Make spack clean env-aware (#44227)

`spack clean <spec>` will now resolve specs based on the active environment if one is active.

If an env is active but no matching spec is found, this will fall back on fully concretizing.

.github/workflows/audit.yaml

@@ -28,7 +28,7 @@ jobs:
       run:
         shell: ${{ matrix.system.shell }}
     steps:
-    - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
     - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d
       with:
         python-version: ${{inputs.python_version}}
@@ -61,7 +61,7 @@ jobs:
           ./share/spack/qa/validate_last_exit.ps1
           spack -d audit externals
           ./share/spack/qa/validate_last_exit.ps1
-    - uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be
+    - uses: codecov/codecov-action@125fc84a9a348dbcf27191600683ec096ec9021c
       if: ${{ inputs.with_coverage == 'true' }}
       with:
         flags: unittests,audits

.github/workflows/bootstrap.yml

@@ -37,7 +37,7 @@ jobs:
               make patch unzip which xz python3 python3-devel tree \
               cmake bison
       - name: Checkout
-        uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
         with:
           fetch-depth: 0
       - name: Bootstrap clingo
@@ -60,7 +60,7 @@ jobs:
         run: |
           brew install cmake bison tree
       - name: Checkout
-        uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
         with:
           fetch-depth: 0
       - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d
@@ -92,7 +92,7 @@ jobs:
         run: |
           sudo rm -rf $(which gpg) $(which gpg2) $(which patchelf)
       - name: Checkout
-        uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
         with:
           fetch-depth: 0
       - name: Bootstrap GnuPG
@@ -121,7 +121,7 @@ jobs:
         run: |
           sudo rm -rf $(which gpg) $(which gpg2) $(which patchelf)
       - name: Checkout
-        uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
         with:
           fetch-depth: 0
       - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d

.github/workflows/build-containers.yml

@@ -56,7 +56,7 @@ jobs:
     if: github.repository == 'spack/spack'
     steps:
       - name: Checkout
-        uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
 
       - uses: docker/metadata-action@8e5442c4ef9f78752691e2d8f8d19755c6f78e81
         id: docker_meta

.github/workflows/ci.yaml

@@ -36,7 +36,7 @@ jobs:
       core: ${{ steps.filter.outputs.core }}
       packages: ${{ steps.filter.outputs.packages }}
     steps:
-      - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
         if: ${{ github.event_name == 'push' }}
         with:
           fetch-depth: 0

.github/workflows/nightly-win-builds.yml

@@ -14,7 +14,7 @@ jobs:
   build-paraview-deps:
     runs-on: windows-latest
     steps:
-    - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
       with:
         fetch-depth: 0
     - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d

.github/workflows/style/requirements.txt

@@ -3,5 +3,5 @@ clingo==5.7.1
 flake8==7.0.0
 isort==5.13.2
 mypy==1.8.0
-types-six==1.16.21.9
+types-six==1.16.21.20240513
 vermin==1.6.0

.github/workflows/unit_tests.yaml

@@ -51,7 +51,7 @@ jobs:
           on_develop: false
 
     steps:
-    - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
       with:
         fetch-depth: 0
     - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d
@@ -91,7 +91,7 @@ jobs:
           UNIT_TEST_COVERAGE: ${{ matrix.python-version == '3.11' }}
       run: |
           share/spack/qa/run-unit-tests
-    - uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be
+    - uses: codecov/codecov-action@125fc84a9a348dbcf27191600683ec096ec9021c
       with:
         flags: unittests,linux,${{ matrix.concretizer }}
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -100,7 +100,7 @@ jobs:
   shell:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
       with:
         fetch-depth: 0
     - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d
@@ -124,7 +124,7 @@ jobs:
           COVERAGE: true
       run: |
           share/spack/qa/run-shell-tests
-    - uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be
+    - uses: codecov/codecov-action@125fc84a9a348dbcf27191600683ec096ec9021c
       with:
         flags: shelltests,linux
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -141,7 +141,7 @@ jobs:
           dnf install -y \
               bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
               make patch tcl unzip which xz
-    - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
     - name: Setup repo and non-root user
       run: |
           git --version
@@ -160,7 +160,7 @@ jobs:
   clingo-cffi:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
       with:
         fetch-depth: 0
     - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d
@@ -185,7 +185,7 @@ jobs:
           SPACK_TEST_SOLVER: clingo
       run: |
           share/spack/qa/run-unit-tests
-    - uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be
+    - uses: codecov/codecov-action@125fc84a9a348dbcf27191600683ec096ec9021c
       with:
         flags: unittests,linux,clingo
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -198,7 +198,7 @@ jobs:
         os: [macos-13, macos-14]
         python-version: ["3.11"]
     steps:
-    - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
       with:
         fetch-depth: 0
     - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d
@@ -223,7 +223,7 @@ jobs:
         $(which spack) solve zlib
         common_args=(--dist loadfile --tx '4*popen//python=./bin/spack-tmpconfig python -u ./bin/spack python' -x)
         $(which spack) unit-test --verbose --cov --cov-config=pyproject.toml --cov-report=xml:coverage.xml "${common_args[@]}"
-    - uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be
+    - uses: codecov/codecov-action@125fc84a9a348dbcf27191600683ec096ec9021c
       with:
         flags: unittests,macos
         token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/valid-style.yml

@@ -18,7 +18,7 @@ jobs:
   validate:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
     - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d
       with:
         python-version: '3.11'
@@ -35,7 +35,7 @@ jobs:
   style:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
       with:
         fetch-depth: 0
     - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d
@@ -70,7 +70,7 @@ jobs:
           dnf install -y \
               bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
               make patch tcl unzip which xz
-      - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
       - name: Setup repo and non-root user
         run: |
           git --version

.github/workflows/windows_python.yml

@@ -15,7 +15,7 @@ jobs:
   unit-tests:
     runs-on: windows-latest
     steps:
-    - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
       with:
         fetch-depth: 0
     - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d
@@ -33,7 +33,7 @@ jobs:
         ./share/spack/qa/validate_last_exit.ps1
         coverage combine -a
         coverage xml
-    - uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be
+    - uses: codecov/codecov-action@125fc84a9a348dbcf27191600683ec096ec9021c
       with:
         flags: unittests,windows
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -41,7 +41,7 @@ jobs:
   unit-tests-cmd:
     runs-on: windows-latest
     steps:
-    - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
       with:
         fetch-depth: 0
     - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d
@@ -59,7 +59,7 @@ jobs:
         ./share/spack/qa/validate_last_exit.ps1
         coverage combine -a
         coverage xml
-    - uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be
+    - uses: codecov/codecov-action@125fc84a9a348dbcf27191600683ec096ec9021c
       with:
         flags: unittests,windows
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -67,7 +67,7 @@ jobs:
   build-abseil:
     runs-on: windows-latest
     steps:
-    - uses: actions/checkout@44c2b7a8a4ea60a981eaca3cf939b5f4305c123b
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
       with:
         fetch-depth: 0
     - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d

README.md

@@ -32,7 +32,7 @@
 
 Spack is a multi-platform package manager that builds and installs
 multiple versions and configurations of software. It works on Linux,
-macOS, and many supercomputers. Spack is non-destructive: installing a
+macOS, Windows, and many supercomputers. Spack is non-destructive: installing a
 new version of a package does not break existing installations, so many
 configurations of the same package can coexist.
 

bin/spack.ps1

@@ -144,3 +144,5 @@ switch($SpackSubCommand)
     "unload" {Invoke-SpackLoad}
     default  {python "$Env:SPACK_ROOT/bin/spack" $SpackCMD_params $SpackSubCommand $SpackSubCommandArgs}
 }
+
+exit $LASTEXITCODE

etc/spack/defaults/cray/packages.yaml

@@ -1,19 +0,0 @@
-# -------------------------------------------------------------------------
-# This file controls default concretization preferences for Spack.
-#
-# Settings here are versioned with Spack and are intended to provide
-# sensible defaults out of the box. Spack maintainers should edit this
-# file to keep it current.
-#
-# Users can override these settings by editing the following files.
-#
-# Per-spack-instance settings (overrides defaults):
-#   $SPACK_ROOT/etc/spack/packages.yaml
-#
-# Per-user settings (overrides default and site settings):
-#   ~/.spack/packages.yaml
-# -------------------------------------------------------------------------
-packages:
-  all:
-    providers:
-      iconv: [glibc, musl, libiconv]

etc/spack/defaults/linux/packages.yaml

@@ -1,19 +0,0 @@
-# -------------------------------------------------------------------------
-# This file controls default concretization preferences for Spack.
-#
-# Settings here are versioned with Spack and are intended to provide
-# sensible defaults out of the box. Spack maintainers should edit this
-# file to keep it current.
-#
-# Users can override these settings by editing the following files.
-#
-# Per-spack-instance settings (overrides defaults):
-#   $SPACK_ROOT/etc/spack/packages.yaml
-#
-# Per-user settings (overrides default and site settings):
-#   ~/.spack/packages.yaml
-# -------------------------------------------------------------------------
-packages:
-  all:
-    providers:
-      iconv: [glibc, musl, libiconv]

etc/spack/defaults/packages.yaml

@@ -38,10 +38,9 @@ packages:
       lapack: [openblas, amdlibflame]
       libc: [glibc, musl]
       libgfortran: [ gcc-runtime ]
-      libglx: [mesa+glx, mesa18+glx]
+      libglx: [mesa+glx]
       libifcore: [ intel-oneapi-runtime ]
       libllvm: [llvm]
-      libosmesa: [mesa+osmesa, mesa18+osmesa]
       lua-lang: [lua, lua-luajit-openresty, lua-luajit]
       luajit: [lua-luajit-openresty, lua-luajit]
       mariadb-client: [mariadb-c-client, mariadb]

lib/spack/docs/build_systems/autotoolspackage.rst

@@ -147,6 +147,15 @@ example, the ``bash`` shell is used to run the ``autogen.sh`` script.
    def autoreconf(self, spec, prefix):
        which("bash")("autogen.sh")
 
+If the ``package.py`` has build instructions in a separate
+:ref:`builder class <multiple_build_systems>`, the signature for a phase changes slightly:
+
+.. code-block:: python
+
+   class AutotoolsBuilder(AutotoolsBuilder):
+      def autoreconf(self, pkg, spec, prefix):
+         which("bash")("autogen.sh")
+
 """""""""""""""""""""""""""""""""""""""
 patching configure or Makefile.in files
 """""""""""""""""""""""""""""""""""""""

lib/spack/docs/build_systems/inteloneapipackage.rst

@@ -25,7 +25,7 @@ use Spack to build packages with the tools.
 The Spack Python class ``IntelOneapiPackage`` is a base class that is
 used by ``IntelOneapiCompilers``, ``IntelOneapiMkl``,
 ``IntelOneapiTbb`` and other classes to implement the oneAPI
-packages. Search for ``oneAPI`` at `<packages.spack.io>`_ for the full
+packages. Search for ``oneAPI`` at `packages.spack.io <https://packages.spack.io>`_ for the full
 list of available oneAPI packages, or use::
 
   spack list -d oneAPI

lib/spack/docs/chain.rst

@@ -11,7 +11,8 @@ Chaining Spack Installations
 
 You can point your Spack installation to another installation to use any
 packages that are installed there. To register the other Spack instance,
-you can add it as an entry to ``upstreams.yaml``:
+you can add it as an entry to ``upstreams.yaml`` at any of the
+:ref:`configuration-scopes`:
 
 .. code-block:: yaml
 
@@ -22,7 +23,8 @@ you can add it as an entry to ``upstreams.yaml``:
       install_tree: /path/to/another/spack/opt/spack
 
 ``install_tree`` must point to the ``opt/spack`` directory inside of the
-Spack base directory.
+Spack base directory, or the location of the ``install_tree`` defined
+in :ref:`config.yaml <config-yaml>`.
 
 Once the upstream Spack instance has been added, ``spack find`` will
 automatically check the upstream instance when querying installed packages,

lib/spack/docs/repositories.rst

@@ -476,9 +476,3 @@ implemented using Python's built-in `sys.path
 :py:mod:`spack.repo` module implements a custom `Python importer
 <https://docs.python.org/2/library/imp.html>`_.
 
-.. warning::
-
-   The mechanism for extending packages is not yet extensively tested,
-   and extending packages across repositories imposes inter-repo
-   dependencies, which may be hard to manage.  Use this feature at your
-   own risk, but let us know if you have a use case for it.

lib/spack/docs/requirements.txt

@@ -6,7 +6,7 @@ python-levenshtein==0.25.1
 docutils==0.20.1
 pygments==2.18.0
 urllib3==2.2.1
-pytest==8.2.0
+pytest==8.2.1
 isort==5.13.2
 black==24.4.2
 flake8==7.0.0

lib/spack/llnl/util/filesystem.py

@@ -843,7 +843,7 @@ def copy_tree(
             if islink(s):
                 link_target = resolve_link_target_relative_to_the_link(s)
                 if symlinks:
-                    target = os.readlink(s)
+                    target = readlink(s)
                     if os.path.isabs(target):
 
                         def escaped_path(path):
@@ -2531,8 +2531,14 @@ def establish_link(self):
 
         # for each binary install dir in self.pkg (i.e. pkg.prefix.bin, pkg.prefix.lib)
         # install a symlink to each dependent library
-        for library, lib_dir in itertools.product(self.rpaths, self.library_dependents):
-            self._link(library, lib_dir)
+
+        # do not rpath for system libraries included in the dag
+        # we should not be modifying libraries managed by the Windows system
+        # as this will negatively impact linker behavior and can result in permission
+        # errors if those system libs are not modifiable by Spack
+        if "windows-system" not in getattr(self.pkg, "tags", []):
+            for library, lib_dir in itertools.product(self.rpaths, self.library_dependents):
+                self._link(library, lib_dir)
 
 
 @system_path_filter

lib/spack/spack/audit.py

@@ -421,6 +421,10 @@ def _check_patch_urls(pkgs, error_cls):
         r"^https?://(?:patch-diff\.)?github(?:usercontent)?\.com/"
         r".+/.+/(?:commit|pull)/[a-fA-F0-9]+\.(?:patch|diff)"
     )
+    github_pull_commits_re = (
+        r"^https?://(?:patch-diff\.)?github(?:usercontent)?\.com/"
+        r".+/.+/pull/\d+/commits/[a-fA-F0-9]+\.(?:patch|diff)"
+    )
     # Only .diff URLs have stable/full hashes:
     # https://forum.gitlab.com/t/patches-with-full-index/29313
     gitlab_patch_url_re = (
@@ -436,14 +440,24 @@ def _check_patch_urls(pkgs, error_cls):
                 if not isinstance(patch, spack.patch.UrlPatch):
                     continue
 
-                if re.match(github_patch_url_re, patch.url):
+                if re.match(github_pull_commits_re, patch.url):
+                    url = re.sub(r"/pull/\d+/commits/", r"/commit/", patch.url)
+                    url = re.sub(r"^(.*)(?<!full_index=1)$", r"\1?full_index=1", url)
+                    errors.append(
+                        error_cls(
+                            f"patch URL in package {pkg_cls.name} "
+                            + "must not be a pull request commit; "
+                            + f"instead use {url}",
+                            [patch.url],
+                        )
+                    )
+                elif re.match(github_patch_url_re, patch.url):
                     full_index_arg = "?full_index=1"
                     if not patch.url.endswith(full_index_arg):
                         errors.append(
                             error_cls(
-                                "patch URL in package {0} must end with {1}".format(
-                                    pkg_cls.name, full_index_arg
-                                ),
+                                f"patch URL in package {pkg_cls.name} "
+                                + f"must end with {full_index_arg}",
                                 [patch.url],
                             )
                         )
@@ -451,9 +465,7 @@ def _check_patch_urls(pkgs, error_cls):
                     if not patch.url.endswith(".diff"):
                         errors.append(
                             error_cls(
-                                "patch URL in package {0} must end with .diff".format(
-                                    pkg_cls.name
-                                ),
+                                f"patch URL in package {pkg_cls.name} must end with .diff",
                                 [patch.url],
                             )
                         )

lib/spack/spack/build_environment.py

@@ -43,7 +43,7 @@
 from collections import defaultdict
 from enum import Flag, auto
 from itertools import chain
-from typing import List, Set, Tuple
+from typing import Dict, List, Set, Tuple
 
 import llnl.util.tty as tty
 from llnl.string import plural
@@ -730,12 +730,28 @@ def _static_to_shared_library(arch, compiler, static_lib, shared_lib=None, **kwa
     return compiler(*compiler_args, output=compiler_output)
 
 
-def get_rpath_deps(pkg):
-    """Return immediate or transitive RPATHs depending on the package."""
-    if pkg.transitive_rpaths:
-        return [d for d in pkg.spec.traverse(root=False, deptype=("link"))]
-    else:
-        return pkg.spec.dependencies(deptype="link")
+def _get_rpath_deps_from_spec(
+    spec: spack.spec.Spec, transitive_rpaths: bool
+) -> List[spack.spec.Spec]:
+    if not transitive_rpaths:
+        return spec.dependencies(deptype=dt.LINK)
+
+    by_name: Dict[str, spack.spec.Spec] = {}
+
+    for dep in spec.traverse(root=False, deptype=dt.LINK):
+        lookup = by_name.get(dep.name)
+        if lookup is None:
+            by_name[dep.name] = dep
+        elif lookup.version < dep.version:
+            by_name[dep.name] = dep
+
+    return list(by_name.values())
+
+
+def get_rpath_deps(pkg: spack.package_base.PackageBase) -> List[spack.spec.Spec]:
+    """Return immediate or transitive dependencies (depending on the package) that need to be
+    rpath'ed. If a package occurs multiple times, the newest version is kept."""
+    return _get_rpath_deps_from_spec(pkg.spec, pkg.transitive_rpaths)
 
 
 def get_rpaths(pkg):

lib/spack/spack/build_systems/cuda.py

@@ -137,11 +137,14 @@ def cuda_flags(arch_list):
         conflicts("%gcc@11.2:", when="+cuda ^cuda@:11.5")
         conflicts("%gcc@12:", when="+cuda ^cuda@:11.8")
         conflicts("%gcc@13:", when="+cuda ^cuda@:12.3")
+        conflicts("%gcc@14:", when="+cuda ^cuda@:12.4")
         conflicts("%clang@12:", when="+cuda ^cuda@:11.4.0")
         conflicts("%clang@13:", when="+cuda ^cuda@:11.5")
         conflicts("%clang@14:", when="+cuda ^cuda@:11.7")
         conflicts("%clang@15:", when="+cuda ^cuda@:12.0")
-        conflicts("%clang@16:", when="+cuda ^cuda@:12.3")
+        conflicts("%clang@16:", when="+cuda ^cuda@:12.1")
+        conflicts("%clang@17:", when="+cuda ^cuda@:12.3")
+        conflicts("%clang@18:", when="+cuda ^cuda@:12.4")
 
         # https://gist.github.com/ax3l/9489132#gistcomment-3860114
         conflicts("%gcc@10", when="+cuda ^cuda@:11.4.0")

lib/spack/spack/build_systems/intel.py

@@ -846,6 +846,7 @@ def scalapack_libs(self):
             "^mpich@2:" in spec_root
             or "^cray-mpich" in spec_root
             or "^mvapich2" in spec_root
+            or "^mvapich" in spec_root
             or "^intel-mpi" in spec_root
             or "^intel-oneapi-mpi" in spec_root
             or "^intel-parallel-studio" in spec_root

lib/spack/spack/ci.py

@@ -44,6 +44,7 @@
 from spack import traverse
 from spack.error import SpackError
 from spack.reporters import CDash, CDashConfiguration
+from spack.reporters.cdash import SPACK_CDASH_TIMEOUT
 from spack.reporters.cdash import build_stamp as cdash_build_stamp
 
 # See https://docs.gitlab.com/ee/ci/yaml/#retry for descriptions of conditions
@@ -683,6 +684,22 @@ def generate_gitlab_ci_yaml(
             "instead.",
         )
 
+    def ensure_expected_target_path(path):
+        """Returns passed paths with all Windows path separators exchanged
+        for posix separators only if copy_only_pipeline is enabled
+
+        This is required as copy_only_pipelines are a unique scenario where
+        the generate job and child pipelines are run on different platforms.
+        To make this compatible w/ Windows, we cannot write Windows style path separators
+        that will be consumed on by the Posix copy job runner.
+
+        TODO (johnwparent): Refactor config + cli read/write to deal only in posix
+        style paths
+        """
+        if copy_only_pipeline and path:
+            path = path.replace("\\", "/")
+        return path
+
     pipeline_mirrors = spack.mirror.MirrorCollection(binary=True)
     deprecated_mirror_config = False
     buildcache_destination = None
@@ -806,7 +823,7 @@ def generate_gitlab_ci_yaml(
             if scope not in include_scopes and scope not in env_includes:
                 include_scopes.insert(0, scope)
         env_includes.extend(include_scopes)
-        env_yaml_root["spack"]["include"] = env_includes
+        env_yaml_root["spack"]["include"] = [ensure_expected_target_path(i) for i in env_includes]
 
         if "gitlab-ci" in env_yaml_root["spack"] and "ci" not in env_yaml_root["spack"]:
             env_yaml_root["spack"]["ci"] = env_yaml_root["spack"].pop("gitlab-ci")
@@ -1227,6 +1244,9 @@ def main_script_replacements(cmd):
             "SPACK_REBUILD_EVERYTHING": str(rebuild_everything),
             "SPACK_REQUIRE_SIGNING": os.environ.get("SPACK_REQUIRE_SIGNING", "False"),
         }
+        output_vars = output_object["variables"]
+        for item, val in output_vars.items():
+            output_vars[item] = ensure_expected_target_path(val)
 
         # TODO: Remove this block in Spack 0.23
         if deprecated_mirror_config and remote_mirror_override:
@@ -1283,7 +1303,6 @@ def main_script_replacements(cmd):
     sorted_output = {}
     for output_key, output_value in sorted(output_object.items()):
         sorted_output[output_key] = output_value
-
     if known_broken_specs_encountered:
         tty.error("This pipeline generated hashes known to be broken on develop:")
         display_broken_spec_messages(broken_specs_url, known_broken_specs_encountered)
@@ -1506,7 +1525,7 @@ def download_and_extract_artifacts(url, work_dir):
     request = Request(url, headers=headers)
     request.get_method = lambda: "GET"
 
-    response = opener.open(request)
+    response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
     response_code = response.getcode()
 
     if response_code != 200:
@@ -2254,7 +2273,7 @@ def create_buildgroup(self, opener, headers, url, group_name, group_type):
 
         request = Request(url, data=enc_data, headers=headers)
 
-        response = opener.open(request)
+        response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
         response_code = response.getcode()
 
         if response_code not in [200, 201]:
@@ -2300,7 +2319,7 @@ def populate_buildgroup(self, job_names):
         request = Request(url, data=enc_data, headers=headers)
         request.get_method = lambda: "PUT"
 
-        response = opener.open(request)
+        response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
         response_code = response.getcode()
 
         if response_code != 200:

lib/spack/spack/cmd/buildcache.py

@@ -13,7 +13,6 @@
 import shutil
 import sys
 import tempfile
-import urllib.request
 from typing import Dict, List, Optional, Tuple, Union
 
 import llnl.util.tty as tty
@@ -54,6 +53,7 @@
 from spack.oci.oci import (
     copy_missing_layers_with_retry,
     get_manifest_and_config_with_retry,
+    list_tags,
     upload_blob_with_retry,
     upload_manifest_with_retry,
 )
@@ -856,10 +856,7 @@ def _config_from_tag(image_ref: ImageReference, tag: str) -> Optional[dict]:
 
 
 def _update_index_oci(image_ref: ImageReference, tmpdir: str, pool: MaybePool) -> None:
-    request = urllib.request.Request(url=image_ref.tags_url())
-    response = spack.oci.opener.urlopen(request)
-    spack.oci.opener.ensure_status(request, response, 200)
-    tags = json.load(response)["tags"]
+    tags = list_tags(image_ref)
 
     # Fetch all image config files in parallel
     spec_dicts = pool.starmap(

lib/spack/spack/cmd/clean.py

@@ -106,7 +106,8 @@ def clean(parser, args):
 
     # Then do the cleaning falling through the cases
     if args.specs:
-        specs = spack.cmd.parse_specs(args.specs, concretize=True)
+        specs = spack.cmd.parse_specs(args.specs, concretize=False)
+        specs = list(spack.cmd.matching_spec_from_env(x) for x in specs)
         for spec in specs:
             msg = "Cleaning build stage [{0}]"
             tty.msg(msg.format(spec.short_spec))

lib/spack/spack/cmd/uninstall.py

@@ -151,7 +151,8 @@ def is_installed(spec):
         key=lambda s: s.dag_hash(),
     )
 
-    return [spec for spec in specs if is_installed(spec)]
+    with spack.store.STORE.db.read_transaction():
+        return [spec for spec in specs if is_installed(spec)]
 
 
 def dependent_environments(
@@ -239,6 +240,8 @@ def get_uninstall_list(args, specs: List[spack.spec.Spec], env: Optional[ev.Envi
             print()
             tty.info("The following environments still reference these specs:")
             colify([e.name for e in other_dependent_envs.keys()], indent=4)
+            if env:
+                msgs.append("use `spack remove` to remove the spec from the current environment")
             msgs.append("use `spack env remove` to remove environments")
         msgs.append("use `spack uninstall --force` to override")
         print()

lib/spack/spack/compilers/__init__.py

@@ -220,10 +220,10 @@ def _compiler_config_from_external(config):
         operating_system = host_platform.operating_system("default_os")
         target = host_platform.target("default_target").microarchitecture
     else:
-        target = spec.target
+        target = spec.architecture.target
         if not target:
-            host_platform = spack.platforms.host()
-            target = host_platform.target("default_target").microarchitecture
+            target = spack.platforms.host().target("default_target")
+        target = target.microarchitecture
 
         operating_system = spec.os
         if not operating_system:

lib/spack/spack/compilers/clang.py

@@ -96,6 +96,8 @@ def verbose_flag(self):
 
     openmp_flag = "-fopenmp"
 
+    # C++ flags based on CMake Modules/Compiler/Clang.cmake
+
     @property
     def cxx11_flag(self):
         if self.real_version < Version("3.3"):
@@ -120,6 +122,24 @@ def cxx17_flag(self):
 
         return "-std=c++17"
 
+    @property
+    def cxx20_flag(self):
+        if self.real_version < Version("5.0"):
+            raise UnsupportedCompilerFlag(self, "the C++20 standard", "cxx20_flag", "< 5.0")
+        elif self.real_version < Version("11.0"):
+            return "-std=c++2a"
+        else:
+            return "-std=c++20"
+
+    @property
+    def cxx23_flag(self):
+        if self.real_version < Version("12.0"):
+            raise UnsupportedCompilerFlag(self, "the C++23 standard", "cxx23_flag", "< 12.0")
+        elif self.real_version < Version("17.0"):
+            return "-std=c++2b"
+        else:
+            return "-std=c++23"
+
     @property
     def c99_flag(self):
         return "-std=c99"
@@ -142,7 +162,10 @@ def c17_flag(self):
     def c23_flag(self):
         if self.real_version < Version("9.0"):
             raise UnsupportedCompilerFlag(self, "the C23 standard", "c23_flag", "< 9.0")
-        return "-std=c2x"
+        elif self.real_version < Version("18.0"):
+            return "-std=c2x"
+        else:
+            return "-std=c23"
 
     @property
     def cc_pic_flag(self):

lib/spack/spack/directory_layout.py

@@ -15,6 +15,7 @@
 
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
+from llnl.util.symlink import readlink
 
 import spack.config
 import spack.hash_types as ht
@@ -181,7 +182,7 @@ def deprecated_file_path(self, deprecated_spec, deprecator_spec=None):
         base_dir = (
             self.path_for_spec(deprecator_spec)
             if deprecator_spec
-            else os.readlink(deprecated_spec.prefix)
+            else readlink(deprecated_spec.prefix)
         )
 
         yaml_path = os.path.join(

lib/spack/spack/environment/environment.py

@@ -22,7 +22,7 @@
 import llnl.util.tty as tty
 import llnl.util.tty.color as clr
 from llnl.util.link_tree import ConflictingSpecsError
-from llnl.util.symlink import symlink
+from llnl.util.symlink import readlink, symlink
 
 import spack.compilers
 import spack.concretize
@@ -662,7 +662,7 @@ def _current_root(self):
         if not os.path.islink(self.root):
             return None
 
-        root = os.readlink(self.root)
+        root = readlink(self.root)
         if os.path.isabs(root):
             return root
 

lib/spack/spack/hooks/absolutify_elf_sonames.py

@@ -13,7 +13,6 @@
 import spack.config
 import spack.relocate
 from spack.util.elf import ElfParsingError, parse_elf
-from spack.util.executable import Executable
 
 
 def is_shared_library_elf(filepath):
@@ -149,10 +148,9 @@ def post_install(spec, explicit=None):
         return
 
     # Should failing to locate patchelf be a hard error?
-    patchelf_path = spack.relocate._patchelf()
-    if not patchelf_path:
+    patchelf = spack.relocate._patchelf()
+    if not patchelf:
         return
-    patchelf = Executable(patchelf_path)
 
     fixes = find_and_patch_sonames(spec.prefix, spec.package.non_bindable_shared_objects, patchelf)
 

lib/spack/spack/oci/oci.py

@@ -11,7 +11,7 @@
 import urllib.parse
 import urllib.request
 from http.client import HTTPResponse
-from typing import NamedTuple, Tuple
+from typing import List, NamedTuple, Tuple
 from urllib.request import Request
 
 import llnl.util.tty as tty
@@ -27,6 +27,7 @@
 import spack.stage
 import spack.traverse
 import spack.util.crypto
+import spack.util.url
 
 from .image import Digest, ImageReference
 
@@ -69,6 +70,42 @@ def with_query_param(url: str, param: str, value: str) -> str:
     )
 
 
+def list_tags(ref: ImageReference, _urlopen: spack.oci.opener.MaybeOpen = None) -> List[str]:
+    """Retrieves the list of tags associated with an image, handling pagination."""
+    _urlopen = _urlopen or spack.oci.opener.urlopen
+    tags = set()
+    fetch_url = ref.tags_url()
+
+    while True:
+        # Fetch tags
+        request = Request(url=fetch_url)
+        response = _urlopen(request)
+        spack.oci.opener.ensure_status(request, response, 200)
+        tags.update(json.load(response)["tags"])
+
+        # Check for pagination
+        link_header = response.headers["Link"]
+
+        if link_header is None:
+            break
+
+        tty.debug(f"OCI tag pagination: {link_header}")
+
+        rel_next_value = spack.util.url.parse_link_rel_next(link_header)
+
+        if rel_next_value is None:
+            break
+
+        rel_next = urllib.parse.urlparse(rel_next_value)
+
+        if rel_next.scheme not in ("https", ""):
+            break
+
+        fetch_url = ref.endpoint(rel_next_value)
+
+    return sorted(tags)
+
+
 def upload_blob(
     ref: ImageReference,
     file: str,

lib/spack/spack/package_base.py

@@ -161,7 +161,11 @@ def windows_establish_runtime_linkage(self):
 
         Performs symlinking to incorporate rpath dependencies to Windows runtime search paths
         """
-        if sys.platform == "win32":
+        # If spec is an external, we should not be modifying its bin directory, as we would
+        # be doing in this method
+        # Spack should in general not modify things it has not installed
+        # we can reasonably expect externals to have their link interface properly established
+        if sys.platform == "win32" and not self.spec.external:
             self.win_rpath.add_library_dependent(*self.win_add_library_dependent())
             self.win_rpath.add_rpath(*self.win_add_rpath())
             self.win_rpath.establish_link()
@@ -2446,9 +2450,18 @@ def rpath(self):
 
         # on Windows, libraries of runtime interest are typically
         # stored in the bin directory
+        # Do not include Windows system libraries in the rpath interface
+        # these libraries are handled automatically by VS/VCVARS and adding
+        # Spack derived system libs into the link path or address space of a program
+        # can result in conflicting versions, which makes Spack packages less useable
         if sys.platform == "win32":
             rpaths = [self.prefix.bin]
-            rpaths.extend(d.prefix.bin for d in deps if os.path.isdir(d.prefix.bin))
+            rpaths.extend(
+                d.prefix.bin
+                for d in deps
+                if os.path.isdir(d.prefix.bin)
+                and "windows-system" not in getattr(d.package, "tags", [])
+            )
         else:
             rpaths = [self.prefix.lib, self.prefix.lib64]
             rpaths.extend(d.prefix.lib for d in deps if os.path.isdir(d.prefix.lib))

lib/spack/spack/platforms/cray.py

@@ -10,6 +10,7 @@
 import archspec.cpu
 
 import llnl.util.tty as tty
+from llnl.util.symlink import readlink
 
 import spack.target
 import spack.version
@@ -133,7 +134,7 @@ def craype_type_and_version(cls):
         # Take the default version from known symlink path
         default_path = os.path.join(craype_dir, "default")
         if os.path.islink(default_path):
-            version = spack.version.Version(os.readlink(default_path))
+            version = spack.version.Version(readlink(default_path))
             return (craype_type, version)
 
         # If no default version, sort available versions and return latest

lib/spack/spack/relocate.py

@@ -566,7 +566,7 @@ def make_link_relative(new_links, orig_links):
         orig_links (list): original links
     """
     for new_link, orig_link in zip(new_links, orig_links):
-        target = os.readlink(orig_link)
+        target = readlink(orig_link)
         relative_target = os.path.relpath(target, os.path.dirname(orig_link))
         os.unlink(new_link)
         symlink(relative_target, new_link)

lib/spack/spack/repo.py

@@ -241,7 +241,7 @@ def get_all_package_diffs(type, rev1="HEAD^1", rev2="HEAD"):
 
     Arguments:
 
-        type (str): String containing one or more of 'A', 'B', 'C'
+        type (str): String containing one or more of 'A', 'R', 'C'
         rev1 (str): Revision to compare against, default is 'HEAD^'
         rev2 (str): Revision to compare to rev1, default is 'HEAD'
 
@@ -264,7 +264,7 @@ def get_all_package_diffs(type, rev1="HEAD^1", rev2="HEAD"):
     lines = [] if not out else re.split(r"\s+", out)
     changed = set()
     for path in lines:
-        pkg_name, _, _ = path.partition(os.sep)
+        pkg_name, _, _ = path.partition("/")
         if pkg_name not in added and pkg_name not in removed:
             changed.add(pkg_name)
 

lib/spack/spack/reporters/cdash.py

@@ -58,7 +58,8 @@
 # Initialize data structures common to each phase's report.
 CDASH_PHASES = set(MAP_PHASES_TO_CDASH.values())
 CDASH_PHASES.add("update")
-
+# CDash request timeout in seconds
+SPACK_CDASH_TIMEOUT = 45
 
 CDashConfiguration = collections.namedtuple(
     "CDashConfiguration", ["upload_url", "packages", "build", "site", "buildstamp", "track"]
@@ -447,7 +448,7 @@ def upload(self, filename):
                 # By default, urllib2 only support GET and POST.
                 # CDash expects this file to be uploaded via PUT.
                 request.get_method = lambda: "PUT"
-                response = opener.open(request)
+                response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
                 if self.current_package_name not in self.buildIds:
                     resp_value = response.read()
                     if isinstance(resp_value, bytes):

lib/spack/spack/rewiring.py

@@ -9,7 +9,7 @@
 import tempfile
 from collections import OrderedDict
 
-from llnl.util.symlink import symlink
+from llnl.util.symlink import readlink, symlink
 
 import spack.binary_distribution as bindist
 import spack.error
@@ -26,7 +26,7 @@ def _relocate_spliced_links(links, orig_prefix, new_prefix):
     in our case. This still needs to be called after the copy to destination
     because it expects the new directory structure to be in place."""
     for link in links:
-        link_target = os.readlink(os.path.join(orig_prefix, link))
+        link_target = readlink(os.path.join(orig_prefix, link))
         link_target = re.sub("^" + orig_prefix, new_prefix, link_target)
         new_link_path = os.path.join(new_prefix, link)
         os.unlink(new_link_path)

lib/spack/spack/solver/asp.py

@@ -314,6 +314,10 @@ def using_libc_compatibility() -> bool:
     return spack.platforms.host().name == "linux"
 
 
+def c_compiler_runs(compiler: spack.compiler.Compiler) -> bool:
+    return compiler.compiler_verbose_output is not None
+
+
 def extend_flag_list(flag_list, new_flags):
     """Extend a list of flags, preserving order and precedence.
 
@@ -1935,6 +1939,11 @@ def _spec_clauses(
             for virtual in virtuals:
                 clauses.append(fn.attr("virtual_on_incoming_edges", spec.name, virtual))
 
+        # If the spec is external and concrete, we allow all the libcs on the system
+        if spec.external and spec.concrete and using_libc_compatibility():
+            for libc in self.libcs:
+                clauses.append(fn.attr("compatible_libc", spec.name, libc.name, libc.version))
+
         # add all clauses from dependencies
         if transitive:
             # TODO: Eventually distinguish 2 deps on the same pkg (build and link)
@@ -2975,6 +2984,13 @@ class CompilerParser:
     def __init__(self, configuration) -> None:
         self.compilers: Set[KnownCompiler] = set()
         for c in all_compilers_in_config(configuration):
+            if using_libc_compatibility() and not c_compiler_runs(c):
+                tty.debug(
+                    f"the C compiler {c.cc} does not exist, or does not run correctly."
+                    f" The compiler {c.spec} will not be used during concretization."
+                )
+                continue
+
             if using_libc_compatibility() and not c.default_libc:
                 warnings.warn(
                     f"cannot detect libc from {c.spec}. The compiler will not be used "

lib/spack/spack/solver/concretize.lp

@@ -1345,8 +1345,10 @@ build(PackageNode) :- not attr("hash", PackageNode, _), attr("node", PackageNode
 % topmost-priority criterion to reuse what is installed.
 %
 % The priority ranges are:
-%   200+        Shifted priorities for build nodes; correspond to priorities 0 - 99.
-%   100 - 199   Unshifted priorities. Currently only includes minimizing #builds.
+%   1000+       Optimizations for concretization errors
+%   300 - 1000  Highest priority optimizations for valid solutions
+%   200 - 299   Shifted priorities for build nodes; correspond to priorities 0 - 99.
+%   100 - 199   Unshifted priorities. Currently only includes minimizing #builds and minimizing dupes.
 %   0   -  99   Priorities for non-built nodes.
 build_priority(PackageNode, 200) :- build(PackageNode), attr("node", PackageNode).
 build_priority(PackageNode, 0)   :- not build(PackageNode), attr("node", PackageNode).
@@ -1394,6 +1396,16 @@ build_priority(PackageNode, 0)   :- not build(PackageNode), attr("node", Package
 %   2. a `#minimize{ 0@2 : #true }.` statement that ensures the criterion
 %      is displayed (clingo doesn't display sums over empty sets by default)
 
+% A condition group specifies one or more specs that must be satisfied.
+% Specs declared first are preferred, so we assign increasing weights and
+% minimize the weights.
+opt_criterion(310, "requirement weight").
+#minimize{ 0@310: #true }.
+#minimize {
+    Weight@310,PackageNode,Group
+    : requirement_weight(PackageNode, Group, Weight)
+}.
+
 % Try hard to reuse installed packages (i.e., minimize the number built)
 opt_criterion(110, "number of packages to build (vs. reuse)").
 #minimize { 0@110: #true }.
@@ -1405,18 +1417,6 @@ opt_criterion(100, "number of nodes from the same package").
 #minimize { ID@100,Package : attr("virtual_node", node(ID, Package)) }.
 #defined optimize_for_reuse/0.
 
-% A condition group specifies one or more specs that must be satisfied.
-% Specs declared first are preferred, so we assign increasing weights and
-% minimize the weights.
-opt_criterion(75, "requirement weight").
-#minimize{ 0@275: #true }.
-#minimize{ 0@75: #true }.
-#minimize {
-    Weight@75+Priority,PackageNode,Group
-    : requirement_weight(PackageNode, Group, Weight),
-      build_priority(PackageNode, Priority)
-}.
-
 % Minimize the number of deprecated versions being used
 opt_criterion(73, "deprecated versions used").
 #minimize{ 0@273: #true }.
@@ -1432,11 +1432,11 @@ opt_criterion(73, "deprecated versions used").
 % 1. Version weight
 % 2. Number of variants with a non default value, if not set
 % for the root package.
-opt_criterion(70, "version weight").
+opt_criterion(70, "version badness (roots)").
 #minimize{ 0@270: #true }.
 #minimize{ 0@70: #true }.
 #minimize {
-    Weight@70+Priority
+    Weight@70+Priority,PackageNode
     : attr("root", PackageNode),
       version_weight(PackageNode, Weight),
       build_priority(PackageNode, Priority)
@@ -1526,13 +1526,14 @@ opt_criterion(30, "non-preferred OS's").
 }.
 
 % Choose more recent versions for nodes
-opt_criterion(25, "version badness").
+opt_criterion(25, "version badness (non roots)").
 #minimize{ 0@225: #true }.
 #minimize{ 0@25: #true }.
 #minimize{
     Weight@25+Priority,node(X, Package)
     : version_weight(node(X, Package), Weight),
       build_priority(node(X, Package), Priority),
+      not attr("root", node(X, Package)),
       not runtime(Package)
 }.
 

lib/spack/spack/solver/libc_compatibility.lp

@@ -10,12 +10,13 @@
 %=============================================================================
 
 % A package cannot be reused if the libc is not compatible with it
-:- provider(node(X, LibcPackage), node(0, "libc")),
-   attr("version", node(X, LibcPackage), LibcVersion),
-   attr("hash", node(R, ReusedPackage), Hash),
-   % Libc packages can be reused without the "compatible_libc" attribute
-   ReusedPackage != LibcPackage,
-   not attr("compatible_libc", node(R, ReusedPackage), LibcPackage, LibcVersion).
+error(100, "Cannot reuse {0} since we cannot determine libc compatibility", ReusedPackage)
+  :- provider(node(X, LibcPackage), node(0, "libc")),
+     attr("version", node(X, LibcPackage), LibcVersion),
+     attr("hash", node(R, ReusedPackage), Hash),
+     % Libc packages can be reused without the "compatible_libc" attribute
+     ReusedPackage != LibcPackage,
+     not attr("compatible_libc", node(R, ReusedPackage), LibcPackage, LibcVersion).
 
 % Check whether the DAG has any built package
 has_built_packages() :- build(X), not external(X).

lib/spack/spack/test/audit.py

@@ -19,6 +19,8 @@
         (["missing-dependency"], ["PKG-DIRECTIVES", "PKG-PROPERTIES"]),
         # The package use a non existing variant in a depends_on directive
         (["wrong-variant-in-depends-on"], ["PKG-DIRECTIVES", "PKG-PROPERTIES"]),
+        # This package has a GitHub pull request commit patch URL
+        (["invalid-github-pull-commits-patch-url"], ["PKG-DIRECTIVES", "PKG-PROPERTIES"]),
         # This package has a GitHub patch URL without full_index=1
         (["invalid-github-patch-url"], ["PKG-DIRECTIVES", "PKG-PROPERTIES"]),
         # This package has invalid GitLab patch URLs

lib/spack/spack/test/bindist.py

@@ -22,6 +22,7 @@
 import archspec.cpu
 
 from llnl.util.filesystem import join_path, visit_directory_tree
+from llnl.util.symlink import readlink
 
 import spack.binary_distribution as bindist
 import spack.caches
@@ -1062,10 +1063,10 @@ def test_tarball_common_prefix(dummy_prefix, tmpdir):
         assert set(os.listdir(os.path.join("prefix2", "share"))) == {"file"}
 
         # Relative symlink should still be correct
-        assert os.readlink(os.path.join("prefix2", "bin", "relative_app_link")) == "app"
+        assert readlink(os.path.join("prefix2", "bin", "relative_app_link")) == "app"
 
         # Absolute symlink should remain absolute -- this is for relocation to fix up.
-        assert os.readlink(os.path.join("prefix2", "bin", "absolute_app_link")) == os.path.join(
+        assert readlink(os.path.join("prefix2", "bin", "absolute_app_link")) == os.path.join(
             dummy_prefix, "bin", "app"
         )
 

lib/spack/spack/test/build_environment.py

@@ -14,6 +14,7 @@
 
 import spack.build_environment
 import spack.config
+import spack.deptypes as dt
 import spack.package_base
 import spack.spec
 import spack.util.spack_yaml as syaml
@@ -716,3 +717,21 @@ def test_build_system_globals_only_set_on_root_during_build(default_mock_concret
     for depth, spec in root.traverse(depth=True, root=True):
         for variable in build_variables:
             assert hasattr(spec.package.module, variable) == should_be_set(depth)
+
+
+def test_rpath_with_duplicate_link_deps():
+    """If we have two instances of one package in the same link sub-dag, only the newest version is
+    rpath'ed. This is for runtime support without splicing."""
+    runtime_1 = spack.spec.Spec("runtime@=1.0")
+    runtime_2 = spack.spec.Spec("runtime@=2.0")
+    child = spack.spec.Spec("child@=1.0")
+    root = spack.spec.Spec("root@=1.0")
+
+    root.add_dependency_edge(child, depflag=dt.LINK, virtuals=())
+    root.add_dependency_edge(runtime_2, depflag=dt.LINK, virtuals=())
+    child.add_dependency_edge(runtime_1, depflag=dt.LINK, virtuals=())
+
+    rpath_deps = spack.build_environment._get_rpath_deps_from_spec(root, transitive_rpaths=True)
+    assert child in rpath_deps
+    assert runtime_2 in rpath_deps
+    assert runtime_1 not in rpath_deps

lib/spack/spack/test/ci.py

@@ -51,7 +51,7 @@ def __init__(self, response_code=200, content_to_read=[]):
         self._content = content_to_read
         self._read = [False for c in content_to_read]
 
-    def open(self, request):
+    def open(self, request, data=None, timeout=object()):
         return self
 
     def getcode(self):

lib/spack/spack/test/cmd/clean.py

@@ -11,6 +11,7 @@
 
 import spack.caches
 import spack.cmd.clean
+import spack.environment as ev
 import spack.main
 import spack.package_base
 import spack.stage
@@ -68,6 +69,20 @@ def test_function_calls(command_line, effects, mock_calls_for_clean):
         assert mock_calls_for_clean[name] == (1 if name in effects else 0)
 
 
+def test_env_aware_clean(mock_stage, install_mockery, mutable_mock_env_path, monkeypatch):
+    e = ev.create("test", with_view=False)
+    e.add("mpileaks")
+    e.concretize()
+
+    def fail(*args, **kwargs):
+        raise Exception("This should not have been called")
+
+    monkeypatch.setattr(spack.spec.Spec, "concretize", fail)
+
+    with e:
+        clean("mpileaks")
+
+
 def test_remove_python_cache(tmpdir, monkeypatch):
     cache_files = ["file1.pyo", "file2.pyc"]
     source_file = "file1.py"

lib/spack/spack/test/cmd/env.py

@@ -15,6 +15,7 @@
 import llnl.util.filesystem as fs
 import llnl.util.link_tree
 import llnl.util.tty as tty
+from llnl.util.symlink import readlink
 
 import spack.cmd.env
 import spack.config
@@ -4414,8 +4415,8 @@ def test_env_view_resolves_identical_file_conflicts(tmp_path, install_mockery, m
     #   view-file/bin/
     #     x                                          # expect this x to be linked
 
-    assert os.readlink(tmp_path / "view" / "bin" / "x") == bottom.bin.x
-    assert os.readlink(tmp_path / "view" / "bin" / "y") == top.bin.y
+    assert readlink(tmp_path / "view" / "bin" / "x") == bottom.bin.x
+    assert readlink(tmp_path / "view" / "bin" / "y") == top.bin.y
 
 
 def test_env_view_ignores_different_file_conflicts(tmp_path, install_mockery, mock_fetch):
@@ -4426,4 +4427,4 @@ def test_env_view_ignores_different_file_conflicts(tmp_path, install_mockery, mo
         install()
         prefix_dependent = e.matching_spec("view-ignore-conflict").prefix
     # The dependent's file is linked into the view
-    assert os.readlink(tmp_path / "view" / "bin" / "x") == prefix_dependent.bin.x
+    assert readlink(tmp_path / "view" / "bin" / "x") == prefix_dependent.bin.x

lib/spack/spack/test/compilers/basics.py

@@ -384,9 +384,18 @@ def test_clang_flags():
     unsupported_flag_test("cxx17_flag", "clang@3.4")
     supported_flag_test("cxx17_flag", "-std=c++1z", "clang@3.5")
     supported_flag_test("cxx17_flag", "-std=c++17", "clang@5.0")
+    unsupported_flag_test("cxx20_flag", "clang@4.0")
+    supported_flag_test("cxx20_flag", "-std=c++2a", "clang@5.0")
+    supported_flag_test("cxx20_flag", "-std=c++20", "clang@11.0")
+    unsupported_flag_test("cxx23_flag", "clang@11.0")
+    supported_flag_test("cxx23_flag", "-std=c++2b", "clang@12.0")
+    supported_flag_test("cxx23_flag", "-std=c++23", "clang@17.0")
     supported_flag_test("c99_flag", "-std=c99", "clang@3.3")
     unsupported_flag_test("c11_flag", "clang@2.0")
     supported_flag_test("c11_flag", "-std=c11", "clang@6.1.0")
+    unsupported_flag_test("c23_flag", "clang@8.0")
+    supported_flag_test("c23_flag", "-std=c2x", "clang@9.0")
+    supported_flag_test("c23_flag", "-std=c23", "clang@18.0")
     supported_flag_test("cc_pic_flag", "-fPIC", "clang@3.3")
     supported_flag_test("cxx_pic_flag", "-fPIC", "clang@3.3")
     supported_flag_test("f77_pic_flag", "-fPIC", "clang@3.3")

lib/spack/spack/test/concretize.py

@@ -1914,11 +1914,11 @@ def test_version_weight_and_provenance(self):
             libc_offset = 1 if spack.solver.asp.using_libc_compatibility() else 0
             criteria = [
                 (num_specs - 1 - libc_offset, None, "number of packages to build (vs. reuse)"),
-                (2, 0, "version badness"),
+                (2, 0, "version badness (non roots)"),
             ]
 
             for criterion in criteria:
-                assert criterion in result.criteria, result_spec
+                assert criterion in result.criteria, criterion
             assert result_spec.satisfies("^b@1.0")
 
     @pytest.mark.only_clingo("Use case not supported by the original concretizer")
@@ -2546,6 +2546,30 @@ def test_include_specs_from_externals_and_libcs(
 
         assert result["deprecated-versions"].satisfies("@1.0.0")
 
+    @pytest.mark.regression("44085")
+    @pytest.mark.only_clingo("Use case not supported by the original concretizer")
+    def test_can_reuse_concrete_externals_for_dependents(self, mutable_config, tmp_path):
+        """Test that external specs that are in the DB can be reused. This means they are
+        preferred to concretizing another external from packages.yaml
+        """
+        packages_yaml = {
+            "externaltool": {"externals": [{"spec": "externaltool@2.0", "prefix": "/fake/path"}]}
+        }
+        mutable_config.set("packages", packages_yaml)
+        # Concretize with gcc@9 to get a suboptimal spec, since we have gcc@10 available
+        external_spec = Spec("externaltool@2 %gcc@9").concretized()
+        assert external_spec.external
+
+        root_specs = [Spec("sombrero")]
+        with spack.config.override("concretizer:reuse", True):
+            solver = spack.solver.asp.Solver()
+            setup = spack.solver.asp.SpackSolverSetup()
+            result, _, _ = solver.driver.solve(setup, root_specs, reuse=[external_spec])
+
+        assert len(result.specs) == 1
+        sombrero = result.specs[0]
+        assert sombrero["externaltool"].dag_hash() == external_spec.dag_hash()
+
 
 @pytest.fixture()
 def duplicates_test_repository():

lib/spack/spack/test/concretize_requirements.py

@@ -1176,3 +1176,46 @@ def test_forward_multi_valued_variant_using_requires(
 
     for constraint in not_expected:
         assert not s.satisfies(constraint)
+
+
+def test_strong_preferences_higher_priority_than_reuse(concretize_scope, mock_packages):
+    """Tests that strong preferences have a higher priority than reusing specs."""
+    reused_spec = Spec("adios2~bzip2").concretized()
+    reuse_nodes = list(reused_spec.traverse())
+    root_specs = [Spec("ascent+adios2")]
+
+    # Check that without further configuration adios2 is reused
+    with spack.config.override("concretizer:reuse", True):
+        solver = spack.solver.asp.Solver()
+        setup = spack.solver.asp.SpackSolverSetup()
+        result, _, _ = solver.driver.solve(setup, root_specs, reuse=reuse_nodes)
+        ascent = result.specs[0]
+    assert ascent["adios2"].dag_hash() == reused_spec.dag_hash(), ascent
+
+    # If we stick a preference, adios2 is not reused
+    update_packages_config(
+        """
+    packages:
+      adios2:
+        prefer:
+        - "+bzip2"
+"""
+    )
+    with spack.config.override("concretizer:reuse", True):
+        solver = spack.solver.asp.Solver()
+        setup = spack.solver.asp.SpackSolverSetup()
+        result, _, _ = solver.driver.solve(setup, root_specs, reuse=reuse_nodes)
+        ascent = result.specs[0]
+
+    assert ascent["adios2"].dag_hash() != reused_spec.dag_hash()
+    assert ascent["adios2"].satisfies("+bzip2")
+
+    # A preference is still preference, so we can override from input
+    with spack.config.override("concretizer:reuse", True):
+        solver = spack.solver.asp.Solver()
+        setup = spack.solver.asp.SpackSolverSetup()
+        result, _, _ = solver.driver.solve(
+            setup, [Spec("ascent+adios2 ^adios2~bzip2")], reuse=reuse_nodes
+        )
+        ascent = result.specs[0]
+    assert ascent["adios2"].dag_hash() == reused_spec.dag_hash(), ascent

lib/spack/spack/test/conftest.py

@@ -2053,3 +2053,11 @@ def _true(x):
 @pytest.fixture()
 def do_not_check_runtimes_on_reuse(monkeypatch):
     monkeypatch.setattr(spack.solver.asp, "_has_runtime_dependencies", _true)
+
+
+@pytest.fixture(autouse=True, scope="session")
+def _c_compiler_always_exists():
+    fn = spack.solver.asp.c_compiler_runs
+    spack.solver.asp.c_compiler_runs = _true
+    yield
+    spack.solver.asp.c_compiler_runs = fn

lib/spack/spack/test/env.py

@@ -813,3 +813,33 @@ def test_deconcretize_then_concretize_does_not_error(mutable_mock_env_path, mock
     assert len(e.concrete_roots()) == 3
     all_root_hashes = set(x.dag_hash() for x in e.concrete_roots())
     assert len(all_root_hashes) == 2
+
+
+@pytest.mark.regression("44216")
+@pytest.mark.only_clingo()
+def test_root_version_weights_for_old_versions(mutable_mock_env_path, mock_packages):
+    """Tests that, when we select two old versions of root specs that have the same version
+    optimization penalty, both are considered.
+    """
+    mutable_mock_env_path.mkdir()
+    spack_yaml = mutable_mock_env_path / ev.manifest_name
+    spack_yaml.write_text(
+        """spack:
+      specs:
+      # allow any version, but the most recent
+      - bowtie@:1.3
+      # allows only the third most recent, so penalty is 2
+      - gcc@1
+      concretizer:
+        unify: true
+    """
+    )
+    e = ev.Environment(mutable_mock_env_path)
+    with e:
+        e.concretize()
+
+    bowtie = [x for x in e.concrete_roots() if x.name == "bowtie"][0]
+    gcc = [x for x in e.concrete_roots() if x.name == "gcc"][0]
+
+    assert bowtie.satisfies("@=1.3.0")
+    assert gcc.satisfies("@=1.0")

lib/spack/spack/test/llnl/util/filesystem.py

@@ -14,7 +14,7 @@
 import pytest
 
 import llnl.util.filesystem as fs
-from llnl.util.symlink import islink, symlink
+from llnl.util.symlink import islink, readlink, symlink
 
 import spack.paths
 
@@ -181,7 +181,7 @@ def test_symlinks_true(self, stage):
 
             assert os.path.exists("dest/a/b2")
             with fs.working_dir("dest/a"):
-                assert os.path.exists(os.readlink("b2"))
+                assert os.path.exists(readlink("b2"))
 
             assert os.path.realpath("dest/f/2") == os.path.abspath("dest/a/b/2")
             assert os.path.realpath("dest/2") == os.path.abspath("dest/1")
@@ -281,7 +281,7 @@ def test_allow_broken_symlinks(self, stage):
             symlink("nonexistant.txt", "source/broken", allow_broken_symlinks=True)
             fs.install_tree("source", "dest", symlinks=True, allow_broken_symlinks=True)
             assert os.path.islink("dest/broken")
-            assert not os.path.exists(os.readlink("dest/broken"))
+            assert not os.path.exists(readlink("dest/broken"))
 
     def test_glob_src(self, stage):
         """Test using a glob as the source."""

lib/spack/spack/test/modules/common.py

@@ -7,6 +7,8 @@
 
 import pytest
 
+from llnl.util.symlink import readlink
+
 import spack.cmd.modules
 import spack.config
 import spack.error
@@ -78,7 +80,7 @@ def test_modules_default_symlink(
 
     link_path = os.path.join(os.path.dirname(mock_module_filename), "default")
     assert os.path.islink(link_path)
-    assert os.readlink(link_path) == mock_module_filename
+    assert readlink(link_path) == mock_module_filename
 
     generator.remove()
     assert not os.path.lexists(link_path)

lib/spack/spack/test/oci/mock_registry.py

@@ -151,7 +151,9 @@ class InMemoryOCIRegistry(DummyServer):
     A third option is to use the chunked upload, but this is not implemented here, because
     it's typically a major performance hit in upload speed, so we're not using it in Spack."""
 
-    def __init__(self, domain: str, allow_single_post: bool = True) -> None:
+    def __init__(
+        self, domain: str, allow_single_post: bool = True, tags_per_page: int = 100
+    ) -> None:
         super().__init__(domain)
         self.router.register("GET", r"/v2/", self.index)
         self.router.register("HEAD", r"/v2/(?P<name>.+)/blobs/(?P<digest>.+)", self.head_blob)
@@ -165,6 +167,9 @@ def __init__(self, domain: str, allow_single_post: bool = True) -> None:
         # If True, allow single POST upload, not all registries support this
         self.allow_single_post = allow_single_post
 
+        # How many tags are returned in a single request
+        self.tags_per_page = tags_per_page
+
         # Used for POST + PUT upload. This is a map from session ID to image name
         self.sessions: Dict[str, str] = {}
 
@@ -280,10 +285,34 @@ def handle_upload(self, req: Request, name: str, digest: Digest):
         return MockHTTPResponse(201, "Created", headers={"Location": f"/v2/{name}/blobs/{digest}"})
 
     def list_tags(self, req: Request, name: str):
+        # Paginate using Link headers, this was added to the spec in the following commit:
+        # https://github.com/opencontainers/distribution-spec/commit/2ed79d930ecec11dd755dc8190409a3b10f01ca9
+
         # List all tags, exclude digests.
-        tags = [_tag for _name, _tag in self.manifests.keys() if _name == name and ":" not in _tag]
-        tags.sort()
-        return MockHTTPResponse.with_json(200, "OK", body={"tags": tags})
+        all_tags = sorted(
+            _tag for _name, _tag in self.manifests.keys() if _name == name and ":" not in _tag
+        )
+
+        query = urllib.parse.parse_qs(urllib.parse.urlparse(req.full_url).query)
+
+        n = int(query["n"][0]) if "n" in query else self.tags_per_page
+
+        if "last" in query:
+            try:
+                offset = all_tags.index(query["last"][0]) + 1
+            except ValueError:
+                return MockHTTPResponse(404, "Not found")
+        else:
+            offset = 0
+
+        tags = all_tags[offset : offset + n]
+
+        if offset + n < len(all_tags):
+            headers = {"Link": f'</v2/{name}/tags/list?last={tags[-1]}&n={n}>; rel="next"'}
+        else:
+            headers = None
+
+        return MockHTTPResponse.with_json(200, "OK", headers=headers, body={"tags": tags})
 
 
 class DummyServerUrllibHandler(urllib.request.BaseHandler):

lib/spack/spack/test/oci/urlopen.py

@@ -6,6 +6,7 @@
 
 import hashlib
 import json
+import random
 import urllib.error
 import urllib.parse
 import urllib.request
@@ -19,6 +20,7 @@
     copy_missing_layers,
     get_manifest_and_config,
     image_from_mirror,
+    list_tags,
     upload_blob,
     upload_manifest,
 )
@@ -670,3 +672,31 @@ def test_retry(url, max_retries, expect_failure, expect_requests):
 
     assert len(server.requests) == expect_requests
     assert sleep_time == [2**i for i in range(expect_requests - 1)]
+
+
+def test_list_tags():
+    # Follows a relatively new rewording of the OCI distribution spec, which is not yet tagged.
+    # https://github.com/opencontainers/distribution-spec/commit/2ed79d930ecec11dd755dc8190409a3b10f01ca9
+    N = 20
+    urlopen = create_opener(InMemoryOCIRegistry("example.com", tags_per_page=5)).open
+    image = ImageReference.from_string("example.com/image")
+    to_tag = lambda i: f"tag-{i:02}"
+
+    # Create N tags in arbitrary order
+    _tags_to_create = [to_tag(i) for i in range(N)]
+    random.shuffle(_tags_to_create)
+    for tag in _tags_to_create:
+        upload_manifest(image.with_tag(tag), default_manifest(), tag=True, _urlopen=urlopen)
+
+    # list_tags should return all tags from all pages in order
+    tags = list_tags(image, urlopen)
+    assert len(tags) == N
+    assert [to_tag(i) for i in range(N)] == tags
+
+    # Test a single request, which should give the first 5 tags
+    assert json.loads(urlopen(image.tags_url()).read())["tags"] == [to_tag(i) for i in range(5)]
+
+    # Test response at an offset, which should exclude the `last` tag.
+    assert json.loads(urlopen(image.tags_url() + f"?last={to_tag(N - 3)}").read())["tags"] == [
+        to_tag(i) for i in range(N - 2, N)
+    ]

lib/spack/spack/test/packaging.py

@@ -16,7 +16,7 @@
 import pytest
 
 from llnl.util import filesystem as fs
-from llnl.util.symlink import symlink
+from llnl.util.symlink import readlink, symlink
 
 import spack.binary_distribution as bindist
 import spack.cmd.buildcache as buildcache
@@ -181,12 +181,12 @@ def test_relocate_links(tmpdir):
         relocate_links(["to_self", "to_dependency", "to_system"], prefix_to_prefix)
 
         # These two are relocated
-        assert os.readlink("to_self") == str(tmpdir.join("new_prefix_a", "file"))
-        assert os.readlink("to_dependency") == str(tmpdir.join("new_prefix_b", "file"))
+        assert readlink("to_self") == str(tmpdir.join("new_prefix_a", "file"))
+        assert readlink("to_dependency") == str(tmpdir.join("new_prefix_b", "file"))
 
         # These two are not.
-        assert os.readlink("to_system") == system_path
-        assert os.readlink("to_self_but_relative") == "relative"
+        assert readlink("to_system") == system_path
+        assert readlink("to_self_but_relative") == "relative"
 
 
 def test_needs_relocation():

lib/spack/spack/test/stage.py

@@ -15,6 +15,7 @@
 import pytest
 
 from llnl.util.filesystem import getuid, mkdirp, partition_path, touch, working_dir
+from llnl.util.symlink import readlink
 
 import spack.error
 import spack.paths
@@ -872,7 +873,7 @@ def _create_files_from_tree(base, tree):
 
 def _create_tree_from_dir_recursive(path):
     if os.path.islink(path):
-        return os.readlink(path)
+        return readlink(path)
     elif os.path.isdir(path):
         tree = {}
         for name in os.listdir(path):

lib/spack/spack/test/url_parse.py

@@ -87,6 +87,13 @@ def test_url_strip_name_suffixes(url, version, expected):
             59,
             "https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow",
         ),
+        (
+            "hpcviewer",
+            30,
+            "2024.02",
+            51,
+            "https://gitlab.com/hpctoolkit/hpcviewer/-/releases/2024.02/downloads/hpcviewer.tgz",
+        ),
         # Version in stem
         ("zlib", 24, "1.2.10", 29, "http://zlib.net/fossils/zlib-1.2.10.tar.gz"),
         (

lib/spack/spack/test/util/util_url.py

@@ -207,3 +207,29 @@ def test_default_download_name_dot_dot():
     assert url_util.default_download_filename("https://example.com/.") == "_"
     assert url_util.default_download_filename("https://example.com/..") == "_."
     assert url_util.default_download_filename("https://example.com/.abcdef") == "_abcdef"
+
+
+def test_parse_link_rel_next():
+    parse = url_util.parse_link_rel_next
+    assert parse(r'</abc>; rel="next"') == "/abc"
+    assert parse(r'</abc>; x=y; rel="next", </def>; x=y; rel="prev"') == "/abc"
+    assert parse(r'</abc>; rel="prev"; x=y, </def>; x=y; rel="next"') == "/def"
+
+    # example from RFC5988
+    assert (
+        parse(
+            r"""</TheBook/chapter2>; title*=UTF-8'de'letztes%20Kapitel; rel="previous","""
+            r"""</TheBook/chapter4>; title*=UTF-8'de'n%c3%a4chstes%20Kapitel; rel="next" """
+        )
+        == "/TheBook/chapter4"
+    )
+
+    assert (
+        parse(r"""<https://example.com/example>; key=";a=b, </c/d>; e=f"; rel="next" """)
+        == "https://example.com/example"
+    )
+
+    assert parse("https://example.com/example") is None
+    assert parse("<https://example.com/example; broken=broken") is None
+    assert parse("https://example.com/example; rel=prev") is None
+    assert parse("https://example.com/example; a=b; c=d; g=h") is None

lib/spack/spack/url.py

@@ -258,7 +258,9 @@ def parse_version_offset(path):
         # 9th Pass: Version in path
         # github.com/repo/name/releases/download/vver/name
         # e.g. https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow
+        # e.g. https://gitlab.com/hpctoolkit/hpcviewer/-/releases/2024.02/downloads/hpcviewer.tgz
         (r"github\.com/[^/]+/[^/]+/releases/download/[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)/", path),
+        (r"gitlab\.com/[^/]+/.+/-/releases/[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)/downloads/", path),
         # e.g. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/ncbi.tar.gz
         (r"(\d[\da-zA-Z._-]*)/[^/]+$", path),
     ]

lib/spack/spack/util/format.py

@@ -21,16 +21,6 @@ def get_version_lines(version_hashes_dict: dict, url_dict: Optional[dict] = None
     version_lines = []
 
     for v, h in version_hashes_dict.items():
-        expand_arg = ""
-
-        # Extract the url for a version if url_dict is provided.
-        url = ""
-        if url_dict is not None and v in url_dict:
-            url = url_dict[v]
-
-        # Add expand_arg since wheels should not be expanded during stanging
-        if url.endswith(".whl") or ".whl#" in url:
-            expand_arg = ", expand=False"
-        version_lines.append(f'    version("{v}", sha256="{h}"{expand_arg})')
+        version_lines.append(f'    version("{v}", sha256="{h}")')
 
     return "\n".join(version_lines)

lib/spack/spack/util/libc.py

@@ -22,7 +22,7 @@ def _libc_from_ldd(ldd: str) -> Optional["spack.spec.Spec"]:
     except Exception:
         return None
 
-    if not re.search(r"\b(?:gnu|glibc|arm)\b", stdout, re.IGNORECASE):
+    if not re.search(r"\bFree Software Foundation\b", stdout):
         return None
 
     version_str = re.match(r".+\(.+\) (.+)", stdout)
@@ -75,7 +75,7 @@ def libc_from_dynamic_linker(dynamic_linker: str) -> Optional["spack.spec.Spec"]
             return spec
         except Exception:
             return None
-    elif re.search(r"\b(?:gnu|glibc|arm)\b", stdout, re.IGNORECASE):
+    elif re.search(r"\bFree Software Foundation\b", stdout):
         # output is like "ld.so (...) stable release version 2.33."
         match = re.search(r"version (\d+\.\d+(?:\.\d+)?)", stdout)
         if not match:

lib/spack/spack/util/spack_yaml.py

@@ -296,8 +296,8 @@ def process_scalar(self):
         if marked(self.event.value):
             self.saved = self.event.value
 
-    def write_line_break(self):
-        super().write_line_break()
+    def write_line_break(self, data=None):
+        super().write_line_break(data)
         if self.saved is None:
             _ANNOTATIONS.append(colorize("@K{---}"))
             return

lib/spack/spack/util/url.py

@@ -10,9 +10,11 @@
 import itertools
 import os
 import posixpath
+import re
 import sys
 import urllib.parse
 import urllib.request
+from typing import Optional
 
 from llnl.path import convert_to_posix_path
 
@@ -254,3 +256,43 @@ def default_download_filename(url: str) -> str:
         valid_name = "_" + valid_name[1:]
 
     return valid_name
+
+
+def parse_link_rel_next(link_value: str) -> Optional[str]:
+    """Return the next link from a Link header value, if any."""
+
+    # Relaxed version of RFC5988
+    uri = re.compile(r"\s*<([^>]+)>\s*")
+    param_key = r"[^;=\s]+"
+    quoted_string = r"\"([^\"]+)\""
+    unquoted_param_value = r"([^;,\s]+)"
+    param = re.compile(rf";\s*({param_key})\s*=\s*(?:{quoted_string}|{unquoted_param_value})\s*")
+
+    data = link_value
+
+    # Parse a list of <url>; key=value; key=value, <url>; key=value; key=value, ... links.
+    while True:
+        uri_match = re.match(uri, data)
+        if not uri_match:
+            break
+        uri_reference = uri_match.group(1)
+        data = data[uri_match.end() :]
+
+        # Parse parameter list
+        while True:
+            param_match = re.match(param, data)
+            if not param_match:
+                break
+            key, quoted_value, unquoted_value = param_match.groups()
+            value = quoted_value or unquoted_value
+            data = data[param_match.end() :]
+
+            if key == "rel" and value == "next":
+                return uri_reference
+
+        if not data.startswith(","):
+            break
+
+        data = data[1:]
+
+    return None

lib/spack/spack/verify.py

@@ -9,6 +9,7 @@
 from typing import Any, Dict
 
 import llnl.util.tty as tty
+from llnl.util.symlink import readlink
 
 import spack.filesystem_view
 import spack.store
@@ -38,7 +39,7 @@ def create_manifest_entry(path: str) -> Dict[str, Any]:
     data: Dict[str, Any] = {"mode": s.st_mode, "owner": s.st_uid, "group": s.st_gid}
 
     if stat.S_ISLNK(s.st_mode):
-        data["dest"] = os.readlink(path)
+        data["dest"] = readlink(path)
 
     elif stat.S_ISREG(s.st_mode):
         data["hash"] = compute_hash(path)
@@ -90,7 +91,7 @@ def check_entry(path, data):
     # instead of `lstat(...).st_mode`. So, ignore mode errors for symlinks.
     if not stat.S_ISLNK(s.st_mode) and s.st_mode != data["mode"]:
         res.add_error(path, "mode")
-    elif stat.S_ISLNK(s.st_mode) and os.readlink(path) != data.get("dest"):
+    elif stat.S_ISLNK(s.st_mode) and readlink(path) != data.get("dest"):
         res.add_error(path, "link")
     elif stat.S_ISREG(s.st_mode):
         # Check file contents against hash and listed as file

share/spack/gitlab/cloud_pipelines/.gitlab-ci.yml

@@ -64,6 +64,11 @@ default:
     SPACK_TARGET_PLATFORM: "linux"
     SPACK_TARGET_ARCH: "ppc64le"
 
+.win64-msvc2019:
+  variables:
+    SPACK_TARGET_PLATFORM: "win64"
+    SPACK_TARGET_ARCH: "x86_64"
+
 ########################################
 # Job templates
 ########################################
@@ -72,6 +77,8 @@ default:
     PIPELINE_MIRROR_TEMPLATE: "single-src-protected-mirrors.yaml.in"
     # TODO: We can remove this when we drop the "deprecated" stack
     PUSH_BUILDCACHE_DEPRECATED: "${PROTECTED_MIRROR_PUSH_DOMAIN}/${CI_COMMIT_REF_NAME}/${SPACK_CI_STACK_NAME}"
+    SPACK_CI_CONFIG_ROOT: "${CI_PROJECT_DIR}/share/spack/gitlab/cloud_pipelines/configs"
+    SPACK_CI_SCRIPTS_ROOT: "${CI_PROJECT_DIR}/share/spack/gitlab/cloud_pipelines/scripts"
 
   rules:
     - if: $SPACK_CI_DISABLE_STACKS =~ /.+/ && $SPACK_CI_STACK_NAME =~ $SPACK_CI_DISABLE_STACKS
@@ -114,16 +121,8 @@ default:
 .generate-common:
   stage: generate
   script:
-    - uname -a || true
-    - grep -E 'vendor|model name' /proc/cpuinfo 2>/dev/null | sort -u || head -n10 /proc/cpuinfo 2>/dev/null || true
-    - nproc || true
-    - cat /proc/loadavg || true
-    - cat /proc/meminfo | grep 'MemTotal\|MemFree' || true
-    - . "./share/spack/setup-env.sh"
     - spack --version
-    - cd share/spack/gitlab/cloud_pipelines/stacks/${SPACK_CI_STACK_NAME}
-    - spack env activate --without-view .
-    - export SPACK_CI_CONFIG_ROOT="${SPACK_ROOT}/share/spack/gitlab/cloud_pipelines/configs"
+    - spack env activate --without-view share/spack/gitlab/cloud_pipelines/stacks/${SPACK_CI_STACK_NAME}
     - spack
       --config-scope "${SPACK_CI_CONFIG_ROOT}"
       --config-scope "${SPACK_CI_CONFIG_ROOT}/${SPACK_TARGET_PLATFORM}"
@@ -134,29 +133,25 @@ default:
       --config-scope "${SPACK_CI_CONFIG_ROOT}"
       --config-scope "${SPACK_CI_CONFIG_ROOT}/${SPACK_TARGET_PLATFORM}"
       --config-scope "${SPACK_CI_CONFIG_ROOT}/${SPACK_TARGET_PLATFORM}/${SPACK_TARGET_ARCH}"
-      ${CI_STACK_CONFIG_SCOPES}
       audit configs
-    - spack python -c "import os,sys; print(os.path.expandvars(sys.stdin.read()))"
-      < "${SPACK_CI_CONFIG_ROOT}/${PIPELINE_MIRROR_TEMPLATE}" > "${SPACK_CI_CONFIG_ROOT}/mirrors.yaml"
+    # Command below needs to be `spack python` due to naming differences accross platforms
+    - spack python ${SPACK_CI_SCRIPTS_ROOT}/common/expand_vars.py
+      "${SPACK_CI_CONFIG_ROOT}/${PIPELINE_MIRROR_TEMPLATE}"
+      "${SPACK_CI_CONFIG_ROOT}/mirrors.yaml"
     - spack config add -f "${SPACK_CI_CONFIG_ROOT}/mirrors.yaml"
-    - mkdir -p "${CI_PROJECT_DIR}/jobs_scratch_dir"
+    - mkdir "${CI_PROJECT_DIR}/jobs_scratch_dir"
     - spack
       --config-scope "${SPACK_CI_CONFIG_ROOT}"
       --config-scope "${SPACK_CI_CONFIG_ROOT}/${SPACK_TARGET_PLATFORM}"
       --config-scope "${SPACK_CI_CONFIG_ROOT}/${SPACK_TARGET_PLATFORM}/${SPACK_TARGET_ARCH}"
-      ${CI_STACK_CONFIG_SCOPES}
       config blame > "${CI_PROJECT_DIR}/jobs_scratch_dir/spack.yaml.blame"
     - spack -v  --color=always
       --config-scope "${SPACK_CI_CONFIG_ROOT}"
       --config-scope "${SPACK_CI_CONFIG_ROOT}/${SPACK_TARGET_PLATFORM}"
       --config-scope "${SPACK_CI_CONFIG_ROOT}/${SPACK_TARGET_PLATFORM}/${SPACK_TARGET_ARCH}"
-      ${CI_STACK_CONFIG_SCOPES}
       ci generate --check-index-only
       --artifacts-root "${CI_PROJECT_DIR}/jobs_scratch_dir"
       --output-file "${CI_PROJECT_DIR}/jobs_scratch_dir/cloud-ci-pipeline.yml"
-  after_script:
-    - cat /proc/loadavg || true
-    - cat /proc/meminfo | grep 'MemTotal\|MemFree' || true
   artifacts:
     paths:
       - "${CI_PROJECT_DIR}/jobs_scratch_dir"
@@ -179,6 +174,16 @@ default:
 # Generate without tags for cases using external runners
 .generate-base:
   extends: [ ".base-job", ".generate-common" ]
+  before_script:
+    - uname -a || true
+    - grep -E 'vendor|model name' /proc/cpuinfo 2>/dev/null | sort -u || head -n10 /proc/cpuinfo 2>/dev/null || true
+    - nproc || true
+    - cat /proc/loadavg || true
+    - cat /proc/meminfo | grep 'MemTotal\|MemFree' || true
+    - . "./share/spack/setup-env.sh"
+  after_script:
+    - cat /proc/loadavg || true
+    - cat /proc/meminfo | grep 'MemTotal\|MemFree' || true
 
 .generate-x86_64:
   extends: [ ".generate-base" ]
@@ -196,6 +201,25 @@ default:
   extends: [ ".generate-base" ]
   tags: ["spack", "public", "medium", "neoverse_v2"]
 
+.generate-win64:
+  extends: [ ".base-job", ".generate-common" ]
+  before_script:
+    - $ErrorActionOld=$ErrorActionPreference
+    - $ErrorActionPreference="SilentlyContinue"
+    - python -c"import psutil;print(psutil.getloadavg())"
+    - (Get-WmiObject Win32_PhysicalMemory | measure-object Capacity -sum).sum/1kb
+    - $ErrorActionPreference=$ErrorActionOld
+    - . .\share\spack\setup-env.ps1
+  after_script:
+    - $ErrorActionOld=$ErrorActionPreference
+    - $ErrorActionPreference="SilentlyContinue"
+    - python -c"import psutil;print(psutil.getloadavg())"
+    - (Get-WmiObject Win32_PhysicalMemory | measure-object Capacity -sum).sum/1kb
+    - $ErrorActionPreference=$ErrorActionOld
+
+  tags: ["spack", "public", "medium", "x86_64-win"]
+  image: "ghcr.io/johnwparent/windows-server21h2:sha-c749cf3"
+
 .generate-deprecated:
   extends: [ ".base-job" ]
   stage: generate
@@ -718,7 +742,7 @@ tutorial-build:
 
 ml-linux-x86_64-cpu-generate:
   extends: [ ".generate-x86_64", .ml-linux-x86_64-cpu, ".tags-x86_64_v4" ]
-  image: ghcr.io/spack/linux-ubuntu22.04-x86_64_v2:v2024-01-29
+  image: ghcr.io/spack/ubuntu-22.04:v2024-05-07
 
 ml-linux-x86_64-cpu-build:
   extends: [ ".build", ".ml-linux-x86_64-cpu" ]
@@ -741,7 +765,7 @@ ml-linux-x86_64-cpu-build:
 
 ml-linux-x86_64-cuda-generate:
   extends: [ ".generate-x86_64", .ml-linux-x86_64-cuda, ".tags-x86_64_v4" ]
-  image: ghcr.io/spack/linux-ubuntu22.04-x86_64_v2:v2024-01-29
+  image: ghcr.io/spack/ubuntu-22.04:v2024-05-07
 
 ml-linux-x86_64-cuda-build:
   extends: [ ".build", ".ml-linux-x86_64-cuda"  ]
@@ -859,6 +883,15 @@ aws-pcluster-build-neoverse_v1:
     - echo $PATH
     - module avail
     - module list
+    - uname -a || true
+    - grep -E 'vendor|model name' /proc/cpuinfo 2>/dev/null | sort -u || head -n10 /proc/cpuinfo 2>/dev/null || true
+    - nproc || true
+    - cat /proc/loadavg || true
+    - cat /proc/meminfo | grep 'MemTotal\|MemFree' || true
+    - . "./share/spack/setup-env.sh"
+  after_script:
+    - cat /proc/loadavg || true
+    - cat /proc/meminfo | grep 'MemTotal\|MemFree' || true
 
 .generate-cray-rhel:
   tags: [ "cray-rhel-zen4", "public" ]
@@ -912,3 +945,25 @@ e4s-cray-sles-build:
   needs:
     - artifacts: True
       job: e4s-cray-sles-generate
+
+#######################################
+# Windows Visualization Tools
+#######################################
+.windows-vis:
+  extends: [".win64-msvc2019"]
+  variables:
+    SPACK_CI_STACK_NAME: windows-vis
+
+windows-vis-generate:
+  extends: [ ".generate-win64", ".windows-vis" ]
+
+windows-vis-build:
+  extends: [ ".build", ".windows-vis"]
+  trigger:
+    include:
+      - artifact: jobs_scratch_dir/cloud-ci-pipeline.yml
+        job: windows-vis-generate
+    strategy: depend
+  needs:
+    - artifacts: True
+      job: windows-vis-generate

share/spack/gitlab/cloud_pipelines/configs/win64/ci.yaml

@@ -0,0 +1,18 @@
+ci:
+  pipeline-gen:
+  - build-job:
+      after_script::
+      - Write-Output "Done"
+
+      before_script::
+      - fsutil 8dot3name set C:\ 0
+      - . .\share\spack\setup-env.ps1
+      - If (Test-Path -path C:\\key\intermediate_ci_signing_key.gpg) { spack.ps1 gpg trust C:\\key\intermediate_ci_signing_key.gpg }
+      - If (Test-Path -path C:\\key\spack_public_key.gpg) { spack.ps1 gpg trust C:\\key\spack_public_key.gpg }
+
+      script::
+      - spack.ps1 env activate --without-view ${SPACK_CONCRETE_ENV_DIR}
+      - spack.ps1 config add "config:install_tree:projections:${SPACK_JOB_SPEC_PKG_NAME}:'morepadding/{hash}'"
+      - mkdir ${SPACK_ARTIFACTS_ROOT}/user_data
+      - spack.ps1 --backtrace ci rebuild | Tee-Object -FilePath "${env:SPACK_ARTIFACTS_ROOT}/user_data/pipeline_out.txt" 2>&1 | Tee-Object -FilePath "${env:SPACK_ARTIFACTS_ROOT}/user_data/pipeline_err.txt"
+      image: "ghcr.io/johnwparent/windows-server21h2:sha-c749cf3"

share/spack/gitlab/cloud_pipelines/configs/win64/config.yaml

@@ -0,0 +1,10 @@
+config:
+  build_stage::
+    - 'C:/spack stage'
+  install_tree:
+    root: "C:/spack install"
+    # Path lengths on windows doesn't support much padding
+    padded_length: 0
+    # Reduce the projections to only including the hash to avoid path length issues
+    projections:
+      all: '{hash}'

share/spack/gitlab/cloud_pipelines/configs/win64/packages.yaml

@@ -0,0 +1,25 @@
+packages:
+  all:
+    target: [x86_64]
+  tbb:
+    require: "intel-tbb"
+  cmake:
+    externals:
+    - spec: cmake@3.28.0-msvc1
+      prefix: "C:\\Program Files\\Microsoft Visual Studio\\2022\\Community\\Common7\\IDE\\CommonExtensions\\Microsoft\\CMake\\CMake"
+    buildable: False
+  ninja:
+    externals:
+    - spec: ninja@1.11.0
+      prefix: "C:\\Program Files\\Microsoft Visual Studio\\2022\\Community\\Common7\\IDE\\CommonExtensions\\Microsoft\\CMake\\Ninja"
+    buildable: False
+  wgl:
+    externals:
+    - spec: wgl@10.0.22621 plat=x64
+      prefix: "C:\\Program Files (x86)\\Windows Kits\\10"
+    buildable: False
+  win-sdk:
+    externals:
+    - spec: win-sdk@10.0.22621 plat=x64
+      prefix: "C:\\Program Files (x86)\\Windows Kits\\10"
+    buildable: False

share/spack/gitlab/cloud_pipelines/configs/win64/x86_64/ci.yaml

@@ -0,0 +1,4 @@
+ci:
+  pipeline-gen:
+  - build-job:
+      tags: [x86_64-win]

share/spack/gitlab/cloud_pipelines/configs/win64/x86_64/packages.yaml

@@ -0,0 +1,3 @@
+packages:
+  all:
+    target: [x86_64]

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

@@ -0,0 +1,10 @@
+import argparse
+import os
+
+parser = argparse.ArgumentParser()
+parser.add_argument("input", type=argparse.FileType("r"))
+parser.add_argument("out", type=argparse.FileType("w"))
+
+args = parser.parse_args()
+
+args.out.write(os.path.expandvars(args.input.read()))

share/spack/gitlab/cloud_pipelines/scripts/pcluster/setup-pcluster.sh

@@ -10,6 +10,7 @@ set -e
 # The best solution would be to have the compilers hash (or packages contents) be part of the
 # individual packages hashes. I don't see this at the moment.
 # Set to the latest tag including a recent oneapi compiler.
+# NOTE: If we update this spack version in the future make sure the compiler version also updates.
 spack_intel_compiler_commit="develop-2023-08-06"
 
 set_pcluster_defaults() {
@@ -23,10 +24,9 @@ set_pcluster_defaults() {
 
 setup_spack() {
     spack compiler add --scope site
-    spack external find --scope site
-    # Remove all autotools/buildtools packages. These versions need to be managed by spack or it will
+    # Do not add  autotools/buildtools packages. These versions need to be managed by spack or it will
     # eventually end up in a version mismatch (e.g. when compiling gmp).
-    spack tags build-tools | xargs -I {} spack config --scope site rm packages:{}
+    spack external find --scope site --tag core-packages
 }
 
 patch_compilers_yaml() {
@@ -99,7 +99,7 @@ install_compilers() {
     # The compilers needs to be in the same install tree as the rest of the software such that the path
     # relocation works correctly. This holds the danger that this part will fail when the current spack gets
     # incompatible with the one in $spack_intel_compiler_commit. Therefore, we make intel installations optional
-    # in package.yaml files.
+    # in package.yaml files and add a fallback `%gcc` version for each application.
     if [ "x86_64" == "$(arch)" ]; then
         (
             CURRENT_SPACK_ROOT=${SPACK_ROOT}

share/spack/gitlab/cloud_pipelines/stacks/aws-isc-aarch64/spack.yaml

@@ -30,8 +30,6 @@ spack:
       variants: +pic +xz
     mesa:
       variants: ~llvm
-    mesa18:
-      variants: ~llvm
     mpich:
       variants: ~wrapperrpath netmod=ofi device=ch4
     ncurses:
@@ -81,7 +79,7 @@ spack:
     - openfoam
     - osu-micro-benchmarks
     - parallel
-    - paraview
+    # - paraview
     - picard
     - quantum-espresso
     - raja

share/spack/gitlab/cloud_pipelines/stacks/aws-isc/spack.yaml

@@ -30,8 +30,6 @@ spack:
       variants: +pic +xz
     mesa:
       variants: ~llvm
-    mesa18:
-      variants: ~llvm
     mpich:
       variants: ~wrapperrpath netmod=ofi device=ch4
     ncurses:
@@ -87,7 +85,7 @@ spack:
     - openfoam
     - osu-micro-benchmarks
     - parallel
-    - paraview
+    # - paraview
     - picard
     - quantum-espresso
 # Build broken for gcc@7.3.1 x86_64_v4 (error: '_mm512_loadu_epi32' was not declared in this scope)

share/spack/gitlab/cloud_pipelines/stacks/aws-pcluster-neoverse_v1/packages.yaml

@@ -19,7 +19,10 @@ packages:
   llvm:
     variants: ~lldb
   mpas-model:
-    require: "precision=single make_target=llvm %arm ^parallelio+pnetcdf"
+    require:
+      - one_of:
+          - "precision=single make_target=llvm %arm ^parallelio+pnetcdf"
+          - "precision=single %gcc ^parallelio+pnetcdf"
   mpich:
     require: "mpich pmi=pmi2 device=ch4 netmod=ofi +slurm"
   nvhpc:

share/spack/gitlab/cloud_pipelines/stacks/aws-pcluster-neoverse_v1/spack.yaml

@@ -2,13 +2,23 @@ spack:
   view: false
 
   definitions:
-  - optimized_configs:
-    - gromacs target=neoverse_v1
-    - gromacs target=neoverse_n1
+  - apps:
+    - gromacs
+    - mpas-model
+    - mpich
+    - openfoam
+    # - quantum-espresso : %gcc@12.3.0 on neoverse_v1 fails.
+    # Root cause: internal compiler error: in compute_live_loop_exits, at tree-ssa-loop-manip.cc:247
+    - wrf
+
+  - targets:
+      - 'target=neoverse_v1'
+      - 'target=neoverse_n1'
 
   specs:
-  - $optimized_configs
-
+  - matrix:
+      - [$apps]
+      - [$targets]
   ci:
     pipeline-gen:
     - build-job:

share/spack/gitlab/cloud_pipelines/stacks/aws-pcluster-x86_64_v4/packages.yaml

@@ -5,13 +5,20 @@ packages:
       - one_of:
           - "cflags=-std=c18 target=x86_64_v4"
           - "cflags=-std=c18 target=x86_64_v3"
-          - "%gcc"
+        when: "%intel"
+  gettext:
+    # Newer gettext cannot build with gcc@12 and old AL2 glibc headers
+    # Older gettext versions do not build correctly with oneapi.
+    require:
+      - one_of:
+          - '@:0.20'
+          - '%oneapi'
   gromacs:
     require:
       - one_of:
-          - "+intel_provided_gcc %intel ^intel-oneapi-mkl target=x86_64_v4"
-          - "+intel_provided_gcc %intel ^intel-oneapi-mkl target=x86_64_v3"
-          - "%gcc"
+          - "+intel_provided_gcc ^intel-oneapi-mkl target=x86_64_v4"
+          - "+intel_provided_gcc ^intel-oneapi-mkl target=x86_64_v3"
+        when: "%intel"
   intel-mpi:
     variants: +external-libfabric
   intel-oneapi-compilers:
@@ -21,15 +28,15 @@ packages:
   lammps:
     require:
       - one_of:
-          - "lammps_sizes=bigbig +molecule +kspace +rigid +asphere +opt +openmp +openmp-package +intel %intel ^intel-oneapi-mkl target=x86_64_v4"
-          - "lammps_sizes=bigbig +molecule +kspace +rigid +asphere +opt +openmp +openmp-package %intel ^intel-oneapi-mkl target=x86_64_v3"
-          - "%gcc"
+          - "lammps_sizes=bigbig +molecule +kspace +rigid +asphere +opt +openmp +openmp-package +intel ^intel-oneapi-mkl target=x86_64_v4"
+          - "lammps_sizes=bigbig +molecule +kspace +rigid +asphere +opt +openmp +openmp-package ^intel-oneapi-mkl target=x86_64_v3"
+        when: "%intel"
   libidn2:
     require:
       - one_of:
           - "cflags=-std=c18 target=x86_64_v4"
           - "cflags=-std=c18 target=x86_64_v3"
-          - '%gcc'
+        when: "%intel"
   libfabric:
     buildable: true
     externals:
@@ -41,13 +48,13 @@ packages:
       - one_of:
           - "cflags=-std=c18 target=x86_64_v4"
           - "cflags=-std=c18 target=x86_64_v3"
-          - "%gcc"
+        when: "%intel"
   mpas-model:
     require:
       - one_of:
-          - "precision=single %intel ^parallelio+pnetcdf target=x86_64_v4"
-          - "precision=single %intel ^parallelio+pnetcdf target=x86_64_v3"
-          - "%gcc"
+          - "precision=single ^parallelio+pnetcdf target=x86_64_v4"
+          - "precision=single ^parallelio+pnetcdf target=x86_64_v3"
+        when: "%intel"
   mpich:
     require:
       - one_of:
@@ -67,9 +74,12 @@ packages:
   palace:
     require:
       - one_of:
-          - "palace %oneapi ^fmt@9.1.0 target=x86_64_v4"
-          - "palace %oneapi ^fmt@9.1.0 target=x86_64_v3"
-          - "%gcc ^fmt@9.1.0"
+          - "palace ^fmt@9.1.0 target=x86_64_v4"
+          - "palace ^fmt@9.1.0 target=x86_64_v3"
+        when: "%oneapi"
+      - one_of:
+          - "palace ^fmt@9.1.0"
+        when: "%gcc"
   pmix:
     require:
       - one_of:
@@ -78,9 +88,9 @@ packages:
   quantum-espresso:
     require:
       - one_of:
-          - "quantum-espresso@6.6 %intel ^intel-oneapi-mkl+cluster target=x86_64_v4"
-          - "quantum-espresso@6.6 %intel ^intel-oneapi-mkl+cluster target=x86_64_v3"
-          - "%gcc"
+          - "quantum-espresso@6.6 ^intel-oneapi-mkl+cluster target=x86_64_v4"
+          - "quantum-espresso@6.6 ^intel-oneapi-mkl+cluster target=x86_64_v3"
+        when: "%intel"
   slurm:
     buildable: false
     externals:
@@ -89,12 +99,13 @@ packages:
   wrf:
     require:
       - one_of:
-          - "wrf@4 build_type=dm+sm %intel target=x86_64_v4"
-          - "wrf@4 build_type=dm+sm %intel target=x86_64_v3"
-          - "wrf@4.2.2 +netcdf_classic fflags=\"-fp-model fast=2 -no-heap-arrays -no-prec-div -no-prec-sqrt -fno-common\" build_type=dm+sm %intel  target=x86_64_v3"
-          - "%gcc"
+          - "wrf@4 build_type=dm+sm target=x86_64_v4"
+          - "wrf@4 build_type=dm+sm target=x86_64_v3"
+          - "wrf@4.2.2 +netcdf_classic fflags=\"-fp-model fast=2 -no-heap-arrays -no-prec-div -no-prec-sqrt -fno-common\" build_type=dm+sm target=x86_64_v3"
+        when: "%intel"
+
   all:
-    compiler: [intel, gcc]
+    compiler: [intel, oneapi, gcc]
     permissions:
       read: world
       write: user

share/spack/gitlab/cloud_pipelines/stacks/aws-pcluster-x86_64_v4/spack.yaml

@@ -2,14 +2,24 @@ spack:
   view: false
 
   definitions:
+  - apps:
+    - gromacs %intel
+    - lammps %intel
+    - mpas-model %intel
+    - openfoam %gcc
+    - palace %oneapi
+    - quantum-espresso %intel
+    # - wrf : While building hdf5 cmake errors out with Detecting Fortran/C Interface: Failed to compile
+    # Root cause: ifort cannot deal with arbitrarily long file names.
 
-  - optimized_configs:
-    - palace target=x86_64_v4
-    - palace target=x86_64_v3
+  - targets:
+      - 'target=x86_64_v4'
+      - 'target=x86_64_v3'
 
   specs:
-  - $optimized_configs
-
+  - matrix:
+      - [$apps]
+      - [$targets]
   ci:
     pipeline-gen:
     - build-job:
@@ -28,5 +38,6 @@ spack:
           # Do not distribute Intel & ARM binaries
           - - for i in $(aws s3 ls --recursive ${SPACK_REMOTE_MIRROR_OVERRIDE}/build_cache/ | grep intel-oneapi | awk '{print $4}' | sed -e 's?^.*build_cache/??g'); do aws s3 rm ${SPACK_REMOTE_MIRROR_OVERRIDE}/build_cache/$i; done
             - for i in $(aws s3 ls --recursive ${SPACK_REMOTE_MIRROR_OVERRIDE}/build_cache/ | grep armpl | awk '{print $4}' | sed -e 's?^.*build_cache/??g'); do aws s3 rm ${SPACK_REMOTE_MIRROR_OVERRIDE}/build_cache/$i; done
+
   cdash:
     build-group: AWS Packages

share/spack/gitlab/cloud_pipelines/stacks/data-vis-sdk/spack.yaml

@@ -12,8 +12,6 @@ spack:
       - one_of: ['@1.14', '@1.12']
     mesa:
       require: "+glx +osmesa +opengl ~opengles +llvm"
-    libosmesa:
-      require: "mesa +osmesa"
     libglx:
       require: "mesa +glx"
     ospray:
@@ -27,16 +25,16 @@ spack:
   - paraview_specs:
     - matrix:
       - - paraview +raytracing
-      - - +qt~osmesa # GUI Support w/ GLX Rendering
-        - ~qt~osmesa # GLX Rendering
-        - ~qt+osmesa # OSMesa Rendering
+      - - +qt ^[virtuals=gl] glx # GUI Support w/ GLX Rendering
+        - ~qt ^[virtuals=gl] glx # GLX Rendering
+        - ^[virtuals=gl] osmesa # OSMesa Rendering
   - visit_specs:
     - matrix:
-      - - visit
-      - - ~gui~osmesa # GLX Rendering
-        - ~gui+osmesa # OSMesa Rendering
+      - - visit~gui
+      - - ^[virtuals=gl] glx # GLX Rendering
+        - ^[virtuals=gl] osmesa # OSMesa Rendering
         # VisIt GUI does not work with Qt 5.14.2
-        # - +gui~osmesa # GUI Support w/ GLX Rendering
+        # - +gui ^[virtuals=gl] glx # GUI Support w/ GLX Rendering
   - sdk_base_spec:
     - matrix:
       - - ecp-data-vis-sdk +ascent +adios2 +cinema +darshan +faodel +hdf5 +pnetcdf

share/spack/gitlab/cloud_pipelines/stacks/developer-tools-manylinux2014/spack.yaml

@@ -56,6 +56,16 @@ spack:
     - openssl certs=system     # must be this, system external does not work
     - libtree
     - patchelf
+    - sed
+    - which
+    - elfutils
+    - fontconfig
+    - font-util
+    - gdb
+    - flex
+    - graphviz
+    - doxygen
+    - meson
 
   - arch:
     - '%gcc target=x86_64_v3'

share/spack/gitlab/cloud_pipelines/stacks/e4s-cray-rhel/spack.yaml

@@ -50,7 +50,7 @@ spack:
       variants: +termlib
     paraview:
       # Don't build GUI support or GLX rendering for HPC/container deployments
-      require: "@5.11 ~qt+osmesa"
+      require: "@5.11 ~qt ^[virtuals=gl] osmesa"
     python:
       version: [3.8.13]
     trilinos:

share/spack/gitlab/cloud_pipelines/stacks/e4s-cray-sles/spack.yaml

@@ -43,7 +43,7 @@ spack:
       variants: +termlib
     paraview:
       # Don't build GUI support or GLX rendering for HPC/container deployments
-      require: "@5.11 ~qt+osmesa"
+      require: "@5.11 ~qt ^[virtuals=gl] osmesa"
     python:
       version: [3.8.13]
     trilinos:

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

@@ -168,7 +168,6 @@ spack:
   - hdf5
   - libcatalyst
   - parallel-netcdf
-  - paraview
   - py-cinemasci
   - sz
   - unifyfs

share/spack/gitlab/cloud_pipelines/stacks/e4s-rocm-external/spack.yaml

@@ -21,7 +21,7 @@ spack:
       variants: threads=openmp
     paraview:
       # Don't build GUI support or GLX rendering for HPC/container deployments
-      require: "@5.11 ~qt+osmesa"
+      require: "@5.11 ~qt ^[virtuals=gl] osmesa"
 
     # ROCm 5.4.3
     comgr:

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

@@ -52,7 +52,7 @@ spack:
       version: [11.8.0]
     paraview:
       # Don't build GUI support or GLX rendering for HPC/container deployments
-      require: "@5.11 ~qt+osmesa"
+      require: "@5.11 ~qt ^[virtuals=gl] osmesa"
 
   specs:
   # CPU

share/spack/gitlab/cloud_pipelines/stacks/gpu-tests/spack.yaml

@@ -31,7 +31,7 @@ spack:
       variants: threads=openmp
     paraview:
       # Don't build GUI support or GLX rendering for HPC/container deployments
-      require: "@5.11 ~qt+osmesa"
+      require: "@5.11 ~qt ^[virtuals=gl] osmesa"
     trilinos:
       require: +amesos +amesos2 +anasazi +aztec +boost +epetra +epetraext
         +ifpack +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu

share/spack/gitlab/cloud_pipelines/stacks/ml-linux-x86_64-cpu/spack.yaml

@@ -79,7 +79,7 @@ spack:
     pipeline-gen:
     - build-job:
         image:
-          name: ghcr.io/spack/linux-ubuntu22.04-x86_64_v2:v2024-01-29
+          name: ghcr.io/spack/ubuntu-22.04:v2024-05-07
           entrypoint: ['']
 
   cdash:

share/spack/gitlab/cloud_pipelines/stacks/ml-linux-x86_64-cuda/spack.yaml

@@ -83,7 +83,7 @@ spack:
     pipeline-gen:
     - build-job:
         image:
-          name: ghcr.io/spack/linux-ubuntu22.04-x86_64_v2:v2024-01-29
+          name: ghcr.io/spack/ubuntu-22.04:v2024-05-07
           entrypoint: ['']
 
   cdash:

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

@@ -22,7 +22,6 @@ spack:
       - conduit  # ^hdf5+shared
       - flux-core
       #- flux-sched
-      #- glvis   # ^mesa-glu@9.0.0 ^mesa18~llvm  # same issue w/chai
       - hypre
       - lbann
       - lvarray ~tests  # per Spack issue #23192  # ~examples

share/spack/gitlab/cloud_pipelines/stacks/windows-vis/spack.yaml

@@ -0,0 +1,12 @@
+# Windows Visualization Stack
+# maintainers:
+# - John Parent (@johnwparent)
+# - Ryan Krattiger (@kwryankrattiger)
+
+spack:
+  view: false
+  specs:
+  - vtk
+
+  cdash:
+    build-group: Windows Visualization (Kitware)

var/spack/repos/builtin.mock/packages/invalid-github-pull-commits-patch-url/package.py

@@ -0,0 +1,20 @@
+# 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 InvalidGithubPullCommitsPatchUrl(Package):
+    """Package that has a GitHub pull request commit patch URL that fails auditing."""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/patch-1.0.tar.gz"
+
+    version("1.0", md5="0123456789abcdef0123456789abcdef")
+
+    patch(
+        "https://github.com/spack/spack/pull/1/commits/b4da28f71e2cef84c6e289afe89aa4bdf7936048.patch?full_index=1",
+        sha256="eae9035b832792549fac00680db5f180a88ff79feb7d7a535b4fd71f9d885e73",
+    )

var/spack/repos/builtin.mock/packages/sombrero/package.py

@@ -0,0 +1,16 @@
+# 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 Sombrero(Package):
+    """Simple package with a dependency on an external spec."""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/b-1.0.tar.gz"
+
+    version("1.0", md5="0123456789abcdef0123456789abcdef")
+    depends_on("externaltool")

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

@@ -36,6 +36,40 @@
 }
 
 _versions = {
+    "24.04": {
+        "RHEL-7": (
+            "064c3ecfd71cba3d8bf639448e899388f58eb7faef4b38f3c1aace625ace8b1e",
+            "https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/24-04/arm-compiler-for-linux_24.04_RHEL-7_aarch64.tar",
+        ),
+        "RHEL-8": (
+            "38f46a3549667d0fbccd947653d3a1a56b630d3bbb1251888c674c463f00dac3",
+            "https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/24-04/arm-compiler-for-linux_24.04_RHEL-8_aarch64.tar",
+        ),
+        "RHEL-9": (
+            "d335db82c8310e1d79c96dc09a19e4d509c5ab17eb6027214bb79cfc75d8229e",
+            "https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/24-04/arm-compiler-for-linux_24.04_RHEL-9_aarch64.tar",
+        ),
+        "SLES-15": (
+            "6f2e090efcd8da2cbeaf63272fac5917f637713f1e86d73cde2ad7268e3a05a2",
+            "https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/24-04/arm-compiler-for-linux_24.04_SLES-15_aarch64.tar",
+        ),
+        "Ubuntu-20.04": (
+            "0d782e6a69a11f90bf3b392313c885a2376c5761f227bf2f68e34e9848ec8e97",
+            "https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/24-04/arm-compiler-for-linux_24.04_Ubuntu-20.04_aarch64.tar",
+        ),
+        "Ubuntu-22.04": (
+            "0bab2e89f0a2359746f89a01251dca763305c5b0dee95cf47b0968dd1cb5f6f6",
+            "https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/24-04/arm-compiler-for-linux_24.04_Ubuntu-22.04_aarch64.tar",
+        ),
+        "AmazonLinux-2": (
+            "cf0bebe2d7123749c919a5f4e36100ad21f08ffbad3b53e477205c08ae973a2d",
+            "https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/24-04/arm-compiler-for-linux_24.04_AmazonLinux-2_aarch64.tar",
+        ),
+        "AmazonLinux-2023": (
+            "035dae8c41a1ac86c8885837978cb712306aa75dc5d26d17aca843b84eaee9f4",
+            "https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/24-04/arm-compiler-for-linux_24.04_AmazonLinux-2023_aarch64.tar",
+        ),
+    },
     "23.10": {
         "RHEL-7": (
             "c3bd4df3e5f6c97369237b0067e0a421dceb9c167d73f22f3da87f5025258314",
@@ -192,34 +226,22 @@ def get_armpl_version_to_3(spec):
 
 
 def get_armpl_prefix(spec):
+    ver = get_armpl_version_to_3(spec)
+    os = get_os(spec.version.string)
     if spec.version.string.startswith("22."):
-        return join_path(
-            spec.prefix,
-            "armpl-{}_AArch64_{}_arm-linux-compiler_aarch64-linux".format(
-                get_armpl_version_to_3(spec), get_os(spec.version.string)
-            ),
-        )
+        return join_path(spec.prefix, f"armpl-{ver}_AArch64_{os}_arm-linux-compiler_aarch64-linux")
     else:
-        return join_path(
-            spec.prefix,
-            "armpl-{}_{}_arm-linux-compiler".format(
-                get_armpl_version_to_3(spec), get_os(spec.version.string)
-            ),
-        )
+        return join_path(spec.prefix, f"armpl-{ver}_{os}_arm-linux-compiler")
 
 
 def get_acfl_prefix(spec):
+    os = get_os(spec.version.string)
     if spec.version.string.startswith("22."):
         return join_path(
-            spec.prefix,
-            "arm-linux-compiler-{0}_Generic-AArch64_{1}_aarch64-linux".format(
-                spec.version, get_os(spec.version.string)
-            ),
+            spec.prefix, f"arm-linux-compiler-{spec.version}_Generic-AArch64_{os}_aarch64-linux"
         )
     else:
-        return join_path(
-            spec.prefix, f"arm-linux-compiler-{spec.version}_{get_os(spec.version.string)}"
-        )
+        return join_path(spec.prefix, f"arm-linux-compiler-{spec.version}_{os}")
 
 
 def get_gcc_prefix(spec):
@@ -227,6 +249,16 @@ def get_gcc_prefix(spec):
     return join_path(spec.prefix, next(dir for dir in dirlist if dir.startswith("gcc")))
 
 
+def get_armpl_suffix(spec):
+    suffix = ""
+    if spec.satisfies("@24:"):
+        suffix += "_ilp64" if spec.satisfies("+ilp64") else "_lp64"
+    else:
+        suffix += "_ilp64" if spec.satisfies("+ilp64") else ""
+    suffix += "_mp" if spec.satisfies("threads=openmp") else ""
+    return suffix
+
+
 class Acfl(Package, CompilerPackage):
     """Arm Compiler combines the optimized tools and libraries from Arm
     with a modern LLVM-based compiler framework.
@@ -235,7 +267,7 @@ class Acfl(Package, CompilerPackage):
     homepage = "https://developer.arm.com/Tools%20and%20Software/Arm%20Compiler%20for%20Linux"
     url = "https://developer.arm.com/-/media/Files/downloads/hpc/arm-compiler-for-linux/23-10/arm-compiler-for-linux_23.10_Ubuntu-22.04_aarch64.tar"
 
-    maintainers("annop-w")
+    maintainers("paolotricerri")
 
     # Build Versions
     for ver, packages in _versions.items():
@@ -310,10 +342,7 @@ def fortran(self):
 
     @property
     def lib_suffix(self):
-        suffix = ""
-        suffix += "_ilp64" if self.spec.satisfies("+ilp64") else ""
-        suffix += "_mp" if self.spec.satisfies("threads=openmp") else ""
-        return suffix
+        return get_armpl_suffix(self.spec)
 
     @property
     def blas_libs(self):
@@ -389,8 +418,9 @@ def setup_run_environment(self, env):
     def check_install(self):
         arm_dir = get_acfl_prefix(self.spec)
         armpl_dir = get_armpl_prefix(self.spec)
+        suffix = get_armpl_suffix(self.spec)
         gcc_dir = get_gcc_prefix(self.spec)
-        armpl_example_dir = join_path(armpl_dir, "examples")
+        armpl_example_dir = join_path(armpl_dir, f"examples{suffix}")
         # run example makefile
         make(
             "-C",
@@ -399,6 +429,7 @@ def check_install(self):
             "F90=" + self.fortran,
             "CPATH=" + join_path(arm_dir, "include"),
             "COMPILER_PATH=" + gcc_dir,
+            "ARMPL_DIR=" + armpl_dir,
         )
         # clean up
         make("-C", armpl_example_dir, "clean")

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

@@ -3,28 +3,31 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
+
 from spack.package import *
 
 
 class Amduprof(Package):
-    """AMD uProf ("MICRO-prof") is a software profiling analysis tool for
-    x86 applications running on Windows, Linux and FreeBSD operating systems
-    and provides event information unique to the AMD "Zen"-based processors
-    and AMD Instinct(tm) MI Series accelerators.
-    """
+    """AMD uProf ("MICRO-prof") is a software profiling analysis tool for x86
+    applications running on Windows, Linux and FreeBSD operating systems and
+    provides event information unique to the AMD "Zen"-based processors and AMD
+    Instinct(tm) MI Series accelerators. AMD uProf enables the developer to better
+    understand the limiters of application performance and evaluate
+    improvements."""
 
     homepage = "https://developer.amd.com/amd-uprof/"
-    url = "https://download.amd.com/developer/eula/uprof/AMDuProf_Linux_x64_4.2.850.tar.bz2"
+    url = f"file://{os.getcwd()}/AMDuProf_Linux_x64_4.2.850.tar.bz2"
+    manual_download = True
 
-    maintainers("zzzoom")
+    maintainers("amd-toolchain-support")
 
     version("4.2.850", sha256="f2d7c4eb9ec9c32845ff8f19874c1e6bcb0fa8ab2c12e73addcbf23a6d1bd623")
 
-    # TODO: build Power Profiling driver on Linux
-    # TODO: ROCm for GPU tracing and profiling
-    # TODO: BCC and eBPF for OS tracing
+    depends_on("binutils@2.27:", type="run")
 
     conflicts("platform=darwin")
+    requires("target=x86_64:", msg="AMD uProf available only on x86_64")
 
     def install(self, spec, prefix):
         install_tree(".", prefix)

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

@@ -21,6 +21,12 @@ class AmrWind(CMakePackage, CudaPackage, ROCmPackage):
     license("BSD-3-Clause")
 
     version("main", branch="main", submodules=True)
+    version(
+        "2.1.0", tag="v2.1.0", commit="bc787f21deca9239928182e27400133934c62658", submodules=True
+    )
+    version(
+        "2.0.0", tag="v2.0.0", commit="ea448365033fc6bc9ee0febeb369b377f4fd8240", submodules=True
+    )
     version(
         "1.4.0", tag="v1.4.0", commit="bdddf133e41a9b7b4c8ce28f1ea1bebec47678f5", submodules=True
     )
@@ -91,7 +97,7 @@ class AmrWind(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("openfast@3.5:", when="@2: +openfast")
     depends_on("helics@:3.3.2", when="+helics")
     depends_on("helics@:3.3.2+mpi", when="+helics+mpi")
-    depends_on("fftw", when="@2: +waves2amr")
+    depends_on("fftw", when="@2.1: +waves2amr")
 
     for arch in CudaPackage.cuda_arch_values:
         depends_on("hypre+cuda cuda_arch=%s" % arch, when="+cuda+hypre cuda_arch=%s" % arch)
@@ -104,7 +110,7 @@ class AmrWind(CMakePackage, CudaPackage, ROCmPackage):
 
     conflicts("+openmp", when="+cuda")
     conflicts("+shared", when="+cuda")
-    conflicts("@:1.4.0", when="+waves2amr")
+    conflicts("@:2.0", when="+waves2amr")
 
     def setup_build_environment(self, env):
         # Avoid compile errors with Intel interprocedural optimization

var/spack/repos/builtin/packages/apple-gl/package.py

@@ -2,34 +2,14 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-
 from spack.package import *
 
 
-class AppleGl(Package):
-    """Shim package for the core OpenGL library from Apple"""
-
+class AppleGlBase(BundlePackage):
     homepage = "https://developer.apple.com/library/archive/documentation/GraphicsImaging/Conceptual/OpenGL-MacProgGuide/opengl_intro/opengl_intro.html"
 
     maintainers("aphecetche")
 
-    has_code = False
-
-    version("4.1.0")
-
-    provides("gl@4.1")
-
-    # Only supported on 'platform=darwin' and compiler=apple-clang
-    conflicts("platform=linux")
-    conflicts("platform=cray")
-    conflicts("platform=windows")
-    conflicts("%gcc")
-    conflicts("%clang")
-    conflicts("%msvc")
-
-    phases = []
-
     def setup_dependent_build_environment(self, env, dependent_spec):
         # we try to setup a build environment with enough hints
         # for the build system to pick up on the Apple framework version
@@ -50,3 +30,16 @@ def headers(self):
     @property
     def libs(self):
         return LibraryList(join_path(self.prefix, "System/Library/Frameworks/OpenGL.framework"))
+
+
+class AppleGl(AppleGlBase):
+    """Shim package for the core OpenGL library from Apple"""
+
+    version("4.1.0")
+
+    provides("gl@4.1")
+
+    requires(
+        "%apple-clang platform=darwin",
+        msg="Apple-GL is only available on Darwin, when using Apple Clang",
+    )