Update feature/ufs_dom from develop 2023/12/12

.gitignore

@@ -6,3 +6,4 @@ latex
 
 *.pyc
 build
+._*

.travis.yml

@@ -20,15 +20,15 @@
 env:
   global:
     - MAIN_REPO=soca
-    - LIB_REPOS="gsw mom6 icepack oops vader ioda ufo saber"
-    - BUILD_OPT="-DBUILD_ICEPACK=ON"
+    - LIB_REPOS="gsw mom6 icepack oasim oops vader ioda ufo saber"
+    - BUILD_OPT="-DBUILD_ICEPACK=ON -DBUILD_OASIM=ON"
     - BUILD_OPT_mom6="-DENABLE_OCEAN_BGC=ON"
     - BUILD_OPT_oops="-DENABLE_QG_MODEL=OFF -DENABLE_LORENZ95_MODEL=OFF"
     - BUILD_OPT_ioda="-DBUILD_PYTHON_BINDINGS=OFF -DBUILD_TESTING=OFF"
     - BUILD_OPT_ufo="-DLOCAL_PATH_TESTFILES_IODA=NONE"
     - BUILD_OPT_saber="-DENABLE_TESTS=OFF"
     - BUILD_OPT_soca="-DENABLE_OCEAN_BGC=ON"
-    - MATCH_REPOS="saber oops ioda ufo mom6 soca"
+    - MATCH_REPOS="saber oops ioda ufo mom6 soca oasim vader"
     - LFS_REPOS=""
     # ENABLE_VALGRIND="ON"
 
@@ -108,13 +108,13 @@ script:
   - |
     # Build code
     docker exec -it jcsda_container bash \
-     -c '. /etc/profile.d/z10_spack_environment.sh && cd /jcsda/work && /jcsda/work/repo.src/${MAIN_REPO}/.github/travisci/build.sh; exit $?' \
+     -c '. /opt/spack-environment/activate.sh && cd /jcsda/work && /jcsda/work/repo.src/${MAIN_REPO}/.github/travisci/build.sh; exit $?' \
      || travis_terminate 1
 
   - |
     # run tests
     docker exec -it jcsda_container bash \
-     -c '. /etc/profile.d/z10_spack_environment.sh && cd /jcsda/work/repo.build/${MAIN_REPO} && ctest --output-on-failure' \
+     -c '. /opt/spack-environment/activate.sh && cd /jcsda/work/repo.build/${MAIN_REPO} && ctest --output-on-failure' \
      || travis_terminate 1
 
 

CMakeLists.txt

@@ -9,7 +9,7 @@
 ################################################################################
 
 cmake_minimum_required( VERSION 3.12 )
-project( soca VERSION 1.5.0 LANGUAGES C CXX Fortran)
+project( soca VERSION 1.6.0 LANGUAGES C CXX Fortran)
 
 find_package(ecbuild 3.3.2 REQUIRED)
 include( ecbuild_system NO_POLICY_SCOPE )
@@ -31,6 +31,13 @@ find_package( vader  1.4.0    REQUIRED)
 find_package( saber  1.7.0    REQUIRED)
 find_package( ioda   2.6.0    REQUIRED)
 find_package( ufo    1.7.0    REQUIRED)
+# fms
+find_package(FMS 2022.04 REQUIRED COMPONENTS R4 R8)
+if (FV3_PRECISION MATCHES DOUBLE OR NOT FV3_PRECISION)
+  add_library(fms ALIAS FMS::fms_r8)
+else()
+  add_library(fms ALIAS FMS::fms_r4)
+endif()
 if(FV3_FORECAST_MODEL MATCHES UFS)
   find_package( ESMF MODULE REQUIRED STATIC)
   find_package( crtm   2.2.3)
@@ -43,13 +50,11 @@ if(FV3_FORECAST_MODEL MATCHES UFS)
   find_package( nemsio REQUIRED)
   find_package( PIO 2.5.3 REQUIRED COMPONENTS C Fortran)
 else()
-  find_package( fms    2020.4.0 REQUIRED)
   find_package( mom6   2020.4.0 REQUIRED)
 endif()
 
-if ( BUILD_ICEPACK )
-  find_package( icepack   1.2.0 REQUIRED)
-endif()
+# Optionally look for icepack
+find_package( icepack 1.2.0 QUIET)
 
 include_directories( ${NETCDF_INCLUDE_DIRS} ${DEPEND_LIB_ROOT}/include_r8 ${DEPEND_LIB_ROOT}/MOM6/mod  )
 include_directories( ${DEPEND_LIB_ROOT}/../ufs-weather-model/src/ufs-weather-model-build/MOM6-interface/mod_solo)

bundle/.gitignore

@@ -1,14 +1,18 @@
 atlas/
 crtm/
-eckit/
-fckit/
 fms/
 gsw/
 icepack/
+ioda-data/
 ioda/
 jedicmake/
 mom6/
+oasim/
 oops/
+saber-data/
 saber/
 soca
+test-data-release/
+ufo-data/
 ufo/
+vader/

bundle/CMakeLists.txt

@@ -1,4 +1,4 @@
-# (C) COPYRIGHT 2018-2020 UCAR
+# (C) COPYRIGHT 2018-2023 UCAR
 #
 # THIS SOFTWARE IS LICENSED UNDER THE TERMS OF THE APACHE LICENCE VERSION 2.0
 # WHICH CAN BE OBTAINED AT HTTP://WWW.APACHE.ORG/LICENSES/LICENSE-2.0.
@@ -14,32 +14,19 @@ include( ecbuild_bundle )
 
 ecbuild_bundle_initialize()
 
-ecbuild_bundle( PROJECT jedicmake GIT "https://github.com/jcsda-internal/jedi-cmake.git" UPDATE BRANCH develop RECURSIVE )
-include( jedicmake/cmake/Functions/git_functions.cmake  )
-
-# ECMWF repos that you probably dont need to build yourself because they
-#  should be in jedi-stack and the containers
-
-option(BUILD_ECKIT "download and build eckit (not needed if in a jedi container)")
-if ( BUILD_ECKIT )
-  ecbuild_bundle( PROJECT eckit  GIT "https://github.com/ecmwf/eckit.git"  UPDATE TAG 1.16.0 )
-endif ()
-
-option(BUILD_FCKIT "download and build fckit (not needed if in a jedi container)")
-if (BUILD_FCKIT)
-  ecbuild_bundle( PROJECT fckit  GIT "https://github.com/jcsda-internal/fckit.git"  UPDATE BRANCH release-stable )
-  # TODO: replace with https://github.com/ecmwf/fckit.git TAG 0.9.2
-endif()
-
-option(BUILD_ATLAS "download and build atlas")
-if (BUILD_ATLAS)
-  ecbuild_bundle( PROJECT atlas  GIT "https://github.com/ecmwf/atlas.git" TAG 0.29.0 )
+# Use external jedi-cmake or build in bundle
+if(DEFINED ENV{jedi_cmake_ROOT})
+  include( $ENV{jedi_cmake_ROOT}/share/jedicmake/Functions/git_functions.cmake )
+else ()
+  ecbuild_bundle( PROJECT jedicmake GIT "https://github.com/jcsda-internal/jedi-cmake.git" UPDATE BRANCH develop RECURSIVE )
+  include( jedicmake/cmake/Functions/git_functions.cmake  )
 endif()
 
 
+#===================================================================================================
 # other optional repositories
-
-option(BUILD_FMS "download and build fms" ON)
+#===================================================================================================
+option(BUILD_FMS "download and build fms" OFF) # NOTE, changed to default=OFF, but this will be removed in the future
 if ( BUILD_FMS )
   ecbuild_bundle( PROJECT fms           GIT "https://github.com/jcsda/FMS.git"                     UPDATE BRANCH release-stable )
 endif ()
@@ -49,17 +36,50 @@ if ( BUILD_ICEPACK )
   ecbuild_bundle( PROJECT icepack         GIT "https://github.com/JCSDA-internal/Icepack.git"         UPDATE BRANCH feature/ecbuild-new )
 endif()
 
-option(BUILD_UFSM6C6 "download and install the UFS" OFF)
+option(BUILD_OASIM "download and build OASIM ocean color forward operator" OFF)
+if ( BUILD_OASIM )
+  ecbuild_bundle( PROJECT oasim         GIT "https://github.com/JCSDA-internal/oasim.git"           UPDATE BRANCH develop )
+endif ()
 
+#===================================================================================================
 # required repositories
-
+#===================================================================================================
+ecbuild_bundle( PROJECT gsw             GIT "https://github.com/jcsda-internal/GSW-Fortran.git"     UPDATE BRANCH develop )
 ecbuild_bundle( PROJECT oops            GIT "https://github.com/jcsda-internal/oops.git"            UPDATE BRANCH develop )
 ecbuild_bundle( PROJECT vader           GIT "https://github.com/jcsda-internal/vader.git"           UPDATE BRANCH develop )
 ecbuild_bundle( PROJECT saber           GIT "https://github.com/jcsda-internal/saber.git"           UPDATE BRANCH develop )
 ecbuild_bundle( PROJECT ioda            GIT "https://github.com/jcsda-internal/ioda.git"            UPDATE BRANCH develop )
-ecbuild_bundle( PROJECT gsw             GIT "https://github.com/jcsda-internal/GSW-Fortran.git"     UPDATE BRANCH develop )
 ecbuild_bundle( PROJECT ufo             GIT "https://github.com/jcsda-internal/ufo.git"             UPDATE BRANCH develop )
 ecbuild_bundle( PROJECT mom6            GIT "https://github.com/jcsda-internal/MOM6.git"            UPDATE BRANCH main-ecbuild RECURSIVE )
 ecbuild_bundle( PROJECT soca            SOURCE "../" )
 
+#===================================================================================================
+# optional test data for the upstream repos
+#===================================================================================================
+option(TEST_IODA "download and ioda-data repo needed for ioda ctests" OFF)
+if ( TEST_IODA )
+  find_branch_name(REPO_DIR_NAME ioda)
+  if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED ${GIT_TAG_FUNC} )
+    ecbuild_bundle( PROJECT ioda-data GIT "https://github.com/JCSDA-internal/ioda-data.git" BRANCH develop UPDATE )
+  endif()
+endif ()
+
+option(TEST_UFO "download and ufo-data repo needed for ufo ctests" OFF)
+if ( TEST_UFO )
+  find_branch_name(REPO_DIR_NAME ufo)
+  if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED ${GIT_TAG_FUNC} )
+    ecbuild_bundle( PROJECT ufo-data GIT "https://github.com/JCSDA-internal/ufo-data.git" BRANCH develop UPDATE )
+  endif()
+endif ()
+
+option(TEST_SABER "download and saber-data repo needed for ioda ctests" OFF)
+if ( TEST_SABER )
+  find_branch_name(REPO_DIR_NAME saber)
+  if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED ${GIT_TAG_FUNC} )
+    ecbuild_bundle( PROJECT saber-data GIT "https://github.com/JCSDA-internal/saber-data.git" BRANCH develop UPDATE )
+  endif()
+endif ()
+
+#===================================================================================================
+
 ecbuild_bundle_finalize()

cmake/soca_compiler_flags.cmake

@@ -5,6 +5,16 @@
 
 add_definitions ( -Duse_libMPI -Duse_netCDF -DSPMD )
 
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+set(CMAKE_C_STANDARD 11)
+set(CMAKE_C_STANDARD_REQUIRED ON)
+set(CMAKE_C_EXTENSIONS OFF)
+set(CMAKE_FORTRAN_STANDARD 08)
+set(CMAKE_FORTRAN_STANDARD_REQUIRED ON)
+set(CMAKE_FORTRAN_EXTENSIONS OFF)
+
 if( NOT CMAKE_BUILD_TYPE MATCHES "Debug" )
   add_definitions( -DNDEBUG )
 endif( )

src/mains/CMakeLists.txt

@@ -1,13 +1,3 @@
-#ecbuild_add_executable( TARGET  soca_dirac.x
-#                        SOURCES Dirac.cc
-#                        LIBS    ${UFS_LIBS}
-#                      )
-
-ecbuild_add_executable( TARGET  test_soca_model.x
-                        SOURCES TestModel.cc
-                        LIBS    ${UFS_LIBS}
-                      )
-
 ecbuild_add_executable( TARGET  soca_forecast.x
                         SOURCES Forecast.cc
                         LIBS    ${UFS_LIBS}
@@ -55,11 +45,6 @@ ecbuild_add_executable( TARGET  soca_ensmeanandvariance.x
                         LIBS    ${UFS_LIBS}
                       )
 
-ecbuild_add_executable( TARGET  soca_ensvariance.x
-                        SOURCES EnsVariance.cc
-                        LIBS   ${UFS_LIBS}
-                      )
-
 ecbuild_add_executable( TARGET  soca_ensrecenter.x
                         SOURCES EnsRecenter.cc
                         LIBS   ${UFS_LIBS}

src/soca/CMakeLists.txt

@@ -29,8 +29,6 @@ target_include_directories(soca PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/..>
   $<INSTALL_INTERFACE:include/soca>)
 
-target_compile_features( soca PUBLIC cxx_std_11 )
-
 target_link_libraries( soca PUBLIC NetCDF::NetCDF_Fortran )
 target_link_libraries( soca PUBLIC fckit )
 target_link_libraries( soca PUBLIC atlas )
@@ -39,20 +37,21 @@ target_link_libraries( soca PUBLIC FMS::fms_r8 )
 target_link_libraries( soca PUBLIC gsw )
 target_link_libraries( soca PUBLIC mom6 )
 target_link_libraries( soca PUBLIC oops )
-target_link_libraries( soca PUBLIC vader )
 target_link_libraries( soca PUBLIC saber )
 target_link_libraries( soca PUBLIC ioda )
 target_link_libraries( soca PUBLIC ufo )
+target_link_libraries( soca PUBLIC vader )
 
 include_directories( ${CMAKE_CURRENT_SOURCE_DIR} ${DEPEND_LIB_ROOT}/mod )
 
-if ( BUILD_ICEPACK )
+if( ${icepack_FOUND} )
   target_link_libraries( soca PUBLIC icepack )
 endif()
 
 # Add source code in the subdirectories
 add_subdirectory(AnalyticInit)
 add_subdirectory(Covariance)
+add_subdirectory(ExplicitDiffusion)
 add_subdirectory(Fields)
 add_subdirectory(Geometry)
 add_subdirectory(GeometryIterator)