Merge pull request #4 from JCSDA/develop

Develop into master

.gitignore

@@ -1 +1,5 @@
+*DS_Store*
 *.swp
+._*
+
+build/

CMakeLists.txt

@@ -1,18 +1,20 @@
-# (C) Copyright 2017 UCAR.
+# (C) Copyright 2017-2020 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.
 
 ################################################################################
-# FV3
+# FV3JEDILM
 ################################################################################
 
 cmake_minimum_required( VERSION 3.3.2 FATAL_ERROR )
 
-project( fv3 C CXX Fortran )
+project( fv3jedilm VERSION 1.0.0 LANGUAGES Fortran C )
 
 set( CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake;${CMAKE_MODULE_PATH} )
 
+set( CMAKE_DIRECTORY_LABELS "fv3-jedi-lm" )
+
 set( ECBUILD_DEFAULT_BUILD_TYPE Release )
 set( ENABLE_OS_TESTS           OFF CACHE BOOL "Disable OS tests" FORCE )
 set( ENABLE_LARGE_FILE_SUPPORT OFF CACHE BOOL "Disable testing of large file support" FORCE )
@@ -29,70 +31,102 @@ ecbuild_requires_macro_version( 2.7 )
 ecbuild_declare_project()
 
 ecbuild_enable_fortran( REQUIRED )
-ecbuild_add_cxx11_flags()
-
-set( FV3_LINKER_LANGUAGE CXX )
 
 ################################################################################
 # Dependencies
 ################################################################################
 
-## Boost
-#set( Boost_MINIMUM_VERSION "1.47" )
-#find_package( Boost ${Boost_MINIMUM_VERSION} REQUIRED
-#              COMPONENTS unit_test_framework )
-#include_directories( ${Boost_INCLUDE_DIR} )
+# MKL / LAPACK
+# Default: use MKL as LAPACK implementation.
+# Set -DENABLE_MKL=Off to disable use of MKL and prefer LAPACK
+option( ENABLE_MKL "Use MKL for LAPACK implementation (if available)" ON )
+if( ENABLE_MKL )
+    find_package( MKL )
+endif()
+if( MKL_FOUND )
+    set( LAPACK_LIBRARIES ${MKL_LIBRARIES} )
+else()
+    find_package( LAPACK REQUIRED )
+endif()
+
+#openMP
+find_package( OpenMP COMPONENTS Fortran )
 
 # MPI
 ecbuild_add_option( FEATURE MPI DEFAULT ON
                     DESCRIPTION "Support for MPI distributed parallelism"
-                    REQUIRED_PACKAGES "MPI COMPONENTS CXX Fortran" )
-ecbuild_find_mpi( COMPONENTS CXX Fortran REQUIRED )
+                    REQUIRED_PACKAGES "MPI COMPONENTS Fortran" )
+ecbuild_find_mpi( COMPONENTS Fortran REQUIRED )
 ecbuild_include_mpi()
-link_libraries(${MPI_CXX_LIBRARIES} ${MPI_Fortran_LIBRARIES})
+link_libraries(${MPI_Fortran_LIBRARIES})
 
 # NetCDF
 set( NETCDF_F90 ON CACHE BOOL "Compile with Fortran NetCDF" )
-find_package( NetCDF REQUIRED )
-include_directories( ${NETCDF_INCLUDE_DIR} )
-
-# fms
-ecbuild_use_package( PROJECT fms REQUIRED )
-include_directories( ${FMS_INCLUDE_DIRS} )
+find_package( NetCDF REQUIRED COMPONENTS Fortran )
+include_directories( ${NETCDF_INCLUDE_DIRS} )
 
-################################################################################
-# Definitions
-################################################################################
+# Set default model
+if (NOT FV3_FORECAST_MODEL MATCHES "GEOS" AND NOT FV3_FORECAST_MODEL MATCHES "UFS")
+  set(FV3_FORECAST_MODEL "FV3CORE")
+endif()
 
-set(COMPDEFS "-DsysLinux;-DESMA64;-DHAS_NETCDF4;-DHAS_NETCDF3;-DH5_HAVE_PARALLEL;-DNETCDF_NEED_NF_MPIIO;-DEIGHT_BYTE;-DSPMD;-DTIMING;-Duse_libMPI;-Duse_netCDF;-DHAVE_SHMEM;-DMAPL_MODE;-DOLDMPP")
-
-add_definitions( ${COMPDEFS} )
+# fms
+if (FV3_FORECAST_MODEL MATCHES "FV3CORE")
+  ecbuild_use_package( PROJECT fms REQUIRED )
+  include_directories( ${FMS_INCLUDE_DIRS} )
+  list( APPEND FV3JEDILM_TPLS fms )
+endif()
+
+# geos
+if(FV3_FORECAST_MODEL MATCHES "GEOS")
+  find_package(MAPL REQUIRED PATHS ${FV3_FORECAST_MODEL_ROOT}/lib/cmake/MAPL )
+  find_package(GEOSgcm REQUIRED PATHS ${FV3_FORECAST_MODEL_ROOT}/lib/cmake/GEOSgcm )
+  if (FV3_PRECISION MATCHES DOUBLE OR NOT FV3_PRECISION)
+    link_libraries(fms_r8)
+  else()
+    link_libraries(fms_r4)
+  endif()
+endif()
+
+# ufs
+if(FV3_FORECAST_MODEL MATCHES "UFS")
+  # Set CMAKE_PREFIX_PATH to include the install location of ufs
+  find_package(fms REQUIRED )
+  find_package(fv3atm REQUIRED )
+  find_package(ufs REQUIRED )
+  link_libraries(fms)
+  link_libraries(NetCDF::NetCDF_Fortran)
+  # Install includes
+  get_target_property(fmsinc fms INTERFACE_INCLUDE_DIRECTORIES)
+  include_directories( ${fmsinc} )
+endif()
 
 ################################################################################
 # Export package info
 ################################################################################
 
-list( APPEND FV3_TPLS MPI fms )
+list( APPEND FV3JEDILM_TPLS MPI )
 
-set( FV3_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_CURRENT_BINARY_DIR}/src
-                      ${CMAKE_Fortran_MODULE_DIRECTORY} )
-set( FV3_LIBRARIES fv3 )
+set( FV3JEDILM_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/src
+                            ${CMAKE_CURRENT_BINARY_DIR}/src
+                            ${CMAKE_Fortran_MODULE_DIRECTORY} )
+set( FV3JEDILM_LIBRARIES fv3jedilm )
 
-get_directory_property( FV3_DEFINITIONS COMPILE_DEFINITIONS )
+get_directory_property( FV3JEDILM_DEFINITIONS COMPILE_DEFINITIONS )
 
-foreach( _tpl ${FV3_TPLS} )
+foreach( _tpl ${FV3JEDILM_TPLS} )
   string( TOUPPER ${_tpl} TPL )
-  list( APPEND FV3_EXTRA_DEFINITIONS   ${${TPL}_DEFINITIONS}  ${${TPL}_TPL_DEFINITIONS}  )
-  list( APPEND FV3_EXTRA_INCLUDE_DIRS  ${${TPL}_INCLUDE_DIRS} ${${TPL}_TPL_INCLUDE_DIRS} )
-  list( APPEND FV3_EXTRA_LIBRARIES     ${${TPL}_LIBRARIES}    ${${TPL}_TPL_LIBRARIES}    )
+  list( APPEND FV3JEDILM_EXTRA_DEFINITIONS   ${${TPL}_DEFINITIONS}  ${${TPL}_TPL_DEFINITIONS}  )
+  list( APPEND FV3JEDILM_EXTRA_INCLUDE_DIRS  ${${TPL}_INCLUDE_DIRS} ${${TPL}_TPL_INCLUDE_DIRS} )
+  list( APPEND FV3JEDILM_EXTRA_LIBRARIES     ${${TPL}_LIBRARIES}    ${${TPL}_TPL_LIBRARIES}    )
 endforeach()
 
 ################################################################################
 # Sources
 ################################################################################
 
-include( fv3_compiler_flags )
-include_directories( ${FV3_INCLUDE_DIRS} ${FV3_EXTRA_INCLUDE_DIRS} )
+include( fv3jedilm_compiler_flags )
+include_directories( ${FV3JEDILM_INCLUDE_DIRS} ${FV3JEDILM_EXTRA_INCLUDE_DIRS} )
 
 add_subdirectory( src )
 
@@ -101,7 +135,7 @@ add_subdirectory( src )
 ################################################################################
 
 # prepares a tar.gz of the sources and/or binaries
-ecbuild_install_project( NAME fv3 )
+ecbuild_install_project( NAME fv3jedilm )
 
 # print the summary of the configuration
 ecbuild_print_summary()

README.md

@@ -1 +1,5 @@
-# fv3
+# Linearized forecast model for FV3-JEDI
+
+The Linearized version (tangent linear and adjoint) of the FV3 dynamical core and GEOS model physics. The scientific parts of this system were built by NASA's Global Modeling and Assimilation Office. The infrastructure parts by the Joint Center for Satellite Data Assimilation, UCAR.
+
+This is not a standalone system and is designed to be built with [FV3-JEDI](https://github.com/JCSDA/fv3-jedi).