containers: Add Fedora 40, 39 (#43847)

* Added Versions of miniconda3: 24.3.0, 24.1.2, 23.11.0, 23.9.0, 23.5.2, 23.5.1, 23.5.0, 23.3.1, 23.1.0

* fixed style

---------

Co-authored-by: James H. Rogers <jhrogers@spear.hpc.msstate.edu>

.github/workflows/audit.yaml

@@ -34,7 +34,7 @@ jobs:
       run: |
           . share/spack/setup-env.sh
           coverage run $(which spack) audit packages
-          coverage run $(which spack) audit externals        
+          coverage run $(which spack) -d audit externals        
           coverage combine
           coverage xml
     - name: Package audits (without coverage)

.github/workflows/build-containers.yml

@@ -50,7 +50,9 @@ jobs:
                      [rockylinux8, 'linux/amd64,linux/arm64', 'rockylinux:8'],
                      [rockylinux9, 'linux/amd64,linux/arm64', 'rockylinux:9'],
                      [fedora37, 'linux/amd64,linux/arm64,linux/ppc64le', 'fedora:37'],
-                     [fedora38, 'linux/amd64,linux/arm64,linux/ppc64le', 'fedora:38']]
+                     [fedora38, 'linux/amd64,linux/arm64,linux/ppc64le', 'fedora:38'],
+                     [fedora39, 'linux/amd64,linux/arm64,linux/ppc64le', 'fedora:39'],
+                     [fedora40, 'linux/amd64,linux/arm64,linux/ppc64le', 'fedora:40']]
     name: Build ${{ matrix.dockerfile[0] }}
     if: github.repository == 'spack/spack'
     steps:

lib/spack/docs/containers.rst

@@ -233,6 +233,12 @@ The OS that are currently supported are summarized in the table below:
    * - Fedora Linux 38
      - ``fedora:38``
      - ``spack/fedora38``
+   * - Fedora Linux 39
+     - ``fedora:39``
+     - ``spack/fedora39``
+   * - Fedora Linux 40
+     - ``fedora:40``
+     - ``spack/fedora40``
 
 
 

lib/spack/docs/packaging_guide.rst

@@ -6435,9 +6435,12 @@ the ``paths`` attribute:
          echo "Target: x86_64-pc-linux-gnu"
          echo "Thread model: posix"
          echo "InstalledDir: /usr/bin"
+     platforms: ["linux", "darwin"]
      results:
      - spec: 'llvm@3.9.1 +clang~lld~lldb'
 
+If the ``platforms`` attribute is present, tests are run only if the current host
+matches one of the listed platforms.
 Each test is performed by first creating a temporary directory structure as
 specified in the corresponding ``layout`` and by then running
 package detection and checking that the outcome matches the expected
@@ -6471,6 +6474,10 @@ package detection and checking that the outcome matches the expected
      - A spec that is expected from detection
      - Any valid spec
      - Yes
+   * - ``results:[0]:extra_attributes``
+     - Extra attributes expected on the associated Spec
+     - Nested dictionary with string as keys, and regular expressions as leaf values
+     - No
 
 """""""""""""""""""""""""""""""
 Reuse tests from other packages

lib/spack/env/cc

@@ -755,7 +755,7 @@ esac
 
 # Linker flags
 case "$mode" in
-    ld|ccld)
+    ccld)
         extend spack_flags_list SPACK_LDFLAGS
         ;;
 esac

lib/spack/spack/audit.py

@@ -1111,4 +1111,76 @@ def _test_detection_by_executable(pkgs, error_cls):
                 details = [msg.format(s, idx) for s in sorted(not_expected)]
                 errors.append(error_cls(summary=summary, details=details))
 
+            matched_detection = []
+            for candidate in expected_specs:
+                try:
+                    idx = specs.index(candidate)
+                except (AttributeError, ValueError):
+                    pass
+
+                matched_detection.append((candidate, specs[idx]))
+
+            def _compare_extra_attribute(_expected, _detected, *, _spec):
+                result = []
+                # Check items are of the same type
+                if not isinstance(_detected, type(_expected)):
+                    _summary = f'{pkg_name}: error when trying to detect "{_expected}"'
+                    _details = [f"{_detected} was detected instead"]
+                    return [error_cls(summary=_summary, details=_details)]
+
+                # If they are string expected is a regex
+                if isinstance(_expected, str):
+                    try:
+                        _regex = re.compile(_expected)
+                    except re.error:
+                        _summary = f'{pkg_name}: illegal regex in "{_spec}" extra attributes'
+                        _details = [f"{_expected} is not a valid regex"]
+                        return [error_cls(summary=_summary, details=_details)]
+
+                    if not _regex.match(_detected):
+                        _summary = (
+                            f'{pkg_name}: error when trying to match "{_expected}" '
+                            f"in extra attributes"
+                        )
+                        _details = [f"{_detected} does not match the regex"]
+                        return [error_cls(summary=_summary, details=_details)]
+
+                if isinstance(_expected, dict):
+                    _not_detected = set(_expected.keys()) - set(_detected.keys())
+                    if _not_detected:
+                        _summary = f"{pkg_name}: cannot detect some attributes for spec {_spec}"
+                        _details = [
+                            f'"{_expected}" was expected',
+                            f'"{_detected}" was detected',
+                        ] + [f'attribute "{s}" was not detected' for s in sorted(_not_detected)]
+                        result.append(error_cls(summary=_summary, details=_details))
+
+                    _common = set(_expected.keys()) & set(_detected.keys())
+                    for _key in _common:
+                        result.extend(
+                            _compare_extra_attribute(_expected[_key], _detected[_key], _spec=_spec)
+                        )
+
+                return result
+
+            for expected, detected in matched_detection:
+                # We might not want to test all attributes, so avoid not_expected
+                not_detected = set(expected.extra_attributes) - set(detected.extra_attributes)
+                if not_detected:
+                    summary = f"{pkg_name}: cannot detect some attributes for spec {expected}"
+                    details = [
+                        f'"{s}" was not detected [test_id={idx}]' for s in sorted(not_detected)
+                    ]
+                    errors.append(error_cls(summary=summary, details=details))
+
+                common = set(expected.extra_attributes) & set(detected.extra_attributes)
+                for key in common:
+                    errors.extend(
+                        _compare_extra_attribute(
+                            expected.extra_attributes[key],
+                            detected.extra_attributes[key],
+                            _spec=expected,
+                        )
+                    )
+
     return errors

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, license, variant
+from spack.directives import conflicts, license, redistribute, variant
 from spack.package_base import InstallError
 from spack.util.environment import EnvironmentModifications
 from spack.util.executable import Executable
@@ -30,7 +30,7 @@ class IntelOneApiPackage(Package):
 
     # oneAPI license does not allow mirroring outside of the
     # organization (e.g. University/Company).
-    redistribute_source = False
+    redistribute(source=False, binary=False)
 
     for c in [
         "target=ppc64:",

lib/spack/spack/container/images.json

@@ -12,9 +12,31 @@
       },
       "os_package_manager": "yum_amazon"
     },
+    "fedora:40": {
+      "bootstrap": {
+        "template": "container/fedora.dockerfile",
+        "image": "docker.io/fedora:40"
+      },
+      "os_package_manager": "dnf",
+      "build": "spack/fedora40",
+      "final": {
+        "image": "docker.io/fedora:40"
+      }
+    },
+    "fedora:39": {
+      "bootstrap": {
+        "template": "container/fedora.dockerfile",
+        "image": "docker.io/fedora:39"
+      },
+      "os_package_manager": "dnf",
+      "build": "spack/fedora39",
+      "final": {
+        "image": "docker.io/fedora:39"
+      }
+    },
     "fedora:38": {
       "bootstrap": {
-        "template": "container/fedora_38.dockerfile",
+        "template": "container/fedora.dockerfile",
         "image": "docker.io/fedora:38"
       },
       "os_package_manager": "dnf",
@@ -25,7 +47,7 @@
     },
     "fedora:37": {
       "bootstrap": {
-        "template": "container/fedora_37.dockerfile",
+        "template": "container/fedora.dockerfile",
         "image": "docker.io/fedora:37"
       },
       "os_package_manager": "dnf",

lib/spack/spack/detection/test.py

@@ -11,6 +11,7 @@
 
 from llnl.util import filesystem
 
+import spack.platforms
 import spack.repo
 import spack.spec
 from spack.util import spack_yaml
@@ -32,6 +33,8 @@ class ExpectedTestResult(NamedTuple):
 
     #: Spec to be detected
     spec: str
+    #: Attributes expected in the external spec
+    extra_attributes: Dict[str, str]
 
 
 class DetectionTest(NamedTuple):
@@ -100,7 +103,10 @@ def _create_executable_scripts(self, mock_executables: MockExecutables) -> List[
 
     @property
     def expected_specs(self) -> List[spack.spec.Spec]:
-        return [spack.spec.Spec(r.spec) for r in self.test.results]
+        return [
+            spack.spec.Spec.from_detection(item.spec, extra_attributes=item.extra_attributes)
+            for item in self.test.results
+        ]
 
 
 def detection_tests(pkg_name: str, repository: spack.repo.RepoPath) -> List[Runner]:
@@ -117,9 +123,13 @@ def detection_tests(pkg_name: str, repository: spack.repo.RepoPath) -> List[Runn
     """
     result = []
     detection_tests_content = read_detection_tests(pkg_name, repository)
+    current_platform = str(spack.platforms.host())
 
     tests_by_path = detection_tests_content.get("paths", [])
     for single_test_data in tests_by_path:
+        if current_platform not in single_test_data.get("platforms", [current_platform]):
+            continue
+
         mock_executables = []
         for layout in single_test_data["layout"]:
             mock_executables.append(
@@ -127,7 +137,11 @@ def detection_tests(pkg_name: str, repository: spack.repo.RepoPath) -> List[Runn
             )
         expected_results = []
         for assertion in single_test_data["results"]:
-            expected_results.append(ExpectedTestResult(spec=assertion["spec"]))
+            expected_results.append(
+                ExpectedTestResult(
+                    spec=assertion["spec"], extra_attributes=assertion.get("extra_attributes", {})
+                )
+            )
 
         current_test = DetectionTest(
             pkg_name=pkg_name, layout=mock_executables, results=expected_results

lib/spack/spack/solver/os_compatibility.lp

@@ -12,6 +12,8 @@
 %=============================================================================
 
 % macOS
+os_compatible("sonoma", "ventura").
+os_compatible("ventura", "monterey").
 os_compatible("monterey", "bigsur").
 os_compatible("bigsur", "catalina").
 

lib/spack/spack/test/cc.py

@@ -127,7 +127,7 @@
 spack_cflags = ["-Wall"]
 spack_cxxflags = ["-Werror"]
 spack_fflags = ["-w"]
-spack_ldflags = ["-L", "foo"]
+spack_ldflags = ["-Wl,--gc-sections", "-L", "foo"]
 spack_ldlibs = ["-lfoo"]
 
 lheaderpad = ["-Wl,-headerpad_max_install_names"]
@@ -279,7 +279,6 @@ def test_ld_flags(wrapper_environment, wrapper_flags):
         test_args,
         ["ld"]
         + test_include_paths
-        + [spack_ldflags[i] + spack_ldflags[i + 1] for i in range(0, len(spack_ldflags), 2)]
         + test_library_paths
         + ["--disable-new-dtags"]
         + test_rpaths
@@ -307,13 +306,14 @@ def test_cc_flags(wrapper_environment, wrapper_flags):
         [real_cc]
         + target_args
         + test_include_paths
-        + [spack_ldflags[i] + spack_ldflags[i + 1] for i in range(0, len(spack_ldflags), 2)]
+        + ["-Lfoo"]
         + test_library_paths
         + ["-Wl,--disable-new-dtags"]
         + test_wl_rpaths
         + test_args_without_paths
         + spack_cppflags
         + spack_cflags
+        + ["-Wl,--gc-sections"]
         + spack_ldlibs,
     )
 
@@ -325,12 +325,13 @@ def test_cxx_flags(wrapper_environment, wrapper_flags):
         [real_cc]
         + target_args
         + test_include_paths
-        + [spack_ldflags[i] + spack_ldflags[i + 1] for i in range(0, len(spack_ldflags), 2)]
+        + ["-Lfoo"]
         + test_library_paths
         + ["-Wl,--disable-new-dtags"]
         + test_wl_rpaths
         + test_args_without_paths
         + spack_cppflags
+        + ["-Wl,--gc-sections"]
         + spack_ldlibs,
     )
 
@@ -342,13 +343,14 @@ def test_fc_flags(wrapper_environment, wrapper_flags):
         [real_cc]
         + target_args
         + test_include_paths
-        + [spack_ldflags[i] + spack_ldflags[i + 1] for i in range(0, len(spack_ldflags), 2)]
+        + ["-Lfoo"]
         + test_library_paths
         + ["-Wl,--disable-new-dtags"]
         + test_wl_rpaths
         + test_args_without_paths
         + spack_fflags
         + spack_cppflags
+        + ["-Wl,--gc-sections"]
         + spack_ldlibs,
     )
 

share/spack/templates/container/fedora_37.dockerfile

@@ -1,29 +0,0 @@
-{% extends "container/bootstrap-base.dockerfile" %}
-{% block install_os_packages %}
-RUN dnf update -y \
- && dnf install -y \
-        bzip2 \
-        curl \
-        file \
-        findutils \
-        gcc-c++ \
-        gcc \
-        gcc-gfortran \
-        git \
-        gnupg2 \
-        hg \
-        hostname \
-        iproute \
-        make \
-        patch \
-        python3 \
-        python3-pip \
-        python3-setuptools \
-        svn \
-        unzip \
-        zstd \
-        xz \
- && pip3 install boto3 \
- && rm -rf /var/cache/dnf \
- && dnf clean all
-{% endblock %}

var/spack/repos/builtin/packages/apple-clang/detection_test.yaml

@@ -9,6 +9,7 @@ paths:
           echo "Target: x86_64-apple-darwin19.5.0"
           echo "Thread model: posix"
           echo "InstalledDir: /Library/Developer/CommandLineTools/usr/bin"
+    platforms: ["darwin"]
     results:
       - spec: 'apple-clang@11.0.0'
   # Apple Clang on Apple M1 (Ventura)
@@ -21,6 +22,7 @@ paths:
           echo "Target: arm64-apple-darwin22.6.0"
           echo "Thread model: posix"
           echo "InstalledDir: /Library/Developer/CommandLineTools/usr/bin"
+    platforms: ["darwin"]
     results:
       - spec: 'apple-clang@15.0.0'
   # Test that missing a compiler prevents the package from being detected
@@ -32,4 +34,5 @@ paths:
           echo "Target: x86_64-apple-darwin19.5.0"
           echo "Thread model: posix"
           echo "InstalledDir: /Library/Developer/CommandLineTools/usr/bin"
+    platforms: ["darwin"]
     results: [ ]

var/spack/repos/builtin/packages/armci-mpi/package.py

@@ -0,0 +1,43 @@
+# 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 ArmciMpi(AutotoolsPackage):
+    """ARMCI-MPI is an implementation of the ARMCI library used by Global Arrays.
+    MPI-3 one-sided communication is used to implement ARMCI.
+    """
+
+    homepage = "https://github.com/pmodels/armci-mpi"
+    url = "https://github.com/pmodels/armci-mpi/archive/refs/tags/v0.4.tar.gz"
+
+    maintainers("jeffhammond")
+
+    license("BSD-3-Clause", checked_by="jeffhammond")
+
+    version("0.4", sha256="bcc3bb189b23bf653dcc69bc469eb86eae5ebc5ad94ab5f83e52ddbdbbebf1b1")
+    version(
+        "0.3.1-beta", sha256="f3eaa8f365fb55123ecd9ced401086b0732e37e4df592b27916d71a67ab34fe9"
+    )
+
+    variant("shared", default=True, description="Builds a shared version of the library")
+    variant("progress", default=False, description="Enable asynchronous progress")
+
+    depends_on("autoconf", type="build")
+    depends_on("automake", type="build")
+    depends_on("libtool", type="build")
+    depends_on("m4", type="build")
+
+    depends_on("mpi")
+
+    def autoreconf(self, spec, prefix):
+        autoreconf("--install", "--verbose", "--force")
+
+    def configure_args(self):
+        args = ["--enable-g"]
+        args.extend(self.enable_or_disable("shared"))
+        args.extend(self.with_or_without("progress"))
+        return args

var/spack/repos/builtin/packages/gcc/detection_test.yaml

@@ -20,8 +20,13 @@ paths:
             echo "mock executable got an unexpected flag: $1"
             exit 1
           fi
+    platforms: ["darwin", "linux"]
     results:
       - spec: "gcc@9.4.0 languages=c,c++"
+        extra_attributes:
+          compilers:
+            c: ".*/bin/gcc"
+            cxx: ".*/bin/g++"
   # Mock a version < 7 of GCC that requires -dumpversion and
   # errors with -dumpfullversion
   - layout:
@@ -37,8 +42,14 @@ paths:
             echo "compilation terminated."
             exit 1
           fi
+    platforms: ["darwin", "linux"]
     results:
       - spec: "gcc@5.5.0 languages=c,c++,fortran"
+        extra_attributes:
+          compilers:
+            c: ".*/bin/gcc-5$"
+            cxx: ".*/bin/g[+][+]-5$"
+            fortran: ".*/bin/gfortran-5$"
   # Multiple compilers present at the same time
   - layout:
       - executables:
@@ -50,7 +61,14 @@ paths:
         script: "echo 10.1.0"
     results:
       - spec: "gcc@6.5.0 languages=c"
+        extra_attributes:
+          compilers:
+            c: ".*/bin/x86_64-linux-gnu-gcc-6$"
       - spec: "gcc@10.1.0 languages=c,c++"
+        extra_attributes:
+          compilers:
+            c: ".*/bin/x86_64-linux-gnu-gcc-10$"
+            cxx: ".*/bin/x86_64-linux-gnu-g[+][+]-10$"
   # Apple clang under disguise as gcc should not be detected
   - layout:
       - executables:
@@ -70,4 +88,5 @@ paths:
             echo "mock executable got an unexpected flag: $1"
             exit 1
           fi
+    platforms: ["darwin"]
     results: []

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

@@ -16,7 +16,6 @@
 
 import spack.platforms
 import spack.util.executable
-from spack.build_environment import dso_suffix
 from spack.operating_systems.mac_os import macos_sdk_path, macos_version
 from spack.package import *
 
@@ -957,76 +956,42 @@ def install_targets(self):
     @property
     def spec_dir(self):
         # e.g. lib/gcc/x86_64-unknown-linux-gnu/4.9.2
-        spec_dir = glob.glob("{0}/gcc/*/*".format(self.prefix.lib))
+        spec_dir = glob.glob(f"{self.prefix.lib}/gcc/*/*")
         return spec_dir[0] if spec_dir else None
 
     @run_after("install")
-    def write_rpath_specs(self):
-        """Generate a spec file so the linker adds a rpath to the libs
-        the compiler used to build the executable.
-
-        .. caution::
-
-           The custom spec file by default with *always* pass ``-Wl,-rpath
-           ...`` to the linker, which will cause the linker to *ignore* the
-           value of ``LD_RUN_PATH``, which otherwise would be saved to the
-           binary as the default rpath. See the mitigation below for how to
-           temporarily disable this behavior.
-
-        Structure the specs file so that users can define a custom spec file
-        to suppress the spack-linked rpaths to facilitate rpath adjustment
-        for relocatable binaries. The custom spec file
-        :file:`{norpath}.spec` will have a single
-        line followed by two blanks lines::
-
-            *link_libgcc_rpath:
-
-
-
-        It can be passed to the GCC linker using the argument
-        ``--specs=norpath.spec`` to disable the automatic rpath and restore
-        the behavior of ``LD_RUN_PATH``."""
+    def write_specs_file(self):
+        """(1) inject an rpath to its runtime library dir, (2) add a default programs search path
+        to <binutils>/bin."""
         if not self.spec_dir:
-            tty.warn(
-                "Could not install specs for {0}.".format(self.spec.format("{name}{@version}"))
-            )
+            tty.warn(f"Could not install specs for {self.spec.format('{name}{@version}')}.")
             return
 
-        gcc = self.spec["gcc"].command
-        lines = gcc("-dumpspecs", output=str).splitlines(True)
-        specs_file = join_path(self.spec_dir, "specs")
-
-        # Save a backup
-        with open(specs_file + ".orig", "w") as out:
-            out.writelines(lines)
-
         # Find which directories have shared libraries
-        rpath_libdirs = []
-        for dir in ["lib", "lib64"]:
+        for dir in ["lib64", "lib"]:
             libdir = join_path(self.prefix, dir)
-            if glob.glob(join_path(libdir, "*." + dso_suffix)):
-                rpath_libdirs.append(libdir)
-
-        if not rpath_libdirs:
-            # No shared libraries
+            if glob.glob(join_path(libdir, "libgcc_s.*")):
+                rpath_dir = libdir
+                break
+        else:
             tty.warn("No dynamic libraries found in lib/lib64")
-            return
+            rpath_dir = None
 
-        # Overwrite the specs file
-        with open(specs_file, "w") as out:
-            for line in lines:
-                out.write(line)
-                if line.startswith("*link_libgcc:"):
-                    # Insert at start of line following link_libgcc, which gets
-                    # inserted into every call to the linker
-                    out.write("%(link_libgcc_rpath) ")
+        specs_file = join_path(self.spec_dir, "specs")
+        with open(specs_file, "w") as f:
+            # rpath
+            if rpath_dir:
+                print("*link_libgcc:", file=f)
+                print(f"+ -rpath={rpath_dir}", file=f)
+                print(file=f)
 
-            # Add easily-overridable rpath string at the end
-            out.write("*link_libgcc_rpath:\n")
-            out.write(" ".join("-rpath " + lib for lib in rpath_libdirs))
-            out.write("\n")
+            # programs search path
+            if self.spec.satisfies("+binutils"):
+                print("*self_spec:", file=f)
+                print(f"+ -B{self.spec['binutils'].prefix.bin}", file=f)
+                print(file=f)
         set_install_permissions(specs_file)
-        tty.info("Wrote new spec file to {0}".format(specs_file))
+        tty.info(f"Wrote new spec file to {specs_file}")
 
     def setup_run_environment(self, env):
         # Search prefix directory for possibly modified compiler names

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

@@ -10,8 +10,9 @@
 from spack.pkg.builtin.gcc_runtime import get_elf_libraries
 
 
+@IntelOneApiPackage.update_description
 class IntelOneapiRuntime(Package):
-    """Package for OneAPI compiler runtime libraries"""
+    """Package for OneAPI compiler runtime libraries redistributables."""
 
     homepage = "https://software.intel.com/content/www/us/en/develop/tools/oneapi.html"
     has_code = False

var/spack/repos/builtin/packages/intel/detection_test.yaml

@@ -15,5 +15,6 @@ paths:
         script: |
           echo "ifort (IFORT) 18.0.5 20180823"
           echo "Copyright (C) 1985-2018 Intel Corporation.  All rights reserved."
+    platforms: ["darwin", "linux"]
     results:
       - spec: 'intel@18.0.5'

var/spack/repos/builtin/packages/julia/julia-1.10-rm-suite-sparse-cuda-stubs.patch

@@ -0,0 +1,16 @@
+diff --git a/base/Makefile b/base/Makefile
+index ad2bb6a63c..493302af78 100644
+--- a/base/Makefile
++++ b/base/Makefile
+@@ -269,11 +269,9 @@ $(eval $(call symlink_system_library,LIBSUITESPARSE,libamd))
+ $(eval $(call symlink_system_library,LIBSUITESPARSE,libcamd))
+ $(eval $(call symlink_system_library,LIBSUITESPARSE,libccolamd))
+ $(eval $(call symlink_system_library,LIBSUITESPARSE,libcholmod))
+-$(eval $(call symlink_system_library,LIBSUITESPARSE,libcholmod_cuda))
+ $(eval $(call symlink_system_library,LIBSUITESPARSE,libcolamd))
+ $(eval $(call symlink_system_library,LIBSUITESPARSE,libumfpack))
+ $(eval $(call symlink_system_library,LIBSUITESPARSE,libspqr))
+-$(eval $(call symlink_system_library,LIBSUITESPARSE,libspqr_cuda))
+ $(eval $(call symlink_system_library,LIBSUITESPARSE,libsuitesparseconfig))
+ # EXCLUDED LIBRARIES (installed/used, but not vendored for use with dlopen):
+ # libunwind

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

@@ -26,6 +26,7 @@ class Julia(MakefilePackage):
     maintainers("vchuravy", "haampie", "giordano")
 
     version("master", branch="master")
+    version("1.10.2", sha256="e3d20c02975da054aeb18d32ed84c5d760d54d2563e45e25017684a5a105d185")
     version("1.9.3", sha256="8d7dbd8c90e71179e53838cdbe24ff40779a90d7360e29766609ed90d982081d")
     version("1.9.2", sha256="015438875d591372b80b09d01ba899657a6517b7c72ed41222298fef9d4ad86b")
     version("1.9.0", sha256="48f4c8a7d5f33d0bc6ce24226df20ab49e385c2d0c3767ec8dfdb449602095b2")
@@ -59,9 +60,24 @@ class Julia(MakefilePackage):
     )
     depends_on("libuv", when="@:1.7")
     depends_on("libuv-julia@1.42.0", when="@1.8.0:1.8.1")
-    depends_on("libuv-julia@1.44.2", when="@1.8.2:")
+    depends_on("libuv-julia@1.44.2", when="@1.8.2:1.9")
+    depends_on("libuv-julia@1.44.3", when="@1.10.0:")
     depends_on("suite-sparse@5.4:5.10", when="@1.6:1.9")
 
+    with when("@1.10.0:1.10"):
+        # libssh2.so.1, libpcre2-8.so.0, libmbedtls.so.14, libmbedcrypto.so.7, libmbedx509.so.1,
+        # libopenlibm.so.4, libblastrampoline.so.5, libgit2.so.1.6, libnghttp2.so.14,
+        # libcurl.so.4
+        depends_on("libblastrampoline@5.8.0:5")
+        depends_on("libgit2@1.6.4:1.6")
+        depends_on("libssh2@1.11.0:1.11")
+        depends_on("llvm@15.0.7 +lld shlib_symbol_version=JL_LLVM_15.0")
+        depends_on("mbedtls@2.28.2:2.28")
+        depends_on("openlibm@0.8.1:0.8", when="+openlibm")
+        depends_on("nghttp2@1.52.0:1.52")
+        depends_on("curl@8.4.0:")
+        depends_on("suite-sparse@7.2.1")
+
     with when("@1.9.0:1.9"):
         # libssh2.so.1, libpcre2-8.so.0, mbedtls.so.14, mbedcrypto.so.7, mbedx509.so.1
         # openlibm.so.4, libblastrampoline.so.5, libgit2.so.1.5, libnghttp2.so.14,
@@ -125,7 +141,7 @@ class Julia(MakefilePackage):
         "llvm",
         when="^llvm@12.0.1",
         patches=patch(
-            "https://raw.githubusercontent.com/spack/patches/master/julia/10cb42f80c2eaad3e9c87cb818b6676f1be26737bdf972c77392d71707386aa4.patch",
+            "https://raw.githubusercontent.com/spack/patches/24ff44c4c5439400747941473c0298a74c1fbcb1/julia/10cb42f80c2eaad3e9c87cb818b6676f1be26737bdf972c77392d71707386aa4.patch",
             sha256="10cb42f80c2eaad3e9c87cb818b6676f1be26737bdf972c77392d71707386aa4",
         ),
     )
@@ -133,7 +149,7 @@ class Julia(MakefilePackage):
         "llvm",
         when="^llvm@13.0.1",
         patches=patch(
-            "https://raw.githubusercontent.com/spack/patches/master/julia/45f72c59ae5cf45461e9cd8b224ca49b739d885c79b3786026433c6c22f83b5f.patch",
+            "https://raw.githubusercontent.com/spack/patches/24ff44c4c5439400747941473c0298a74c1fbcb1/julia/45f72c59ae5cf45461e9cd8b224ca49b739d885c79b3786026433c6c22f83b5f.patch",
             sha256="45f72c59ae5cf45461e9cd8b224ca49b739d885c79b3786026433c6c22f83b5f",
         ),
     )
@@ -141,10 +157,18 @@ class Julia(MakefilePackage):
         "llvm",
         when="^llvm@14.0.6",
         patches=patch(
-            "https://raw.githubusercontent.com/spack/patches/master/julia/f3def26930832532bbcd861d41b31ae03db993bc2b3510f89ef831a30bd3e099.patch",
+            "https://raw.githubusercontent.com/spack/patches/24ff44c4c5439400747941473c0298a74c1fbcb1/julia/f3def26930832532bbcd861d41b31ae03db993bc2b3510f89ef831a30bd3e099.patch",
             sha256="f3def26930832532bbcd861d41b31ae03db993bc2b3510f89ef831a30bd3e099",
         ),
     )
+    depends_on(
+        "llvm",
+        when="^llvm@15.0.7",
+        patches=patch(
+            "https://raw.githubusercontent.com/spack/patches/24ff44c4c5439400747941473c0298a74c1fbcb1/julia/25cdc0271e7722d4a7cc6f72abcb17bfe205fc741bbe3716a21759c3eee7d32c.patch",
+            sha256="25cdc0271e7722d4a7cc6f72abcb17bfe205fc741bbe3716a21759c3eee7d32c",
+        ),
+    )
 
     # Patches for libuv
     depends_on(
@@ -234,6 +258,11 @@ class Julia(MakefilePackage):
     # Make sure Julia sets -DNDEBUG when including LLVM header files.
     patch("llvm-NDEBUG.patch", when="@1.7.0:1.7")
 
+    # suite-sparse@7.2.1 sometimes builds cuda stub libraries and Julia build
+    # system deals with them, but we don't compile them, so we remove the code
+    # which is creating symlinks to those libraries.
+    patch("julia-1.10-rm-suite-sparse-cuda-stubs.patch", when="@1.10.0:1.10")
+
     def patch(self):
         # The system-libwhich-libblastrampoline.patch causes a rebuild of docs as it
         # touches the main Makefile, so we reset the a/m-time to doc/_build's.

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

@@ -16,13 +16,13 @@ class Libcatalyst(CMakePackage):
 
     homepage = "https://gitlab.kitware.com/paraview/catalyst"
     git = "https://gitlab.kitware.com/paraview/catalyst.git"
-    url = "https://gitlab.kitware.com/api/v4/projects/paraview%2Fcatalyst/packages/generic/catalyst/v2.0.0/catalyst-v2.0.0.tar.gz"
+    url = "https://gitlab.kitware.com/api/v4/projects/5912/packages/generic/catalyst/v2.0.0/catalyst-v2.0.0.tar.gz"
 
     license("BSD-3-Clause")
 
     maintainers("mathstuf", "ayenpure")
     version("master", branch="master")
-    version("2.0.0-rc4", sha256="cb491e4ccd344156cc2494f65b9f38885598c16d12e1016c36e2ee0bc3640863")
+    version("2.0.0", sha256="5842b690bd8afa635414da9b9c5e5d79fa37879b0d382428d0d8e26ba5374828")
 
     variant("mpi", default=False, description="Enable MPI support")
     variant("conduit", default=False, description="Use external Conduit for Catalyst")

var/spack/repos/builtin/packages/llvm/detection_test.yaml

@@ -14,6 +14,7 @@ paths:
           echo "Target: x86_64-pc-linux-gnu"
           echo "Thread model: posix"
           echo "InstalledDir: /usr/bin"
+    platforms: ["darwin", "linux"]
     results:
       - spec: 'llvm@3.9.1 +clang~lld~lldb'
   # Multiple LLVM packages in the same prefix
@@ -40,6 +41,7 @@ paths:
           echo "Target: x86_64-pc-linux-gnu"
           echo "Thread model: posix"
           echo "InstalledDir: /usr/bin"
+    platforms: ["darwin", "linux"]
     results:
       - spec: 'llvm@8.0.0+clang+lld+lldb'
       - spec: 'llvm@3.9.1+clang~lld~lldb'
@@ -53,4 +55,5 @@ paths:
         echo "Target: x86_64-apple-darwin19.5.0"
         echo "Thread model: posix"
         echo "InstalledDir: /Library/Developer/CommandLineTools/usr/bin"
+    platforms: ["darwin"]
     results: []

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

@@ -936,7 +936,9 @@ def cmake_args(self):
 
         cmake_args.append(from_variant("LIBOMP_TSAN_SUPPORT", "libomp_tsan"))
 
-        if self.compiler.name == "gcc":
+        # From clang 16 onwards we use a more precise --gcc-install-dir flag in post-install
+        # generated config files.
+        if self.spec.satisfies("@:15 %gcc"):
             cmake_args.append(define("GCC_INSTALL_PREFIX", self.compiler.prefix))
 
         if self.spec.satisfies("~code_signing platform=darwin"):
@@ -976,12 +978,24 @@ def cmake_args(self):
                         runtimes_order.index(x) if x in runtimes_order else len(runtimes_order)
                     )
                 )
+
+            # CMake args passed just to runtimes
+            runtime_cmake_args = [define("CMAKE_INSTALL_RPATH_USE_LINK_PATH", True)]
+
+            # When building runtimes, just-built clang has to know where GCC is.
+            gcc_install_dir_flag = get_gcc_install_dir_flag(spec, self.compiler)
+            if gcc_install_dir_flag:
+                runtime_cmake_args.extend(
+                    [
+                        define("CMAKE_C_FLAGS", gcc_install_dir_flag),
+                        define("CMAKE_CXX_FLAGS", gcc_install_dir_flag),
+                    ]
+                )
+
             cmake_args.extend(
                 [
                     define("LLVM_ENABLE_RUNTIMES", runtimes),
-                    define(
-                        "RUNTIMES_CMAKE_ARGS", [define("CMAKE_INSTALL_RPATH_USE_LINK_PATH", True)]
-                    ),
+                    define("RUNTIMES_CMAKE_ARGS", runtime_cmake_args),
                 ]
             )
 
@@ -1031,6 +1045,19 @@ def post_install(self):
         with working_dir(self.build_directory):
             install_tree("bin", join_path(self.prefix, "libexec", "llvm"))
 
+        cfg_files = []
+        if spec.satisfies("+clang"):
+            cfg_files.extend(("clang.cfg", "clang++.cfg"))
+        if spec.satisfies("@19: +flang"):
+            # The config file is `flang.cfg` even though the executable is `flang-new`.
+            # `--gcc-install-dir` / `--gcc-toolchain` support was only added in LLVM 19.
+            cfg_files.append("flang.cfg")
+        gcc_install_dir_flag = get_gcc_install_dir_flag(spec, self.compiler)
+        if gcc_install_dir_flag:
+            for cfg in cfg_files:
+                with open(os.path.join(self.prefix.bin, cfg), "w") as f:
+                    print(gcc_install_dir_flag, file=f)
+
     def llvm_config(self, *args, **kwargs):
         lc = Executable(self.prefix.bin.join("llvm-config"))
         if not kwargs.get("output"):
@@ -1042,6 +1069,18 @@ def llvm_config(self, *args, **kwargs):
             return ret
 
 
+def get_gcc_install_dir_flag(spec: Spec, compiler) -> Optional[str]:
+    """Get the --gcc-install-dir=... flag, so that clang does not do a system scan for GCC."""
+    if not spec.satisfies("@16: %gcc"):
+        return None
+    gcc = Executable(compiler.cc)
+    libgcc_path = gcc("-print-file-name=libgcc.a", output=str, fail_on_error=False).strip()
+    if not os.path.isabs(libgcc_path):
+        return None
+    libgcc_dir = os.path.dirname(libgcc_path)
+    return f"--gcc-install-dir={libgcc_dir}" if os.path.exists(libgcc_dir) else None
+
+
 def get_llvm_targets_to_build(spec):
     targets = spec.variants["targets"].value
 

var/spack/repos/builtin/packages/miniconda3/package.py

@@ -10,6 +10,60 @@
 from spack.util.environment import EnvironmentModifications
 
 _versions = {
+    "24.3.0": {
+        "Linux-x86_64": (
+            "96a44849ff17e960eeb8877ecd9055246381c4d4f2d031263b63fa7e2e930af1",
+            "https://repo.anaconda.com/miniconda/Miniconda3-py312_24.3.0-0-Linux-x86_64.sh",
+        )
+    },
+    "24.1.2": {
+        "Linux-x86_64": (
+            "b978856ec3c826eb495b60e3fffe621f670c101150ebcbdeede4f961f22dc438",
+            "https://repo.anaconda.com/miniconda/Miniconda3-py312_24.1.2-0-Linux-x86_64.sh",
+        )
+    },
+    "23.11.0": {
+        "Linux-x86_64": (
+            "c9ae82568e9665b1105117b4b1e499607d2a920f0aea6f94410e417a0eff1b9c",
+            "https://repo.anaconda.com/miniconda/Miniconda3-py311_23.11.0-2-Linux-x86_64.sh",
+        )
+    },
+    "23.9.0": {
+        "Linux-x86_64": (
+            "43651393236cb8bb4219dcd429b3803a60f318e5507d8d84ca00dafa0c69f1bb",
+            "https://repo.anaconda.com/miniconda/Miniconda3-py311_23.9.0-0-Linux-x86_64.sh",
+        )
+    },
+    "23.5.2": {
+        "Linux-x86_64": (
+            "634d76df5e489c44ade4085552b97bebc786d49245ed1a830022b0b406de5817",
+            "https://repo.anaconda.com/miniconda/Miniconda3-py311_23.5.2-0-Linux-x86_64.sh",
+        )
+    },
+    "23.5.1": {
+        "Linux-x86_64": (
+            "333779c9cae3fe14735949a8dcb9657b9e55ada69e9c60f191c5d582b2deac20",
+            "https://repo.anaconda.com/miniconda/Miniconda3-py311_23.5.1-0-Linux-x86_64.sh",
+        )
+    },
+    "23.5.0": {
+        "Linux-x86_64": (
+            "61a5c087893f6210176045931b89ee6e8760c17abd9c862b2cab4c1b7d00f7c8",
+            "https://repo.anaconda.com/miniconda/Miniconda3-py311_23.5.0-3-Linux-x86_64.sh",
+        )
+    },
+    "23.3.1": {
+        "Linux-x86_64": (
+            "aef279d6baea7f67940f16aad17ebe5f6aac97487c7c03466ff01f4819e5a651",
+            "https://repo.anaconda.com/miniconda/Miniconda3-py310_23.3.1-0-Linux-x86_64.sh",
+        )
+    },
+    "23.1.0": {
+        "Linux-x86_64": (
+            "32d73e1bc33fda089d7cd9ef4c1be542616bd8e437d1f77afeeaf7afdb019787",
+            "https://repo.anaconda.com/miniconda/Miniconda3-py310_23.1.0-1-Linux-x86_64.sh",
+        )
+    },
     "22.11.1": {
         "Linux-x86_64": (
             "00938c3534750a0e4069499baf8f4e6dc1c2e471c86a59caa0dd03f4a9269db6",

var/spack/repos/builtin/packages/osg-ca-certs/package.py

@@ -11,9 +11,8 @@ class OsgCaCerts(Package):
     in the OpenSSL 1.0.* format."""
 
     homepage = "http://repo.opensciencegrid.org/cadist"
-    url = "https://github.com/opensciencegrid/osg-certificates/archive/v1.109.igtf.1.117/osg-certificates-1.109.igtf.1.117.tar.gz"
+    git = "https://github.com/opensciencegrid/osg-certificates.git"
 
-    _osg_base_url = "https://github.com/opensciencegrid/osg-certificates/archive/v{osg_version}.igtf.{igtf_version}/osg-certificates-{osg_version}.igtf.{igtf_version}.tar.gz"
     _igtf_base_url = "https://dist.eugridpma.info/distribution/igtf/{igtf_version}/igtf-policy-installation-bundle-{igtf_version}.tar.gz"
     _letsencrypt_base_url = "https://github.com/opensciencegrid/letsencrypt-certificates/archive/v{letsencrypt_version}/letsencrypt-certificates.tar.gz"
 
@@ -21,29 +20,17 @@ class OsgCaCerts(Package):
 
     releases = [
         {
-            "osg_version": "1.110",
-            "igtf_version": "1.119",
-            "osg_sha256": "025969d415bf27c1609699caf63d0d79540a01df500187195f2bd973fe69e00d",
-            "igtf_sha256": "cc4db07a86fc27f0e0dfd15c797d1a0da7b5620f4b611dbb686543712b2f335a",
-        },
-        {
-            "osg_version": "1.109",
-            "igtf_version": "1.117",
-            "osg_sha256": "41e12c05aedb4df729bf326318cc29b9b79eb097564fd68c6af2e1448ec74f75",
-            "igtf_sha256": "130d4d95cd65d01d2db250ee24c539341e3adc899b7eff1beafef1ba4674807d",
-        },
+            "osg_version": "1.119",
+            "igtf_version": "1.128",
+            "osg_commit": "1f7abbe392e339aae28625a4016bc98d58ad7cab",
+            "igtf_sha256": "1385e2206b4088cbad94264e2c252ad431f075f88a427cdee4ed523df95b9ab7",
+        }
     ]
 
     for release in releases:
         _version = "{0}.igtf.{1}".format(release["osg_version"], release["igtf_version"])
 
-        version(
-            _version,
-            url=_osg_base_url.format(
-                osg_version=release["osg_version"], igtf_version=release["igtf_version"]
-            ),
-            sha256=release["osg_sha256"],
-        )
+        version(_version, commit=release["osg_commit"])
 
         resource(
             name="igtf-{igtf_version}".format(igtf_version=release["igtf_version"]),

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

@@ -15,7 +15,7 @@ class Sos(AutotoolsPackage):
     # notify when the package is updated.
     maintainers("rscohn2")
 
-    license("GPL-2.0-or-later")
+    license("BSD-3-Clause")
 
     version("1.5.2", sha256="c9df8c6ab43890e5d8970467c188ae2fad736845875ca4c370ff047dbb37d017")
     version("1.5.1", sha256="0a6303dcbdd713ef2d83c617c1eb821227603c98cb9816c53585fd993da8a984")
@@ -24,12 +24,47 @@ class Sos(AutotoolsPackage):
 
     variant("xpmem", default=False, description="Enable xpmem for transport")
     variant("ofi", default=True, description="Enable ofi for transport")
+    variant(
+        "manual-progress",
+        default=False,
+        description="Enable intermittent progress calls in transport layer",
+    )
+    variant(
+        "ofi-manual-progress",
+        default=False,
+        when="+ofi",
+        description="Use FI_MANUAL_PROGRESS for data progress control mode",
+    )
     variant("shr-atomics", default=False, description="Enable shared memory atomic operations")
+    variant(
+        "av-map",
+        default=False,
+        description="Enable av-map instead of av-table in the OFI transport",
+    )
+    variant(
+        "completion-polling",
+        default=False,
+        description="Enable polling in quiet, fence, and local completion operations",
+    )
+    variant(
+        "thread-completion",
+        default=False,
+        description="Support SHMEM_THREAD_MULTIPLE in OFI transport using FI_THREAD_COMPLETION",
+    )
+    variant("error-checking", default=False, description="Enable error checking for SHMEM calls")
+    variant(
+        "lengthy-tests",
+        default=False,
+        description="Execute long running tests as part of 'make check'",
+    )
+    variant("rpath", default=True, description="Use rpath in compiler wrappers ")
+    variant("hard-polling", default=False, description="Enable hard polling of wait calls")
 
     depends_on("autoconf", type="build")
     depends_on("automake", type="build")
     depends_on("libtool", type="build")
     depends_on("m4", type="build")
+    depends_on("hydra", type=("build", "run"), when="+ofi")
 
     depends_on("libfabric", type="link", when="+ofi")
     depends_on("xpmem", type="link", when="+xpmem")
@@ -39,8 +74,6 @@ class Sos(AutotoolsPackage):
     filter_compiler_wrappers("oshcc", "oshc++", "oshcc", "oshfort", relative_root="bin")
 
     def setup_dependent_build_environment(self, env, dependent_spec):
-        self.setup_compiler_environment(env)
-
         # Enable the osh wrappers to use spack wrappers when inside spack
         # with env variables
         env.set("SHMEM_CC", spack_cc)
@@ -57,5 +90,14 @@ def configure_args(self):
         args.extend(self.with_or_without("ofi"))
         # This option is not compatiable with remote atomics
         args.extend(self.enable_or_disable("shr-atomics"))
+        args.extend(self.enable_or_disable("av-map"))
+        args.extend(self.enable_or_disable("completion-polling"))
+        args.extend(self.enable_or_disable("thread-completion"))
+        args.extend(self.enable_or_disable("error-checking"))
+        args.extend(self.enable_or_disable("lengthy-tests"))
+        args.extend(self.enable_or_disable("rpath"))
+        args.extend(self.enable_or_disable("manual-progress"))
+        args.extend(self.enable_or_disable("ofi-manual-progress"))
+        args.extend(self.enable_or_disable("hard-polling"))
         args.append("--enable-pmi-simple")
         return args

var/spack/repos/builtin/packages/tests-sos/package.py

@@ -0,0 +1,32 @@
+# 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 TestsSos(AutotoolsPackage):
+    """Sandia OpenSHMEM unit tests and performance testing suite."""
+
+    homepage = "https://github.com/openshmem-org/tests-sos"
+    url = "https://github.com/openshmem-org/tests-sos/archive/refs/tags/v1.5.2.tar.gz"
+
+    maintainers("jack-morrison")
+
+    version("1.5.2", sha256="3a063963ef779419aadc6b21ff2f1e4dcdd3e95fa8ed23545434e56757f3187f")
+
+    depends_on("autoconf", type="build")
+    depends_on("automake", type="build")
+    depends_on("libtool", type="build")
+    depends_on("m4", type="build")
+    depends_on("sos", type=("build", "run"))
+
+    def autoreconf(self, spec, prefix):
+        bash = which("bash")
+        bash("./autogen.sh")
+
+    def setup_build_environment(self, env):
+        env.set("CC", "oshcc")
+        env.set("CXX", "oshc++")
+        env.set("FC", "oshfort")

var/spack/repos/builtin/packages/xlc/detection_test.yaml

@@ -13,6 +13,7 @@ paths:
         script: |
           echo "IBM XL Fortran for Linux, V16.1.1 (5725-C73, 5765-J13)"
           echo "Version: 16.01.0001.0006"
+    platforms: ["linux"]
     results:
       - spec: "xlc+r@16.1"
       - spec: "xlc~r@16.1"

var/spack/repos/builtin/packages/xlf/detection_test.yaml

@@ -6,6 +6,7 @@ paths:
         script: |
           echo "IBM XL Fortran for Linux, V16.1.1 (5725-C73, 5765-J13)"
           echo "Version: 16.01.0001.0006"
+    platforms: ["linux"]
     results:
       - spec: "xlf+r@16.1"
       - spec: "xlf~r@16.1"