Add fv3-jedi and its dependencies (SkyLab 8 version)

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

@@ -35,6 +35,10 @@ 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("netcdf-fortran", when="@v3.1.0-skylabv7")
 
     depends_on("[email protected]_emc", when="@2.3.0 +fix")
     depends_on("[email protected]_emc", when="@=2.4.0 +fix")
@@ -45,6 +49,50 @@ 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")
+    depends_on("ecbuild", type=("build"), when="@v3.1.0-skylabv7")
+
+    # Spack gets confused by the different repository url, so we use direct URLs here.
+
+    version(
+        "v3.1.0-skylabv7",
+        url="https://www.github.com/JCSDA/crtmv3/tarball/90d52eec1f97bb5a098c9834c4499a17de4ff35b",
+        sha256="0751ddad9a0304e62902a11faa1e693b84ad2b338512f8d2c1a03e5cc573a947",
+    )
+    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.
+    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/builtin/packages/ecmwf-atlas/package.py

@@ -20,6 +20,7 @@ class EcmwfAtlas(CMakePackage):
 
     version("master", branch="master")
     version("develop", branch="develop")
+    version("0.36.0", sha256="39bf748aa7b22df80b9791fbb6b4351ed9a9f85587b58fc3225314278a2a68f8")
     version("0.35.1", sha256="7a344aaa8a1378d989a7bb883eb741852c5fa494630be6d8c88e477e4b9c5be1")
     version("0.35.0", sha256="5a4f898ffb4a33c738b6f86e4e2a4c8e26dfd56d3c3399018081487374e29e97")
     version("0.34.0", sha256="48536742cec0bc268695240843ac0e232e2b5142d06b19365688d9ea44dbd9ba")
@@ -29,6 +30,7 @@ class EcmwfAtlas(CMakePackage):
     version("0.31.0", sha256="fa4ff8665544b8e19f79d171c540a9ca8bfc4127f52a3c4d4d618a2fe23354d7")
 
     depends_on("ecbuild", type=("build"))
+    depends_on("[email protected]:", type=("build"), when="@0.36.0:")
     depends_on("eckit@:1.23", when="@:0.33")
     depends_on("[email protected]:", when="@0.34:")
     depends_on("boost cxxstd=14 visibility=hidden", when="@0.26.0:0.33.99", type=("build", "run"))

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("[email protected]:", 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("[email protected]:", 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 +1,72 @@
+# 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("1.4.0", commit="05cc1ae63252ca535f3db0fdca9a8a996329fc8f")
+    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("[email protected]:", 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", "link", "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="@1.2:1.4")
+    # fv3-jedi-linearmodel needs to install its Fortran modules.
+    patch("src.CMakeLists.txt.patch", when="@1.2:1.4")

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.16.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/CMakeLists.txt.18.patch

@@ -0,0 +1,20 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -17,6 +17,8 @@ set( CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake;${CMAKE_MODULE_PATH})
+
+ 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 )
+@@ -217,7 +219,7 @@ if (FV3_FORECAST_MODEL MATCHES UFS)
+ endif()
+
+ add_subdirectory( src )
+-add_subdirectory( test )
++#add_subdirectory( test )
+
+ if( ENABLE_FV3JEDI_DOC )
+     add_subdirectory( Documents )

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 )