H220

.gitignore

@@ -0,0 +1 @@
+build*/

.gitmodules

@@ -1,6 +1,7 @@
 [submodule "fix"]
 	path = fix
 	url = gerrit:GSI-fix
+
 [submodule "libsrc"]
 	path = libsrc
 	url = gerrit:GSI-libsrc

CMakeLists.txt

@@ -6,6 +6,7 @@ if( NOT DEFINED ENV{CC} )
   find_path( intelComp "ifort" )
   find_path( pgiComp "pgf90" )
   if( crayComp )
+    message("Setting CrayLinuxEnvironment")
     set(CMAKE_SYSTEM_NAME "CrayLinuxEnvironment")
     set(CMAKE_C_COMPILER "${crayComp}/cc")
     set(CMAKE_CXX_COMPILER "${crayComp}/CC")
@@ -32,68 +33,125 @@ endif()
 project(GSI)
   enable_language (Fortran)
   option(USE_WRF "Find WRF object files and build regional GSI model" ON)
+  option(USE_BASELIBS "Look for and use GMAO Baselibs" OFF)
   option(BUILD_GLOBAL "Build GSI without WRF (regional) module " OFF)
-  option(BUILD_GSI "Build the GSI model" ON)
   option(BUILD_ENKF "Build the Enkf executable " ON)
-  option(BUILD_GFS "Build the Enkf with GFS module " ON)
-  option(BUILD_NMMB "Build the Enkf with NMMB module " OFF)
-  option(BUILD_WRF "Build the Enkf with WRF module " OFF)
-  option(BUILD_CORELIBS "Build the Core libraries " OFF)
+  option(USE_BASELINE "Use baseline control runs" ON)
+  SET(ENKF_MODE "GFS" CACHE STRING "EnKF build mode: GFS, WRF, NMMB")
+  string(TOUPPER ${ENKF_MODE} ENKF_MODE)
+  if (ENKF_MODE MATCHES "^GFS$")
+    message("Build the EnKF with GFS module")
+    option(BUILD_GFS "Build the Enkf with GFS module " ON)
+    option(BUILD_NMMB "Build the Enkf with NMMB module " OFF)
+    option(BUILD_WRF "Build the Enkf with WRF module " OFF)
+  elseif (ENKF_MODE MATCHES "^WRF$")
+    message("Build the EnKF with WRF module")
+    option(BUILD_GFS "Build the Enkf with GFS module " OFF)
+    option(BUILD_NMMB "Build the Enkf with NMMB module " OFF)
+    option(BUILD_WRF "Build the Enkf with WRF module " ON)
+  elseif (ENKF_MODE MATCHES "^NMMB$")
+    message("Build the EnKF with NMMB module")
+    option(BUILD_GFS "Build the Enkf with GFS module " OFF)
+    option(BUILD_NMMB "Build the Enkf with NMMB module " ON)
+    option(BUILD_WRF "Build the Enkf with WRF module " OFF)
+  else()
+    message("unkown ENKF_MODE: ${ENKF_MODE} !\nBuild the EnKF with GFS module by default")
+    option(BUILD_GFS "Build the Enkf with GFS module " ON)
+    option(BUILD_NMMB "Build the Enkf with NMMB module " OFF)
+    option(BUILD_WRF "Build the Enkf with WRF module " OFF)
+  endif()
   option(BUILD_UTIL "Build the Enkf utilities " OFF)
+
+  option(BUILD_UTIL_COM "Build community utilities " OFF)
+  option(BUILD_ENKF_PREPROCESS_ARW "Build enkf preprocess for ARW " OFF)
+  option(BUILD_COV_CALC "Build the Desroziers utility" OFF)
+  option(BUILD_NCDIAG "Build the NCDIAG libraries" ON)
+  option(BUILD_NCDIAG_SERIAL "Build the serial NCDIAG libraries" ON)
   option(BUILD_REG_TESTING "Build the Regression Testing Suite" ON)
   option(BUILD_UNIT_TESTING "Build the Unit Testing Suite" OFF)
+  option(MPI3 "Build EnKF with MPI3" OFF)
+  option(BUILD_GSDCLOUD_ARW "Build the GSD cloud analysis " OFF)
   cmake_minimum_required(VERSION 2.8)
   set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
   set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/lib")
   SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
   SET(ARCHIVE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
   set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
   set(CMAKE_INCLUDE_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/include")
+  set(CMAKE_INCLUDE_4_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/include4")
   set(Fortran_MODULE_DIRECTORY "${PROJECT_BINARY_DIR}/include")
   set(CMAKE_Fortran_MODULE_DIRECTORY "${PROJECT_BINARY_DIR}/include")
   file(MAKE_DIRECTORY ${CMAKE_INCLUDE_OUTPUT_DIRECTORY})
+  file(MAKE_DIRECTORY ${CMAKE_INCLUDE_4_OUTPUT_DIRECTORY})
   include(${CMAKE_SOURCE_DIR}/cmake/Modules/setPlatformVariables.cmake)
-  include(${CMAKE_SOURCE_DIR}/cmake/Modules/setCompilerFlags.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/setIntelFlags.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/setGNUFlags.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/setPGIFlags.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/setHOST.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/platforms/Cheyenne.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/platforms/Discover.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/platforms/Generic.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/platforms/Gaea.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/platforms/Jet.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/platforms/S4.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/platforms/Hera.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/platforms/WCOSS-C.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/platforms/WCOSS-D.cmake)
+  include(${CMAKE_SOURCE_DIR}/cmake/Modules/platforms/WCOSS.cmake)
   if(BUILD_REG_TESTING)
     set(CTEST_TEST_TIMEOUT 86400 )
     find_package(GSICONTROL)
     include( CTest )
   endif(BUILD_REG_TESTING)
+  if(MPI3)
+    set( MPI3FLAG "-DMPI3" CACHE INTERNAL "" )
+  else()
+    set( MPI3FLAG "" CACHE INTERNAL "" )
+  endif()
+
 
   cmake_policy(SET CMP0009 NEW)
-  site_name(HOSTNAME)
-  string(REGEX MATCH "s4-" HOST-S4 ${HOSTNAME} )
-  string(REGEX MATCH "tfe[0-9]" HOST-Theia ${HOSTNAME} )
-  string(REGEX MATCH "g[0-9][0-9]a" HOST-Gyre ${HOSTNAME} )
-  string(REGEX MATCH "t[0-9][0-9]a" HOST-Tide ${HOSTNAME} )
-  string(REGEX MATCH "llogin" HOST-Luna ${HOSTNAME} )
-  string(REGEX MATCH "slogin" HOST-Surge ${HOSTNAME} )
-  if( HOST-S4 )
-    set( host "S4" )
-    setS4()
-  elseif(( HOST-Tide ) OR ( HOST-Gyre ) )
-    set( host "WCOSS" )
-    setWCOSS()
-  elseif( HOST-Theia )
-    set( host "THEIA" )
-    setTHEIA()
-  elseif( ( crayComp ) OR ( HOST-Luna) OR ( HOST-Surge ) )
-    find_path( crayComp "ftn" )
-    set( host "LUNA" )
-    setCRAY()
-  else(  )
-    set( host "GENERIC" )
-    setGeneric()
+  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)
     set (CMAKE_BUILD_TYPE RELEASE CACHE STRING
-        "Choose the type of build, options are: None Debug Release."
+        "Choose the type of build, options are: PRODUCTION Debug Release."
         FORCE)
   endif (NOT CMAKE_BUILD_TYPE)
-  set(CMAKE_Fortran_FLAGS_RELEASE "")
+
+  STRING(COMPARE EQUAL ${CMAKE_BUILD_TYPE} "RelWithDebInfo" BUILD_RELEASE)
+  STRING(COMPARE EQUAL ${CMAKE_BUILD_TYPE} "PRODUCTION" BUILD_PRODUCTION)
+  STRING(COMPARE EQUAL ${CMAKE_BUILD_TYPE} "PROFILE" BUILD_PROFILE)
+  if( BUILD_PRODUCTION )
+    set( CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/exec )
+  endif()
+  if( BUILD_PROFILE )
+    set(CMAKE_SKIP_RPATH "TRUE")
+    if(NOT ENV{TAU_MAKEFILE}) 
+      message("Must set TAU MAKEFILE environment variable to build in profiling mode")
+      exit()
+    endif()
+  endif()
+
+  if(BUILD_GSDCLOUD_ARW)
+    set(GSDCLOUDOPT "-DRR_CLOUDANALYSIS" CACHE INTERNAL "" )
+  else(BUILD_GSDCLOUD_ARW)
+    set( GSDCLOUDOPT "" CACHE INTERNAL "" )
+  endif(BUILD_GSDCLOUD_ARW)
+
+  set(CMAKE_Fortran_FLAGS_RELEASE "")  
   if (CMAKE_CXX_COMPILER_ID MATCHES "GNU*")
     message("Setting GNU flags")
     setGNU()
@@ -105,38 +163,44 @@ project(GSI)
     setPGI()
   endif()
 
-  set(intsize 4)
-  set(doublesize 4)
-  set(libsuffix "_i${intsize}r${doublesize}")
 
-  if( NOT(HOST-Luna) AND NOT(HOST-Surge) )
-    find_package(MPI REQUIRED)
-  endif()
+  find_package(MPI REQUIRED)
+  message("MPI version is ${MPI_Fortran_VERSION}")
+  message("MPI f90 version is ${MPI_Fortran_HAVE_F90_MODULE}")
+  message("MPI f08 version is ${MPI_Fortran_HAVE_F08_MODULE}")
+
   add_definitions(${MPI_Fortran_COMPILE_FLAGS})
   include_directories(${MPI_Fortran_INCLUDE_DIRS} ${MPI_INCLUDE_PATH} "./" ${CMAKE_INCLUDE_OUTPUT_DIRECTORY})
   link_directories(${MPI_Fortran_LIBRARIES} ${ARCHIVE_OUTPUT_PATH} )
-
-
-  find_package( NetCDF REQUIRED)
-  if(NETCDF4)
-    if(CMAKE_MAJOR_VERSION GREATER 2)
-      find_package( HDF5 COMPONENTS C HL Fortran_HL REQUIRED )
-    else()
-      find_package( HDF5 )
+# if( (HOST-Discover) AND (NOT HOST-Generic))
+  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( CURL )
   endif()
-  if( NOT crayComp )
-    message(" trying to find lapack")
+  if(( NOT HOST-WCOSS_D ) AND ( NOT HOST-WCOSS_C ) AND ( NOT HOST-Gaea ) ) 
+    message(" trying to find lapack, ${host}")
     find_package( LAPACK )
   endif()
-  if(USE_WRF)
+# build the WRF I/O libraries
+  if(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()
+
   # default installation
   get_filename_component (default_prefix ".." ABSOLUTE)
-  set (CMAKE_INSTALL_PREFIX ${default_prefix} CACHE STRING "set prefix"
-        FORCE)
+# set (CMAKE_INSTALL_PREFIX ${default_prefix} CACHE STRING "set prefix"
+#       FORCE)
 
 
   # FFLAGS depend on the compiler
@@ -148,49 +212,102 @@ project(GSI)
 
   if(BUILD_CORELIBS )
     message("setting values for corelibs")
-    set(BUILD_CRTM "ON" CACHE STRING "Build the CRTM library" )
     set(BUILD_BACIO "ON" CACHE STRING "Build the BACIO library" )
     set(BUILD_BUFR "ON" CACHE STRING "Build the BUFR library" )
     set(BUILD_SFCIO "ON" CACHE STRING "Build the SFCIO library" )
     set(BUILD_SIGIO "ON" CACHE STRING "Build the SIGIO library" )
     set(BUILD_NEMSIO "ON" CACHE STRING "Build the NEMSIO library" )
     set(BUILD_SP "ON" CACHE STRING "Build the SP library" )
-    set(BUILD_EMC "ON" CACHE STRING "Build the EMC library" )
+    set(BUILD_CRTM "ON" CACHE STRING "Build the CRTM library" )
+    set(BUILD_W3EMC "ON" CACHE STRING "Build the EMC library" )
     set(BUILD_NCO "ON" CACHE STRING "Build the NCO library" )
-    set(FIND_SRC ON )
-  else()
-    set(FIND_SRC OFF)
-  endif()
-  find_package( CORELIBS )
-  if(BUILD_CORELIBS)
-    add_subdirectory(core-libs)
   endif()
+  find_package( BACIO )
+  find_package( BUFR )
+  find_package( SIGIO )
+  find_package( NEMSIO )
+  find_package( CRTM )
+  find_package( SP )
+  find_package( SFCIO )
+  find_package( W3EMC )
+  find_package( W3NCO )
 
-  add_subdirectory(src)
-  add_subdirectory(src/enkf)
+  if(BUILD_NCDIAG)
+    set(NCDIAG_INCS "${PROJECT_BINARY_DIR}/libsrc/ncdiag/include")
+    add_subdirectory(src/ncdiag)
+    set(NCDIAG_LIBRARIES ncdiag )
+  endif(BUILD_NCDIAG)
 
-  set(GSILIB gsilib)
+  find_package( BACIO )
+  find_package( BUFR )
+  find_package( SIGIO )
+  find_package( NEMSIO )
+  find_package( CRTM )
+  find_package( SP )
+  find_package( SFCIO )
+  find_package( W3EMC )
+  find_package( W3NCO )
 
+  if(BUILD_GSDCLOUD_ARW)
+    set(GSDCLOUD_DIR "${CMAKE_SOURCE_DIR}/libsrc/GSD/gsdcloud")
+    set(gsdcloud gsdcloud_arw)
+    add_subdirectory(libsrc/GSD/gsdcloud)
+    set(GSDCLOUD_LIBRARY ${gsdcloud} )
+  else(BUILD_GSDCLOUD_ARW)
+    set(GSDCLOUD_LIBRARY "")
+  endif(BUILD_GSDCLOUD_ARW)
+
+  add_subdirectory(src/gsi)
+  if(BUILD_ENKF)
+    add_subdirectory(src/enkf)
+  endif(BUILD_ENKF) 
+  if(BUILD_UTIL)
+    add_subdirectory(util/EnKF/gfs/src)
+    add_subdirectory(util/Ozone_Monitor/nwprod/oznmon_shared.v2.0.0/sorc/oznmon_horiz.fd)
+    add_subdirectory(util/Ozone_Monitor/nwprod/oznmon_shared.v2.0.0/sorc/oznmon_time.fd)
+    add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared.v3.0.0/sorc/verf_radang.fd)
+    add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared.v3.0.0/sorc/verf_radbcoef.fd)
+    add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared.v3.0.0/sorc/verf_radbcor.fd)
+    add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared.v3.0.0/sorc/verf_radtime.fd)
+  endif(BUILD_UTIL) 
+  find_package( NDATE )
+  if( NOT NDATE )
+     add_subdirectory(util/ndate)
+  endif()
+  if(BUILD_ENKF_PREPROCESS_ARW)
+    add_subdirectory(util/EnKF/arw/src)
+  endif(BUILD_ENKF_PREPROCESS_ARW)
+  if(BUILD_UTIL_COM)
+    add_subdirectory(util/Analysis_Utilities/read_diag)
+    add_subdirectory(util/radar_process/radialwind)
+    add_subdirectory(util/radar_process/reflectivity)
+    add_subdirectory(util/bufr_tools)
+  endif(BUILD_UTIL_COM)
+  if(BUILD_COV_CALC)
+    add_subdirectory(util/Correlated_Obs)
+  endif (BUILD_COV_CALC)
   if(BUILD_UNIT_TESTING)
     set(CTEST_TEST_TIMEOUT 400 )
     find_package(GSICONTROL)
     include( CTest )
     add_subdirectory(unit-tests)
   endif(BUILD_UNIT_TESTING)
   if(BUILD_REG_TESTING)
+    if(USE_BASELINE) 
+      set(BASELINE_FLAG "1")
+    else()      
+      set(BASELINE_FLAG "0")
+    endif(USE_BASELINE)
     if(USE_WRF)
-      file(WRITE "${PROJECT_BINARY_DIR}/regression_var.out" "${CMAKE_SOURCE_DIR}/regression/regression_var.sh ${host} ${CMAKE_SOURCE_DIR}/.. ${PROJECT_BINARY_DIR} ${CMAKE_SOURCE_DIR} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/gsi.x${debug_suffix} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/enkf_gfs.x${debug_suffix} ${GSICONTROL} ${ENKFCONTROL} ")
-      set( REG_TEST_NAMES "global_T62;global_T62_ozonly;global_4dvar_T62;global_4denvar_T126;global_lanczos_T62;arw_netcdf;
-          arw_binary;nmm_binary;nmm_netcdf;nmmb_nems_4denvar;hwrf_nmm_d2;hwrf_nmm_d3;rtma;global_enkf_T62")
+      file(WRITE "${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} ${BASELINE_FLAG} ")
+      set( REG_TEST_NAMES "global_T62;global_T62_ozonly;global_4dvar_T62;global_4denvar_T126;global_fv3_4denvar_T126;global_lanczos_T62;arw_netcdf;
+          arw_binary;nmm_binary;nmm_netcdf;nmmb_nems_4denvar;hwrf_nmm_d2;hwrf_nmm_d3;rtma;global_enkf_T62;netcdf_fv3_regional;global_C96_fv3aero")
     else()
-      file(WRITE "${PROJECT_BINARY_DIR}/regression_var.out" "${CMAKE_SOURCE_DIR}/regression/regression_var.sh ${host} ${CMAKE_SOURCE_DIR}/.. ${PROJECT_BINARY_DIR} ${CMAKE_SOURCE_DIR} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/gsi_global.x${debug_suffix} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/enkf.x${debug_suffix} ${GSICONTROL} ${ENKFCONTROL} ")
-      set( REG_TEST_NAMES "global_T62;global_T62_ozonly;global_4dvar_T62;global_lanczos_T62;global_nemsio_T62")
+      file(WRITE "${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")
     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})
     endforeach( REG_TEST )
     set_tests_properties( ${REG_TEST_NAMES} PROPERTIES TIMEOUT 86400 )
   endif()
-  if(BUILD_UTIL)
-    add_subdirectory(util/EnKF/gfs/src)
-  endif(BUILD_UTIL)

clean

@@ -0,0 +1,23 @@
+#!/bin/sh
+
+set -xe
+
+echo "Cleaning up the build and/or exec dir for ProdGSI ..."
+if [[ "$1" == '-a' ]] ; then
+
+if [[ -d build ]] ; then
+  rm -r ./build
+fi
+if [[ -d exec ]] ; then
+  rm -r ./exec
+fi
+
+else
+
+if [[ -d build ]] ; then
+  rm -r ./build
+fi
+
+fi
+
+exit