merge the latest master branch from the authoritative repo

comgsi · May 19, 2021 · aa4f372 · aa4f372
2 parents 0552149 + 1162d92
commit aa4f372
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Showing 886 changed files with 34,259 additions and 68,969 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -107,18 +107,14 @@ project(GSI)
   endif(BUILD_REG_TESTING)
 
   cmake_policy(SET CMP0009 NEW)
+  cmake_policy(SET CMP0054 NEW)
+  cmake_policy(SET CMP0074 NEW)
   find_package(OpenMP)
   message("found openmp with flag ${OPENMP_Fortran_FLAGS}")
 
 # Set Host specific flags and options
   setHOST()
 
-  if(FIND_HDF5_HL)
-    find_package(HDF5 COMPONENTS C HL Fortran_HL )
-  elseif(FIND_HDF5)
-    find_package(HDF5)
-  endif()
-
   MESSAGE(${CMAKE_CURRENT_SOURCE_DIR})
   # make sure that the default is a RELEASE
   if (NOT CMAKE_BUILD_TYPE)
@@ -172,25 +168,18 @@ project(GSI)
   if( USE_BASELIBS )
     find_package(Baselibs REQUIRED)
   else()
-    find_package( NetCDF REQUIRED)
-    if(NETCDF4)
-      if(CMAKE_MAJOR_VERSION GREATER 2)
-        find_package( ZLIB )
-      endif()
-      find_package( CURL )
-    endif()
+    find_package( NetCDF COMPONENTS C Fortran REQUIRED)
   endif()
   if(( NOT HOST-WCOSS_D ) AND ( NOT HOST-WCOSS_C ) AND ( NOT HOST-Gaea ) ) 
     message(" trying to find lapack, ${host}")
     find_package( LAPACK )
   endif()
 # build the WRF I/O libraries
-  if(DEFINED ENV{GSIWRF_LIB})
-    set(wrflib "$ENV{GSIWRF_LIB}" CACHE INTERNAL "WRFIO library" )
+  if(DEFINED ENV{GSIWRFIO_LIB})
+    set(wrflib "$ENV{GSIWRFIO_LIB}" CACHE INTERNAL "WRFIO library" )
   elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/libsrc/wrflib)
     add_subdirectory(libsrc/wrflib)
   else()
-    message("libsrc/wrflib not pulled from git, looking for WRF dependencies locally")
     message("libsrc/wrflib not pulled from git, looking for WRF dependencies locally")
     find_package( WRF )
   endif()
@@ -204,7 +193,7 @@ project(GSI)
   # FFLAGS depend on the compiler
   get_filename_component (Fortran_COMPILER_NAME ${CMAKE_Fortran_COMPILER} NAME)
   set(CFLAGS "-I. -DFortranByte=char -DFortranInt=int -DFortranLlong='long long' -O3  -Dfunder")
-  set (CMAKE_Fortran_INC_FLAGS "-I ./ -I ${CORE_INCS} -I ${NETCDF_INCLUDES} ")
+  set (CMAKE_Fortran_INC_FLAGS "-I ./ -I ${CORE_INCS} -I ${NETCDF_INCLUDE_DIRS} ")
   set (CFLAGS_N "-I. -DFortranByte=char -DFortranInt=int -DFortranLlong='long long'  -O3  -Dfunder")
 
 
@@ -271,12 +260,18 @@ project(GSI)
   endif(BUILD_ENKF) 
   if(BUILD_UTIL)
     add_subdirectory(util/EnKF/gfs/src)
-    add_subdirectory(util/Ozone_Monitor/nwprod/oznmon_shared.v2.0.0/sorc/oznmon_horiz.fd)
-    add_subdirectory(util/Ozone_Monitor/nwprod/oznmon_shared.v2.0.0/sorc/oznmon_time.fd)
-    add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared.v3.0.0/sorc/verf_radang.fd)
-    add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared.v3.0.0/sorc/verf_radbcoef.fd)
-    add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared.v3.0.0/sorc/verf_radbcor.fd)
-    add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared.v3.0.0/sorc/verf_radtime.fd)
+    add_subdirectory(util/Ozone_Monitor/nwprod/oznmon_shared/sorc/oznmon_horiz.fd)
+    add_subdirectory(util/Ozone_Monitor/nwprod/oznmon_shared/sorc/oznmon_time.fd)
+    add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared/sorc/verf_radang.fd)
+    add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared/sorc/verf_radbcoef.fd)
+    add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared/sorc/verf_radbcor.fd)
+    add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared/sorc/verf_radtime.fd)
+    add_subdirectory(util/Conventional_Monitor/nwprod/conmon_shared/sorc/conmon_grads_lev.fd)
+    add_subdirectory(util/Conventional_Monitor/nwprod/conmon_shared/sorc/conmon_grads_mandlev.fd)
+    add_subdirectory(util/Conventional_Monitor/nwprod/conmon_shared/sorc/conmon_grads_sfc.fd)
+    add_subdirectory(util/Conventional_Monitor/nwprod/conmon_shared/sorc/conmon_grads_sfctime.fd)
+    add_subdirectory(util/Conventional_Monitor/nwprod/conmon_shared/sorc/conmon_grads_sig.fd)
+    add_subdirectory(util/Conventional_Monitor/nwprod/conmon_shared/sorc/conmon_time.fd)
   endif(BUILD_UTIL) 
   find_package( NDATE )
   if( NOT NDATE )
@@ -309,10 +304,10 @@ project(GSI)
     if(USE_WRF)
       file(WRITE "${PROJECT_BINARY_DIR}/regression_var.out" "${CMAKE_SOURCE_DIR}/regression/regression_var.sh ${host} ${CMAKE_SOURCE_DIR}/.. ${PROJECT_BINARY_DIR} ${CMAKE_SOURCE_DIR} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${GSIEXEC} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${ENKFEXEC} ${GSICONTROL} ${ENKFCONTROL} ${BASELINE_FLAG} ")
       set( REG_TEST_NAMES "global_T62;global_T62_ozonly;global_4dvar_T62;global_4denvar_T126;global_fv3_4denvar_T126;;global_fv3_4denvar_C192;global_lanczos_T62;arw_netcdf;
-          arw_binary;nmm_binary;nmm_netcdf;nmmb_nems_4denvar;hwrf_nmm_d2;hwrf_nmm_d3;rtma;global_enkf_T62;netcdf_fv3_regional;global_C96_fv3aero")
+          arw_binary;nmm_binary;nmm_netcdf;nmmb_nems_4denvar;hwrf_nmm_d2;hwrf_nmm_d3;rtma;global_enkf_T62;netcdf_fv3_regional;global_C96_fv3aero;global_C96_fv3aerorad")
     else()
       file(WRITE "${PROJECT_BINARY_DIR}/regression_var.out" "${CMAKE_SOURCE_DIR}/regression/regression_var.sh ${host} ${CMAKE_SOURCE_DIR}/.. ${PROJECT_BINARY_DIR} ${CMAKE_SOURCE_DIR} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${GSIEXEC} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${ENKFEXEC} ${GSICONTROL} ${ENKFCONTROL} ${BASELINE_FLAG} ")
-      set( REG_TEST_NAMES "global_T62;global_T62_ozonly;global_4dvar_T62;global_lanczos_T62;global_nemsio_T62;global_C96_fv3aero")
+      set( REG_TEST_NAMES "global_T62;global_T62_ozonly;global_4dvar_T62;global_lanczos_T62;global_nemsio_T62;global_C96_fv3aero;global_C96_fv3aerorad")
     endif()
     foreach( REG_TEST ${REG_TEST_NAMES} )
       add_test(NAME ${REG_TEST} WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/regression COMMAND regression_driver.sh ${REG_TEST} ${PROJECT_BINARY_DIR})

diff --git a/cmake/Modules/FindBUFR.cmake b/cmake/Modules/FindBUFR.cmake
@@ -11,8 +11,8 @@ endif()
 
 set( NO_DEFAULT_PATH )
 if(NOT BUILD_BUFR )
-  if(DEFINED ENV{BUFR_LIBd} )
-    set(BUFR_LIBRARY $ENV{BUFR_LIBd} )
+  if(DEFINED ENV{BUFR_LIBd_DA} )
+    set(BUFR_LIBRARY $ENV{BUFR_LIBd_DA} )
     message("BUFR library ${BUFR_LIBRARY} set via Environment variable")
   else()
   find_library( BUFR_LIBRARY 

diff --git a/cmake/Modules/FindCORELIBS.cmake b/cmake/Modules/FindCORELIBS.cmake
@@ -102,8 +102,8 @@ else()
     set( w3nco "w3nco${libsuffix}")
 endif()
 if(NOT  BUILD_BUFR  )
-  if(DEFINED ENV{BUFR_LIBd} )
-    set(BUFR_LIBRARY $ENV{BUFR_LIBd} )
+  if(DEFINED ENV{BUFR_LIBd_DA} )
+    set(BUFR_LIBRARY $ENV{BUFR_LIBd_DA} )
   else()
   find_library( BUFR_LIBRARY 
     NAMES libbufr.a libbufr_d_64.a libbufr_i4r8.a libbufr_v${BUFR_VER}_d_64.a