Merge remote-tracking branch 'origin/development' into cice5_esm1p6

packages/access-esm1p6/package.py

@@ -8,7 +8,8 @@
 from spack.package import *
 
 class AccessEsm1p6(BundlePackage):
-    """ACCESS-ESM1.6 bundle contains the coupled UM7, CICE4 and MOM5 models.
+    """ACCESS-ESM1.6 bundle contains the coupled UM7, CICE4/CICE5 and MOM5
+       models.
 
     ACCESS-ESM1.6 comprises of:
 
@@ -17,21 +18,54 @@ class AccessEsm1p6(BundlePackage):
     * The CABLE land surface model with biogeochemistry (CASA-CNP) (CABLE2.4)
     * The GFDL MOM5 ocean model at 1 degree resolution
     * The WOMBATlite ocean BGC model (generic tracer version)
-    * The LANL CICE4.1 sea ice model (version as ACCESS1.4)
+    * The LANL CICE4.1 sea ice model (version as ACCESS1.4). CICE5 for testing.
     * The OASIS-MCT coupler
     """
 
     homepage = "https://www.access-nri.org.au"
 
     git = "https://github.com/ACCESS-NRI/ACCESS-ESM1.6.git"
 
-    maintainers("dougiesquire")
+    maintainers("dougiesquire", "harshula")
 
     version("latest")
 
-    depends_on("[email protected]", type="run")
-    depends_on("[email protected] type=ACCESS-ESM", type="run")
+    variant(
+        "cice",
+        default="4",
+        description="Choose the version of the CICE sea-ice model.",
+        values=("4", "5"),
+        multi=False,
+    )
+    variant(
+        "generic-tracers",
+        default=True,
+        description="Enable generic tracers.",
+    )
+    variant(
+        "um",
+        default="access-esm1.6",
+        description="Choose the branch of um7.",
+        values=("access-esm1.5", "access-esm1.6"),
+        multi=False,
+    )
+
+    depends_on("[email protected]", type="run", when="cice=4")
+    depends_on("[email protected]", type="run", when="cice=5")
+    # TODO: Use the access-esm1.6 branch when it has been confirmed that
+    #       MOM5 master supports building with generic tracers disabled.
+    depends_on(
+        "[email protected] type=ACCESS-CM",
+        type="run",
+        when="~generic-tracers",
+    )
+    depends_on(
+        "[email protected] type=ACCESS-ESM",
+        type="run",
+        when="+generic-tracers",
+    )
     # um7 is in a private repository
-    depends_on("[email protected]", type="run")
+    depends_on("[email protected]", type="run", when="um=access-esm1.5")
+    depends_on("[email protected]", type="run", when="um=access-esm1.6")
 
     # There is no need for install() since there is no code.

packages/access-fms/package.py

@@ -0,0 +1,63 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# Copyright 2024 ACCESS-NRI
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import find_headers, find_libraries
+
+# Based on upstream $spack/var/spack/repos/builtin/packages/fms/package.py
+class AccessFms(CMakePackage):
+    """GFDL's Flexible Modeling System (FMS) is a software environment
+    that supports the efficient development, construction, execution,
+    and scientific interpretation of atmospheric, oceanic, and climate
+    system models. This is ACCESS-NRI's fork."""
+
+    homepage = "https://github.com/ACCESS-NRI/FMS"
+    git = "https://github.com/ACCESS-NRI/FMS.git"
+
+    license("LGPL-3.0-or-later")
+
+    maintainers("harshula")
+
+    version("master", branch="master")
+    # TODO: Needs to be changed once changes to build system enter master.
+    version("development", branch="development", preferred=True)
+
+    variant("gfs_phys", default=True, description="Use GFS Physics")
+    variant("large_file", default=False, description="Enable compiler definition -Duse_LARGEFILE.")
+    variant(
+        "internal_file_nml",
+        default=True,
+        description="Enable compiler definition -DINTERNAL_FILE_NML.",
+    )
+
+    depends_on("netcdf-c")
+    depends_on("netcdf-fortran")
+    depends_on("mpi")
+
+    def url_for_version(self, version):
+        return "https://github.com/ACCESS-NRI/FMS/tarball/{0}".format(version)
+
+    @property
+    def headers(self):
+        return find_headers(
+            "*", root=self.prefix, recursive=True
+        )
+
+    @property
+    def libs(self):
+        libraries = ["libfms_r4", "libfms_r8"]
+        return find_libraries(
+            libraries, root=self.prefix, shared=False, recursive=True
+        )
+
+    def cmake_args(self):
+        args = [
+            self.define_from_variant("GFS_PHYS"),
+            self.define_from_variant("LARGEFILE", "large_file"),
+            self.define_from_variant("INTERNAL_FILE_NML"),
+        ]
+
+        return args

packages/access-generic-tracers/package.py

@@ -0,0 +1,38 @@
+# Copyright 2013-2024 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 find_libraries
+
+class AccessGenericTracers(CMakePackage):
+    """This is a fork of the NOAA-GFDL/ocean_BGC repo managed by NOAA-GFDL.
+    It contains a collection of tracers and associated code for use with
+    the MOM and GOLD ocean models. This fork includes generic tracer
+    implementations of the suite of WOMBAT models used in ACCESS earth-system
+    models."""
+
+    homepage = "https://github.com/ACCESS-NRI/GFDL-generic-tracers"
+    git = "https://github.com/ACCESS-NRI/GFDL-generic-tracers.git"
+
+    maintainers("harshula")
+
+    version("master", branch="master")
+    # TODO: Needs to be changed once changes to build system enter master.
+    version("development", branch="development", preferred=True)
+
+    depends_on("access-mocsy")
+    depends_on("access-fms")
+    depends_on("mpi")
+
+    def url_for_version(self, version):
+        return "https://github.com/ACCESS-NRI/GFDL-generic-tracers/tarball/{0}".format(version)
+
+    @property
+    def libs(self):
+        libraries = find_libraries(
+            "libgtracers", root=self.prefix, shared=False, recursive=True
+        )
+        # mocsy is an internal lib dependency of this static library.
+        # Hence we need to propagate it.
+        return libraries + self.spec["access-mocsy"].libs

packages/access-mocsy/package.py

@@ -0,0 +1,108 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# Copyright 2024 ACCESS-NRI
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import find_libraries, install, join_path, mkdirp
+
+# https://spack.readthedocs.io/en/latest/build_systems/makefilepackage.html
+class AccessMocsy(MakefilePackage):
+    """Routines to model ocean carbonate system thermodynamics. ACCESS NRI's fork."""
+
+    homepage = "https://www.access-nri.org.au"
+    git = "https://github.com/ACCESS-NRI/mocsy.git"
+
+    maintainers("harshula")
+
+    version("master", branch="master")
+    version("mom5", branch="mom5", preferred=True)
+
+    # Need: self.spec["mpi"].mpifc
+    depends_on("mpi")
+
+    _header = join_path("src", "mocsy_DNADHeaders.h")
+    _libname = "libmocsy.a"
+    _pcfile = "mocsy.pc"
+    _pkgdir = "pkgconfig"
+    _modfiles = [
+        "dual_num_auto_diff.mod",
+        "mocsy_buffesm.mod",
+        "mocsy_constants.mod",
+        "mocsy_depth2press.mod",
+        "mocsy_derivauto.mod",
+        "mocsy_derivnum.mod",
+        "mocsy_errors.mod",
+        "mocsy_f2pco2.mod",
+        "mocsy_gasx.mod",
+        "mocsy_p2fco2.mod",
+        "mocsy_p80.mod",
+        "mocsy_phsolvers.mod",
+        "mocsy_rho.mod",
+        "mocsy_rhoinsitu.mod",
+        "mocsy_singledouble.mod",
+        "mocsy_sw_adtg.mod",
+        "mocsy_sw_ptmp.mod",
+        "mocsy_sw_temp.mod",
+        "mocsy_tis.mod",
+        "mocsy_tpot.mod",
+        "mocsy_vars.mod",
+        "mocsy_varsolver.mod",
+    ]
+
+    def url_for_version(self, version):
+        return "https://github.com/ACCESS-NRI/mocsy/tarball/{0}".format(version)
+
+    @property
+    def libs(self):
+        return find_libraries(
+            "libmocsy", root=self.prefix, shared=False, recursive=True
+        )
+
+    def _create_pkgconf(self, spec, prefix):
+
+        text = f"""\
+prefix={prefix}
+exec_prefix=${{prefix}}
+libdir=${{exec_prefix}}/lib
+includedir=${{prefix}}/include
+
+Name: mocsy
+Description: Routines to model ocean carbonate system thermodynamics.
+Version: 2024.08.1
+Libs: -L${{libdir}} -lmocsy
+Cflags: -I${{includedir}}
+Fflags: -I${{includedir}}
+"""
+
+        with open(join_path(self.stage.source_path, self._pcfile), "w", encoding="utf-8") as pc:
+            nchars_written = pc.write(text)
+
+        if nchars_written < len(text):
+            raise OSError
+
+    def build(self, spec, prefix):
+        build = Executable("make")
+        build(
+            self._libname,
+            "FC=" + self.spec["mpi"].mpifc,
+            # Copied from MOM5/bin/mkmf.template.nci
+            "FCFLAGS=-fno-alias -safe-cray-ptr -fpe0 -ftz -assume byterecl -i4 -r8 -traceback -nowarn -check noarg_temp_created -assume nobuffered_io -convert big_endian -grecord-gcc-switches -align all -g3 -O2 -xCORE-AVX2 -debug all -check none",
+            "F90=" + self.spec["mpi"].mpifc
+        )
+        self._create_pkgconf(spec, prefix)
+
+    def install(self, spec, prefix):
+
+        # Creates prefix.lib too
+        pkgconfdir = join_path(prefix.lib, self._pkgdir)
+        mkdirp(pkgconfdir)
+        mkdirp(prefix.include)
+
+        install(join_path(self.stage.source_path, self._libname), prefix.lib)
+        install(join_path(self.stage.source_path, self._header), prefix.include)
+        for f in self._modfiles:
+            install(join_path(self.stage.source_path, f), prefix.include)
+        install(join_path(self.stage.source_path, self._pcfile), pkgconfdir)
+

packages/access-test/package.py

@@ -0,0 +1,26 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# Copyright 2024 ACCESS-NRI
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+class AccessTest(BundlePackage):
+    """ACCESS-TEST bundle is for testing ACCESS-NRI infrastructure."""
+
+    homepage = "https://www.access-nri.org.au"
+
+    git = "https://github.com/ACCESS-NRI/ACCESS-TEST.git"
+
+    maintainers("harshula")
+
+    version("latest")
+
+    variant("deterministic", default=False, description="Deterministic build.")
+
+    depends_on("oasis3-mct+deterministic", when="+deterministic", type="run")
+    depends_on("oasis3-mct~deterministic", when="~deterministic", type="run")
+
+    # There is no need for install() since there is no code.