Merge branch 'jcsda_emc_spack_stack' into feature/fv3_jedi

lib/jcsda-emc/spack-stack/stack/meta_modules.py

@@ -259,9 +259,14 @@ def setup_meta_modules():
     module_choice = module_config["default"]["enable"][0]
     logging.info("  ... configured to use {} modules".format(module_choice))
 
-    # Prevent the use of tcl modules on macOS because sed syntax is different
-    if module_choice == "tcl" and sys.platform == "darwin":
-        raise Exception("Use of tcl modules on macOS not supported - sed syntax differs")
+    # Need to set a few variables when tcl modules are used
+    if module_choice == "tcl":
+        module_replace_patterns = ["is-loaded", "module load", "depends-on"]
+        # sed syntax differs on macOS
+        if sys.platform == "darwin":
+            sed_syntax_fix = "''"
+        else:
+            sed_syntax_fix = ""
 
     # Top-level module directory
     module_dir = substitute_config_vars(module_config["default"]["roots"][module_choice])
@@ -297,8 +302,13 @@ def setup_meta_modules():
     # Then, check for mpi providers - recursively for compilers
     mpi_dict = get_matched_dict(module_dir, mpi_candidate_list, compiler_candidate_list)
     if not mpi_dict:
-        raise Exception("No matching MPI providers found")
-    logging.info(" ... stack mpi providers: '{}'".format(mpi_dict))
+        user_input = input(
+            "No matching MPI providers found, proceed without creating MPI module hierarchy? (yes/no): "
+        )
+        if not user_input.lower() in ["yes", "y"]:
+            raise Exception("No matching MPI providers found")
+    else:
+        logging.info(" ... stack mpi providers: '{}'".format(mpi_dict))
 
     # For some environments, there are only compiler+mpi-dependent modules,
     # and therefore the compiler itself is not recorded in compiler_dict.
@@ -422,18 +432,13 @@ def setup_meta_modules():
                         logging.debug(
                             "  ... ... ... removing compiler prefices in {}".format(filepath)
                         )
-                        cmd = "sed -i 's#is-loaded {}/{}/#is-loaded #g' {}".format(
-                            compiler_name, compiler_version, filepath
-                        )
-                        status = os.system(cmd)
-                        if not status == 0:
-                            raise Exception("Error while calling '{}'".format(cmd))
-                        cmd = "sed -i 's#load {}/{}/#load #g' {}".format(
-                            compiler_name, compiler_version, filepath
-                        )
-                        status = os.system(cmd)
-                        if not status == 0:
-                            raise Exception("Error while calling '{}'".format(cmd))
+                        for pattern in module_replace_patterns:
+                            cmd = "sed -i {4} 's#{0} {1}/{2}/#{0} #g' {3}".format(
+                                pattern, compiler_name, compiler_version, filepath, sed_syntax_fix
+                            )
+                            status = os.system(cmd)
+                            if not status == 0:
+                                raise Exception("Error while calling '{}'".format(cmd))
 
             # Read compiler template into module_content string
             with open(COMPILER_TEMPLATES[module_choice]) as f:
@@ -646,40 +651,34 @@ def setup_meta_modules():
                                         filepath
                                     )
                                 )
+                                # Search patterns
+                                patterns = ["is-loaded", "module load", "depends-on"]
                                 # First, compiler-only dependent modules
-                                cmd = "sed -i 's#is-loaded {}/{}/#is-loaded #g' {}".format(
-                                    compiler_name, compiler_version, filepath
-                                )
-                                status = os.system(cmd)
-                                if not status == 0:
-                                    raise Exception("Error while calling '{}'".format(cmd))
-                                cmd = "sed -i 's#load {}/{}/#load #g' {}".format(
-                                    compiler_name, compiler_version, filepath
-                                )
-                                status = os.system(cmd)
-                                if not status == 0:
-                                    raise Exception("Error while calling '{}'".format(cmd))
+                                for pattern in module_replace_patterns:
+                                    cmd = "sed -i {4} 's#{0} {1}/{2}/#{0} #g' {3}".format(
+                                        pattern,
+                                        compiler_name,
+                                        compiler_version,
+                                        filepath,
+                                        sed_syntax_fix,
+                                    )
+                                    status = os.system(cmd)
+                                    if not status == 0:
+                                        raise Exception("Error while calling '{}'".format(cmd))
                                 # Then, compiler+mpi-dependent modules
-                                cmd = "sed -i 's#is-loaded {}/{}/{}/{}/#is-loaded #g' {}".format(
-                                    mpi_name,
-                                    mpi_version,
-                                    compiler_name,
-                                    compiler_version,
-                                    filepath,
-                                )
-                                status = os.system(cmd)
-                                if not status == 0:
-                                    raise Exception("Error while calling '{}'".format(cmd))
-                                cmd = "sed -i 's#load {}/{}/{}/{}/#load #g' {}".format(
-                                    mpi_name,
-                                    mpi_version,
-                                    compiler_name,
-                                    compiler_version,
-                                    filepath,
-                                )
-                                status = os.system(cmd)
-                                if not status == 0:
-                                    raise Exception("Error while calling '{}'".format(cmd))
+                                for pattern in module_replace_patterns:
+                                    cmd = "sed -i {6} 's#{0} {1}/{2}/{3}/{4}/#{0} #g' {5}".format(
+                                        pattern,
+                                        mpi_name,
+                                        mpi_version,
+                                        compiler_name,
+                                        compiler_version,
+                                        filepath,
+                                        sed_syntax_fix,
+                                    )
+                                    status = os.system(cmd)
+                                    if not status == 0:
+                                        raise Exception("Error while calling '{}'".format(cmd))
 
                     # Read compiler lua template into module_content string
                     with open(MPI_TEMPLATES[module_choice]) as f:
@@ -698,7 +697,10 @@ def setup_meta_modules():
                         f.write(module_content)
                     logging.info("  ... writing {}".format(mpi_module_file))
 
-    del package_name
+    try:
+        del package_name
+    except:
+        pass
     # Create python modules. Need to accommodate both external
     # Python distributions and spack-built Python distributions.
     # If there is no package config info for Python, then we are
@@ -748,10 +750,21 @@ def setup_meta_modules():
                     python_dict = get_matched_dict(compiler_install_dir, python_candidate_list)
             logging.info(" ... stack python providers: '{}'".format(python_dict))
             if not python_dict:
-                raise Exception(
-                    """No matching Python version found. Make sure that the
-Python version in the package config matches what spack installed."""
+                user_input = input(
+                    "No matching Python version found found, proceed without creating Python modules? (yes/no): "
                 )
+                if not user_input.lower() in ["yes", "y"]:
+                    raise Exception(
+                        """"No matching Python version found. Make sure that the
+Python version in the package config matches what spack installed."""
+                    )
+                else:
+                    logging.info(
+                        "Metamodule generation completed successfully in {}".format(
+                            meta_module_dir
+                        )
+                    )
+                    return
 
     for compiler_name in compiler_dict.keys():
         for compiler_version in compiler_dict[compiler_name]:

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

@@ -13,6 +13,7 @@ class Awscli(PythonPackage):
 
     pypi = "awscli/awscli-1.16.308.tar.gz"
 
+    version("1.29.41", sha256="c029edd2c0bd72fb49cefe1a8f83ce2b46ba31ab45769677f7ba0771461078cb")
     version("1.27.84", sha256="a27a7d1f3efa9dd2acf9d8bd72b939337d53da4ac71721cde6d5dff94aa446f7")
     version("1.27.56", sha256="58fd7122547db71646c053c914bd4f9b673356dd8c9520ae6d35560a8aec208b")
     version("1.16.308", sha256="3632fb1db2538128509a7b5e89f2a2c4ea3426bec139944247bddc4d79bf7603")
@@ -22,22 +23,24 @@ class Awscli(PythonPackage):
     depends_on("[email protected]:", when="@1.25:", type=("build", "run"))
 
     # py-botocore is pinned to the patch version number
+    depends_on("[email protected]", when="@1.29.41", type=("build", "run"))
     depends_on("[email protected]", when="@1.27.84", type=("build", "run"))
     depends_on("[email protected]", when="@1.27.56", type=("build", "run"))
     depends_on("[email protected]", when="@1.16.308", type=("build", "run"))
     depends_on("[email protected]", when="@1.16.179", type=("build", "run"))
 
-    depends_on("[email protected]:0.4.4", when="@1.27", type=("build", "run"))
+    depends_on("[email protected]:0.4.4", when="@1.27:", type=("build", "run"))
     depends_on("[email protected]:0.3.9", when="@1.16", type=("build", "run"))
 
-    depends_on("[email protected]:0.16", when="@1.27", type=("build", "run"))
+    depends_on("[email protected]:0.16", when="@1.27:", type=("build", "run"))
     depends_on("[email protected]:0.15", when="@1.16", type=("build", "run"))
 
+    depends_on("[email protected]:6.0", when="@1.29", type=("build", "run"))
     depends_on("[email protected]:5.4", when="@1.27", type=("build", "run"))
     depends_on("[email protected]:5.2", when="@1.16", type=("build", "run"))
 
-    depends_on("[email protected]:4.7", when="@1.27", type=("build", "run"))
+    depends_on("[email protected]:4.7", when="@1.27:", type=("build", "run"))
     depends_on("[email protected]:3.5.0", when="@1.16", type=("build", "run"))
 
-    depends_on("[email protected]:0.6", when="@1.27", type=("build", "run"))
+    depends_on("[email protected]:0.6", when="@1.27:", type=("build", "run"))
     depends_on("[email protected]:0.2", when="@1.16", type=("build", "run"))

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

@@ -90,7 +90,7 @@ def _setup_bufr_environment(self, env, suffix):
         lib = find_libraries(libname + append, root=self.prefix, shared=shared, recursive=True)
         lib_envname = "BUFR_LIB{0}".format(suffix) + append
         inc_envname = "BUFR_INC{0}".format(suffix) + append
-        include_dir = "include_{0}".format(suffix)
+        include_dir = "{0}_{1}".format(self.prefix.include.bufr, suffix)
 
         env.set(lib_envname, lib[0])
         env.set(inc_envname, include_dir)

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

@@ -18,6 +18,7 @@ class Eckit(CMakePackage):
 
     maintainers("skosukhin", "climbfuji")
 
+    version("1.24.4", sha256="b6129eb4f7b8532aa6905033e4cf7d09aadc8547c225780fea3db196e34e4671")
     version("1.23.1", sha256="cd3c4b7a3a2de0f4a59f00f7bab3178dd59c0e27900d48eaeb357975e8ce2f15")
     version("1.23.0", sha256="3cac55ddf7036ecd32cb0974a1ec3a2d347de574ab3a2c0bb6c6f8982e5a7a09")
     version("1.22.1", sha256="a3463d07e47e3bd3e5efa13fdc03d7d3a30ada919ccec3259c6c9c7da4cfdfd9")

var/spack/repos/builtin/packages/ecmwf-atlas/intel_vectorization_v0p34.patch

@@ -0,0 +1,11 @@
+--- a/cmake/atlas_compile_flags.cmake	2023-07-10 04:13:02.000000000 -0600
++++ b/cmake/atlas_compile_flags.cmake	2023-08-21 14:29:10.000000000 -0600
+@@ -21,6 +21,8 @@
+
+ endif()
+
++ecbuild_add_cxx_flags("-fp-speculation=safe")
++
+ if( CMAKE_CXX_COMPILER_ID MATCHES NVHPC )
+   ecbuild_add_cxx_flags("--diag_suppress declared_but_not_referenced --display_error_number" NAME atlas_cxx_disable_warnings )
+   # For all the variables with side effects (constructor/dectructor functionality)

var/spack/repos/builtin/packages/ecmwf-atlas/package.py

@@ -20,21 +20,26 @@ class EcmwfAtlas(CMakePackage):
 
     version("master", branch="master")
     version("develop", branch="develop")
+    version("0.34.0", sha256="48536742cec0bc268695240843ac0e232e2b5142d06b19365688d9ea44dbd9ba")
     version("0.33.0", sha256="a91fffe9cecb51c6ee8549cbc20f8279e7b1f67dd90448e6c04c1889281b0600")
     version("0.32.1", sha256="3d1a46cb7f50e1a6ae9e7627c158760e132cc9f568152358e5f78460f1aaf01b")
     version("0.31.1", sha256="fa9274c74c40c2115b9c6120a7040e357b0c7f37b20b601b684d2a83a479cdfb")
     version("0.31.0", sha256="fa4ff8665544b8e19f79d171c540a9ca8bfc4127f52a3c4d4d618a2fe23354d7")
 
     depends_on("ecbuild", type=("build"))
-    depends_on("eckit")
-    depends_on("boost cxxstd=14 visibility=hidden", when="@0.26.0:", type=("build", "run"))
+    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"))
+    depends_on("boost cxxstd=17 visibility=hidden", when="@0.34.0:", type=("build", "run"))
     variant("fckit", default=True)
-    depends_on("fckit", when="+fckit")
+    depends_on("fckit@:0.10", when="@:0.33 +fckit")
+    depends_on("[email protected]:", when="@0.34: +fckit")
     depends_on("python")
 
     patch("clang_include_array.patch", when="%apple-clang")
     patch("clang_include_array.patch", when="%clang")
-    patch("intel_vectorization.patch", when="%intel")
+    patch("intel_vectorization_v0p33.patch", when="@:0.33 %intel")
+    patch("intel_vectorization_v0p34.patch", when="@0.34: %intel")
 
     variant(
         "build_type",
@@ -43,7 +48,7 @@ class EcmwfAtlas(CMakePackage):
         values=("Debug", "Release", "RelWithDebInfo"),
     )
 
-    variant('openmp', default=True, description='Use OpenMP?')
+    variant("openmp", default=True, description="Use OpenMP?")
     depends_on("llvm-openmp", when="+openmp %apple-clang", type=("build", "run"))
     variant("shared", default=True)
 
@@ -61,7 +66,7 @@ class EcmwfAtlas(CMakePackage):
 
     def cmake_args(self):
         args = [
-            self.define_from_variant('ENABLE_OMP', 'openmp'),
+            self.define_from_variant("ENABLE_OMP", "openmp"),
             self.define_from_variant("ENABLE_FCKIT", "fckit"),
             self.define_from_variant("ENABLE_TRANS", "trans"),
             self.define_from_variant("ENABLE_EIGEN", "eigen"),
@@ -74,8 +79,8 @@ def cmake_args(self):
 
     @when("+fismahigh")
     def patch(self):
-        filter_file("http://www\.ecmwf\.int", "", "cmake/atlas-import.cmake.in")
-        filter_file("int\.ecmwf", "", "cmake/atlas-import.cmake.in")
+        filter_file("http://www\.ecmwf\.int", "", "cmake/atlas-import.cmake.in")  # noqa: W605
+        filter_file("int\.ecmwf", "", "cmake/atlas-import.cmake.in")  # noqa: W605
         filter_file('http[^"]+', "", "cmake/atlas_export.cmake")
         patterns = [".travis.yml", "tools/install*.sh", "tools/github-sha.sh"]
         for pattern in patterns:

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

@@ -29,6 +29,7 @@ class Esmf(MakefilePackage):
     # Develop is a special name for spack and is always considered the newest version
     version("develop", branch="develop")
     # generate chksum with spack checksum [email protected]
+    version("8.5.0", sha256="acd0b2641587007cc3ca318427f47b9cae5bfd2da8d2a16ea778f637107c29c4")
     version("8.4.2", sha256="969304efa518c7859567fa6e65efd960df2b4f6d72dbf2c3f29e39e4ab5ae594")
     version("8.4.1", sha256="1b54cee91aacaa9df400bd284614cbb0257e175f6f3ec9977a2d991ed8aa1af6")
     version(
@@ -42,7 +43,7 @@ class Esmf(MakefilePackage):
         sha256="0ff43ede83d1ac6beabd3d5e2a646f7574174b28a48d1b9f2c318a054ba268fd",
         deprecated=True,
     )
-    version("8.3.0b09", commit="5b7e546c4b")
+    version("8.3.0b09", commit="5b7e546c4b", deprecated=True)
     version("8.2.0", sha256="27866c31fdb63c58e78211de970470ca02d274f5d4d6d97e94284d63b1c1d9e4")
     version("8.1.1", sha256="629690c7a488e84ac7252470349458d7aaa98b54c260f8b3911a2e2f3e713dd0")
     version(
@@ -221,6 +222,11 @@ def setup_build_environment(self, env):
         elif self.compiler.name == "intel" or self.compiler.name == "oneapi":
             env.set("ESMF_COMPILER", "intel")
         elif self.compiler.name in ["clang", "apple-clang"]:
+            # Turn off OpenMP with both versions of clang compilers
+            # to avoid having to add clang OpenMP libraries to the
+            # Fortran linker command.
+            env.set("ESMF_OPENMP", "OFF")
+            #
             env.set("ESMF_COMPILER", "gfortranclang")
             with self.compiler.compiler_environment():
                 gfortran_major_version = int(