasstage_ic_${HALF_CYCLE} PROPERTIES LABELS "manual")
+ set_tests_properties(${test_name}_gdas_stage_ic_${HALF_CYCLE} PROPERTIES LABELS "manual")
 
- # 1/2 cycle gdasfcst
- message(STATUS "preparing 1/2 cycle gdasfcst for ${pslot} ctest")
- add_test(NAME ${test_name}_gdasfcst_${HALF_CYCLE}
- COMMAND /bin/bash -c "${PROJECT_SOURCE_DIR}/test/gw-ci/run_exp.sh ${pslot} gdasfcst_seg0 ${HALF_CYCLE}"
+ # 1/2 cycle gdas_fcst
+ message(STATUS "preparing 1/2 cycle gdas_fcst for ${pslot} ctest")
+ add_test(NAME ${test_name}_gdas_fcst_${HALF_CYCLE}
+ COMMAND /bin/bash -c "${PROJECT_SOURCE_DIR}/test/gw-ci/run_exp.sh ${pslot} gdas_fcst_seg0 ${HALF_CYCLE}"
  WORKING_DIRECTORY ${RUNTESTS})
- set_tests_properties(${test_name}_gdasfcst_${HALF_CYCLE} PROPERTIES LABELS "manual")
+ set_tests_properties(${test_name}_gdas_fcst_${HALF_CYCLE} PROPERTIES LABELS "manual")
 
  # Select the list of tasks to run for the full cycle
  message(STATUS "Tasks ${TASK_LIST}")
@@ -54,12 +54,12 @@ if (WORKFLOW_TESTS)
  set(pslot "WCDA-3DVAR-C48mx500")
  set(YAML_PATH ${HOMEgfs}/ci/cases/pr/C48mx500_3DVarAOWCDA.yaml)
  set(TASK_LIST
- "gdasprepoceanobs"
- "gdasmarinebmat"
- "gdasmarineanlinit"
- "gdasmarineanlvar"
- "gdasmarineanlchkpt"
- "gdasmarineanlfinal"
+ "gdas_prepoceanobs"
+ "gdas_marinebmat"
+ "gdas_marineanlinit"
+ "gdas_marineanlvar"
+ "gdas_marineanlchkpt"
+ "gdas_marineanlfinal"
  )
  add_cycling_tests(${pslot} ${YAML_PATH} ${HOMEgfs} ${RUNTESTS} ${PROJECT_SOURCE_DIR} "${TASK_LIST}")
 endif()
@@ -85,15 +85,15 @@ if (RUN_GW_CI)
  set(pslot "GFSv17-3DVAR-C384mx025")
  set(YAML_PATH ${HOMEgfs}/ci/cases/gfsv17/C384mx025_3DVarAOWCDA.yaml)
  set(TASK_LIST
- "gdasprepoceanobs"
- "gdasmarinebmat"
- "gdasmarineanlinit"
- "gdasmarineanlvar"
- "gdasmarineanlchkpt"
- "gdasmarineanlfinal"
- "gdasocnanalvrfy"
- "gdasprep"
- "gdasanal"
+ "gdas_prepoceanobs"
+ "gdas_marinebmat"
+ "gdas_marineanlinit"
+ "gdas_marineanlvar"
+ "gdas_marineanlchkpt"
+ "gdas_marineanlfinal"
+ "gdas_ocnanalvrfy"
+ "gdas_prep"
+ "gdas_anal"
  )
  add_cycling_tests(${pslot} ${YAML_PATH} ${HOMEgfs} ${RUNTESTS} ${PROJECT_SOURCE_DIR} "${TASK_LIST}")
 endif()
diff --git a/ush/detect_machine.sh b/ush/detect_machine.sh
@@ -24,6 +24,9 @@ case $(hostname -f) in
  gaea5[1-8]) MACHINE_ID=gaea ;; ### gaea51-58
  gaea5[1-8].ncrc.gov) MACHINE_ID=gaea ;; ### gaea51-58
 
+ gaea6[1-8]) MACHINE_ID=gaeac6 ;; ### gaea61-68
+ gaea6[1-8].ncrc.gov) MACHINE_ID=gaeac6 ;; ### gaea61-68
+
  hfe0[1-9]) MACHINE_ID=hera ;; ### hera01-09
  hfe1[0-2]) MACHINE_ID=hera ;; ### hera10-12
  hecflow01) MACHINE_ID=hera ;; ### heraecflow01