meshlab: allow downloads of vendored components

* Nalu: updating Trilinos recipe a bit

Basic changes to build/install nalu properly using Spack.
Some more changes would be nice for instance adding an
option to build against Trilinos master or develop. Adding
a dependency on googletest to avoid the annoying build
failures in the unit-tests.

* Nalu: adding release 1.6.0

Nalu v1.6.0 can build cleanly against Trilinos 14.0.0 with the
proposed changes. The only other combo is master / master but
than one is "floating" as these branch evolve over time. When a
new Nalu comes out we might want to add another fixed version to
keep this recipes up to date!

lib/spack/spack/build_systems/oneapi.py

@@ -14,7 +14,7 @@
 from llnl.util.link_tree import LinkTree
 
 from spack.build_environment import dso_suffix
-from spack.directives import conflicts, variant
+from spack.directives import conflicts, license, variant
 from spack.package_base import InstallError
 from spack.util.environment import EnvironmentModifications
 from spack.util.executable import Executable
@@ -26,6 +26,7 @@ class IntelOneApiPackage(Package):
     """Base class for Intel oneAPI packages."""
 
     homepage = "https://software.intel.com/oneapi"
+    license("https://intel.ly/393CijO")
 
     # oneAPI license does not allow mirroring outside of the
     # organization (e.g. University/Company).

lib/spack/spack/ci.py

@@ -1947,9 +1947,9 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
         entrypoint_script.append(["echo", f"Re-run install script using:\n\t{install_mechanism}"])
         # Allow interactive
         if IS_WINDOWS:
-            entrypoint_script.extend(["&", "($args -Join ' ')", "-NoExit"])
+            entrypoint_script.append(["&", "($args -Join ' ')", "-NoExit"])
         else:
-            entrypoint_script.extend(["exec", "$@"])
+            entrypoint_script.append(["exec", "$@"])
 
         process_command(
             "entrypoint", entrypoint_script, work_dir, run=False, exit_on_failure=False

lib/spack/spack/cmd/install.py

@@ -420,10 +420,9 @@ def install_with_active_env(env: ev.Environment, args, install_kwargs, reporter_
         with reporter_factory(specs_to_install):
             env.install_specs(specs_to_install, **install_kwargs)
     finally:
-        # TODO: this is doing way too much to trigger
-        # views and modules to be generated.
-        with env.write_transaction():
-            env.write(regenerate=True)
+        if env.views:
+            with env.write_transaction():
+                env.write(regenerate=True)
 
 
 def concrete_specs_from_cli(args, install_kwargs):

lib/spack/spack/compilers/msvc.py

@@ -199,7 +199,7 @@ def __init__(self, *args, **kwargs):
         # for a fortran compiler
         if paths[2]:
             # If this found, it sets all the vars
-            oneapi_root = os.getenv("ONEAPI_ROOT")
+            oneapi_root = os.path.join(self.cc, "../../..")
             oneapi_root_setvars = os.path.join(oneapi_root, "setvars.bat")
             oneapi_version_setvars = os.path.join(
                 oneapi_root, "compiler", str(self.ifx_version), "env", "vars.bat"

lib/spack/spack/installer.py

@@ -119,7 +119,7 @@ def __init__(self, pkg_count: int):
         self.pkg_ids: Set[str] = set()
 
     def next_pkg(self, pkg: "spack.package_base.PackageBase"):
-        pkg_id = package_id(pkg)
+        pkg_id = package_id(pkg.spec)
 
         if pkg_id not in self.pkg_ids:
             self.pkg_num += 1
@@ -221,12 +221,12 @@ def _handle_external_and_upstream(pkg: "spack.package_base.PackageBase", explici
     # consists in module file generation and registration in the DB.
     if pkg.spec.external:
         _process_external_package(pkg, explicit)
-        _print_installed_pkg(f"{pkg.prefix} (external {package_id(pkg)})")
+        _print_installed_pkg(f"{pkg.prefix} (external {package_id(pkg.spec)})")
         return True
 
     if pkg.spec.installed_upstream:
         tty.verbose(
-            f"{package_id(pkg)} is installed in an upstream Spack instance at "
+            f"{package_id(pkg.spec)} is installed in an upstream Spack instance at "
             f"{pkg.spec.prefix}"
         )
         _print_installed_pkg(pkg.prefix)
@@ -403,7 +403,7 @@ def _install_from_cache(
         return False
     t.stop()
 
-    pkg_id = package_id(pkg)
+    pkg_id = package_id(pkg.spec)
     tty.debug(f"Successfully extracted {pkg_id} from binary cache")
 
     _write_timer_json(pkg, t, True)
@@ -484,7 +484,7 @@ def _process_binary_cache_tarball(
         if download_result is None:
             return False
 
-    tty.msg(f"Extracting {package_id(pkg)} from binary cache")
+    tty.msg(f"Extracting {package_id(pkg.spec)} from binary cache")
 
     with timer.measure("install"), spack.util.path.filter_padding():
         binary_distribution.extract_tarball(pkg.spec, download_result, force=False, timer=timer)
@@ -513,7 +513,7 @@ def _try_install_from_binary_cache(
     if not spack.mirror.MirrorCollection(binary=True):
         return False
 
-    tty.debug(f"Searching for binary cache of {package_id(pkg)}")
+    tty.debug(f"Searching for binary cache of {package_id(pkg.spec)}")
 
     with timer.measure("search"):
         matches = binary_distribution.get_mirrors_for_spec(pkg.spec, index_only=True)
@@ -610,7 +610,7 @@ def get_dependent_ids(spec: "spack.spec.Spec") -> List[str]:
 
     Returns: list of package ids
     """
-    return [package_id(d.package) for d in spec.dependents()]
+    return [package_id(d) for d in spec.dependents()]
 
 
 def install_msg(name: str, pid: int, install_status: InstallStatus) -> str:
@@ -720,7 +720,7 @@ def log(pkg: "spack.package_base.PackageBase") -> None:
     dump_packages(pkg.spec, packages_dir)
 
 
-def package_id(pkg: "spack.package_base.PackageBase") -> str:
+def package_id(spec: "spack.spec.Spec") -> str:
     """A "unique" package identifier for installation purposes
 
     The identifier is used to track build tasks, locks, install, and
@@ -732,10 +732,10 @@ def package_id(pkg: "spack.package_base.PackageBase") -> str:
     Args:
         pkg: the package from which the identifier is derived
     """
-    if not pkg.spec.concrete:
+    if not spec.concrete:
         raise ValueError("Cannot provide a unique, readable id when the spec is not concretized.")
 
-    return f"{pkg.name}-{pkg.version}-{pkg.spec.dag_hash()}"
+    return f"{spec.name}-{spec.version}-{spec.dag_hash()}"
 
 
 class BuildRequest:
@@ -765,7 +765,7 @@ def __init__(self, pkg: "spack.package_base.PackageBase", install_args: dict):
         self.pkg.last_phase = install_args.pop("stop_at", None)  # type: ignore[attr-defined]
 
         # Cache the package id for convenience
-        self.pkg_id = package_id(pkg)
+        self.pkg_id = package_id(pkg.spec)
 
         # Save off the original install arguments plus standard defaults
         # since they apply to the requested package *and* dependencies.
@@ -780,9 +780,9 @@ def __init__(self, pkg: "spack.package_base.PackageBase", install_args: dict):
         # are not able to return full dependents for all packages across
         # environment specs.
         self.dependencies = set(
-            package_id(d.package)
+            package_id(d)
             for d in self.pkg.spec.dependencies(deptype=self.get_depflags(self.pkg))
-            if package_id(d.package) != self.pkg_id
+            if package_id(d) != self.pkg_id
         )
 
     def __repr__(self) -> str:
@@ -832,7 +832,7 @@ def get_depflags(self, pkg: "spack.package_base.PackageBase") -> int:
         depflag = dt.LINK | dt.RUN
         include_build_deps = self.install_args.get("include_build_deps")
 
-        if self.pkg_id == package_id(pkg):
+        if self.pkg_id == package_id(pkg.spec):
             cache_only = self.install_args.get("package_cache_only")
         else:
             cache_only = self.install_args.get("dependencies_cache_only")
@@ -927,7 +927,7 @@ def __init__(
             raise ValueError(f"{self.pkg.name} must have a concrete spec")
 
         # The "unique" identifier for the task's package
-        self.pkg_id = package_id(self.pkg)
+        self.pkg_id = package_id(self.pkg.spec)
 
         # The explicit build request associated with the package
         if not isinstance(request, BuildRequest):
@@ -965,9 +965,9 @@ def __init__(
         # if use traverse for transitive dependencies, then must remove
         # transitive dependents on failure.
         self.dependencies = set(
-            package_id(d.package)
+            package_id(d)
             for d in self.pkg.spec.dependencies(deptype=self.request.get_depflags(self.pkg))
-            if package_id(d.package) != self.pkg_id
+            if package_id(d) != self.pkg_id
         )
 
         # Handle bootstrapped compiler
@@ -983,7 +983,7 @@ def __init__(
             dep.constrain(f"os={str(arch_spec.os)}")
             dep.constrain(f"target={arch_spec.target.microarchitecture.family.name}:")
             dep.concretize()
-            dep_id = package_id(dep.package)
+            dep_id = package_id(dep)
             self.dependencies.add(dep_id)
 
         # List of uninstalled dependencies, which is used to establish
@@ -1194,7 +1194,7 @@ def _add_bootstrap_compilers(
         """
         packages = _packages_needed_to_bootstrap_compiler(compiler, architecture, pkgs)
         for comp_pkg, is_compiler in packages:
-            pkgid = package_id(comp_pkg)
+            pkgid = package_id(comp_pkg.spec)
             if pkgid not in self.build_tasks:
                 self._add_init_task(comp_pkg, request, is_compiler, all_deps)
             elif is_compiler:
@@ -1241,7 +1241,7 @@ def _add_init_task(
         """
         task = BuildTask(pkg, request, is_compiler, 0, 0, STATUS_ADDED, self.installed)
         for dep_id in task.dependencies:
-            all_deps[dep_id].add(package_id(pkg))
+            all_deps[dep_id].add(package_id(pkg.spec))
 
         self._push_task(task)
 
@@ -1276,7 +1276,7 @@ def _check_deps_status(self, request: BuildRequest) -> None:
         err = "Cannot proceed with {0}: {1}"
         for dep in request.traverse_dependencies():
             dep_pkg = dep.package
-            dep_id = package_id(dep_pkg)
+            dep_id = package_id(dep)
 
             # Check for failure since a prefix lock is not required
             if spack.store.STORE.failure_tracker.has_failed(dep):
@@ -1409,7 +1409,7 @@ def _cleanup_task(self, pkg: "spack.package_base.PackageBase") -> None:
         Args:
             pkg: the package being installed
         """
-        self._remove_task(package_id(pkg))
+        self._remove_task(package_id(pkg.spec))
 
         # Ensure we have a read lock to prevent others from uninstalling the
         # spec during our installation.
@@ -1423,7 +1423,7 @@ def _ensure_install_ready(self, pkg: "spack.package_base.PackageBase") -> None:
         Args:
             pkg: the package being locally installed
         """
-        pkg_id = package_id(pkg)
+        pkg_id = package_id(pkg.spec)
         pre = f"{pkg_id} cannot be installed locally:"
 
         # External packages cannot be installed locally.
@@ -1465,7 +1465,7 @@ def _ensure_locked(
             "write",
         ], f'"{lock_type}" is not a supported package management lock type'
 
-        pkg_id = package_id(pkg)
+        pkg_id = package_id(pkg.spec)
         ltype, lock = self.locks.get(pkg_id, (lock_type, None))
         if lock and ltype == lock_type:
             return ltype, lock
@@ -1601,7 +1601,7 @@ def _add_tasks(self, request: BuildRequest, all_deps):
             for dep in request.traverse_dependencies():
                 dep_pkg = dep.package
 
-                dep_id = package_id(dep_pkg)
+                dep_id = package_id(dep)
                 if dep_id not in self.build_tasks:
                     self._add_init_task(dep_pkg, request, False, all_deps)
 
@@ -1913,7 +1913,7 @@ def _flag_installed(
             dependent_ids: set of the package's dependent ids, or None if the dependent ids are
                 limited to those maintained in the package (dependency DAG)
         """
-        pkg_id = package_id(pkg)
+        pkg_id = package_id(pkg.spec)
 
         if pkg_id in self.installed:
             # Already determined the package has been installed
@@ -2309,7 +2309,7 @@ def __init__(self, pkg: "spack.package_base.PackageBase", install_args: dict):
 
         # info/debug information
         self.pre = _log_prefix(pkg.name)
-        self.pkg_id = package_id(pkg)
+        self.pkg_id = package_id(pkg.spec)
 
     def run(self) -> bool:
         """Main entry point from ``build_process`` to kick off install in child."""

lib/spack/spack/solver/asp.py

@@ -3371,7 +3371,7 @@ def _is_reusable(spec: spack.spec.Spec, packages, local: bool) -> bool:
         return False
 
     if not spec.external:
-        return True
+        return _has_runtime_dependencies(spec)
 
     # Cray external manifest externals are always reusable
     if local:
@@ -3396,6 +3396,19 @@ def _is_reusable(spec: spack.spec.Spec, packages, local: bool) -> bool:
     return False
 
 
+def _has_runtime_dependencies(spec: spack.spec.Spec) -> bool:
+    if not WITH_RUNTIME:
+        return True
+
+    if spec.compiler.name == "gcc" and not spec.dependencies("gcc-runtime"):
+        return False
+
+    if spec.compiler.name == "oneapi" and not spec.dependencies("intel-oneapi-runtime"):
+        return False
+
+    return True
+
+
 class Solver:
     """This is the main external interface class for solving.
 

lib/spack/spack/solver/concretize.lp

@@ -80,6 +80,7 @@ unification_set(SetID, VirtualNode)
 
 
 #defined multiple_unification_sets/1.
+#defined runtime/1.
 
 %----
 % Rules to break symmetry and speed-up searches
@@ -1494,18 +1495,20 @@ opt_criterion(40, "compiler mismatches that are not from CLI").
 #minimize{ 0@240: #true }.
 #minimize{ 0@40: #true }.
 #minimize{
-    1@40+Priority,PackageNode,DependencyNode
-    : compiler_mismatch(PackageNode, DependencyNode),
-      build_priority(PackageNode, Priority)
+    1@40+Priority,PackageNode,node(ID, Dependency)
+    : compiler_mismatch(PackageNode, node(ID, Dependency)),
+      build_priority(node(ID, Dependency), Priority),
+      not runtime(Dependency)
 }.
 
 opt_criterion(39, "compiler mismatches that are not from CLI").
 #minimize{ 0@239: #true }.
 #minimize{ 0@39: #true }.
 #minimize{
-    1@39+Priority,PackageNode,DependencyNode
-    : compiler_mismatch_required(PackageNode, DependencyNode),
-      build_priority(PackageNode, Priority)
+    1@39+Priority,PackageNode,node(ID, Dependency)
+    : compiler_mismatch_required(PackageNode, node(ID, Dependency)),
+      build_priority(node(ID, Dependency), Priority),
+      not runtime(Dependency)
 }.
 
 opt_criterion(30, "non-preferred OS's").
@@ -1522,9 +1525,10 @@ opt_criterion(25, "version badness").
 #minimize{ 0@225: #true }.
 #minimize{ 0@25: #true }.
 #minimize{
-    Weight@25+Priority,PackageNode
-    : version_weight(PackageNode, Weight),
-      build_priority(PackageNode, Priority)
+    Weight@25+Priority,node(X, Package)
+    : version_weight(node(X, Package), Weight),
+      build_priority(node(X, Package), Priority),
+      not runtime(Package)
 }.
 
 % Try to use all the default values of variants
@@ -1543,9 +1547,10 @@ opt_criterion(15, "non-preferred compilers").
 #minimize{ 0@215: #true }.
 #minimize{ 0@15: #true }.
 #minimize{
-    Weight@15+Priority,PackageNode
-    : node_compiler_weight(PackageNode, Weight),
-      build_priority(PackageNode, Priority)
+    Weight@15+Priority,node(X, Package)
+    : node_compiler_weight(node(X, Package), Weight),
+      build_priority(node(X, Package), Priority),
+      not runtime(Package)
 }.
 
 % Minimize the number of mismatches for targets in the DAG, try
@@ -1554,18 +1559,55 @@ opt_criterion(10, "target mismatches").
 #minimize{ 0@210: #true }.
 #minimize{ 0@10: #true }.
 #minimize{
-    1@10+Priority,PackageNode,Dependency
-    : node_target_mismatch(PackageNode, Dependency),
-      build_priority(PackageNode, Priority)
+    1@10+Priority,PackageNode,node(ID, Dependency)
+    : node_target_mismatch(PackageNode, node(ID, Dependency)),
+      build_priority(node(ID, Dependency), Priority),
+      not runtime(Dependency)
 }.
 
 opt_criterion(5, "non-preferred targets").
 #minimize{ 0@205: #true }.
 #minimize{ 0@5: #true }.
 #minimize{
-    Weight@5+Priority,PackageNode
-    : node_target_weight(PackageNode, Weight),
-      build_priority(PackageNode, Priority)
+    Weight@5+Priority,node(X, Package)
+    : node_target_weight(node(X, Package), Weight),
+      build_priority(node(X, Package), Priority),
+      not runtime(Package)
+}.
+
+
+% Minimize the number of compiler mismatches for runtimes
+opt_criterion(4, "compiler mismatches (runtimes)").
+#minimize{ 0@204: #true }.
+#minimize{ 0@4: #true }.
+#minimize{
+    1@4,PackageNode,node(ID, Dependency)
+    : compiler_mismatch(PackageNode, node(ID, Dependency)), runtime(Dependency)
+}.
+#minimize{
+    1@4,PackageNode,node(ID, Dependency)
+    : compiler_mismatch_required(PackageNode, node(ID, Dependency)), runtime(Dependency)
+}.
+
+
+% Choose more recent versions for runtimes
+opt_criterion(3, "version badness (runtimes)").
+#minimize{ 0@203: #true }.
+#minimize{ 0@3: #true }.
+#minimize{
+    Weight@3,node(X, Package)
+    : version_weight(node(X, Package), Weight),
+      runtime(Package)
+}.
+
+% Choose best target for runtimes
+opt_criterion(2, "non-preferred targets (runtimes)").
+#minimize{ 0@202: #true }.
+#minimize{ 0@2: #true }.
+#minimize{
+    Weight@2,node(X, Package)
+    : node_target_weight(node(X, Package), Weight),
+      runtime(Package)
 }.
 
 % Choose more recent versions for nodes

lib/spack/spack/target.py

@@ -142,7 +142,7 @@ def optimization_flags(self, compiler):
         # custom spec.
         compiler_version = compiler.version
         version_number, suffix = archspec.cpu.version_components(compiler.version)
-        if not version_number or suffix not in ("", "apple"):
+        if not version_number or suffix:
             # Try to deduce the underlying version of the compiler, regardless
             # of its name in compilers.yaml. Depending on where this function
             # is called we might get either a CompilerSpec or a fully fledged

lib/spack/spack/test/cmd/compiler.py

@@ -112,10 +112,10 @@ def test_compiler_find_no_apple_gcc(no_compilers_yaml, working_env, mock_executa
 @pytest.mark.regression("37996")
 def test_compiler_remove(mutable_config, mock_packages):
     """Tests that we can remove a compiler from configuration."""
-    assert spack.spec.CompilerSpec("gcc@=4.8.0") in spack.compilers.all_compiler_specs()
-    args = spack.util.pattern.Bunch(all=True, compiler_spec="gcc@4.8.0", add_paths=[], scope=None)
+    assert spack.spec.CompilerSpec("gcc@=9.4.0") in spack.compilers.all_compiler_specs()
+    args = spack.util.pattern.Bunch(all=True, compiler_spec="gcc@9.4.0", add_paths=[], scope=None)
     spack.cmd.compiler.compiler_remove(args)
-    assert spack.spec.CompilerSpec("gcc@=4.8.0") not in spack.compilers.all_compiler_specs()
+    assert spack.spec.CompilerSpec("gcc@=9.4.0") not in spack.compilers.all_compiler_specs()
 
 
 @pytest.mark.regression("37996")
@@ -124,10 +124,10 @@ def test_removing_compilers_from_multiple_scopes(mutable_config, mock_packages):
     site_config = spack.config.get("compilers", scope="site")
     spack.config.set("compilers", site_config, scope="user")
 
-    assert spack.spec.CompilerSpec("gcc@=4.8.0") in spack.compilers.all_compiler_specs()
-    args = spack.util.pattern.Bunch(all=True, compiler_spec="gcc@4.8.0", add_paths=[], scope=None)
+    assert spack.spec.CompilerSpec("gcc@=9.4.0") in spack.compilers.all_compiler_specs()
+    args = spack.util.pattern.Bunch(all=True, compiler_spec="gcc@9.4.0", add_paths=[], scope=None)
     spack.cmd.compiler.compiler_remove(args)
-    assert spack.spec.CompilerSpec("gcc@=4.8.0") not in spack.compilers.all_compiler_specs()
+    assert spack.spec.CompilerSpec("gcc@=9.4.0") not in spack.compilers.all_compiler_specs()
 
 
 @pytest.mark.not_on_windows("Cannot execute bash script on Windows")

lib/spack/spack/test/cmd/spec.py

@@ -31,7 +31,7 @@ def test_spec():
 
 
 @pytest.mark.only_clingo("Known failure of the original concretizer")
-def test_spec_concretizer_args(mutable_config, mutable_database):
+def test_spec_concretizer_args(mutable_config, mutable_database, do_not_check_runtimes_on_reuse):
     """End-to-end test of CLI concretizer prefs.
 
     It's here to make sure that everything works from CLI

lib/spack/spack/test/concretize.py

@@ -254,7 +254,7 @@ def gcc11_with_flags(compiler_factory):
 # This must use the mutable_config fixture because the test
 # adjusting_default_target_based_on_compiler uses the current_host fixture,
 # which changes the config.
-@pytest.mark.usefixtures("mutable_config", "mock_packages")
+@pytest.mark.usefixtures("mutable_config", "mock_packages", "do_not_check_runtimes_on_reuse")
 class TestConcretize:
     def test_concretize(self, spec):
         check_concretize(spec)
@@ -614,7 +614,7 @@ def test_my_dep_depends_on_provider_of_my_virtual_dep(self):
         spec.normalize()
         spec.concretize()
 
-    @pytest.mark.parametrize("compiler_str", ["clang", "gcc", "gcc@10.2.1", "clang@:12.0.0"])
+    @pytest.mark.parametrize("compiler_str", ["clang", "gcc", "gcc@10.2.1", "clang@:15.0.0"])
     def test_compiler_inheritance(self, compiler_str):
         spec_str = "mpileaks %{0}".format(compiler_str)
         spec = Spec(spec_str).concretized()
@@ -877,7 +877,7 @@ def test_concretize_anonymous_dep(self, spec_str):
             # Unconstrained versions select default compiler (gcc@4.5.0)
             ("bowtie@1.4.0", "%gcc@10.2.1"),
             # Version with conflicts and no valid gcc select another compiler
-            ("bowtie@1.3.0", "%clang@12.0.0"),
+            ("bowtie@1.3.0", "%clang@15.0.0"),
             # If a higher gcc is available still prefer that
             ("bowtie@1.2.2 os=redhat6", "%gcc@11.1.0"),
         ],
@@ -1439,7 +1439,7 @@ def test_os_selection_when_multiple_choices_are_possible(
     @pytest.mark.regression("22718")
     @pytest.mark.parametrize(
         "spec_str,expected_compiler",
-        [("mpileaks", "%gcc@10.2.1"), ("mpileaks ^mpich%clang@12.0.0", "%clang@12.0.0")],
+        [("mpileaks", "%gcc@10.2.1"), ("mpileaks ^mpich%clang@15.0.0", "%clang@15.0.0")],
     )
     def test_compiler_is_unique(self, spec_str, expected_compiler):
         s = Spec(spec_str).concretized()
@@ -1727,7 +1727,7 @@ def test_reuse_with_unknown_package_dont_raise(self, tmpdir, temporary_store, mo
         [
             (["libelf", "libelf@0.8.10"], 1),
             (["libdwarf%gcc", "libelf%clang"], 2),
-            (["libdwarf%gcc", "libdwarf%clang"], 4),
+            (["libdwarf%gcc", "libdwarf%clang"], 3),
             (["libdwarf^libelf@0.8.12", "libdwarf^libelf@0.8.13"], 4),
             (["hdf5", "zmpi"], 3),
             (["hdf5", "mpich"], 2),

lib/spack/spack/test/concretize_compiler_runtimes.py

@@ -7,6 +7,8 @@
 
 import pytest
 
+import archspec.cpu
+
 import spack.paths
 import spack.repo
 import spack.solver.asp
@@ -24,9 +26,7 @@ def _concretize_with_reuse(*, root_str, reused_str):
     reused_spec = spack.spec.Spec(reused_str).concretized()
     setup = spack.solver.asp.SpackSolverSetup(tests=False)
     driver = spack.solver.asp.PyclingoDriver()
-    result, _, _ = driver.solve(
-        setup, [spack.spec.Spec(f"{root_str} ^{reused_str}")], reuse=[reused_spec]
-    )
+    result, _, _ = driver.solve(setup, [spack.spec.Spec(f"{root_str}")], reuse=[reused_spec])
     root = result.specs[0]
     return root, reused_spec
 
@@ -47,7 +47,7 @@ def enable_runtimes():
 
 
 def test_correct_gcc_runtime_is_injected_as_dependency(runtime_repo):
-    s = spack.spec.Spec("a%gcc@10.2.1 ^b%gcc@4.8.0").concretized()
+    s = spack.spec.Spec("a%gcc@10.2.1 ^b%gcc@9.4.0").concretized()
     a, b = s["a"], s["b"]
 
     # Both a and b should depend on the same gcc-runtime directly
@@ -78,9 +78,28 @@ def test_external_nodes_do_not_have_runtimes(runtime_repo, mutable_config, tmp_p
     "root_str,reused_str,expected,nruntime",
     [
         # The reused runtime is older than we need, thus we'll add a more recent one for a
-        ("a%gcc@10.2.1", "b%gcc@4.8.0", {"a": "gcc-runtime@10.2.1", "b": "gcc-runtime@4.8.0"}, 2),
+        ("a%gcc@10.2.1", "b%gcc@9.4.0", {"a": "gcc-runtime@10.2.1", "b": "gcc-runtime@9.4.0"}, 2),
         # The root is compiled with an older compiler, thus we'll reuse the runtime from b
-        ("a%gcc@4.8.0", "b%gcc@10.2.1", {"a": "gcc-runtime@10.2.1", "b": "gcc-runtime@10.2.1"}, 1),
+        ("a%gcc@9.4.0", "b%gcc@10.2.1", {"a": "gcc-runtime@10.2.1", "b": "gcc-runtime@10.2.1"}, 1),
+        # Same as before, but tests that we can reuse from a more generic target
+        pytest.param(
+            "a%gcc@9.4.0",
+            "b%gcc@10.2.1 target=x86_64",
+            {"a": "gcc-runtime@10.2.1 target=x86_64", "b": "gcc-runtime@10.2.1 target=x86_64"},
+            1,
+            marks=pytest.mark.skipif(
+                str(archspec.cpu.host().family) != "x86_64", reason="test data is x86_64 specific"
+            ),
+        ),
+        pytest.param(
+            "a%gcc@10.2.1",
+            "b%gcc@9.4.0 target=x86_64",
+            {"a": "gcc-runtime@10.2.1 target=x86_64", "b": "gcc-runtime@9.4.0 target=x86_64"},
+            2,
+            marks=pytest.mark.skipif(
+                str(archspec.cpu.host().family) != "x86_64", reason="test data is x86_64 specific"
+            ),
+        ),
     ],
 )
 def test_reusing_specs_with_gcc_runtime(root_str, reused_str, expected, nruntime, runtime_repo):
@@ -104,8 +123,8 @@ def test_reusing_specs_with_gcc_runtime(root_str, reused_str, expected, nruntime
     [
         # Ensure that, whether we have multiple runtimes in the DAG or not,
         # we always link only the latest version
-        ("a%gcc@10.2.1", "b%gcc@4.8.0", ["gcc-runtime@10.2.1"], ["gcc-runtime@4.8.0"]),
-        ("a%gcc@4.8.0", "b%gcc@10.2.1", ["gcc-runtime@10.2.1"], ["gcc-runtime@4.8.0"]),
+        ("a%gcc@10.2.1", "b%gcc@9.4.0", ["gcc-runtime@10.2.1"], ["gcc-runtime@9.4.0"]),
+        ("a%gcc@9.4.0", "b%gcc@10.2.1", ["gcc-runtime@10.2.1"], ["gcc-runtime@9.4.0"]),
     ],
 )
 def test_views_can_handle_duplicate_runtime_nodes(

lib/spack/spack/test/concretize_preferences.py

@@ -105,7 +105,7 @@ def test_preferred_variants_from_wildcard(self):
 
     @pytest.mark.parametrize(
         "compiler_str,spec_str",
-        [("gcc@=4.8.0", "mpileaks"), ("clang@=12.0.0", "mpileaks"), ("gcc@=4.8.0", "openmpi")],
+        [("gcc@=9.4.0", "mpileaks"), ("clang@=15.0.0", "mpileaks"), ("gcc@=9.4.0", "openmpi")],
     )
     def test_preferred_compilers(self, compiler_str, spec_str):
         """Test preferred compilers are applied correctly"""

lib/spack/spack/test/conftest.py

@@ -2013,3 +2013,12 @@ def _factory(*, spec, operating_system):
 def host_architecture_str():
     """Returns the broad architecture family (x86_64, aarch64, etc.)"""
     return str(archspec.cpu.host().family)
+
+
+def _true(x):
+    return True
+
+
+@pytest.fixture()
+def do_not_check_runtimes_on_reuse(monkeypatch):
+    monkeypatch.setattr(spack.solver.asp, "_has_runtime_dependencies", _true)

lib/spack/spack/test/data/config/compilers.yaml

@@ -1,6 +1,6 @@
 compilers:
 - compiler:
-    spec: gcc@=4.8.0
+    spec: gcc@=9.4.0
     operating_system: {linux_os.name}{linux_os.version}
     paths:
       cc: /path/to/gcc
@@ -10,7 +10,7 @@ compilers:
     modules: []
     target: {target}
 - compiler:
-    spec: gcc@=4.8.0
+    spec: gcc@=9.4.0
     operating_system: redhat6
     paths:
       cc: /path/to/gcc
@@ -20,7 +20,7 @@ compilers:
     modules: []
     target: {target}
 - compiler:
-    spec: clang@=12.0.0
+    spec: clang@=15.0.0
     operating_system: {linux_os.name}{linux_os.version}
     paths:
       cc: /path/to/clang

lib/spack/spack/test/data/config/packages.yaml

@@ -16,7 +16,7 @@ packages:
   externalvirtual:
     buildable: False
     externals:
-    - spec: externalvirtual@2.0%clang@12.0.0
+    - spec: externalvirtual@2.0%clang@15.0.0
       prefix: /path/to/external_virtual_clang
     - spec: externalvirtual@1.0%gcc@10.2.1
       prefix: /path/to/external_virtual_gcc

lib/spack/spack/test/data/modules/lmod/complex_hierarchy.yaml

@@ -4,7 +4,7 @@ lmod:
   hash_length: 0
 
   core_compilers:
-    - 'clang@12.0.0'
+    - 'clang@15.0.0'
 
   core_specs:
     - 'mpich@3.0.1'

lib/spack/spack/test/data/modules/lmod/core_compilers.yaml

@@ -2,4 +2,4 @@ enable:
   - lmod
 lmod:
   core_compilers:
-    - 'clang@12.0.0'
+    - 'clang@15.0.0'

lib/spack/spack/test/data/modules/lmod/core_compilers_at_equal.yaml

@@ -2,4 +2,4 @@ enable:
   - lmod
 lmod:
   core_compilers:
-    - 'clang@=12.0.0'
+    - 'clang@=15.0.0'

lib/spack/spack/test/installer.py

@@ -136,7 +136,7 @@ def test_get_dependent_ids(install_mockery, mock_packages):
     spec.concretize()
     assert spec.concrete
 
-    pkg_id = inst.package_id(spec.package)
+    pkg_id = inst.package_id(spec)
 
     # Grab the sole dependency of 'a', which is 'b'
     dep = spec.dependencies()[0]
@@ -385,7 +385,7 @@ def test_ensure_locked_have(install_mockery, tmpdir, capsys):
     const_arg = installer_args(["trivial-install-test-package"], {})
     installer = create_installer(const_arg)
     spec = installer.build_requests[0].pkg.spec
-    pkg_id = inst.package_id(spec.package)
+    pkg_id = inst.package_id(spec)
 
     with tmpdir.as_cwd():
         # Test "downgrade" of a read lock (to a read lock)
@@ -456,17 +456,15 @@ def _pl(db, spec, timeout):
 
 def test_package_id_err(install_mockery):
     s = spack.spec.Spec("trivial-install-test-package")
-    pkg_cls = spack.repo.PATH.get_pkg_class(s.name)
     with pytest.raises(ValueError, match="spec is not concretized"):
-        inst.package_id(pkg_cls(s))
+        inst.package_id(s)
 
 
 def test_package_id_ok(install_mockery):
     spec = spack.spec.Spec("trivial-install-test-package")
     spec.concretize()
     assert spec.concrete
-    pkg = spec.package
-    assert pkg.name in inst.package_id(pkg)
+    assert spec.name in inst.package_id(spec)
 
 
 def test_fake_install(install_mockery):
@@ -726,7 +724,7 @@ def test_check_deps_status_external(install_mockery, monkeypatch):
     installer._check_deps_status(request)
 
     for dep in request.spec.traverse(root=False):
-        assert inst.package_id(dep.package) in installer.installed
+        assert inst.package_id(dep) in installer.installed
 
 
 def test_check_deps_status_upstream(install_mockery, monkeypatch):
@@ -739,7 +737,7 @@ def test_check_deps_status_upstream(install_mockery, monkeypatch):
     installer._check_deps_status(request)
 
     for dep in request.spec.traverse(root=False):
-        assert inst.package_id(dep.package) in installer.installed
+        assert inst.package_id(dep) in installer.installed
 
 
 def test_add_bootstrap_compilers(install_mockery, monkeypatch):
@@ -1111,7 +1109,7 @@ def test_install_fail_fast_on_detect(install_mockery, monkeypatch, capsys):
     const_arg = installer_args(["b"], {"fail_fast": False})
     const_arg.extend(installer_args(["c"], {"fail_fast": True}))
     installer = create_installer(const_arg)
-    pkg_ids = [inst.package_id(spec.package) for spec, _ in const_arg]
+    pkg_ids = [inst.package_id(spec) for spec, _ in const_arg]
 
     # Make sure all packages are identified as failed
     #
@@ -1186,7 +1184,7 @@ def test_install_lock_installed_requeue(install_mockery, monkeypatch, capfd):
     const_arg = installer_args(["b"], {})
     b, _ = const_arg[0]
     installer = create_installer(const_arg)
-    b_pkg_id = inst.package_id(b.package)
+    b_pkg_id = inst.package_id(b)
 
     def _prep(installer, task):
         installer.installed.add(b_pkg_id)
@@ -1196,7 +1194,7 @@ def _prep(installer, task):
         monkeypatch.setattr(inst.PackageInstaller, "_ensure_locked", _not_locked)
 
     def _requeued(installer, task, install_status):
-        tty.msg("requeued {0}".format(inst.package_id(task.pkg)))
+        tty.msg("requeued {0}".format(inst.package_id(task.pkg.spec)))
 
     # Flag the package as installed
     monkeypatch.setattr(inst.PackageInstaller, "_prepare_for_install", _prep)
@@ -1262,7 +1260,7 @@ def test_install_skip_patch(install_mockery, mock_fetch):
     installer.install()
 
     spec, install_args = const_arg[0]
-    assert inst.package_id(spec.package) in installer.installed
+    assert inst.package_id(spec) in installer.installed
 
 
 def test_install_implicit(install_mockery, mock_fetch):

lib/spack/spack/test/modules/lmod.py

@@ -29,7 +29,7 @@
 ]
 
 
-@pytest.fixture(params=["clang@=12.0.0", "gcc@=10.2.1"])
+@pytest.fixture(params=["clang@=15.0.0", "gcc@=10.2.1"])
 def compiler(request):
     return request.param
 
@@ -59,7 +59,7 @@ def test_layout_for_specs_compiled_with_core_compilers(
         we can use both ``compiler@version`` and ``compiler@=version`` to specify a core compiler.
         """
         module_configuration(modules_config)
-        module, spec = factory("libelf%clang@12.0.0")
+        module, spec = factory("libelf%clang@15.0.0")
         assert "Core" in module.layout.available_path_parts
 
     def test_file_layout(self, compiler, provider, factory, module_configuration):
@@ -78,7 +78,7 @@ def test_file_layout(self, compiler, provider, factory, module_configuration):
         # is transformed to r"Core" if the compiler is listed among core
         # compilers
         # Check that specs listed as core_specs are transformed to "Core"
-        if compiler == "clang@=12.0.0" or spec_string == "mpich@3.0.1":
+        if compiler == "clang@=15.0.0" or spec_string == "mpich@3.0.1":
             assert "Core" in layout.available_path_parts
         else:
             assert compiler.replace("@=", "/") in layout.available_path_parts

share/spack/gitlab/cloud_pipelines/configs/ci.yaml

@@ -27,12 +27,12 @@ ci:
       - - spack config blame mirrors
         - spack --color=always --backtrace ci rebuild --tests > >(tee ${SPACK_ARTIFACTS_ROOT}/user_data/pipeline_out.txt) 2> >(tee ${SPACK_ARTIFACTS_ROOT}/user_data/pipeline_err.txt >&2)
       after_script:
-      - - ./bin/spack python ${CI_PROJECT_DIR}/share/spack/gitlab/cloud_pipelines/scripts/common/aggregate_package_logs.spack.py
-          --prefix /home/software/spack:${CI_PROJECT_DIR}/opt/spack
-          --log install_times.json
-          ${SPACK_ARTIFACTS_ROOT}/user_data/install_times.json
       - - cat /proc/loadavg || true
         - cat /proc/meminfo | grep 'MemTotal\|MemFree' || true
+      - - time python ${CI_PROJECT_DIR}/share/spack/gitlab/cloud_pipelines/scripts/common/aggregate_package_logs.spack.py
+          --prefix /home/software/spack:${CI_PROJECT_DIR}/opt/spack
+          --log install_times.json
+          ${SPACK_ARTIFACTS_ROOT}/user_data/install_times.json || true
       variables:
         CI_JOB_SIZE: "default"
         CI_GPG_KEY_ROOT: /mnt/key

share/spack/gitlab/cloud_pipelines/scripts/common/aggregate_package_logs.spack.py

@@ -37,10 +37,14 @@ def find_logs(prefix, filename):
 
     # Look in the list of prefixes for logs
     for prefix in prefixes:
-        logs = find_logs(prefix, args.log)
+        print(f"Walking {prefix}")
+        logs = [log for log in find_logs(prefix, args.log)]
+        print(f"  * found {len(logs)} logs")
         for log in logs:
+            print(f"  * appending data for {log}")
             with open(log) as fd:
                 data.append(json.load(fd))
 
+    print(f"Writing {args.output_file}")
     with open(args.output_file, "w") as fd:
         json.dump(data, fd)

share/spack/gitlab/cloud_pipelines/stacks/e4s-neoverse_v1/spack.yaml

@@ -240,7 +240,6 @@ spack:
   - umpire ~shared +cuda cuda_arch=75
   # INCLUDED IN ECP DAV CUDA
   - adios2 +cuda cuda_arch=75
-  - paraview +cuda cuda_arch=75
   - vtk-m +cuda cuda_arch=75
   - zfp +cuda cuda_arch=75
   # --
@@ -248,6 +247,7 @@ spack:
   # - axom +cuda cuda_arch=75       # axom: https://github.com/spack/spack/issues/29520
   # - cusz +cuda cuda_arch=75       # cusz: https://github.com/spack/spack/issues/38787
   # - dealii +cuda cuda_arch=75     # slepc: make[1]: *** internal error: invalid --jobserver-auth string 'fifo:/tmp/GMfifo1313'.
+  # - paraview +cuda cuda_arch=75   # Error building some cuda componets in paraview
   # - ecp-data-vis-sdk +adios2 +hdf5 +vtkm +zfp +paraview +cuda cuda_arch=75  # embree: https://github.com/spack/spack/issues/39534
   # - lammps +cuda cuda_arch=75     # lammps: needs NVIDIA driver
   # - lbann +cuda cuda_arch=75      # lbann: https://github.com/spack/spack/issues/38788
@@ -287,7 +287,6 @@ spack:
   - umpire ~shared +cuda cuda_arch=80
   # INCLUDED IN ECP DAV CUDA
   - adios2 +cuda cuda_arch=80
-  - paraview +cuda cuda_arch=80
   - vtk-m +cuda cuda_arch=80
   - zfp +cuda cuda_arch=80
   # --
@@ -295,6 +294,7 @@ spack:
   # - axom +cuda cuda_arch=80       # axom: https://github.com/spack/spack/issues/29520
   # - cusz +cuda cuda_arch=80       # cusz: https://github.com/spack/spack/issues/38787
   # - dealii +cuda cuda_arch=80     # slepc: make[1]: *** internal error: invalid --jobserver-auth string 'fifo:/tmp/GMfifo1313'.
+  # - paraview +cuda cuda_arch=80   # Error building some cuda componets in paraview
   # - ecp-data-vis-sdk +adios2 +hdf5 +vtkm +zfp +paraview +cuda cuda_arch=80 # embree: https://github.com/spack/spack/issues/39534
   # - lammps +cuda cuda_arch=80     # lammps: needs NVIDIA driver
   # - lbann +cuda cuda_arch=80      # lbann: https://github.com/spack/spack/issues/38788

share/spack/gitlab/cloud_pipelines/stacks/e4s/spack.yaml

@@ -103,7 +103,7 @@ spack:
   - kokkos +openmp
   - kokkos-kernels +openmp
   - laghos
-  - lammps
+  - lammps +amoeba +asphere +bocs +body +bpm +brownian +cg-dna +cg-spica +class2 +colloid +colvars +compress +coreshell +dielectric +diffraction +dipole +dpd-basic +dpd-meso +dpd-react +dpd-smooth +drude +eff +electrode +extra-compute +extra-dump +extra-fix +extra-molecule +extra-pair +fep +granular +interlayer +kspace +lepton +machdyn +manybody +mc +meam +mesont +misc +ml-iap +ml-pod +ml-snap +mofff +molecule +openmp-package +opt +orient +peri +phonon +plugin +poems +qeq +reaction +reaxff +replica +rigid +shock +sph +spin +srd +tally +uef +voronoi +yaff
   - lbann
   - legion
   - libnrm
@@ -119,6 +119,7 @@ spack:
   - mpifileutils ~xattr
   - nccmp
   - nco
+  - nekbone +mpi
   - netlib-scalapack
   - nrm
   - nvhpc
@@ -186,6 +187,7 @@ spack:
   # --
   # - geopm                           # geopm: https://github.com/spack/spack/issues/38795
   # - glvis                           # glvis: https://github.com/spack/spack/issues/42839
+  # - nek5000 +mpi +visit             # nek5000:  Error: AttributeError: 'str' object has no attribute 'propagate': 'VISIT_INSTALL="' + spec["visit"].prefix.bin + '"',
 
   # PYTHON PACKAGES
   - opencv +python3
@@ -207,6 +209,7 @@ spack:
   - py-seaborn
   - py-tensorflow
   - py-torch
+  - py-deephyper
 
   # # CUDA NOARCH
   # - bricks +cuda

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

@@ -331,10 +331,7 @@ class Acts(CMakePackage, CudaPackage):
     depends_on("python@3.8:", when="+python @19.11:19")
     depends_on("python@3.8:", when="+python @21:")
     depends_on("py-onnxruntime@:1.12", when="+onnx @:23.2")
-    # FIXME py-onnxruntime@1.12: required but not yet available
-    # Ref: https://github.com/spack/spack/pull/37064
-    # depends_on("py-onnxruntime@1.12:", when="+onnx @23.3:")
-    conflicts("+onnx", when="@23.3:", msg="py-onnxruntime@1.12: required but not yet available")
+    depends_on("py-onnxruntime@1.12:", when="+onnx @23.3:")
     depends_on("py-pybind11 @2.6.2:", when="+python @18:")
     depends_on("py-pytest", when="+python +unit_tests")
 

var/spack/repos/builtin/packages/adios2/package.py

@@ -26,13 +26,11 @@ class Adios2(CMakePackage, CudaPackage, ROCmPackage):
 
     version("master", branch="master")
     version(
-        "2.10.0-rc1", sha256="8b72142bd5aabfb80c7963f524df11b8721c09ef20caea6df5fb00c31a7747c0"
-    )
-    version(
-        "2.9.2",
-        sha256="78309297c82a95ee38ed3224c98b93d330128c753a43893f63bbe969320e4979",
+        "2.10.0",
+        sha256="e5984de488bda546553dd2f46f047e539333891e63b9fe73944782ba6c2d95e4",
         preferred=True,
     )
+    version("2.9.2", sha256="78309297c82a95ee38ed3224c98b93d330128c753a43893f63bbe969320e4979")
     version("2.9.1", sha256="ddfa32c14494250ee8a48ef1c97a1bf6442c15484bbbd4669228a0f90242f4f9")
     version("2.9.0", sha256="69f98ef58c818bb5410133e1891ac192653b0ec96eb9468590140f2552b6e5d1")
     version("2.8.3", sha256="4906ab1899721c41dd918dddb039ba2848a1fb0cf84f3a563a1179b9d6ee0d9f")
@@ -225,7 +223,7 @@ class Adios2(CMakePackage, CudaPackage, ROCmPackage):
 
     # cmake: find threads package first
     # https://github.com/ornladios/ADIOS2/pull/3893
-    patch("2.9.2-cmake-find-threads-package-first.patch", when="@2.9.2:")
+    patch("2.9.2-cmake-find-threads-package-first.patch", when="@2.9")
 
     @when("%fj")
     def patch(self):

var/spack/repos/builtin/packages/amr-wind/package.py

@@ -20,6 +20,7 @@ class AmrWind(CMakePackage, CudaPackage, ROCmPackage):
     license("BSD-3-Clause")
 
     version("main", branch="main", submodules=True)
+    version("0.9.0", tag="v0.9.0", submodules=True)
 
     variant("hypre", default=True, description="Enable Hypre integration")
     variant("ascent", default=False, description="Enable Ascent integration")
@@ -31,9 +32,22 @@ class AmrWind(CMakePackage, CudaPackage, ROCmPackage):
     variant("shared", default=True, description="Build shared libraries")
     variant("tests", default=True, description="Activate regression tests")
     variant("tiny_profile", default=False, description="Activate tiny profile")
+    variant("hdf5", default=False, description="Enable HDF5 plots with ZFP compression")
+    variant("umpire", default=False, description="Enable Umpire")
+    variant("sycl", default=False, description="Enable SYCL backend")
+    variant("gpu-aware-mpi", default=False, description="gpu-aware-mpi")
 
     depends_on("hypre~int64@2.20.0:", when="+hypre")
     depends_on("hypre+mpi", when="+hypre+mpi")
+    depends_on("hdf5~mpi", when="+hdf5~mpi")
+    depends_on("hdf5+mpi", when="+hdf5+mpi")
+    depends_on("h5z-zfp", when="+hdf5")
+    depends_on("zfp", when="+hdf5")
+    depends_on("hypre+umpire", when="+umpire")
+    depends_on("hypre+sycl", when="+sycl")
+    depends_on("hypre+gpu-aware-mpi", when="+gpu-aware-mpi")
+    depends_on("hypre@2.29.0:", when="@0.9.0:+hypre")
+
     for arch in CudaPackage.cuda_arch_values:
         depends_on("hypre+cuda cuda_arch=%s" % arch, when="+cuda+hypre cuda_arch=%s" % arch)
     for arch in ROCmPackage.amdgpu_targets:
@@ -88,6 +102,13 @@ def cmake_args(self):
         if "+mpi" in self.spec:
             args.append(define("MPI_HOME", self.spec["mpi"].prefix))
 
+        if "+hdf5" in self.spec:
+            cmake_options.append(self.define("AMR_WIND_ENABLE_HDF5", True))
+            cmake_options.append(self.define("AMR_WIND_ENABLE_HDF5_ZFP", True))
+            # Help AMReX understand if HDF5 is parallel or not.
+            # Building HDF5 with CMake as Spack does, causes this inspection to break.
+            cmake_options.append(self.define("HDF5_IS_PARALLEL", spec.satisfies("+mpi")))
+
         if "+cuda" in self.spec:
             amrex_arch = [
                 "{0:.1f}".format(float(i) / 10.0) for i in self.spec.variants["cuda_arch"].value
@@ -100,4 +121,16 @@ def cmake_args(self):
             targets = self.spec.variants["amdgpu_target"].value
             args.append("-DAMReX_AMD_ARCH=" + ";".join(str(x) for x in targets))
 
+        if "+sycl" in self.spec:
+            cmake_options.append(self.define("AMR_WIND_ENABLE_SYCL", True))
+            requires(
+                "%dpcpp",
+                "%oneapi",
+                policy="one_of",
+                msg=(
+                    "AMReX's SYCL GPU Backend requires DPC++ (dpcpp) "
+                    "or the oneAPI CXX (icpx) compiler."
+                ),
+            )
+
         return args

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

@@ -26,6 +26,7 @@ class Amrex(CMakePackage, CudaPackage, ROCmPackage):
     license("BSD-3-Clause")
 
     version("develop", branch="development")
+    version("24.04", sha256="77a91e75ad0106324a44ca514e1e8abc54f2fc2d453406441c871075726a8167")
     version("24.03", sha256="024876fe65838d1021fcbf8530b992bff8d9be1d3f08a1723c4e2e5f7c28b427")
     version("24.02", sha256="286cc3ca29daa69c8eafc1cd7a572662dec9eb78631ac3d33a1260868fdc6996")
     version("24.01", sha256="83dbd4dad6dc51fa4a80aad0347b15ee5a6d816cf4abcd87f7b0e2987d8131b7")

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

@@ -131,6 +131,8 @@ class Bazel(Package):
     # Bazel-4.0.0 does not compile with gcc-11
     # Newer versions of grpc and abseil dependencies are needed but are not in bazel-4.0.0
     conflicts("@4.0.0", when="%gcc@11:")
+    # https://github.com/bazelbuild/bazel/issues/18642
+    conflicts("@:6", when="%gcc@13:")
 
     executables = ["^bazel$"]
 

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

@@ -43,7 +43,7 @@ class Datatransferkit(CMakePackage):
     depends_on("trilinos+openmp", when="+openmp")
     depends_on("trilinos+stratimikos+belos", when="@master")
     depends_on("trilinos@13:13.4.1", when="@3.1-rc2:3.1-rc3")
-    depends_on("trilinos@14:", when="@3.1.0:")
+    depends_on("trilinos@14.2:", when="@3.1.0:")
 
     def cmake_args(self):
         spec = self.spec

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

@@ -6,37 +6,93 @@
 from spack.package import *
 
 
-class Exawind(CMakePackage):
+class Exawind(CMakePackage, CudaPackage, ROCmPackage):
     """Multi-application driver for Exawind project."""
 
     homepage = "https://github.com/Exawind/exawind-driver"
     git = "https://github.com/Exawind/exawind-driver.git"
 
-    maintainers("jrood-nrel", "psakievich")
+    maintainers("jrood-nrel")
 
     tags = ["ecp", "ecp-apps"]
 
+    # Testing is currently always enabled, but should be optional in the future
+    # to avoid cloning the mesh submodule
+    version("master", branch="main", submodules=True)
+    version("1.0.0", tag="v1.0.0", submodules=True)
     license("Apache-2.0")
 
-    version("master", branch="main")
+    variant("openfast", default=False, description="Enable OpenFAST integration")
+    variant("hypre", default=True, description="Enable hypre solver")
+    variant("stk_simd", default=False, description="Enable SIMD in STK")
+    variant("umpire", default=False, description="Enable Umpire")
+    variant("tiny_profile", default=False, description="Turn on AMR-wind with tiny profile")
+    variant("sycl", default=False, description="Enable SYCL backend for AMR-Wind")
+    variant("gpu-aware-mpi", default=False, description="gpu-aware-mpi")
 
-    depends_on("trilinos+stk")
-    depends_on("tioga+shared~nodegid")
-    depends_on("nalu-wind+hypre+openfast+tioga+wind-utils")
-    depends_on("amr-wind+hypre+mpi+netcdf+openfast")
-    depends_on("openfast+cxx+shared@2.6.0:")
+    conflicts("amr-wind+hypre", when="+sycl")
+
+    for arch in CudaPackage.cuda_arch_values:
+        depends_on("amr-wind+cuda cuda_arch=%s" % arch, when="+cuda cuda_arch=%s" % arch)
+        depends_on("nalu-wind+cuda cuda_arch=%s" % arch, when="+cuda cuda_arch=%s" % arch)
+
+    for arch in ROCmPackage.amdgpu_targets:
+        depends_on("amr-wind+rocm amdgpu_target=%s" % arch, when="+rocm amdgpu_target=%s" % arch)
+        depends_on("nalu-wind+rocm amdgpu_target=%s" % arch, when="+rocm amdgpu_target=%s" % arch)
+
+    depends_on("nalu-wind+tioga")
+    depends_on("amr-wind+netcdf+mpi")
+    depends_on("tioga~nodegid")
     depends_on("yaml-cpp@0.6:")
+    depends_on("nalu-wind+openfast", when="+openfast")
+    depends_on("amr-wind+hypre", when="+hypre~sycl")
+    depends_on("amr-wind~hypre", when="~hypre")
+    depends_on("nalu-wind+hypre", when="+hypre")
+    depends_on("nalu-wind~hypre", when="~hypre")
+    depends_on("amr-wind+sycl", when="+sycl")
+    depends_on("nalu-wind+umpire", when="+umpire")
+    depends_on("amr-wind+umpire", when="+umpire")
+    depends_on("amr-wind+tiny_profile", when="+tiny_profile")
+    depends_on("nalu-wind+gpu-aware-mpi", when="+gpu-aware-mpi")
+    depends_on("amr-wind+gpu-aware-mpi", when="+gpu-aware-mpi")
+    depends_on("nalu-wind@2.0.0:", when="@1.0.0:")
+    depends_on("amr-wind@0.9.0:", when="@1.0.0:")
+    depends_on("tioga@1.0.0:", when="@1.0.0:")
 
     def cmake_args(self):
         spec = self.spec
 
-        args = [
-            self.define("Trilinos_DIR", spec["trilinos"].prefix),
-            self.define("TIOGA_DIR", spec["tioga"].prefix),
-            self.define("Nalu-Wind_DIR", spec["nalu-wind"].prefix),
-            self.define("AMR-Wind_DIR", spec["amr-wind"].prefix),
-            self.define("OpenFAST_DIR", spec["openfast"].prefix),
-            self.define("YAML-CPP_DIR", spec["yaml-cpp"].prefix),
-        ]
+        args = [self.define("MPI_HOME", spec["mpi"].prefix)]
+
+        if "+umpire" in self.spec:
+            args.append(self.define_from_variant("EXAWIND_ENABLE_UMPIRE", "umpire"))
+            args.append(self.define("UMPIRE_DIR", self.spec["umpire"].prefix))
+
+        if spec.satisfies("+cuda"):
+            args.append(self.define("EXAWIND_ENABLE_CUDA", True))
+            args.append(self.define("CUDAToolkit_ROOT", self.spec["cuda"].prefix))
+            args.append(self.define("EXAWIND_CUDA_ARCH", self.spec.variants["cuda_arch"].value))
+
+        if spec.satisfies("+rocm"):
+            targets = self.spec.variants["amdgpu_target"].value
+            args.append(self.define("EXAWIND_ENABLE_ROCM", True))
+            args.append(self.define("CMAKE_CXX_COMPILER", self.spec["hip"].hipcc))
+            args.append(self.define("CMAKE_HIP_ARCHITECTURES", ";".join(str(x) for x in targets)))
+            args.append(self.define("AMDGPU_TARGETS", ";".join(str(x) for x in targets)))
+            args.append(self.define("GPU_TARGETS", ";".join(str(x) for x in targets)))
+
+        if spec.satisfies("^amr-wind+hdf5"):
+            args.append(self.define("H5Z_ZFP_USE_STATIC_LIBS", True))
+
+        if spec.satisfies("^amr-wind+ascent"):
+            args.append(self.define("CMAKE_EXE_LINKER_FLAGS", self.compiler.openmp_flag))
 
         return args
+
+    def setup_build_environment(self, env):
+        if "~stk_simd" in self.spec:
+            env.append_flags("CXXFLAGS", "-DUSE_STK_SIMD_NONE")
+        if "+rocm" in self.spec:
+            env.set("OMPI_CXX", self.spec["hip"].hipcc)
+            env.set("MPICH_CXX", self.spec["hip"].hipcc)
+            env.set("MPICXX_CXX", self.spec["hip"].hipcc)

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

@@ -72,6 +72,28 @@ class Fastjet(AutotoolsPackage):
     )
     variant("atlas", default=False, description="Patch to make random generator thread_local")
 
+    available_plugins = (
+        conditional("atlascone", when="@2.4.0:"),
+        conditional("cdfcones", when="@2.1.0:"),
+        conditional("cmsiterativecone", when="@2.4.0:"),
+        conditional("d0runicone", when="@3.0.0:"),
+        conditional("d0runiicone", when="@2.4.0:"),
+        conditional("eecambridge", when="@2.4.0:"),
+        conditional("gridjet", when="@3.0.0:"),
+        conditional("jade", when="@2.4.0:"),
+        conditional("nesteddefs", when="@2.4.0:"),
+        conditional("pxcone", when="@2.1.0:"),
+        conditional("siscone", when="@2.1.0:"),
+        conditional("trackjet", when="@2.4.0:"),
+    )
+    variant(
+        "plugins",
+        multi=True,
+        values=("all", "cxx") + available_plugins,
+        default="all",
+        description="List of plugins to enable, or 'cxx' or 'all'",
+    )
+
     patch("atlas.patch", when="@:3.3 +atlas", level=0)
     patch(
         "https://gitlab.cern.ch/sft/lcgcmake/-/raw/23c82f269b8e5df0190e20b7fbe06db16b24d667/externals/patches/fastjet-3.4.1.patch",
@@ -81,7 +103,21 @@ class Fastjet(AutotoolsPackage):
     )
 
     def configure_args(self):
-        extra_args = ["--enable-allplugins"]
+        extra_args = []
+        plugins = self.spec.variants["plugins"].value
+        if "all" in plugins:
+            extra_args += ["--enable-allplugins"]
+        elif "cxx" in plugins:
+            extra_args += ["--enable-allcxxplugins"]
+        else:
+            for plugin in self.available_plugins:
+                # conditional returns an iterable _ConditionalVariantValues
+                for v in plugin:
+                    # this version does not support this plugin
+                    if not self.spec.satisfies(v.when):
+                        continue
+                    enabled = v.value in plugins
+                    extra_args += [f"--{'enable' if enabled else 'disable'}-{v.value}"]
         extra_args += self.enable_or_disable("shared")
         extra_args += self.enable_or_disable("auto-ptr")
         if self.spec.variants["thread-safety"].value == "limited":

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

@@ -25,6 +25,7 @@ class FftwBase(AutotoolsPackage):
     )
     variant("openmp", default=False, description="Enable OpenMP support.")
     variant("mpi", default=True, description="Activate MPI support")
+    variant("shared", default=True, description="Build shared libraries")
 
     depends_on("mpi", when="+mpi")
     depends_on("llvm-openmp", when="%apple-clang +openmp")
@@ -104,7 +105,9 @@ def setup_build_environment(self, env):
 
     def configure(self, spec, prefix):
         # Base options
-        options = ["--prefix={0}".format(prefix), "--enable-shared", "--enable-threads"]
+        options = ["--prefix={0}".format(prefix), "--enable-threads"]
+        options.extend(self.enable_or_disable("shared"))
+
         if not self.compiler.f77 or not self.compiler.fc:
             options.append("--disable-fortran")
         if spec.satisfies("@:2"):

var/spack/repos/builtin/packages/g2/package.py

@@ -20,6 +20,7 @@ class G2(CMakePackage):
     maintainers("AlexanderRichert-NOAA", "Hang-Lei-NOAA", "edwardhartnett")
 
     version("develop", branch="develop")
+    version("3.4.9", sha256="6edc33091f6bd2acb191182831499c226a1c3992c3acc104d6363528b12dfbae")
     version("3.4.8", sha256="071a6f799c4c4fdfd5d0478152a0cbb9d668d12d71c78d5bda71845fc5580a7f")
     version("3.4.7", sha256="d6530611e3a515122f11ed4aeede7641f6f8932ef9ee0d4828786572767304dc")
     version("3.4.6", sha256="c4b03946365ce0bacf1e10e8412a5debd72d8671d1696aa4fb3f3adb119175fe")

var/spack/repos/builtin/packages/g2c/package.py

@@ -18,6 +18,7 @@ class G2c(CMakePackage):
     maintainers("AlexanderRichert-NOAA", "Hang-Lei-NOAA", "edwardhartnett")
 
     version("develop", branch="develop")
+    version("1.9.0", sha256="5554276e18bdcddf387a08c2dd23f9da310c6598905df6a2a244516c22ded9aa")
     version("1.8.0", sha256="4ce9f5a7cb0950699fe08ebc5a463ab4d09ef550c050391a319308a2494f971f")
     version("1.7.0", sha256="73afba9da382fed73ed8692d77fa037bb313280879cd4012a5e5697dccf55175")
     version("1.6.4", sha256="5129a772572a358296b05fbe846bd390c6a501254588c6a223623649aefacb9d")

var/spack/repos/builtin/packages/g2tmpl/package.py

@@ -18,6 +18,20 @@ class G2tmpl(CMakePackage):
     maintainers("edwardhartnett", "AlexanderRichert-NOAA", "Hang-Lei-NOAA")
 
     version("develop", branch="develop")
+    version("1.11.0", sha256="00fde3b37c6b4d1f0eaf60f230159298ffcb47349a076c3bd6afa20c7ed791a9")
     version("1.10.2", sha256="4063361369f3691f75288c801fa9d1a2414908b7d6c07bbf69d4165802e2a7fc")
     version("1.10.1", sha256="0be425e5128fabb89915a92261aa75c27a46a3e115e00c686fc311321e5d1e2a")
     version("1.10.0", sha256="dcc0e40b8952f91d518c59df7af64e099131c17d85d910075bfa474c8822649d")
+
+    variant("shared", default=False, description="Build shared library")
+
+    def cmake_args(self):
+        args = [
+            self.define_from_variant("BUILD_SHARED_LIBS", "shared"),
+            self.define("BUILD_TESTING", self.run_tests),
+        ]
+        return args
+
+    def check(self):
+        with working_dir(self.builder.build_directory):
+            make("test")

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

@@ -32,6 +32,7 @@ class Gdal(CMakePackage, AutotoolsPackage, PythonExtension):
 
     license("MIT")
 
+    version("3.8.5", sha256="e8b4df2a8a7d25272f867455c0c230459545972f81f0eff2ddbf6a6f60dcb1e4")
     version("3.8.4", sha256="0c53ced95d29474236487202709b49015854f8e02e35e44ed0f4f4e12a7966ce")
     version("3.8.3", sha256="ae2d160f65016e208eca34ff14490ec4511f1fa03fd386ac130449d15e82929d")
     version("3.8.2", sha256="dc2921ee1cf7a5c0498e94d15fb9ab9c9689c296363a1d021fc3293dd242b4db")

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

@@ -3,10 +3,11 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack.build_systems import autotools, cmake
 from spack.package import *
 
 
-class Gperftools(AutotoolsPackage):
+class Gperftools(AutotoolsPackage, CMakePackage):
     """Google's fast malloc/free implementation, especially for
     multi-threaded applications.  Contains tcmalloc, heap-checker,
     heap-profiler, and cpu-profiler.
@@ -19,6 +20,8 @@ class Gperftools(AutotoolsPackage):
 
     license("BSD-3-Clause")
 
+    build_system(conditional("cmake", when="@2.8.1:"), "autotools", default="cmake")
+
     version("2.15", sha256="c69fef855628c81ef56f12e3c58f2b7ce1f326c0a1fe783e5cae0b88cbbe9a80")
     version("2.14", sha256="6b561baf304b53d0a25311bd2e29bc993bed76b7c562380949e7cb5e3846b299")
     version("2.13", sha256="4882c5ece69f8691e51ffd6486df7d79dbf43b0c909d84d3c0883e30d27323e7")
@@ -43,21 +46,38 @@ class Gperftools(AutotoolsPackage):
     )
 
     depends_on("unwind", when="+libunwind")
+    depends_on("cmake@3.12:", type="build", when="build_system=cmake")
 
     # Linker error: src/base/dynamic_annotations.cc:46: undefined reference to
     # `TCMallocGetenvSafe'
     conflicts("target=ppc64:", when="@2.14")
     conflicts("target=ppc64le:", when="@2.14")
 
-    def configure_args(self):
-        args = []
-        args += self.enable_or_disable("sized-delete", variant="sized_delete")
-        args += self.enable_or_disable(
-            "dynamic-sized-delete-support", variant="dynamic_sized_delete_support"
-        )
-        args += self.enable_or_disable("debugalloc")
-        args += self.enable_or_disable("libunwind")
-        if self.spec.satisfies("+libunwind"):
-            args += ["LDFLAGS=-lunwind"]
+    # the autotools build system creates an explicit list of -L <system dir> flags that end up
+    # before the -L <spack dir> flags, which causes the system libunwind to be linked instead of
+    # the spack libunwind. This is a workaround to fix that.
+    conflicts("+libunwind", when="build_system=autotools")
 
-        return args
+
+class CMakeBuilder(cmake.CMakeBuilder):
+    def cmake_args(self):
+        return [
+            self.define_from_variant("gperftools_sized_delete", "sized_delete"),
+            self.define_from_variant(
+                "gperftools_dynamic_sized_delete_support", "dynamic_sized_delete_support"
+            ),
+            self.define_from_variant("GPERFTOOLS_BUILD_DEBUGALLOC", "debugalloc"),
+            self.define_from_variant("gperftools_enable_libunwind", "libunwind"),
+        ]
+
+
+class AutotooolsBuilder(autotools.AutotoolsBuilder):
+    def configure_args(self):
+        return [
+            *self.enable_or_disable("sized-delete", variant="sized_delete"),
+            *self.enable_or_disable(
+                "dynamic-sized-delete-support", variant="dynamic_sized_delete_support"
+            ),
+            *self.enable_or_disable("debugalloc"),
+            *self.enable_or_disable("libunwind"),
+        ]

var/spack/repos/builtin/packages/grib-util/package.py

@@ -22,6 +22,7 @@ class GribUtil(CMakePackage):
     version("1.2.3", sha256="b17b08e12360bb8ad01298e615f1b4198e304b0443b6db35fe990a817e648ad5")
 
     variant("openmp", default=False, description="Use OpenMP multithreading")
+    variant("tests", default=False, description="Enable this variant when installing with --test")
 
     depends_on("jasper")
     depends_on("libpng")
@@ -30,15 +31,19 @@ class GribUtil(CMakePackage):
     requires("^w3emc precision=4,d", when="^w3emc@2.10:")
     depends_on("w3nco", when="@:1.2.3")
     depends_on("g2")
+    depends_on("g2c@1.8: +utils", when="+tests")
     depends_on("bacio")
     depends_on("ip")
-    depends_on("ip@:3.3.3", when="@:1.2.4")
-    depends_on("sp")
+    requires("^ip precision=d", when="^ip@4.1:")
+    depends_on("ip@:3.3.3", when="@:1.2")
+    depends_on("sp", when="^ip@:4")
+    requires("^sp precision=d", when="^ip@:4 ^sp@2.4:")
 
     def cmake_args(self):
         args = [
             self.define_from_variant("OPENMP", "openmp"),
             self.define("BUILD_TESTING", self.run_tests),
+            self.define("G2C_COMPARE", self.run_tests),
         ]
         return args
 

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

@@ -72,6 +72,7 @@ class Hypre(AutotoolsPackage, CudaPackage, ROCmPackage):
     variant("int64", default=False, description="Use 64bit integers")
     variant("mixedint", default=False, description="Use 64bit integers while reducing memory use")
     variant("complex", default=False, description="Use complex values")
+    variant("gpu-aware-mpi", default=False, description="Use gpu-aware mpi")
     variant("mpi", default=True, description="Enable MPI support")
     variant("openmp", default=False, description="Enable OpenMP support")
     variant("debug", default=False, description="Build debug instead of optimized version")
@@ -300,6 +301,9 @@ def configure_args(self):
             configure_args.append("--with-magma-lib=%s" % spec["magma"].libs)
             configure_args.append("--with-magma")
 
+        if "+gpu-aware-mpi" in spec:
+            options.append("--enable-gpu-aware-mpi")
+
         configure_args.extend(self.enable_or_disable("fortran"))
 
         return configure_args

var/spack/repos/builtin/packages/intel-oneapi-inspector/package.py

@@ -24,6 +24,12 @@ class IntelOneapiInspector(IntelOneApiLibraryPackageWithSdk):
 
     homepage = "https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/inspector.html"
 
+    version(
+        "2024.1.0",
+        url="https://registrationcenter-download.intel.com/akdlm/IRC_NAS/891acaab-a5b4-4a3c-9f36-60dca629e410/l_inspector_oneapi_p_2024.1.0.158_offline.sh",
+        sha256="b4e4e2e395ad98ce025a6bf26950fc39c2f54c905a1a9c88cb129109a5dd0936",
+        expand=False,
+    )
     version(
         "2024.0.0",
         url="https://registrationcenter-download.intel.com/akdlm//IRC_NAS/44ae6846-719c-49bd-b196-b16ce5835a1e/l_inspector_oneapi_p_2024.0.0.49433_offline.sh",

var/spack/repos/builtin/packages/intel-oneapi-itac/package.py

@@ -27,6 +27,12 @@ class IntelOneapiItac(IntelOneApiPackage):
 
     maintainers("rscohn2")
 
+    version(
+        "2022.1.0",
+        url="https://registrationcenter-download.intel.com/akdlm/IRC_NAS/644eec67-83d9-4bdd-be0d-d90587ec72ed/l_itac_oneapi_p_2022.1.0.158_offline.sh",
+        sha256="2a1f4be6b349d1629006ee72087b361a5f3e714bddd1ef932045d0c03c0b20e8",
+        expand=False,
+    )
     version(
         "2022.0.0",
         url="https://registrationcenter-download.intel.com/akdlm//IRC_NAS/e83526f5-7e0f-4708-9e0d-47f1e65f29aa/l_itac_oneapi_p_2022.0.0.49690_offline.sh",

var/spack/repos/builtin/packages/intel-oneapi-runtime/package.py

@@ -15,6 +15,9 @@ class IntelOneapiRuntime(Package):
 
     homepage = "https://software.intel.com/content/www/us/en/develop/tools/oneapi.html"
     has_code = False
+    license("https://intel.ly/393CijO")
+
+    maintainers("rscohn2")
 
     tags = ["runtime"]
 

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

@@ -0,0 +1,36 @@
+# 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 *
+
+
+class Libfort(CMakePackage):
+    """libfort is a simple crossplatform library to create formatted text tables."""
+
+    homepage = "https://github.com/seleznevae/libfort"
+    url = "https://github.com/seleznevae/libfort/archive/refs/tags/v0.4.2.tar.gz"
+
+    license("MIT")
+
+    version("0.4.2", sha256="8f7b03f1aa526e50c9828f09490f3c844b73d5f9ca72493fe81931746f75e489")
+
+    variant("enable_astyle", default=False, description="Enable astyle")
+    variant("enable_wchar", default=True, description="Enable wchar support")
+    variant("enable_utf8", default=True, description="Enable utf8 support")
+    variant("enable_testing", default=True, description="Enables building tests and examples")
+    variant("shared", default=False, description="Build shared library")
+
+    depends_on("cmake@3.0.0:", type="build")
+
+    def cmake_args(self):
+        args = [
+            self.define_from_variant("FORT_ENABLE_ASTYLE", "enable_astyle"),
+            self.define_from_variant("FORT_ENABLE_WCHAR", "enable_wchar"),
+            self.define_from_variant("FORT_ENABLE_UTF8", "enable_utf8"),
+            self.define_from_variant("FORT_ENABLE_TESTING", "enable_testing"),
+            self.define_from_variant("BUILD_SHARED_LIBS", "shared"),
+        ]
+
+        return args

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

@@ -0,0 +1,44 @@
+# 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 *
+
+
+class Meshlab(CMakePackage):
+    """The open source mesh processing system."""
+
+    homepage = "https://www.meshlab.net"
+    url = "https://github.com/cnr-isti-vclab/meshlab/archive/refs/tags/MeshLab-2023.12.tar.gz"
+    git = "https://github.com/cnr-isti-vclab/meshlab.git"
+
+    maintainers("wdconinc")
+
+    license("GPL-3.0", checked_by="wdconinc")
+
+    version("main", branch="main", submodules=True)
+    version("2023.12", commit="2dbd2f4b12df3b47d8777b2b4a43cabd9e425735", submodules=True)
+
+    variant("double_scalar", default=False, description="Type to use for scalars")
+
+    depends_on("eigen")
+    depends_on("glew")
+    depends_on("mpfr")
+    depends_on("qt@5.15: +opengl")
+
+    def cmake_args(self):
+        args = [
+            self.define_from_variant("MESHLAB_BUILD_WITH_DOUBLE_SCALAR", "double_scalar"),
+            # E57 and Nexus plugins fail on gcc-13 due to missing include cstdint,
+            # but patching is cumbersome since build process downloads their source.
+            # Ref: https://github.com/asmaloney/libE57Format/pull/176
+            self.define("MESHLAB_ALLOW_DOWNLOAD_SOURCE_LIBE57", False),
+            # Ref: https://github.com/cnr-isti-vclab/corto/pull/44
+            self.define("MESHLAB_ALLOW_DOWNLOAD_SOURCE_NEXUS", False),
+        ]
+
+        for bundle in "LIBIGL", "LEVMAR", "LIB3DS", "EMBREE", "NEXUS", "QHULL", "STRUCTURE_SYNTH", "TINYGLTF", "MUPARSER", "BOOST", "OPENCTM", "U3D", "LIBE57", "CGAL", "XERCES":
+            args.append(self.define(f"MESHLAB_ALLOW_DOWNLOAD_SOURCE_{bundle}", False))
+
+        return args

var/spack/repos/builtin/packages/nalu-wind/package.py

@@ -15,7 +15,7 @@ def _parse_float(val):
         return False
 
 
-class NaluWind(CMakePackage, CudaPackage):
+class NaluWind(CMakePackage, CudaPackage, ROCmPackage):
     """Nalu-Wind: Wind energy focused variant of Nalu."""
 
     homepage = "https://nalu-wind.readthedocs.io"
@@ -26,6 +26,7 @@ class NaluWind(CMakePackage, CudaPackage):
     tags = ["ecp", "ecp-apps"]
 
     version("master", branch="master")
+    version("2.0.0", tag="v2.0.0")
 
     variant("pic", default=True, description="Position independent code")
     variant(
@@ -45,12 +46,31 @@ class NaluWind(CMakePackage, CudaPackage):
     variant("hypre", default=True, description="Compile with Hypre support")
     variant("trilinos-solvers", default=True, description="Compile with Trilinos Solvers support")
     variant("catalyst", default=False, description="Compile with Catalyst support")
+    variant("shared", default=True, description="Build shared libraries")
     variant("fftw", default=False, description="Compile with FFTW support")
+    variant("fsi", default=False, description="Enable fluid-structure-interaction models")
     variant("boost", default=False, description="Enable Boost integration")
+    variant("gpu-aware-mpi", default=False, description="gpu-aware-mpi")
     variant("wind-utils", default=False, description="Build wind-utils")
+    variant("umpire", default=False, description="Enable Umpire")
+    conflicts(
+        "+shared",
+        when="+cuda",
+        msg="invalid device functions are generated with shared libs and cuda",
+    )
+    conflicts(
+        "+shared",
+        when="+rocm",
+        msg="invalid device functions are generated with shared libs and rocm",
+    )
+    conflicts("+cuda", when="+rocm")
+    conflicts("+rocm", when="+cuda")
 
     depends_on("mpi")
     depends_on("yaml-cpp@0.5.3:")
+    depends_on("openfast@4.0.0:+cxx+netcdf", when="+fsi")
+    depends_on("trilinos@13.4.1+exodus+zoltan+stk", when="@=2.0.0")
+    depends_on("hypre@2.29.0:", when="@2.0.0:+hypre")
     depends_on(
         "trilinos@13:+exodus+tpetra+zoltan+stk~superlu-dist~superlu+hdf5+shards~hypre+gtest"
     )
@@ -76,12 +96,42 @@ class NaluWind(CMakePackage, CudaPackage):
             "hypre@develop +mpi+cuda~int64~superlu-dist cuda_arch={0}".format(_arch),
             when="+hypre+cuda cuda_arch={0}".format(_arch),
         )
+    for _arch in ROCmPackage.amdgpu_targets:
+        depends_on(
+            "trilinos@13.4.0.2022.10.27: "
+            "~shared+exodus+tpetra+zoltan+stk~superlu-dist~superlu"
+            "+hdf5+shards~hypre+gtest+rocm amdgpu_target={0}".format(_arch),
+            when="+rocm amdgpu_target={0}".format(_arch),
+        )
+        depends_on(
+            "hypre+rocm amdgpu_target={0}".format(_arch),
+            when="+hypre+rocm amdgpu_target={0}".format(_arch),
+        )
+
     depends_on("trilinos-catalyst-ioss-adapter", when="+catalyst")
     depends_on("fftw+mpi", when="+fftw")
     depends_on("nccmp")
     # indirect dependency needed to make original concretizer work
     depends_on("netcdf-c+parallel-netcdf")
     depends_on("boost +filesystem +iostreams cxxstd=14", when="+boost")
+    supported_cxxstd = ["17"]
+    variant(
+        "cxxstd", default="17", values=supported_cxxstd, multi=False, description="cxx standard"
+    )
+    for std in supported_cxxstd:
+        depends_on("trilinos cxxstd=%s" % std, when="cxxstd=%s" % std)
+
+    def setup_build_environment(self, env):
+        if "~stk_simd" in self.spec:
+            env.append_flags("CXXFLAGS", "-DUSE_STK_SIMD_NONE")
+        if "+cuda" in self.spec:
+            env.set("CUDA_LAUNCH_BLOCKING", "1")
+            env.set("CUDA_MANAGED_FORCE_DEVICE_ALLOC", "1")
+            env.set("OMPI_CXX", self.spec["kokkos-nvcc-wrapper"].kokkos_cxx)
+            env.set("MPICH_CXX", self.spec["kokkos-nvcc-wrapper"].kokkos_cxx)
+            env.set("MPICXX_CXX", self.spec["kokkos-nvcc-wrapper"].kokkos_cxx)
+        if "+rocm" in self.spec:
+            env.append_flags("CXXFLAGS", "-fgpu-rdc")
 
     def cmake_args(self):
         spec = self.spec
@@ -95,22 +145,26 @@ def cmake_args(self):
             self.define_from_variant("ENABLE_CUDA", "cuda"),
             self.define_from_variant("ENABLE_WIND_UTILS", "wind-utils"),
             self.define_from_variant("ENABLE_BOOST", "boost"),
+            self.define_from_variant("CMAKE_CXX_STANDARD", "cxxstd"),
+            self.define_from_variant("BUILD_SHARED_LIBS", "shared"),
+            self.define_from_variant("ENABLE_OPENFAST", "openfast"),
+            self.define_from_variant("ENABLE_TIOGA", "tioga"),
+            self.define_from_variant("ENABLE_HYPRE", "hypre"),
+            self.define_from_variant("ENABLE_TRILINOS_SOLVERS", "trilinos-solvers"),
+            self.define_from_variant("ENABLE_PARAVIEW_CATALYST", "catalyst"),
+            self.define_from_variant("ENABLE_FFTW", "fftw"),
+            self.define_from_variant("ENABLE_UMPIRE", "umpire"),
         ]
 
-        args.append(self.define_from_variant("ENABLE_OPENFAST", "openfast"))
         if "+openfast" in spec:
             args.append(self.define("OpenFAST_DIR", spec["openfast"].prefix))
 
-        args.append(self.define_from_variant("ENABLE_TIOGA", "tioga"))
         if "+tioga" in spec:
             args.append(self.define("TIOGA_DIR", spec["tioga"].prefix))
 
-        args.append(self.define_from_variant("ENABLE_HYPRE", "hypre"))
         if "+hypre" in spec:
             args.append(self.define("HYPRE_DIR", spec["hypre"].prefix))
 
-        args.append(self.define_from_variant("ENABLE_TRILINOS_SOLVERS", "trilinos-solvers"))
-        args.append(self.define_from_variant("ENABLE_PARAVIEW_CATALYST", "catalyst"))
         if "+catalyst" in spec:
             args.append(
                 self.define(
@@ -118,7 +172,6 @@ def cmake_args(self):
                 )
             )
 
-        args.append(self.define_from_variant("ENABLE_FFTW", "fftw"))
         if "+fftw" in spec:
             args.append(self.define("FFTW_DIR", spec["fftw"].prefix))
 
@@ -131,6 +184,15 @@ def cmake_args(self):
                 ]
             )
 
+        if "+umpire" in spec:
+            args.append(self.define("UMPIRE_DIR", spec["umpire"].prefix))
+
+        if "+rocm" in spec:
+            args.append(self.define("CMAKE_CXX_COMPILER", spec["hip"].hipcc))
+            args.append(self.define("ENABLE_ROCM", True))
+            targets = spec.variants["amdgpu_target"].value
+            args.append(self.define("GPU_TARGETS", ";".join(str(x) for x in targets)))
+
         if "darwin" in spec.architecture:
             args.append(self.define("CMAKE_MACOSX_RPATH", "ON"))
 

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

@@ -15,9 +15,14 @@ class Nalu(CMakePackage):
     """
 
     homepage = "https://github.com/NaluCFD/Nalu"
+    url = "https://github.com/NaluCFD/Nalu/archive/refs/tags/v1.6.0.tar.gz"
     git = "https://github.com/NaluCFD/Nalu.git"
 
     version("master", branch="master")
+    version("1.6.0", sha256="2eafafe25ed44a7bc1429881f8f944b9794ca51b1e1b29c28a45b91520c7cf97")
+
+    depends_on("trilinos@master", when="@master")
+    depends_on("trilinos@=14.0.0", when="@1.6.0")
 
     # Options
     variant(
@@ -31,16 +36,15 @@ class Nalu(CMakePackage):
 
     # Required dependencies
     depends_on("mpi")
-    depends_on("yaml-cpp@0.5.3:", when="+shared")
-    depends_on("yaml-cpp~shared@0.5.3:", when="~shared")
+    depends_on("yaml-cpp@0.5.3:0.6.2", when="+shared")
+    depends_on("yaml-cpp~shared@0.5.3:0.6.2", when="~shared")
     # Cannot build Trilinos as a shared library with STK on Darwin
     # which is why we have a 'shared' variant for Nalu
     # https://github.com/trilinos/Trilinos/issues/2994
     depends_on(
         "trilinos"
-        "+mpi+exodus+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost"
-        "~superlu-dist+superlu+hdf5+shards~hypre"
-        "@master"
+        "+mpi+exodus+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost+gtest"
+        "~superlu-dist+superlu+hdf5+shards~hypre gotype=long"
     )
     depends_on("trilinos~shared", when="~shared")
     # Optional dependencies

var/spack/repos/builtin/packages/openfast/hub_seg_fault.patch

@@ -0,0 +1,17 @@
+diff --git a/modules/openfast-library/src/FAST_Solver.f90 b/modules/openfast-library/src/FAST_Solver.f90
+index 364d0b78..10056965 100644
+--- a/modules/openfast-library/src/FAST_Solver.f90
++++ b/modules/openfast-library/src/FAST_Solver.f90
+@@ -607,9 +607,9 @@ SUBROUTINE AD_InputSolve_IfW( p_FAST, u_AD, y_IfW, y_OpFM, ErrStat, ErrMsg )
+       end if
+
+       if (u_AD%rotors(1)%NacelleMotion%NNodes > 0) then
+-         u_AD%rotors(1)%InflowOnNacelle(1) = y_OpFM%u(node)
+-         u_AD%rotors(1)%InflowOnNacelle(2) = y_OpFM%v(node)
+-         u_AD%rotors(1)%InflowOnNacelle(3) = y_OpFM%w(node)
++         u_AD%rotors(1)%InflowOnNacelle(1) = y_OpFM%u(1)
++         u_AD%rotors(1)%InflowOnNacelle(2) = y_OpFM%v(1)
++         u_AD%rotors(1)%InflowOnNacelle(3) = y_OpFM%w(1)
+          node = node + 1
+       else
+          u_AD%rotors(1)%InflowOnNacelle = 0.0_ReKi

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

@@ -13,6 +13,7 @@ class Openfast(CMakePackage):
     git = "https://github.com/OpenFAST/openfast.git"
 
     maintainers("jrood-nrel")
+    patch("hub_seg_fault.patch", when="@2.7:3.2")
 
     license("Apache-2.0")
 

var/spack/repos/builtin/packages/paraview/kits_with_catalyst_5_12.patch

@@ -0,0 +1,21 @@
+From 65ec5b0604576474141def0ba7f0c7b94f6b32ee Mon Sep 17 00:00:00 2001
+From: Ryan Krattiger <ryan.krattiger@kitware.com>
+Date: Fri, 8 Mar 2024 09:17:03 -0600
+
+---
+ VTK/IO/CatalystConduit/vtk.module | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/VTK/IO/CatalystConduit/vtk.module b/VTK/IO/CatalystConduit/vtk.module
+index c67f5a099d5..18e706e8c9f 100644
+--- a/VTK/IO/CatalystConduit/vtk.module
++++ b/VTK/IO/CatalystConduit/vtk.module
+@@ -5,7 +5,7 @@ LIBRARY_NAME
+ DESCRIPTION
+   Catalyst implementation for VTK, including Conduit to/from VTK conversion.
+ KIT
+-  VTK::IO
++  VTK::Parallel
+ SPDX_LICENSE_IDENTIFIER
+   BSD-3-Clause
+ SPDX_COPYRIGHT_TEXT

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

@@ -31,13 +31,11 @@ class Paraview(CMakePackage, CudaPackage, ROCmPackage):
 
     version("master", branch="master", submodules=True)
     version(
-        "5.12.0-RC3", sha256="6aaa46ff295126707294482e6ba24bd0ec0d68cf6bb5f56f145f8bcc53fc3f70"
-    )
-    version(
-        "5.11.2",
-        sha256="5c5d2f922f30d91feefc43b4a729015dbb1459f54c938896c123d2ac289c7a1e",
+        "5.12.0",
+        sha256="d289afe7b48533e2ca4a39a3b48d3874bfe67cf7f37fdd2131271c57e64de20d",
         preferred=True,
     )
+    version("5.11.2", sha256="5c5d2f922f30d91feefc43b4a729015dbb1459f54c938896c123d2ac289c7a1e")
     version("5.11.1", sha256="5cc2209f7fa37cd3155d199ff6c3590620c12ca4da732ef7698dec37fa8dbb34")
     version("5.11.0", sha256="9a0b8fe8b1a2cdfd0ace9a87fa87e0ec21ee0f6f0bcb1fdde050f4f585a25165")
     version("5.10.1", sha256="520e3cdfba4f8592be477314c2f6c37ec73fb1d5b25ac30bdbd1c5214758b9c2")
@@ -319,6 +317,8 @@ class Paraview(CMakePackage, CudaPackage, ROCmPackage):
 
     patch("exodusII-netcdf4.9.0.patch", when="@5.10.0:5.10.2")
 
+    patch("kits_with_catalyst_5_12.patch", when="@5.12.0")
+
     generator("ninja", "make", default="ninja")
     # https://gitlab.kitware.com/paraview/paraview/-/issues/21223
     conflicts("generator=ninja", when="%xl")

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

@@ -23,6 +23,7 @@ class Precice(CMakePackage):
     license("LGPL-3.0-or-later")
 
     version("develop", branch="develop")
+    version("3.1.0", sha256="11e7d3d4055ee30852c0e83692ca7563acaa095bd223ebdbd5c8c851b3646d37")
     version("3.0.0", sha256="efe6cf505d9305af89c6da1fdba246199a75a1c63a6a22103773ed95341879ba")
     version("2.5.1", sha256="a5a37d3430eac395e885eb9cbbed9d0980a15e96c3e44763a3769fa7301e3b3a")
     version("2.5.0", sha256="76ec6ee0d1a66f6f3d3d2d11f03cfc5aa7ef4d9e5deb9b7a4b4455ec7f796c00")
@@ -71,7 +72,8 @@ class Precice(CMakePackage):
     depends_on("pkgconfig", type="build", when="@2.2:")
 
     # Boost components
-    depends_on("boost+filesystem+log+program_options+system+test+thread")
+    depends_on("boost+log+program_options+system+test+thread")
+    depends_on("boost+filesystem", when="@:3.0.0")
     depends_on("boost+signals", when="@:2.3")
 
     # Baseline versions

var/spack/repos/builtin/packages/py-amqp/package.py

@@ -13,12 +13,20 @@ class PyAmqp(PythonPackage):
 
     license("BSD-3-Clause")
 
+    version("5.2.0", sha256="a1ecff425ad063ad42a486c902807d1482311481c8ad95a72694b2975e75f7fd")
+    version("5.1.1", sha256="2c1b13fecc0893e946c65cbd5f36427861cffa4ea2201d8f6fca22e2a373b5e2")
     version("5.0.9", sha256="1e5f707424e544078ca196e72ae6a14887ce74e02bd126be54b7c03c971bef18")
+    version("5.0.6", sha256="03e16e94f2b34c31f8bf1206d8ddd3ccaa4c315f7f6a1879b7b1210d229568c2")
     version("5.0.1", sha256="9881f8e6fe23e3db9faa6cfd8c05390213e1d1b95c0162bc50552cad75bffa5f")
+    version("5.0.0", sha256="1183b66e54a5c533b679d9f557b31c5b31d26701761f2bbd144054cce58f3588")
     version("2.6.1", sha256="70cdb10628468ff14e57ec2f751c7aa9e48e7e3651cfd62d431213c0c4e58f21")
+    version("2.6.0", sha256="24dbaff8ce4f30566bb88976b398e8c4e77637171af3af6f1b9650f48890e60b")
     version("2.5.2", sha256="77f1aef9410698d20eaeac5b73a87817365f457a507d82edf292e12cbb83b08d")
+    version("2.5.1", sha256="19a917e260178b8d410122712bac69cb3e6db010d68f6101e7307508aded5e68")
+    version("2.5.0", sha256="cbb6f87d53cac612a594f982b717cc1c54c6a1e17943a0a0d32dc6cc9e2120c8")
     version("2.4.2", sha256="043beb485774ca69718a35602089e524f87168268f0d1ae115f28b88d27f92d7")
     version("2.4.1", sha256="6816eed27521293ee03aa9ace300a07215b11fee4e845588a9b863a7ba30addb")
+    version("2.4.0", sha256="9f181e4aef6562e6f9f45660578fc1556150ca06e836ecb9e733e6ea10b48464")
 
     depends_on("python@2.7:2.8,3.5:", type=("build", "run"))
     depends_on("python@3.6:", type=("build", "run"), when="@5.0.9:")

var/spack/repos/builtin/packages/py-billiard/package.py

@@ -13,6 +13,7 @@ class PyBilliard(PythonPackage):
 
     license("BSD-3-Clause")
 
+    version("4.2.0", sha256="9a3c3184cb275aa17a732f93f65b20c525d3d9f253722d26a82194803ade5a2c")
     version("3.6.4.0", sha256="299de5a8da28a783d51b197d496bef4f1595dd023a93a4f59dde1886ae905547")
     version("3.6.3.0", sha256="d91725ce6425f33a97dfa72fb6bfef0e47d4652acd98a032bd1a7fbf06d5fa6a")
     version("3.6.1.0", sha256="b8809c74f648dfe69b973c8e660bcec00603758c9db8ba89d7719f88d5f01f26")

var/spack/repos/builtin/packages/py-celery/package.py

@@ -9,10 +9,11 @@
 class PyCelery(PythonPackage):
     """Celery - Distributed Task Queue."""
 
-    pypi = "celery/celery-4.2.1.tar.gz"
+    pypi = "celery/celery-5.3.6.tar.gz"
 
     license("BSD-3-Clause")
 
+    version("5.3.6", sha256="870cc71d737c0200c397290d730344cc991d13a057534353d124c9380267aab9")
     version("5.2.3", sha256="e2cd41667ad97d4f6a2f4672d1c6a6ebada194c619253058b5f23704aaadaa82")
     version("5.0.0", sha256="313930fddde703d8e37029a304bf91429cd11aeef63c57de6daca9d958e1f255")
     version("4.4.7", sha256="d220b13a8ed57c78149acf82c006785356071844afe0b27012a4991d44026f9f")
@@ -53,24 +54,34 @@ class PyCelery(PythonPackage):
     depends_on("python@2.7:2.8,3.4:", type=("build", "run"))
 
     depends_on("py-setuptools", type=("build", "run"))
-    depends_on("py-setuptools@59.1.1:59.6", type=("build", "run"), when="@5.2.3:")
+    depends_on("py-setuptools@59.1.1:59.6", type=("build", "run"), when="@5.2.3:5.2.4")
 
     depends_on("py-redis@3.2.0:", when="+redis", type=("build", "run"))
     depends_on("py-redis@3.4.1:3,4.0.2:", when="@5.2.3:+redis", type=("build", "run"))
     depends_on("py-sqlalchemy", when="+sqlalchemy", type=("build", "run"))
 
     depends_on("py-click@7.0:7", when="@5.0.0:5.0", type=("build", "run"))
-    depends_on("py-click@8.0.3:8", when="@5.2.0:", type=("build", "run"))
+    depends_on("py-click@8.0.3:8", when="@5.2", type=("build", "run"))
+    depends_on("py-click@8.1.2:", when="@5.3:", type=("build", "run"))
     depends_on("py-click-didyoumean@0.0.3:", when="@5.0.0:5", type=("build", "run"))
     depends_on("py-click-plugins@1.1.1:", when="@5.0.3:", type=("build", "run"))
     depends_on("py-click-repl@:0.1.6", when="@5.0.0:5.0", type=("build", "run"))
     depends_on("py-click-repl@0.2.0:", when="@5.2.0:", type=("build", "run"))
-    depends_on("py-pytz@2019.3:", type=("build", "run"))
-    depends_on("py-pytz@2021.3:", type=("build", "run"), when="@5.2.3")
-    depends_on("py-billiard@3.6.3.0:3", type=("build", "run"))
-    depends_on("py-billiard@3.6.4.0:3", type=("build", "run"), when="@5.2.3")
+    depends_on("py-pytz@2019.3:", type=("build", "run"), when="@:5.2")
+    depends_on("py-pytz@2021.3:", type=("build", "run"), when="@5.2.3:5.2.99")
+    depends_on("py-billiard@3.6.3", type=("build", "run"), when="@:5.0.99")
+    depends_on("py-billiard@3.6.4.0:3.99", type=("build", "run"), when="@5.1.0:5.2")
+    depends_on("py-billiard@4.2.0:5.0", type=("build", "run"), when="@5.3.0:")
     depends_on("py-kombu@4.6.11", when="@4.3.0:4", type=("build", "run"))
-    depends_on("py-kombu@5.0.0:", when="@5.0.0:5.0", type=("build", "run"))
-    depends_on("py-kombu@5.2.3:5", when="@5.2.0:5.2", type=("build", "run"))
+    depends_on("py-kombu@5.0.0:", when="@5.0", type=("build", "run"))
+    depends_on("py-kombu@5.1.0:", when="@5.1", type=("build", "run"))
+    depends_on("py-kombu@5.2.1", when="@5.2.0", type=("build", "run"))
+    depends_on("py-kombu@5.2.2", when="@5.2.1:5.2.2", type=("build", "run"))
+    depends_on("py-kombu@5.2.3", when="@5.2.3:5.2.99", type=("build", "run"))
+    depends_on("py-kombu@5.3.0", when="@5.3.0", type=("build", "run"))
+    depends_on("py-kombu@5.3.1", when="@5.3.1", type=("build", "run"))
+    depends_on("py-kombu@5.3.2", when="@5.3.4", type=("build", "run"))
+    depends_on("py-kombu@5.3.3", when="@5.3.5", type=("build", "run"))
+    depends_on("py-kombu@5.3.4:5.3.5", when="@5.3.6", type=("build", "run"))
     depends_on("py-vine@1.3.0", when="@4.3.0:4", type=("build", "run"))
     depends_on("py-vine@5.0.0:5", when="@5.0.0:5", type=("build", "run"))

var/spack/repos/builtin/packages/py-deephyper/package.py

@@ -20,22 +20,32 @@ class PyDeephyper(PythonPackage):
     license("BSD-3-Clause")
 
     version("master", branch="master")
+    version("0.6.0", sha256="cda2dd7c74bdca4203d9cd637c4f441595f77bae6d77ef8e4a056b005357de34")
     version("0.4.2", sha256="ee1811a22b08eff3c9098f63fbbb37f7c8703e2f878f2bdf2ec35a978512867f")
 
     depends_on("python@3.7:3.9", type=("build", "run"))
+    depends_on("python@3.7:3.11", type=("build", "run"), when="@0.6.0")
 
+    depends_on("py-setuptools@42:", type="build", when="@0.6.0")
     depends_on("py-setuptools@40:49.1", type="build")
     depends_on("py-wheel@0.36.2", type="build")
-    depends_on("py-cython@0.29.24:2", type="build")
+    depends_on("py-cython@0.29.24:", type="build", when="@0.6.0")
+    depends_on("py-cython@0.29.24:2", type="build", when="@0.4.2")
 
     depends_on("py-configspace@0.4.20:", type=("build", "run"))
     depends_on("py-dm-tree", type=("build", "run"))
-    depends_on("py-jinja2@:3.0", type=("build", "run"))
+    depends_on("py-jinja2@:3.1", type=("build", "run"), when="@0.6.0")
+    depends_on("py-jinja2@:3.0", type=("build", "run"), when="@0.4.2")
+    depends_on("py-numpy@1.20:", type=("build", "run"), when="@0.6.0")
     depends_on("py-numpy", type=("build", "run"))
     depends_on("py-pandas@0.24.2:", type=("build", "run"))
     depends_on("py-packaging", type=("build", "run"))
+    depends_on(
+        "py-packaging@20.5:", type=("build", "run"), when="@0.6.0 target=aarch64: platform=darwin"
+    )
     depends_on("py-scikit-learn@0.23.1:", type=("build", "run"))
+    depends_on("py-scipy@1.7:", type=("build", "run"), when="@0.6.0")
     depends_on("py-scipy@0.19.1:", type=("build", "run"))
     depends_on("py-tqdm@4.64.0:", type=("build", "run"))
     depends_on("py-pyyaml", type=("build", "run"))
-    depends_on("py-tinydb", type=("build", "run"))
+    depends_on("py-tinydb", type=("build", "run"), when="@0.4.2")

var/spack/repos/builtin/packages/py-jax/package.py

@@ -22,11 +22,31 @@ class PyJax(PythonPackage):
     pypi = "jax/jax-0.2.25.tar.gz"
 
     license("Apache-2.0")
-    maintainers("adamjstewart")
+    maintainers("adamjstewart", "jonas-eschle")
 
+    version("0.4.26", sha256="2cce025d0a279ec630d550524749bc8efe25d2ff47240d2a7d4cfbc5090c5383")
     version("0.4.25", sha256="a8ee189c782de2b7b2ffb64a8916da380b882a617e2769aa429b71d79747b982")
+    version("0.4.24", sha256="4a6b6fd026ddd22653c7fa2fac1904c3de2dbe845b61ede08af9a5cc709662ae")
     version("0.4.23", sha256="2a229a5a758d1b803891b2eaed329723f6b15b4258b14dc0ccb1498c84963685")
+    version("0.4.22", sha256="801434dda6e14f82a45fff753969a33281ab22fb2a50fe801b651390321057ba")
+    version("0.4.21", sha256="c97fd0d2751d6e1eb15aa2052ff7cfdc129f8fafc2c14cd779720658926a587b")
+    version("0.4.20", sha256="ea96a763a8b1a9374639d1159ab4de163461d01cd022f67c34c09581b71ed2ac")
+    version("0.4.19", sha256="29f87f9a50964d3ca5eeb2973de3462f0e8b4eca6d46027894a0e9a903420601")
+    version("0.4.18", sha256="776cf33890100803e98f45f9af10aa727271c6993d4e766c069118733c928132")
+    version("0.4.17", sha256="d7508a69e87835f534cb07a2f21d79cc1cb8c4cfdcf7fb010927267ef7355f1d")
     version("0.4.16", sha256="e2ca82c9bf973c2c1c01f5340a583692b31f277aa3abd0544229c1fe5fa44b02")
+    version("0.4.15", sha256="2aa123ccef591e355dea94a6e714b6559f8e1d6368a576a223f97d031ece0d15")
+    version("0.4.14", sha256="18fed3881f26e8b13c8cb46eeeea3dba9eb4d48e3714d8e8f2304dd6e237083d")
+    version("0.4.13", sha256="03bfe6749dfe647f16f15f6616638adae6c4a7ca7167c75c21961ecfd3a3baaa")
+    version("0.4.12", sha256="d2de9a2388ffe002f16506d3ad1cc6e34d7536b98948e49c7e05bbcfe8e57998")
+    version("0.4.11", sha256="8b1cd443b698339df8d8807578ee141e5b67e36125b3945b146f600177d60d79")
+    version("0.4.10", sha256="1bf0f2720f778f2937301a16a4d5cd3497f13a4d6c970c24a88918a81816a888")
+    version("0.4.9", sha256="1ed135cd08f48e4baf10f6eafdb4a4cdae781f9052b5838c09c91a9f4fa75f09")
+    version("0.4.8", sha256="08116481f7336db16c24812bfb5e6f9786915f4c2f6ff4028331fa69e7535202")
+    version("0.4.7", sha256="5e7002d74db25f97c99b979d4ba1233b1ef26e1597e5fc468ad11d1c8a9dc4f8")
+    version("0.4.6", sha256="d06ea8fba4ed315ec55110396058cb48c8edb2ab0b412f28c8a123beee9e58ab")
+    version("0.4.5", sha256="1633e56d34b18ddfa7d2a216ce214fa6fa712d36552532aaa71da416aede7268")
+    version("0.4.4", sha256="39b07e07343ed7c74492ee5e75db77456d3afdd038a322671f09fc748f6392cb")
     version("0.4.3", sha256="d43f08f940aa30eb339965cfb3d6bee2296537b0dc2f0c65ccae3009279529ae")
     version(
         "0.3.23",
@@ -58,7 +78,33 @@ class PyJax(PythonPackage):
 
     # See jax/_src/lib/__init__.py
     # https://github.com/google/jax/commit/8be057de1f50756fe7522f7e98b2f30fad56f7e4
-    for v in ["0.4.25", "0.4.23", "0.4.16", "0.4.3", "0.3.23"]:
+    for v in [
+        "0.4.26",
+        "0.4.25",
+        "0.4.24",
+        "0.4.23",
+        "0.4.22",
+        "0.4.21",
+        "0.4.20",
+        "0.4.19",
+        "0.4.18",
+        "0.4.17",
+        "0.4.16",
+        "0.4.15",
+        "0.4.14",
+        "0.4.13",
+        "0.4.12",
+        "0.4.11",
+        "0.4.10",
+        "0.4.9",
+        "0.4.8",
+        "0.4.7",
+        "0.4.6",
+        "0.4.5",
+        "0.4.4",
+        "0.4.3",
+        "0.3.23",
+    ]:
         depends_on(f"py-jaxlib@:{v}", when=f"@{v}", type=("build", "run"))
 
     # See _minimum_jaxlib_version in jax/version.py

var/spack/repos/builtin/packages/py-jaxlib/package.py

@@ -20,9 +20,19 @@ class PyJaxlib(PythonPackage, CudaPackage):
     license("Apache-2.0")
     maintainers("adamjstewart")
 
+    version("0.4.26", sha256="ddc14da1eaa34f23430d40ad9b9585088575cac439a2fa1c6833a247e1b221fd")
     version("0.4.25", sha256="fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8")
     version("0.4.24", sha256="c4e6963c2c36f634a9a1765e476a1ed4e6c4a7954465ebf72e29f344c28ddc28")
+    version("0.4.23", sha256="e4c06d62ba54becffd91abc862627b8b11b79c5a77366af8843b819665b6d568")
+    version("0.4.21", sha256="8d57f66d00b9c0b824b1eff84adda5b765a412b3f316ef7c773632d1edbf9477")
+    version("0.4.20", sha256="058410d2bc12f7562c7b01e0c8cd587cb68059c12f78bc945055e5ddc445f5fd")
+    version("0.4.19", sha256="51242b217a1f82474e42d24f09ed5dedff951eeb4579c6e49e706d1adfd6949d")
     version("0.4.16", sha256="85c8bc050abe0a2cf62e8cfc7edb4904dd3807924b5714ec6277f291c576b5ca")
+    version("0.4.14", sha256="9f309476a8f6337717b059b8d10b5859b4134c30cf8f1220bb70379b5e2744a4")
+    version("0.4.11", sha256="bdfc45f33970beba5caf28d061668a4863f05994deea26791db50ea605fc2e36")
+    version("0.4.7", sha256="0578d5dd5035b5225cadb6a62ca5f93dd76b70292268502fc01a0fd9ca7001d0")
+    version("0.4.6", sha256="2c9bf8962815bc54ef524e33dc8eda9d165d379fe87e0df210f316adead27787")
+    version("0.4.4", sha256="881f402c7983b56b185e182d5315dd64c9f5320be96213d0415996ece1826806")
     version("0.4.3", sha256="2104735dc22be2b105e5517bd5bc6ae97f40e8e9e54928cac1585c6112a3d910")
     version(
         "0.3.22",
@@ -40,9 +50,12 @@ class PyJaxlib(PythonPackage, CudaPackage):
     # build/build.py
     depends_on("py-build", when="@0.4.14:", type="build")
 
+    # Based on PyPI wheels
+    depends_on("python@3.9:3.12", when="@0.4.17:", type=("build", "run"))
+    depends_on("python@3.9:3.11", when="@0.4.14:0.4.16", type=("build", "run"))
+    depends_on("python@3.8:3.11", when="@0.4.6:0.4.13", type=("build", "run"))
+
     # jaxlib/setup.py
-    depends_on("python@3.9:", when="@0.4.14:", type=("build", "run"))
-    depends_on("python@3.8:", when="@0.4:", type=("build", "run"))
     depends_on("py-setuptools", type="build")
     depends_on("py-scipy@1.9:", when="@0.4.19:", type=("build", "run"))
     depends_on("py-scipy@1.7:", when="@0.4.7:", type=("build", "run"))
@@ -63,12 +76,16 @@ class PyJaxlib(PythonPackage, CudaPackage):
     depends_on("bazel@4.2.1", when="@0.1.75:0.1.76", type="build")
     depends_on("bazel@4.1.0", when="@0.1.70:0.1.74", type="build")
 
-    # README.md
-    depends_on("cuda@11.4:", when="@0.4:+cuda")
+    # jaxlib/setup.py
+    depends_on("cuda@12.1.105:", when="@0.4.26:+cuda")
+    depends_on("cuda@11.8:", when="@0.4.11:+cuda")
+    depends_on("cuda@11.4:", when="@0.4.0:0.4.7+cuda")
     depends_on("cuda@11.1:", when="@0.3+cuda")
     # https://github.com/google/jax/issues/12614
     depends_on("cuda@11.1:11.7.0", when="@0.1+cuda")
-    depends_on("cudnn@8.2:", when="@0.4:+cuda")
+
+    depends_on("cudnn@8.8:", when="@0.4.11:+cuda")
+    depends_on("cudnn@8.2:", when="@0.4:0.4.7+cuda")
     depends_on("cudnn@8.0.5:", when="+cuda")
 
     # Historical dependencies
@@ -83,7 +100,7 @@ class PyJaxlib(PythonPackage, CudaPackage):
     )
 
     # https://github.com/google/jax/issues/19992
-    conflicts("@0.4.16:0.4.25", when="target=ppc64le:")
+    conflicts("@0.4.4:", when="target=ppc64le:")
 
     def patch(self):
         self.tmp_path = tempfile.mkdtemp(prefix="spack")

var/spack/repos/builtin/packages/py-kombu/package.py

@@ -13,7 +13,17 @@ class PyKombu(PythonPackage):
 
     license("BSD-3-Clause")
 
+    version("5.3.5", sha256="30e470f1a6b49c70dc6f6d13c3e4cc4e178aa6c469ceb6bcd55645385fc84b93")
+    version("5.3.4", sha256="0bb2e278644d11dea6272c17974a3dbb9688a949f3bb60aeb5b791329c44fadc")
+    version("5.3.3", sha256="1491df826cfc5178c80f3e89dd6dfba68e484ef334db81070eb5cb8094b31167")
+    version("5.3.2", sha256="0ba213f630a2cb2772728aef56ac6883dc3a2f13435e10048f6e97d48506dbbd")
+    version("5.3.1", sha256="fbd7572d92c0bf71c112a6b45163153dea5a7b6a701ec16b568c27d0fd2370f2")
+    version("5.3.0", sha256="d084ec1f96f7a7c37ba9e816823bdbc08f0fc7ddb3a5be555805e692102297d8")
+    version("5.2.4", sha256="37cee3ee725f94ea8bb173eaab7c1760203ea53bbebae226328600f9d2799610")
     version("5.2.3", sha256="81a90c1de97e08d3db37dbf163eaaf667445e1068c98bfd89f051a40e9f6dbbd")
+    version("5.2.2", sha256="0f5d0763fb916808f617b886697b2be28e6bc35026f08e679697fc814b48a608")
+    version("5.2.1", sha256="f262a2adc71b53e5b7dad4933bbdee65d8766ca4df6a9043b13edaad2144aaec")
+    version("5.1.0", sha256="01481d99f4606f6939cdc9b637264ed353ee9e3e4f62cfb582324142c41a572d")
     version("5.0.2", sha256="f4965fba0a4718d47d470beeb5d6446e3357a62402b16c510b6a2f251e05ac3c")
     version("4.6.11", sha256="ca1b45faac8c0b18493d02a8571792f3c40291cf2bcf1f55afed3d8f3aa7ba74")
     version("4.6.6", sha256="1760b54b1d15a547c9a26d3598a1c8cdaf2436386ac1f5561934bc8a3cbbbd86")
@@ -26,15 +36,19 @@ class PyKombu(PythonPackage):
     variant("redis", default=False, description="Use redis transport")
 
     depends_on("py-setuptools", type="build")
-    # "pytz>dev" in tests_require: setuptools parser changed in v60 and errors.
-    depends_on("py-setuptools@:59", when="@4.6:5.2", type="build")
+    depends_on("py-amqp@2.4", when="@4.3.0:4.5.0", type=("build", "run"))
+    depends_on("py-amqp@2.5.0", when="@4.6.0:4.6.3", type=("build", "run"))
+    depends_on("py-amqp@2.5.1", when="@4.6.4:4.6.5", type=("build", "run"))
+    depends_on("py-amqp@2.5.2:2.5.99", when="@4.6.6:4.6.8", type=("build", "run"))
+    depends_on("py-amqp@2.6.0:2.99", when="@4.6.9:5.0.1", type=("build", "run"))
+    depends_on("py-amqp@5.0.0:5.0.5", when="@5.0.2:5.0.99", type=("build", "run"))
+    depends_on("py-amqp@5.0.6:5.0.8", when="@5.1.0:5.2.2", type=("build", "run"))
+    depends_on("py-amqp@5.0.9:5.1.0", when="@5.2.3:5.2.4", type=("build", "run"))
+    depends_on("py-amqp@5.1.1:5.1.99", when="@5.3.0:5.3.5", type=("build", "run"))
 
-    depends_on("py-amqp@2.5.2:2.5", when="@:4.6.6", type=("build", "run"))
-    depends_on("py-amqp@2.6.0:2.6", when="@4.6.7:4", type=("build", "run"))
-    depends_on("py-amqp@5.0.0:5", when="@5.0.0:5.0.2", type=("build", "run"))
-    depends_on("py-amqp@5.0.9:5.0", when="@5.2.3", type=("build", "run"))
     depends_on("py-vine", when="@5.1.0:", type=("build", "run"))
     depends_on("py-importlib-metadata@0.18:", type=("build", "run"), when="^python@:3.7")
     depends_on("py-cached-property", type=("build", "run"), when="^python@:3.7")
 
     depends_on("py-redis@3.4.1:3,4.0.2:", when="+redis", type=("build", "run"))
+    depends_on("py-backports-zoneinfo@0.2.1:", when="^python@:3.8", type=("build", "run"))

var/spack/repos/builtin/packages/py-pip/package.py

@@ -2,8 +2,8 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
 import os
+import sys
 
 from spack.package import *
 
@@ -44,6 +44,15 @@ class PyPip(Package, PythonExtension):
     # Uses collections.MutableMapping
     depends_on("python@:3.9", when="@:19.1", type=("build", "run"))
 
+    resource(
+        name="pip-bootstrap",
+        url="https://bootstrap.pypa.io/pip/zipapp/pip-22.3.1.pyz",
+        checksum="c9363c70ad91d463f9492a8a2c89f60068f86b0239bd2a6aa77367aab5fefb3e",
+        when="platform=windows",
+        placement={"pip-22.3.1.pyz": "pip.pyz"},
+        expand=False,
+    )
+
     def url_for_version(self, version):
         url = "https://files.pythonhosted.org/packages/{0}/p/pip/pip-{1}-{0}-none-any.whl"
         if version >= Version("21"):
@@ -58,7 +67,14 @@ def install(self, spec, prefix):
         # itself, see:
         # https://discuss.python.org/t/bootstrapping-a-specific-version-of-pip/12306
         whl = self.stage.archive_file
-        args = [os.path.join(whl, "pip")] + std_pip_args + ["--prefix=" + prefix, whl]
+        args = std_pip_args + ["--prefix=" + prefix, whl]
+        if sys.platform == "win32":
+            # On Windows for newer versions of pip, you must bootstrap pip first.
+            # In order to achieve this, use the pip.pyz zipapp version of pip to
+            # bootstrap the pip wheel install.
+            args.insert(0, os.path.join(self.stage.source_path, "pip.pyz"))
+        else:
+            args.insert(0, os.path.join(whl, "pip"))
         python(*args)
 
     def setup_dependent_package(self, module, dependent_spec):

var/spack/repos/builtin/packages/py-pymatgen/package.py

@@ -52,3 +52,8 @@ class PyPymatgen(PythonPackage):
     depends_on("py-uncertainties@3.1.4:", when="@2021.1.1:", type=("build", "run"))
     depends_on("py-pybtex", when="@2022.1.9:", type=("build", "run"))
     depends_on("py-tqdm", when="@2022.1.9:", type=("build", "run"))
+
+    # <<< manual changes
+    # https://github.com/materialsproject/pymatgen/commit/29b5b909e109cb04d4b118d0de5b3929819b9378
+    depends_on("py-cython@:2", when="@:2023.7.16", type="build")
+    # manual changes >>>

var/spack/repos/builtin/packages/py-tatsu/package.py

@@ -24,3 +24,8 @@ class PyTatsu(PythonPackage):
     depends_on("py-setuptools", type="build")
     # optional dependency, otherwise falls back to standard implementation
     depends_on("py-regex@2018.8:", type=("build", "run"), when="+future_regex")
+
+    # <<< manual changes
+    # https://github.com/neogeny/TatSu/commit/a4fd84a2785fb0820ed65fe80ebd768458643b66
+    depends_on("python@:3.9", type=("build", "run"), when="@:4")
+    # manual changes >>>

var/spack/repos/builtin/packages/py-triton/package.py

@@ -19,5 +19,6 @@ class PyTriton(PythonPackage):
     depends_on("py-setuptools@40.8:", type="build")
     depends_on("cmake@3.18:", type="build")
     depends_on("py-filelock", type=("build", "run"))
+    depends_on("zlib-api", type="link")
 
     build_directory = "python"

var/spack/repos/builtin/packages/py-zfit/package.py

@@ -18,15 +18,17 @@ class PyZfit(PythonPackage):
     maintainers("jonas-eschle")
     license("BSD-3-Clause", checked_by="jonas-eschle")
 
-    # TODO: reactivate once TF 2.15 is ready https://github.com/spack/spack/pull/41069
-    # version("0.18.1", sha256="fbc6b3a636d8dc74fb2e69dfec5855f534c4583ec18efac9e9107ad45b18eb43")
-    # version("0.18.0", sha256="21d9479480f74945c67707b715780693bd4e94062c551bf41fe04a2eddb47fab")
+    tags = ["likelihood", "statistics", "inference", "fitting", "hep"]
+
+    version("0.18.2", sha256="099b111e135937966b4c6342c7738731f112aea33e1b9f4a9785d2eac9e530f1")
+    version("0.18.1", sha256="fbc6b3a636d8dc74fb2e69dfec5855f534c4583ec18efac9e9107ad45b18eb43")
+    version("0.18.0", sha256="21d9479480f74945c67707b715780693bd4e94062c551bf41fe04a2eddb47fab")
     version("0.17.0", sha256="cd60dfc360c82666af4e8dddd78edb0ab95a095b9dd0868457f0981dc03afa5a")
     version("0.16.0", sha256="b3b170af23b61d7e265d6fb1bab1d052003f3fb41b3c537527cc1e5a1066dc10")
     version("0.15.5", sha256="00a1138429e8a7f830c9e229b9c0bcd6071b95dadd8c87eb81191079fb679225")
     version("0.14.1", sha256="66d1e349403f1d6c6350138d0f2b422046bcbdfb34fd95453dadae29a8b0c98a")
 
-    depends_on("python@3.8:3.11", type=("build", "run"))
+    depends_on("python@3.9:3.11", type=("build", "run"))
     depends_on("py-setuptools@42:", type="build")
     depends_on("py-setuptools-scm-git-archive", type="build")
     depends_on("py-setuptools-scm@3.4:+toml", type="build")
@@ -37,9 +39,8 @@ class PyZfit(PythonPackage):
     # TODO: remove "build" once fixed in spack that tests need "run", not "build"
     with default_args(type=("build", "run")):
 
-        # TODO: reactivate once TF 2.15 is ready https://github.com/spack/spack/pull/41069
-        # depends_on("py-tensorflow@2.15", type=("run"), when="@0.18")
-        # depends_on("py-tensorflow-probability@0.23", type=("run"), when="@0.18")
+        depends_on("py-tensorflow@2.15", type=("run"), when="@0.18")
+        depends_on("py-tensorflow-probability@0.23", type=("run"), when="@0.18")
 
         depends_on("py-tensorflow@2.13", when="@0.15:0.17")
         depends_on("py-tensorflow-probability@0.21", when="@0.16:0.17")
@@ -54,7 +55,7 @@ class PyZfit(PythonPackage):
         with when("+hs3"):
             depends_on("py-asdf")
 
-        depends_on("py-attrs", when="@0.15:18.0")
+        depends_on("py-attrs", when="@0.15:")
         depends_on("py-typing-extensions", when="^python@:3.8")
         depends_on("py-boost-histogram")
         depends_on("py-colorama")

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

@@ -54,7 +54,7 @@ class Rivet(AutotoolsPackage):
 
     depends_on("hepmc", when="hepmc=2")
     depends_on("hepmc3", when="hepmc=3")
-    depends_on("fastjet")
+    depends_on("fastjet plugins=cxx")
     depends_on("fastjet@3.4.0:", when="@3.1.7:")
     depends_on("fjcontrib")
     depends_on("python", type=("build", "run"))

var/spack/repos/builtin/packages/rocm-opencl/package.py

@@ -82,6 +82,19 @@ def url_for_version(self, version):
             placement="rocclr",
             when=f"@{d_version}",
         )
+    # For avx build, the start address of values_ buffer in KernelParameters is not
+    # correct as it is computed based on 16-byte alignment.
+    patch(
+        "https://github.com/ROCm/clr/commit/c4f773db0b4ccbbeed4e3d6c0f6bff299c2aa3f0.patch?full_index=1",
+        sha256="5bb9b0e08888830ccf3a0a658529fe25f4ee62b5b8890f349bf2cc914236eb2f",
+        when="@5.7:",
+    )
+    patch(
+        "https://github.com/ROCm/clr/commit/7868876db742fb4d44483892856a66d2993add03.patch?full_index=1",
+        sha256="7668b2a710baf4cb063e6b00280fb75c4c3e0511575e8298a9c7ae5143f60b33",
+        when="@5.7:",
+    )
+
     # Patch to set package installation path for OpenCL.
     patch("0001-fix-build-error-rocm-opencl-5.1.0.patch", when="@5.1")
 

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

@@ -39,7 +39,11 @@ class Scotch(CMakePackage, MakefilePackage):
 
     build_system(conditional("cmake", when="@7:"), "makefile", default="cmake")
     variant("threads", default=True, description="use POSIX Pthreads within Scotch and PT-Scotch")
-    variant("mpi_thread", default=False, description="use multi-threaded algorithms")
+    variant(
+        "mpi_thread",
+        default=False,
+        description="use multi-threaded algorithms in conjunction with MPI",
+    )
     variant("mpi", default=True, description="Compile parallel libraries")
     variant("compression", default=True, description="May use compressed files")
     variant("esmumps", default=False, description="Compile esmumps (needed by mumps)")
@@ -48,6 +52,7 @@ class Scotch(CMakePackage, MakefilePackage):
         "metis", default=False, description="Expose vendored METIS/ParMETIS libraries and wrappers"
     )
     variant("int64", default=False, description="Use int64_t for SCOTCH_Num typedef")
+    variant("noarch", default=False, description="Unset SPACK_TARGET_ARGS")
     variant(
         "link_error_lib",
         default=False,
@@ -69,6 +74,9 @@ class Scotch(CMakePackage, MakefilePackage):
     patch("libscotchmetis-return-6.0.5a.patch", when="@6.0.5a")
     patch("libscotch-scotcherr-link-7.0.1.patch", when="@7.0.1 +link_error_lib")
 
+    # Avoid OpenMPI segfaults by using MPI_Comm_F2C for parmetis communicator
+    patch("parmetis-mpi.patch", when="@6.1.1:7.0.3 +metis ^openmpi")
+
     # Vendored dependency of METIS/ParMETIS conflicts with standard
     # installations
     conflicts("metis", when="+metis")
@@ -127,6 +135,10 @@ def cmake_args(self):
 
         return args
 
+    @when("+noarch")
+    def setup_build_environment(self, env):
+        env.unset("SPACK_TARGET_ARGS")
+
 
 class MakefileBuilder(spack.build_systems.makefile.MakefileBuilder):
     build_directory = "src"

var/spack/repos/builtin/packages/scotch/parmetis-mpi.patch

@@ -0,0 +1,127 @@
+diff --git a/src/libscotchmetis/parmetis_dgraph_order_f.c b/src/libscotchmetis/parmetis_dgraph_order_f.c
+index 44c2ede..549a834 100644
+--- a/src/libscotchmetis/parmetis_dgraph_order_f.c
++++ b/src/libscotchmetis/parmetis_dgraph_order_f.c
+@@ -46,7 +46,7 @@
+ /**                # Version 6.0  : from : 13 sep 2012     **/
+ /**                                 to   : 18 may 2019     **/
+ /**                # Version 7.0  : from : 21 jan 2023     **/
+-/**                                 to   : 21 jan 2023     **/
++/**                                 to   : 30 jun 2023     **/
+ /**                                                        **/
+ /************************************************************/
+ 
+@@ -76,11 +76,14 @@ const SCOTCH_Num * const    numflag,                    \
+ const SCOTCH_Num * const    options,                    \
+ SCOTCH_Num * const          order,                      \
+ SCOTCH_Num * const          sizes,                      \
+-MPI_Comm * const            commptr,                    \
++const MPI_Fint * const      commptr,                    \
+ int * const                 revaptr),                   \
+ (vtxdist, xadj, adjncy, numflag, options, order, sizes, commptr, revaptr))
+ {
+-  *revaptr = SCOTCH_ParMETIS_V3_NodeND (vtxdist, xadj, adjncy, numflag, options, order, sizes, commptr);
++  MPI_Comm            commdat;
++
++  commdat = MPI_Comm_f2c (*commptr);
++  *revaptr = SCOTCH_ParMETIS_V3_NodeND (vtxdist, xadj, adjncy, numflag, options, order, sizes, &commdat);
+ }
+ 
+ /*******************/
+@@ -101,10 +104,13 @@ const SCOTCH_Num * const    numflag,                                \
+ const SCOTCH_Num * const    options,                                \
+ SCOTCH_Num * const          order,                                  \
+ SCOTCH_Num * const          sizes,                                  \
+-MPI_Comm * const            commptr),                               \
++const MPI_Fint * const      commptr),                               \
+ (vtxdist, xadj, adjncy, numflag, options, order, sizes, commptr))
+ {
+-  METISNAMEU (ParMETIS_V3_NodeND) (vtxdist, xadj, adjncy, numflag, options, order, sizes, commptr);
++  MPI_Comm            commdat;
++
++  commdat = MPI_Comm_f2c (*commptr);
++  METISNAMEU (ParMETIS_V3_NodeND) (vtxdist, xadj, adjncy, numflag, options, order, sizes, &commdat);
+ }
+ 
+ #endif /* SCOTCH_METIS_PREFIX */
+diff --git a/src/libscotchmetis/parmetis_dgraph_part_f.c b/src/libscotchmetis/parmetis_dgraph_part_f.c
+index 2b76818..3bf66af 100644
+--- a/src/libscotchmetis/parmetis_dgraph_part_f.c
++++ b/src/libscotchmetis/parmetis_dgraph_part_f.c
+@@ -44,7 +44,7 @@
+ /**                # Version 6.0  : from : 13 sep 2012     **/
+ /**                                 to   : 18 may 2019     **/
+ /**                # Version 7.0  : from : 21 jan 2023     **/
+-/**                                 to   : 21 jan 2023     **/
++/**                                 to   : 30 jun 2023     **/
+ /**                                                        **/
+ /************************************************************/
+ 
+@@ -81,12 +81,15 @@ const float * const         ubvec,                          \
+ const SCOTCH_Num * const    options,                        \
+ SCOTCH_Num * const          edgecut,                        \
+ SCOTCH_Num * const          part,                           \
+-MPI_Comm * const            commptr,                        \
++const MPI_Fint * const      commptr,                        \
+ int * const                 revaptr),                       \
+ (vtxdist, xadj, adjncy, vwgt, adjwgt, wgtflag, numflag, ncon, nparts, tpwgts, ubvec, options, edgecut, part, commptr, revaptr))
+ {
++  MPI_Comm            commdat;
++
++  commdat = MPI_Comm_f2c (*commptr);
+   *revaptr = SCOTCH_ParMETIS_V3_PartKway (vtxdist, xadj, adjncy, vwgt, adjwgt, wgtflag, numflag,
+-                                          ncon, nparts, tpwgts, ubvec, options, edgecut, part, commptr);
++                                          ncon, nparts, tpwgts, ubvec, options, edgecut, part, &commdat);
+ }
+ 
+ /*
+@@ -111,12 +114,15 @@ const float * const         ubvec,                                  \
+ const SCOTCH_Num * const    options,                                \
+ SCOTCH_Num * const          edgecut,                                \
+ SCOTCH_Num * const          part,                                   \
+-MPI_Comm * const            commptr,                                \
++const MPI_Fint * const      commptr,                                \
+ int * const                 revaptr),                               \
+ (vtxdist, xadj, adjncy, vwgt, adjwgt, wgtflag, numflag, ndims, xyz, ncon, nparts, tpwgts, ubvec, options, edgecut, part, commptr, revaptr))
+ {
++  MPI_Comm            commdat;
++
++  commdat = MPI_Comm_f2c (*commptr);
+   *revaptr = SCOTCH_ParMETIS_V3_PartGeomKway (vtxdist, xadj, adjncy, vwgt, adjwgt, wgtflag, numflag,
+-                                              ndims, xyz, ncon, nparts, tpwgts, ubvec, options, edgecut, part, commptr);
++                                              ndims, xyz, ncon, nparts, tpwgts, ubvec, options, edgecut, part, &commdat);
+ }
+ 
+ /*******************/
+@@ -144,10 +150,13 @@ const float * const         ubvec,                                      \
+ const SCOTCH_Num * const    options,                                    \
+ SCOTCH_Num * const          edgecut,                                    \
+ SCOTCH_Num * const          part,                                       \
+-MPI_Comm * const            commptr),                                   \
++const MPI_Fint * const      commptr),                                   \
+ (vtxdist, xadj, adjncy, vwgt, adjwgt, wgtflag, numflag, ncon, nparts, tpwgts, ubvec, options, edgecut, part, commptr))
+ {
+-  METISNAMEU (ParMETIS_V3_PartKway) (vtxdist, xadj, adjncy, vwgt, adjwgt, wgtflag, numflag, ncon, nparts, tpwgts, ubvec, options, edgecut, part, commptr);
++  MPI_Comm            commdat;
++
++  commdat = MPI_Comm_f2c (*commptr);
++  METISNAMEU (ParMETIS_V3_PartKway) (vtxdist, xadj, adjncy, vwgt, adjwgt, wgtflag, numflag, ncon, nparts, tpwgts, ubvec, options, edgecut, part, &commdat);
+ }
+ 
+ /*
+@@ -172,10 +181,13 @@ const float * const         ubvec,
+ const SCOTCH_Num * const    options,                                            \
+ SCOTCH_Num * const          edgecut,                                            \
+ SCOTCH_Num * const          part,                                               \
+-MPI_Comm * const            commptr),                                           \
++const MPI_Fint * const      commptr),                                           \
+ (vtxdist, xadj, adjncy, vwgt, adjwgt, wgtflag, numflag, ndims, xyz, ncon, nparts, tpwgts, ubvec, options, edgecut, part, commptr))
+ {
+-  METISNAMEU (ParMETIS_V3_PartGeomKway) (vtxdist, xadj, adjncy, vwgt, adjwgt, wgtflag, numflag, ndims, xyz, ncon, nparts, tpwgts, ubvec, options, edgecut, part, commptr);
++  MPI_Comm            commdat;
++
++  commdat = MPI_Comm_f2c (*commptr);
++  METISNAMEU (ParMETIS_V3_PartGeomKway) (vtxdist, xadj, adjncy, vwgt, adjwgt, wgtflag, numflag, ndims, xyz, ncon, nparts, tpwgts, ubvec, options, edgecut, part, &commdat);
+ }
+ 
+ #endif /* SCOTCH_METIS_PREFIX */

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

@@ -92,6 +92,9 @@ class Slate(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("scalapack", when="@:2022.07.00", type="test")
     depends_on("python", type="test")
     depends_on("hipify-clang", when="@:2021.05.02 +rocm ^hip@5:")
+    depends_on("comgr", when="+rocm")
+    depends_on("rocblas", when="+rocm")
+    depends_on("rocsolver", when="+rocm")
 
     requires("%oneapi", when="+sycl", msg="slate+sycl must be compiled with %oneapi")
 
@@ -166,9 +169,11 @@ def test(self):
         test_dir = join_path(self.test_suite.current_test_cache_dir, "examples", "build")
         with working_dir(test_dir, create=True):
             cmake_bin = join_path(self.spec["cmake"].prefix.bin, "cmake")
+            # This package must directly depend on all packages listed here.
+            # Otherwise, it will not work when some packages are external to spack.
             deps = "slate blaspp lapackpp mpi"
             if self.spec.satisfies("+rocm"):
-                deps += " rocblas hip llvm-amdgpu comgr hsa-rocr-dev rocsolver"
+                deps += " rocblas hip llvm-amdgpu comgr hsa-rocr-dev rocsolver "
             prefixes = ";".join([self.spec[x].prefix for x in deps.split()])
             self.run_test(cmake_bin, ["-DCMAKE_PREFIX_PATH=" + prefixes, ".."])
             make()

var/spack/repos/builtin/packages/tinyxml2/package.py

@@ -14,6 +14,10 @@ class Tinyxml2(CMakePackage):
 
     license("Zlib")
 
+    version("10.0.0", sha256="3bdf15128ba16686e69bce256cc468e76c7b94ff2c7f391cc5ec09e40bff3839")
+    version("9.0.0", sha256="cc2f1417c308b1f6acc54f88eb70771a0bf65f76282ce5c40e54cfe52952702c")
+    version("8.0.0", sha256="6ce574fbb46751842d23089485ae73d3db12c1b6639cda7721bf3a7ee862012c")
+    version("7.0.0", sha256="fa0d1c745d65d4d833e62cb183e23c2034dc7a35ec1a4977e808bdebb9b4fe60")
     version("6.2.0", sha256="cdf0c2179ae7a7931dba52463741cf59024198bbf9673bf08415bcb46344110f")
     version("4.0.1", sha256="14b38ef25cc136d71339ceeafb4856bb638d486614103453eccd323849267f20")
     version("4.0.0", sha256="90add44f06de081047d431c08d7269c25b4030e5fe19c3bc8381c001ce8f258c")
@@ -21,3 +25,13 @@ class Tinyxml2(CMakePackage):
     version("2.2.0", sha256="f891224f32e7a06bf279290619cec80cc8ddc335c13696872195ffb87f5bce67")
     version("2.1.0", sha256="4bdd6569fdce00460bf9cda0ff5dcff46d342b4595900d849cc46a277a74cce6")
     version("2.0.2", sha256="3cc3aa09cd1ce77736f23488c7cb24e65e11daed4e870ddc8d352aa4070c7c74")
+
+    variant("shared", default=False, description="Build shared library")
+
+    def cmake_args(self):
+        args = []
+
+        if self.spec.satisfies("+shared"):
+            args.append("-DBUILD_SHARED_LIBS=ON")
+
+        return args

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

@@ -20,6 +20,7 @@ class Tioga(CMakePackage):
     # The original TIOGA repo has possibly been abandoned,
     # so work on TIOGA has continued in the Exawind project
     version("develop", git="https://github.com/Exawind/tioga.git", branch="exawind")
+    version("1.0.0", git="https://github.com/Exawind/tioga.git", tag="v1.0.0")
     version("master", branch="master")
 
     variant("shared", default=sys.platform != "darwin", description="Build shared libraries")

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

@@ -103,6 +103,13 @@ class Trilinos(CMakePackage, CudaPackage, ROCmPackage):
     variant("uvm", default=False, when="@13.2: +cuda", description="Turn on UVM for CUDA build")
     variant("wrapper", default=False, description="Use nvcc-wrapper for CUDA build")
 
+    # Makes the Teuchos Memory Management classes (Teuchos::RCP, Teuchos::Ptr, Teuchos::Array,
+    # Teuchos::ArrayView, and Teuchos::ArrayRCP) thread-safe. Requires at least the OMP kokkos
+    # backend to be enabled. Without, this seemingly does nothing
+    variant(
+        "threadsafe", default=False, when="+openmp", description="Enable threadsafe in Teuchos"
+    )
+
     # TPLs (alphabet order)
     variant("adios2", default=False, description="Enable ADIOS2")
     variant("boost", default=False, description="Compile with Boost")
@@ -633,6 +640,7 @@ def define_enable(suffix, value=None):
                 define_trilinos_enable(
                     "EXPLICIT_INSTANTIATION", "explicit_template_instantiation"
                 ),
+                define_from_variant("Trilinos_ENABLE_THREAD_SAFE", "threadsafe"),
             ]
         )