Add fv3-jedi and its dependencies

var/spack/repos/builtin/packages/crtm/package.py

@@ -42,6 +42,9 @@ class Crtm(CMakePackage):
     depends_on("netcdf-fortran", when="@v2.4-jedi.2")
     depends_on("netcdf-fortran", when="@v2.4.1-jedi")
     depends_on("netcdf-fortran", when="@v3.0.0-rc.1")
+    depends_on("netcdf-fortran", when="@v3.0.0-skylabv5")
+    depends_on("netcdf-fortran", when="@v3.0.0-skylabv5-1")
+    depends_on("netcdf-fortran", when="@v3.0.0-skylabv6")
 
     depends_on("crtm-fix@2.3.0_emc", when="@2.3.0 +fix")
     depends_on("crtm-fix@2.4.0_emc", when="@=2.4.0 +fix")
@@ -52,6 +55,46 @@ class Crtm(CMakePackage):
     depends_on("ecbuild", type=("build"), when="@v2.4-jedi.2")
     depends_on("ecbuild", type=("build"), when="@v2.4.1-jedi")
     depends_on("ecbuild", type=("build"), when="@v3.0.0-rc.1")
+    depends_on("ecbuild", type=("build"), when="@v3.0.0-skylabv5")
+    depends_on("ecbuild", type=("build"), when="@v3.0.0-skylabv5-1")
+    depends_on("ecbuild", type=("build"), when="@v3.0.0-skylabv6")
+
+    # Spack gets confused by the different repository url, so we use direct URLs here.
+
+    # version("v3.0.0-skylabv6", commit="a31ed458fb702b235bccbe1693d2badffb241d05")
+    version(
+        "v3.0.0-skylabv6",
+        url="https://www.github.com/JCSDA/crtmv3/tarball/a31ed458fb702b235bccbe1693d2badffb241d05",
+        sha256="719b1070a2864e2ccc8334f195f276a555ebe3d3b1363f3dc6430b049080e4d6",
+    )
+
+    # Slightly after the Skylab 5 release to fix https://github.com/JCSDA/CRTMv3/pull/48.
+    # TODO: Push for a distinct tag in the CRTMv3 repository.
+    version(
+        "v3.0.0-skylabv5-1",
+        url="https://www.github.com/JCSDA/crtmv3/tarball/d15810f5538d4cf041e94ebfbb41b403d82bed13",
+        sha256="fa0f050ae29d3d7d71da4b97c5dfd74ad90c98c3645fd35340efa1410cf76cf3",
+    )
+
+    # The official release for Skylab 5, but it's buggy. See https://github.com/JCSDA/CRTMv3/pull/48.
+    version(
+        "v3.0.0-skylabv5",
+        url="https://www.github.com/JCSDA/crtmv3/tarball/74cdc9428f56a11ce0dcd3ac7ddff00097b7b61c",
+        sha256="033abf0dde10b29043f3cde8c4b4285a32e5886599d174ab83ef6f5a2132e3d6",
+    )
+
+    version(
+        "v2.4.1-jedi.1", sha256="94ff24051382d544c2e200a937bfe7d2047f6393a3e22f64284d5dc70e791ca6"
+    )
+    version(
+        "v2.4.1-jedi", sha256="fd8bf4db4f2a3b420b4186de84483ba2a36660519dffcb1e0ff14bfe8c6f6a14"
+    )
+
+    # Both of these have big binary file blobs
+    #  Corrects polarization angle biases for NOAA-21 and fixes WMO satellite and sensor ids.
+    version("v2.4.0_emc.2", commit="50fde6ae9caeaca3f5c8c3a39aca7e594eab451a")
+    #  Adds new NOAA-21 and ancillary files for VIIRS.
+    version("v2.4.0_emc.1", commit="eaf322287691d5d204167e1a929117ba6b9c2e23")
 
     version(
         "v2.4.1-jedi", sha256="fd8bf4db4f2a3b420b4186de84483ba2a36660519dffcb1e0ff14bfe8c6f6a14"

var/spack/repos/jcsda-emc/packages/GFDL_atmos_cubed_sphere/CMakeLists.txt.patch

@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -9,6 +9,8 @@
+
+ cmake_minimum_required( VERSION 3.3.2 FATAL_ERROR )
+
++find_package( ecbuild 3.6 REQUIRED HINTS ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/../ecbuild)
++
+ project( fv3 VERSION 1.2.0 LANGUAGES C CXX Fortran )
+
+ set( CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake;${CMAKE_MODULE_PATH} )

var/spack/repos/jcsda-emc/packages/GFDL_atmos_cubed_sphere/package.py

@@ -0,0 +1,29 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class GfdlAtmosCubedSphere(CMakePackage):
+    """The GFDL atmos_cubed_sphere dynamical core code"""
+
+    homepage = "https://github.com/JCSDA/GFDL_atmos_cubed_sphere"
+    git = "https://github.com/JCSDA/GFDL_atmos_cubed_sphere.git"
+
+    maintainers = ["climbfuji"]
+
+    version("1.2.0.jcsda", commit="61450b4e3e80bb96b26c5f3808ce60b5e5cb4207")
+
+    depends_on("ecbuild", type=("build"))
+    depends_on("ecbuild@3.3.2:", type=("build"), when="@1.7.0:")
+    depends_on("fms@release-jcsda")
+    depends_on("jedi-cmake", type=("build"))
+    depends_on("llvm-openmp", when="%apple-clang", type=("build", "run"))
+    depends_on("mpi")
+    depends_on("netcdf-c")
+    depends_on("netcdf-fortran")
+
+    # find_package(ecbuild REQUIRED) is needed when using ecbuild.
+    patch("CMakeLists.txt.patch", when="@1.2.0.jcsda")

var/spack/repos/jcsda-emc/packages/femps/CMakeLists.txt.patch

@@ -0,0 +1,12 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -4,6 +4,8 @@
+
+ cmake_minimum_required( VERSION 3.3.2 FATAL_ERROR )
+
++find_package( ecbuild 3.6 REQUIRED HINTS ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/../ecbuild)
++
+ project( femps VERSION 1.2.0 LANGUAGES Fortran )
+
+ set( CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake;${CMAKE_MODULE_PATH})
+

var/spack/repos/jcsda-emc/packages/femps/package.py

@@ -0,0 +1,30 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class Femps(CMakePackage):
+    """Finite Element Mesh Poisson Solver"""
+
+    homepage = "https://github.com/JCSDA/femps"
+    git = "https://github.com/JCSDA/femps.git"
+
+    maintainers = ["climbfuji"]
+
+    version("1.2.0", commit="a22e458c1742695479db9011ddb6bcbf31de39fe")
+
+    depends_on("ecbuild", type=("build"))
+    depends_on("ecbuild@3.3.2:", type=("build"), when="@1.7.0:")
+    depends_on("jedi-cmake", type=("build"))
+    depends_on("llvm-openmp", when="%apple-clang", type=("build", "run"))
+    depends_on("mpi")
+    depends_on("netcdf-c")
+    depends_on("netcdf-fortran")
+
+    # find_package(ecbuild REQUIRED) is needed when using ecbuild.
+    patch("CMakeLists.txt.patch", when="@1.2.0")
+    # femps needs to install its Fortran modules.
+    patch("src.femps.CMakeLists.txt.patch", when="@1.2.0")

var/spack/repos/jcsda-emc/packages/femps/src.femps.CMakeLists.txt.patch

@@ -0,0 +1,16 @@
+--- a/src/femps/CMakeLists.txt
++++ b/src/femps/CMakeLists.txt
+@@ -25,3 +25,12 @@ ecbuild_add_library( TARGET          femps
+
+ target_include_directories( femps INTERFACE $<BUILD_INTERFACE:${CMAKE_Fortran_MODULE_DIRECTORY}>
+                                             $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
++
++# Fortran module output directory for build and install interfaces
++set( MODULE_DIR module/${PROJECT_NAME}/${CMAKE_Fortran_COMPILER_ID}/${CMAKE_Fortran_COMPILER_VERSION} )
++set_target_properties( ${PROJECT_NAME} PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/${MODULE_DIR} )
++install( DIRECTORY ${CMAKE_BINARY_DIR}/${MODULE_DIR}/ DESTINATION ${MODULE_DIR} )
++target_include_directories( femps INTERFACE
++                            $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/${MODULE_DIR}>
++                            $<INSTALL_INTERFACE:${MODULE_DIR}> )
++
+

var/spack/repos/jcsda-emc/packages/fv3-jedi-linearmodel/CMakeLists.txt.patch

@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt	2023-10-12 11:02:44
++++ b/CMakeLists.txt	2023-10-12 11:03:11
+@@ -15,6 +15,8 @@
+
+ set( CMAKE_DIRECTORY_LABELS "fv3-jedi-lm" )
+
++find_package( ecbuild 3.6 REQUIRED HINTS ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/../ecbuild)
++
+ 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 )

var/spack/repos/jcsda-emc/packages/fv3-jedi-linearmodel/package.py

@@ -0,0 +1,71 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class Fv3JediLinearmodel(CMakePackage):
+    """Tangent linear and adjoint versions of FV3 dynamical core and GEOS physics"""
+
+    homepage = "https://github.com/JCSDA/fv3-jedi-linearmodel"
+    git = "https://github.com/JCSDA/fv3-jedi-linearmodel.git"
+
+    maintainers = ["climbfuji"]
+
+    version("1.3.0", commit="9758fbd44166fc1e1d745ca9ab7e9e5e6071955f")
+    version("1.2.0", commit="d47cea97c659e8a11e9e64c23092bef06227ebde")
+    version("develop", branch="develop", no_cache=True)
+
+    variant(
+        "forecast_model",
+        default="FV3CORE",
+        description="fv3 forecast model",
+        values=("FV3CORE", "GEOS", "UFS"),
+    )
+    # Note that the options for mkl, mpi, and openmp are lazily written in fv3-jedi-linearmodel.
+    # These options just turn on a find_package call. If a package is already found, for example by
+    # one of the package dependencies, then that component is silently used even if the user
+    # toggles it off. This is a bug and should be fixed eventually.
+    variant("mkl", default=False, description="Use MKL for LAPACK implementation (if available)")
+    variant("mpi", default=True, description="Support for MPI distributed parallelism")
+    variant("openmp", default=True, description="Build with OpenMP support")
+
+    conflicts("forecast_model=GEOS", msg="FV3-JEDI-LINEARMODEL: GEOS to be implemented.")
+    conflicts("forecast_model=UFS", msg="FV3-JEDI-LINEARMODEL: UFS to be implemented.")
+
+    depends_on("ecbuild", type=("build"))
+    depends_on("ecbuild@3.3.2:", type=("build"), when="@1.7.0:")
+    depends_on("fms@release-jcsda", when="forecast_model=FV3CORE")
+    depends_on("fms@release-jcsda", when="forecast_model=UFS")
+    depends_on("jedi-cmake", type=("build"))
+    depends_on("lapack", when="~mkl")
+    depends_on("llvm-openmp", when="+openmp %apple-clang", type=("build", "run"))
+    depends_on("mkl", when="+mkl")
+    depends_on("mpi", when="+mpi")
+    depends_on("netcdf-fortran")
+    depends_on("netcdf-c~mpi", when="~mpi")
+    depends_on("netcdf-c+mpi", when="+mpi")
+
+    # Future: GEOS needs
+    # - MAPL (underway at GMAO)
+    # - GEOSgcm
+    # - fms r8 or r4
+
+    # Future: UFS needs
+    # - stochastic_physics
+    # - ccpp
+    # - ccppphys
+    # - fv3atm
+    # - ufs
+    # - FMS::fms_r8
+
+    def cmake_args(self):
+        res = [self.define_from_variant("FV3_FORECAST_MODEL", "forecast_model")]
+        return res
+
+    # find_package(ecbuild REQUIRED) is needed when using ecbuild.
+    patch("CMakeLists.txt.patch", when="@1.2:1.3")
+    # fv3-jedi-linearmodel needs to install its Fortran modules.
+    patch("src.CMakeLists.txt.patch", when="@1.2:1.3")

var/spack/repos/jcsda-emc/packages/fv3-jedi-linearmodel/src.CMakeLists.txt.patch

@@ -0,0 +1,16 @@
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -36,3 +37,12 @@ target_include_directories( fv3jedilm INTERFACE $<BUILD_INTERFACE:${CMAKE_Fortra
+ if(CMAKE_Fortran_COMPILER_ID MATCHES GNU AND CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER_EQUAL 10)
+     target_compile_options(fv3jedilm PRIVATE $<$<COMPILE_LANGUAGE:Fortran>:-fallow-argument-mismatch>)
+ endif()
++
++# Fortran module output directory for build and install interfaces
++set( MODULE_DIR module/${PROJECT_NAME}/${CMAKE_Fortran_COMPILER_ID}/${CMAKE_Fortran_COMPILER_VERSION} )
++set_target_properties( ${PROJECT_NAME} PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/${MODULE_DIR} )
++install( DIRECTORY ${CMAKE_BINARY_DIR}/${MODULE_DIR}/ DESTINATION ${MODULE_DIR} )
++target_include_directories( fv3jedilm INTERFACE
++                            $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/${MODULE_DIR}>
++                            $<INSTALL_INTERFACE:${MODULE_DIR}> )
++
+

var/spack/repos/jcsda-emc/packages/fv3-jedi/CMakeLists.txt.patch

@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt	2023-10-12 11:36:48
++++ b/CMakeLists.txt	2023-10-12 11:37:13
+@@ -17,6 +17,8 @@
+
+ set( CMAKE_DIRECTORY_LABELS "fv3-jedi" )
+
++find_package( ecbuild 3.6 REQUIRED HINTS ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/../ecbuild)
++
+ 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 )

var/spack/repos/jcsda-emc/packages/fv3-jedi/cmake.fv3jedi_extra_macros.cmake.patch

@@ -0,0 +1,27 @@
+--- a/cmake/fv3jedi_extra_macros.cmake
++++ b/cmake/fv3jedi_extra_macros.cmake
+@@ -21,6 +21,24 @@ macro( LINK_FILES_DIR filelist dst_dir )
+   endforeach(FILENAME)
+ endmacro()
+
++# macro to create a symlink from src to dst
++function(CREATE_SYMLINK src dst)
++    foreach (FILENAME ${ARGN})
++        execute_process( COMMAND ${CMAKE_COMMAND} -E create_symlink
++            ${src}/${FILENAME}
++            ${dst}/${FILENAME} )
++        endforeach(FILENAME)
++endfunction(CREATE_SYMLINK)
++
++# macro to create a symlink from src to dst with just filename
++function(CREATE_SYMLINK_FILENAME src dst)
++    foreach (FILENAME ${ARGN})
++        get_filename_component(filename ${FILENAME} NAME )
++        execute_process( COMMAND ${CMAKE_COMMAND} -E create_symlink
++            ${src}/${FILENAME}
++            ${dst}/${filename} )
++        endforeach(FILENAME)
++endfunction(CREATE_SYMLINK_FILENAME)
+
+ # Macro to include GFS restart files in testing
+ macro( GFS_FILES_BKG path date )

var/spack/repos/jcsda-emc/packages/fv3-jedi/package.py

@@ -0,0 +1,95 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class Fv3Jedi(CMakePackage):
+    """Interface between JEDI and FV3 based models"""
+
+    homepage = "https://github.com/JCSDA/fv3-jedi"
+    git = "https://github.com/JCSDA/fv3-jedi.git"
+
+    maintainers = ["climbfuji"]
+
+    version("develop", branch="develop", no_cache=True)
+    version("1.7.0", commit="75fa0544ae7c6b5446460bef8cb7663f3fe1acad")
+    version("1.6.0", commit="3c20ebd2657d4b8df35103207a1e83535b67469c")
+
+    variant(
+        "forecast_model",
+        default="FV3CORE",
+        description="fv3 forecast model",
+        values=("FV3CORE", "GEOS", "UFS"),
+    )
+    variant("geos-aero", default=False, description="Enable usage of geos-aero")
+    variant("gsibec", default=True, description="FV3-SABER block GSI")
+    # Note that the option for openmp is lazily written in fv3-jedi.
+    # It just enables a find_package call. If a package is already found, for example by
+    # one of the package dependencies, then that component is silently used even if the user
+    # toggles it off. This is a bug and should be fixed eventually.
+    variant("openmp", default=True, description="Build with OpenMP support")
+    variant("ropp", default=False, description="Enable usage of ropp")
+    variant("sp", default=True, description="Enable usage of ncep-sp")
+
+    conflicts("forecast_model=GEOS", msg="FV3-JEDI: GEOS to be implemented.")
+    conflicts("forecast_model=UFS", msg="FV3-JEDI: UFS to be implemented.")
+    conflicts("+geos-aero", msg="FV3-JEDI: geos-aero to be implemented.")
+    # Note: the ropp code needs a JCSDA-internal repository.
+    conflicts("+ropp", msg="FV3-JEDI: ropp to be implemented.")
+
+    # Required components
+    depends_on("crtm")
+    depends_on("crtm@2.2.3:", when="@:1.5.0")
+    depends_on("crtm@v3.0.0-skylabv5-1", when="@1.6.0")
+    depends_on("crtm@v3.0.0-skylabv6", when="@1.7.0")
+    depends_on("ecbuild", type=("build"))
+    depends_on("ecbuild@3.3.2:", type=("build"), when="@1.6.0")
+    depends_on("ecmwf-atlas")
+    depends_on("ecmwf-atlas@0.33.0", when="@1.6.0")
+    depends_on("femps@1.0.0:")
+    depends_on("jedi-cmake", type=("build"))
+    depends_on("mpi")
+    # fv3-jedi depends on netcdf-fortran, which always depends on netcdf-c. However, netcdf-c
+    # has the mpi options, and netcdf-fortran does not.
+    depends_on("netcdf-fortran")
+    depends_on("netcdf-c+mpi")
+    depends_on("oops")
+    depends_on("oops@1.7.0", when="@1.6.0")
+    depends_on("oops@1.8.0", when="@1.7.0")
+    depends_on("saber")
+    depends_on("saber@1.7.0", when="@1.6.0")
+    depends_on("saber@1.8.0", when="@1.7.0")
+    depends_on("ufo")
+    depends_on("ufo@1.7.0", when="@1.6.0")
+    depends_on("ufo@1.8.0", when="@1.7.0")
+    depends_on("vader")
+    depends_on("vader@1.4.0", when="@1.6.0")
+    depends_on("vader@1.5.0", when="@1.7.0")
+
+    depends_on("fms", when="forecast_model=FV3CORE")
+    depends_on("fv3-jedi-linearmodel@1.0.0:", when="forecast_model=FV3CORE")
+
+    # Optional components
+    depends_on("GFDL_atmos_cubed_sphere", when="forecast_model=FV3CORE")
+    depends_on("gsibec", when="+gsibec")
+    depends_on("gsibec@1.1.2:", when="@1.6:1.7 +gsibec")
+    depends_on("llvm-openmp", when="+openmp %apple-clang", type=("build", "run"))
+    depends_on("sp", when="+sp")
+
+    def cmake_args(self):
+        res = [
+            self.define_from_variant("FV3_FORECAST_MODEL", "forecast_model"),
+            self.define_from_variant("OPENMP", "openmp"),
+        ]
+        return res
+
+    # find_package(ecbuild REQUIRED) is needed when using ecbuild.
+    patch("CMakeLists.txt.patch", when="@1.6:1.7")
+    # fv3-jedi is improperly including git_functions.cmake via an environment variable.
+    # It should instead use the jedicmake_FUNCTIONS variable, which is exported by jedi-cmake.
+    patch("test.CMakeLists.txt.patch", when="@1.6:1.7")
+    # fv3-jedi depends on these macros that are defined (and not exported) in ufo.
+    patch("cmake.fv3jedi_extra_macros.cmake.patch", when="@1.6:1.7")