crypto.py: reduce allocations

* all-libary: add voronoi support and git version

---------

Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>

lib/spack/docs/getting_started.rst

@@ -1326,6 +1326,7 @@ Required:
 * Microsoft Visual Studio
 * Python
 * Git
+* 7z
 
 Optional:
 * Intel Fortran (needed for some packages)
@@ -1391,6 +1392,13 @@ as the project providing Git support on Windows. This is additionally the recomm
 for installing Git on Windows, a link to which can be found above. Spack requires the
 utilities vendored by this project.
 
+"""
+7zip
+"""
+
+A tool for extracting ``.xz`` files is required for extracting source tarballs. The latest 7zip
+can be located at https://sourceforge.net/projects/sevenzip/.
+
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Step 2: Install and setup Spack
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

lib/spack/spack/compilers/intel.py

@@ -124,8 +124,8 @@ def setup_custom_environment(self, pkg, env):
         # Edge cases for Intel's oneAPI compilers when using the legacy classic compilers:
         # Always pass flags to disable deprecation warnings, since these warnings can
         # confuse tools that parse the output of compiler commands (e.g. version checks).
-        if self.real_version >= Version("2021") and self.real_version <= Version("2023"):
+        if self.real_version >= Version("2021") and self.real_version < Version("2024"):
             env.append_flags("SPACK_ALWAYS_CFLAGS", "-diag-disable=10441")
             env.append_flags("SPACK_ALWAYS_CXXFLAGS", "-diag-disable=10441")
-        if self.real_version >= Version("2021") and self.real_version <= Version("2024"):
+        if self.real_version >= Version("2021") and self.real_version < Version("2025"):
             env.append_flags("SPACK_ALWAYS_FFLAGS", "-diag-disable=10448")

lib/spack/spack/compilers/oneapi.py

@@ -155,10 +155,10 @@ def setup_custom_environment(self, pkg, env):
         # icx+icpx+ifx or icx+icpx+ifort. But to be on the safe side (some users may
         # want to try to swap icpx against icpc, for example), and since the Intel LLVM
         # compilers accept these diag-disable flags, we apply them for all compilers.
-        if self.real_version >= Version("2021") and self.real_version <= Version("2023"):
+        if self.real_version >= Version("2021") and self.real_version < Version("2024"):
             env.append_flags("SPACK_ALWAYS_CFLAGS", "-diag-disable=10441")
             env.append_flags("SPACK_ALWAYS_CXXFLAGS", "-diag-disable=10441")
-        if self.real_version >= Version("2021") and self.real_version <= Version("2024"):
+        if self.real_version >= Version("2021") and self.real_version < Version("2025"):
             env.append_flags("SPACK_ALWAYS_FFLAGS", "-diag-disable=10448")
 
         # 2024 release bumped the libsycl version because of an ABI

lib/spack/spack/config.py

@@ -672,12 +672,11 @@ def set(self, path: str, value: Any, scope: Optional[str] = None) -> None:
             return
 
         parts = process_config_path(path)
-        section = parts[0]
+        section = parts.pop(0)
 
         section_data = self.get_config(section, scope=scope)
 
-        full_data = {section: section_data}
-        data = full_data
+        data = section_data
         while len(parts) > 1:
             key = parts.pop(0)
 
@@ -700,7 +699,7 @@ def set(self, path: str, value: Any, scope: Optional[str] = None) -> None:
         # update new value
         data[parts[0]] = value
 
-        self.update_config(section, full_data[section], scope=scope)
+        self.update_config(section, section_data, scope=scope)
 
     def __iter__(self):
         """Iterate over scopes in this configuration."""

lib/spack/spack/stage.py

@@ -176,14 +176,13 @@ def _resolve_paths(candidates):
 
 # Cached stage path root
 _stage_root = None
-_default_stage_config = ["$tmpdir/$user/spack-stage", "$user_cache_path/stage"]
 
 
 def get_stage_root():
     global _stage_root
 
     if _stage_root is None:
-        candidates = spack.config.get("config:build_stage", _default_stage_config)
+        candidates = spack.config.get("config:build_stage")
         if isinstance(candidates, str):
             candidates = [candidates]
 

lib/spack/spack/test/config.py

@@ -1208,16 +1208,8 @@ def test_internal_config_list_override(mock_low_high_config, write_config_file):
 def test_set_section_override(mock_low_high_config, write_config_file):
     write_config_file("config", config_merge_list, "low")
     wanted_list = config_override_list["config"]["build_stage:"]
-
-    # Ensure test validity:
-    assert wanted_list != mock_low_high_config.get("config:build_stage")
-
-    # Test both bare section with full value and section override in path
     with spack.config.override("config::build_stage", wanted_list):
         assert mock_low_high_config.get("config:build_stage") == wanted_list
-    with spack.config.override("config::", {"build_stage": wanted_list}):
-        assert mock_low_high_config.get("config:build_stage") == wanted_list
-
     assert config_merge_list["config"]["build_stage"] == mock_low_high_config.get(
         "config:build_stage"
     )

lib/spack/spack/test/stage.py

@@ -754,18 +754,6 @@ def test_get_stage_root_bad_path(self, clear_stage_root):
         # Make sure the cached stage path values are unchanged.
         assert spack.stage._stage_root is None
 
-    def test_get_stage_root_empty(self, clear_stage_root, monkeypatch, tmpdir):
-        expected = str(tmpdir)
-        monkeypatch.setattr(spack.stage, "_default_stage_config", [expected])
-        # build stage set to empty by user is respected and errors
-        with spack.config.override("config:build_stage::", []):
-            with pytest.raises(spack.stage.StageError):
-                spack.stage.get_stage_root()
-
-        # No build stage set (config section set to empty) uses default
-        with spack.config.override("config::", {}):
-            assert spack.stage.get_stage_root() == expected
-
     @pytest.mark.parametrize(
         "path,purged",
         [

lib/spack/spack/util/crypto.py

@@ -4,7 +4,8 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import hashlib
-from typing import BinaryIO, Callable, Dict, Optional
+import os
+from typing import Callable, Dict, Optional
 
 import llnl.util.tty as tty
 
@@ -80,20 +81,24 @@ def hash_fun_for_digest(hexdigest: str) -> HashFactory:
     return hash_fun_for_algo(hash_algo_for_digest(hexdigest))
 
 
-def checksum_stream(hashlib_algo: HashFactory, fp: BinaryIO, *, block_size: int = 2**20) -> str:
+def checksum_stream(hashlib_algo: HashFactory, fp, *, block_size: int = 2**20) -> str:
     """Returns a hex digest of the stream generated using given algorithm from hashlib."""
     hasher = hashlib_algo()
-    while True:
-        data = fp.read(block_size)
-        if not data:
-            break
-        hasher.update(data)
+    with memoryview(bytearray(block_size)) as view:
+        while True:
+            n = fp.readinto(view)
+            if n == block_size:
+                hasher.update(view)
+            else:
+                hasher.update(view[:n])
+                break
     return hasher.hexdigest()
 
 
 def checksum(hashlib_algo: HashFactory, filename: str, *, block_size: int = 2**20) -> str:
     """Returns a hex digest of the filename generated using an algorithm from hashlib."""
     with open(filename, "rb") as f:
+        block_size = min(block_size, os.fstat(f.fileno()).st_size)
         return checksum_stream(hashlib_algo, f, block_size=block_size)
 
 

lib/spack/spack/util/elf.py

@@ -7,7 +7,7 @@
 import re
 import struct
 from struct import calcsize, unpack, unpack_from
-from typing import BinaryIO, Dict, List, NamedTuple, Optional, Pattern, Tuple
+from typing import BinaryIO, Callable, Dict, List, NamedTuple, Optional, Pattern, Tuple
 
 
 class ElfHeader(NamedTuple):
@@ -476,6 +476,31 @@ def get_interpreter(path: str) -> Optional[str]:
         return None
 
 
+def _delete_dynamic_array_entry(
+    f: BinaryIO, elf: ElfFile, should_delete: Callable[[int, int], bool]
+) -> None:
+    f.seek(elf.pt_dynamic_p_offset)
+    dynamic_array_fmt = elf.byte_order + ("qQ" if elf.is_64_bit else "lL")
+    dynamic_array_size = calcsize(dynamic_array_fmt)
+    new_offset = elf.pt_dynamic_p_offset  # points to the new dynamic array
+    old_offset = elf.pt_dynamic_p_offset  # points to the current dynamic array
+    for _ in range(elf.pt_dynamic_p_filesz // dynamic_array_size):
+        data = read_exactly(f, dynamic_array_size, "Malformed dynamic array entry")
+        tag, val = unpack(dynamic_array_fmt, data)
+
+        if tag == ELF_CONSTANTS.DT_NULL or not should_delete(tag, val):
+            if new_offset != old_offset:
+                f.seek(new_offset)
+                f.write(data)
+                f.seek(old_offset + dynamic_array_size)
+            new_offset += dynamic_array_size
+
+        if tag == ELF_CONSTANTS.DT_NULL:
+            break
+
+        old_offset += dynamic_array_size
+
+
 def delete_rpath(path: str) -> None:
     """Modifies a binary to remove the rpath. It zeros out the rpath string and also drops the
     DT_R(UN)PATH entry from the dynamic section, so it doesn't show up in 'readelf -d file', nor
@@ -492,29 +517,22 @@ def delete_rpath(path: str) -> None:
         f.seek(rpath_offset)
         f.write(new_rpath_string)
 
-        # Next update the dynamic array
-        f.seek(elf.pt_dynamic_p_offset)
-        dynamic_array_fmt = elf.byte_order + ("qQ" if elf.is_64_bit else "lL")
-        dynamic_array_size = calcsize(dynamic_array_fmt)
-        new_offset = elf.pt_dynamic_p_offset  # points to the new dynamic array
-        old_offset = elf.pt_dynamic_p_offset  # points to the current dynamic array
-        for _ in range(elf.pt_dynamic_p_filesz // dynamic_array_size):
-            data = read_exactly(f, dynamic_array_size, "Malformed dynamic array entry")
-            tag, _ = unpack(dynamic_array_fmt, data)
+        # Delete DT_RPATH / DT_RUNPATH entries from the dynamic section
+        _delete_dynamic_array_entry(
+            f, elf, lambda tag, _: tag == ELF_CONSTANTS.DT_RPATH or tag == ELF_CONSTANTS.DT_RUNPATH
+        )
 
-            # Overwrite any entry that is not DT_RPATH or DT_RUNPATH, including DT_NULL
-            if tag != ELF_CONSTANTS.DT_RPATH and tag != ELF_CONSTANTS.DT_RUNPATH:
-                if new_offset != old_offset:
-                    f.seek(new_offset)
-                    f.write(data)
-                    f.seek(old_offset + dynamic_array_size)
-                new_offset += dynamic_array_size
 
-            # End of the dynamic array
-            if tag == ELF_CONSTANTS.DT_NULL:
-                break
+def delete_needed_from_elf(f: BinaryIO, elf: ElfFile, needed: bytes) -> None:
+    """Delete a needed library from the dynamic section of an ELF file"""
+    if not elf.has_needed or needed not in elf.dt_needed_strs:
+        return
 
-            old_offset += dynamic_array_size
+    offset = elf.dt_needed_strtab_offsets[elf.dt_needed_strs.index(needed)]
+
+    _delete_dynamic_array_entry(
+        f, elf, lambda tag, val: tag == ELF_CONSTANTS.DT_NEEDED and val == offset
+    )
 
 
 class CStringType:

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

@@ -8,8 +8,8 @@ packages:
   gromacs:
     require:
       - one_of:
-          - "gromacs@2021.3 %arm ^fftw ^openmpi"
-          - "gromacs@2021.3 %gcc ^armpl-gcc ^openmpi"
+          - "gromacs@2024.3 %arm ^fftw ^openmpi"
+          - "gromacs@2024.3 %gcc ^armpl-gcc ^openmpi"
   libfabric:
     buildable: true
     externals:

var/spack/repos/builtin/packages/adol-c/package.py

@@ -153,3 +153,8 @@ def install_additional_files(self):
                     join_path(source_directory, "ADOL-C", "examples", "additional_examples")
                 ):
                     Executable("./checkpointing/checkpointing")()
+
+    @property
+    def libs(self):
+        """The name of the library differs from the package name => own libs handling."""
+        return find_libraries(["libadolc"], root=self.prefix, shared=True, recursive=True)

var/spack/repos/builtin/packages/all-library/package.py

@@ -15,21 +15,30 @@ class AllLibrary(CMakePackage):
 
     homepage = "http://slms.pages.jsc.fz-juelich.de/websites/all-website/"
     url = "https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing/-/archive/v0.9.2/loadbalancing-v0.9.2.tar.gz"
+    git = "https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing.git"
 
     maintainers("junghans")
 
     license("BSD-3-Clause", checked_by="junghans")
 
+    version("master", branch="master")
     version("0.9.2", sha256="2b4ef52c604c3c0c467712d0912a33c82177610b67edc14df1e034779c6ddb71")
 
     variant("fortran", default=False, description="Build with fortran support")
     variant("shared", default=True, description="Build shared libraries")
     variant("vtk", default=False, description="Build with vtk support")
+    variant(
+        "voronoi",
+        default=False,
+        description="Enable voronoi-based loadbalancing scheme",
+        when="@0.9.3:",
+    )
 
     depends_on("c", type="build")
     depends_on("cxx", type="build")
     depends_on("fortran", type="build", when="+fortran")
     depends_on("vtk", when="+vtk")
+    depends_on("voropp", when="+voronoi")
 
     depends_on("mpi")
 
@@ -39,6 +48,7 @@ def cmake_args(self):
             self.define_from_variant("CM_ALL_FORTRAN", "fortran"),
             self.define_from_variant("CM_ALL_USE_F08", "fortran"),
             self.define_from_variant("CM_ALL_VTK_OUTPUT", "vtk"),
+            self.define_from_variant("CM_ALL_VORONOI", "voronoi"),
         ]
 
         if self.run_tests:

var/spack/repos/builtin/packages/cray-libsci/package.py

@@ -13,6 +13,8 @@ class CrayLibsci(Package):
     homepage = "https://docs.nersc.gov/development/libraries/libsci/"
     has_code = False  # Skip attempts to fetch source that is not available
 
+    version("23.02.1.1")
+    version("22.11.1.2")
     version("21.08.1.2")
     version("20.06.1")
     version("20.03.1")

var/spack/repos/builtin/packages/cray-mpich/package.py

@@ -18,6 +18,10 @@ class CrayMpich(Package):
 
     maintainers("haampie")
 
+    version("8.1.25")
+    version("8.1.24")
+    version("8.1.21")
+    version("8.1.14")
     version("8.1.7")
     version("8.1.0")
     version("8.0.16")

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

@@ -3,6 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import glob
 import os
 import re
 
@@ -11,7 +12,7 @@
 from llnl.util import tty
 
 from spack.package import *
-from spack.util.elf import parse_elf
+from spack.util.elf import delete_needed_from_elf, parse_elf
 
 
 class GccRuntime(Package):
@@ -72,6 +73,9 @@ def install(self, spec, prefix):
         for path, name in libraries:
             install(path, os.path.join(prefix.lib, name))
 
+        if spec.platform in ("linux", "freebsd"):
+            _drop_libgfortran_zlib(prefix.lib)
+
     def _get_libraries_macho(self):
         """Same as _get_libraries_elf but for Mach-O binaries"""
         cc = Executable(self.compiler.cc)
@@ -124,6 +128,22 @@ def headers(self):
         return HeaderList([])
 
 
+def _drop_libgfortran_zlib(lib_dir: str) -> None:
+    """Due to a bug in GCC's autotools setup (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=87182),
+    libz sometimes appears as a redundant system dependency of libgfortran. Delete it."""
+    libraries = glob.glob(os.path.join(lib_dir, "libgfortran*.so*"))
+    if len(libraries) == 0:
+        return
+    with open(libraries[0], "rb+") as f:
+        elf = parse_elf(f, dynamic_section=True)
+        if not elf.has_needed:
+            return
+        libz = next((x for x in elf.dt_needed_strs if x.startswith(b"libz.so")), None)
+        if libz is None:
+            return
+        delete_needed_from_elf(f, elf, libz)
+
+
 def get_elf_libraries(compiler, libraries):
     """Get the GCC runtime libraries for ELF binaries"""
     cc = Executable(compiler.cc)

var/spack/repos/builtin/packages/gdk-pixbuf/package.py

@@ -12,33 +12,36 @@ class GdkPixbuf(MesonPackage):
     GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3."""
 
     homepage = "https://gitlab.gnome.org/GNOME/gdk-pixbuf"
-    url = "https://ftp.acc.umu.se/pub/gnome/sources/gdk-pixbuf/2.40/gdk-pixbuf-2.40.0.tar.xz"
     git = "https://gitlab.gnome.org/GNOME/gdk-pixbuf"
-    list_url = "https://ftp.acc.umu.se/pub/gnome/sources/gdk-pixbuf/"
+    url = "https://gitlab.gnome.org/GNOME/gdk-pixbuf/-/archive/2.40.0/gdk-pixbuf-2.40.0.tar.gz"
+
+    # Falling back to the gitlab source since the mirror here seems to be broken
+    # url = "https://ftp.acc.umu.se/pub/gnome/sources/gdk-pixbuf/2.40/gdk-pixbuf-2.40.0.tar.xz"
+    # list_url = "https://ftp.acc.umu.se/pub/gnome/sources/gdk-pixbuf/"
     list_depth = 1
 
     license("LGPL-2.1-or-later", checked_by="wdconinc")
 
-    version("2.42.12", sha256="b9505b3445b9a7e48ced34760c3bcb73e966df3ac94c95a148cb669ab748e3c7")
+    version("2.42.12", sha256="d41966831b3d291fcdfe31f683bea4b3f03241d591ddbe550b5db873af3da364")
     # https://nvd.nist.gov/vuln/detail/CVE-2022-48622
     version(
         "2.42.10",
-        sha256="ee9b6c75d13ba096907a2e3c6b27b61bcd17f5c7ebeab5a5b439d2f2e39fe44b",
+        sha256="87a086c51d9705698b22bd598a795efaccf61e4db3a96f439dcb3cd90506dab8",
         deprecated=True,
     )
     version(
         "2.42.9",
-        sha256="28f7958e7bf29a32d4e963556d241d0a41a6786582ff6a5ad11665e0347fc962",
+        sha256="226d950375907857b23c5946ae6d30128f08cd75f65f14b14334c7a9fb686e36",
         deprecated=True,
     )
     version(
         "2.42.6",
-        sha256="c4a6b75b7ed8f58ca48da830b9fa00ed96d668d3ab4b1f723dcf902f78bde77f",
+        sha256="c4f3a84a04bc7c5f4fbd97dce7976ab648c60628f72ad4c7b79edce2bbdb494d",
         deprecated=True,
     )
     version(
         "2.42.2",
-        sha256="83c66a1cfd591d7680c144d2922c5955d38b4db336d7cd3ee109f7bcf9afef15",
+        sha256="249b977279f761979104d7befbb5ee23f1661e29d19a36da5875f3a97952d13f",
         deprecated=True,
     )
 

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

@@ -27,11 +27,29 @@ class Gromacs(CMakePackage, CudaPackage):
     url = "https://ftp.gromacs.org/gromacs/gromacs-2022.2.tar.gz"
     list_url = "https://ftp.gromacs.org/gromacs"
     git = "https://gitlab.com/gromacs/gromacs.git"
+
     maintainers("mabraham", "eirrgang", "junghans")
 
     license("GPL-2.0-or-later", when="@:4.5")
     license("LGPL-2.1-or-later", when="@4.6:")
 
+    # Deprecation policy:
+    #
+    # GROMACS makes an annual major release and supports it with fixes
+    # in minor updates for about two years. Each such annual release
+    # series is supported in spack for those two years, then marked as
+    # deprecated in Spack. Deprecated versions can be removed after
+    # the next major release of GROMACS is supported in Spack. Users
+    # needing such an old version can either do a manual installation
+    # or get an older version of Spack.
+    #
+    # Exception: Version 2019.6 is the last version capable of tabulated
+    # interactions used in the so-called "group scheme." It will be marked
+    # as deprecated only after equivalent functionality is available in
+    # a major release of GROMACS, then removed as above.
+    #
+    # Exception: Otherwise, versions before 2022 will be removed when
+    # 2025 is supported.
     version("main", branch="main")
     version("master", branch="main", deprecated=True)
     version("2024.3", sha256="bbda056ee59390be7d58d84c13a9ec0d4e3635617adf2eb747034922cba1f029")
@@ -51,45 +69,197 @@ class Gromacs(CMakePackage, CudaPackage):
     version("2022.2", sha256="656404f884d2fa2244c97d2a5b92af148d0dbea94ad13004724b3fcbf45e01bf")
     version("2022.1", sha256="85ddab5197d79524a702c4959c2c43be875e0fc471df3a35224939dce8512450")
     version("2022", sha256="fad60d606c02e6164018692c6c9f2c159a9130c2bf32e8c5f4f1b6ba2dda2b68")
-    version("2021.7", sha256="4db7bbbfe5424de48373686ec0e8c5bfa7175d5cd74290ef1c1e840e6df67f06")
-    version("2021.6", sha256="52df2c1d7586fd028d9397985c68bd6dd26e6e905ead382b7e6c473d087902c3")
-    version("2021.5", sha256="eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6")
-    version("2021.4", sha256="cb708a3e3e83abef5ba475fdb62ef8d42ce8868d68f52dafdb6702dc9742ba1d")
-    version("2021.3", sha256="e109856ec444768dfbde41f3059e3123abdb8fe56ca33b1a83f31ed4575a1cc6")
-    version("2021.2", sha256="d940d865ea91e78318043e71f229ce80d32b0dc578d64ee5aa2b1a4be801aadb")
-    version("2021.1", sha256="bc1d0a75c134e1fb003202262fe10d3d32c59bbb40d714bc3e5015c71effe1e5")
-    version("2021", sha256="efa78ab8409b0f5bf0fbca174fb8fbcf012815326b5c71a9d7c385cde9a8f87b")
-    version("2020.7", sha256="744158d8f61b0d36ffe89ec934519b7e0981a7af438897740160da648d36c2f0")
-    version("2020.6", sha256="d8bbe57ed3c9925a8cb99ecfe39e217f930bed47d5268a9e42b33da544bdb2ee")
-    version("2020.5", sha256="7b6aff647f7c8ee1bf12204d02cef7c55f44402a73195bd5f42cf11850616478")
-    version("2020.4", sha256="5519690321b5500c7951aaf53ff624042c3edd1a5f5d6dd1f2d802a3ecdbf4e6")
-    version("2020.3", sha256="903183691132db14e55b011305db4b6f4901cc4912d2c56c131edfef18cc92a9")
-    version("2020.2", sha256="7465e4cd616359d84489d919ec9e4b1aaf51f0a4296e693c249e83411b7bd2f3")
-    version("2020.1", sha256="e1666558831a3951c02b81000842223698016922806a8ce152e8f616e29899cf")
-    version("2020", sha256="477e56142b3dcd9cb61b8f67b24a55760b04d1655e8684f979a75a5eec40ba01")
+    version(
+        "2021.7",
+        sha256="4db7bbbfe5424de48373686ec0e8c5bfa7175d5cd74290ef1c1e840e6df67f06",
+        deprecated=True,
+    )
+    version(
+        "2021.6",
+        sha256="52df2c1d7586fd028d9397985c68bd6dd26e6e905ead382b7e6c473d087902c3",
+        deprecated=True,
+    )
+    version(
+        "2021.5",
+        sha256="eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6",
+        deprecated=True,
+    )
+    version(
+        "2021.4",
+        sha256="cb708a3e3e83abef5ba475fdb62ef8d42ce8868d68f52dafdb6702dc9742ba1d",
+        deprecated=True,
+    )
+    version(
+        "2021.3",
+        sha256="e109856ec444768dfbde41f3059e3123abdb8fe56ca33b1a83f31ed4575a1cc6",
+        deprecated=True,
+    )
+    version(
+        "2021.2",
+        sha256="d940d865ea91e78318043e71f229ce80d32b0dc578d64ee5aa2b1a4be801aadb",
+        deprecated=True,
+    )
+    version(
+        "2021.1",
+        sha256="bc1d0a75c134e1fb003202262fe10d3d32c59bbb40d714bc3e5015c71effe1e5",
+        deprecated=True,
+    )
+    version(
+        "2021",
+        sha256="efa78ab8409b0f5bf0fbca174fb8fbcf012815326b5c71a9d7c385cde9a8f87b",
+        deprecated=True,
+    )
+    version(
+        "2020.7",
+        sha256="744158d8f61b0d36ffe89ec934519b7e0981a7af438897740160da648d36c2f0",
+        deprecated=True,
+    )
+    version(
+        "2020.6",
+        sha256="d8bbe57ed3c9925a8cb99ecfe39e217f930bed47d5268a9e42b33da544bdb2ee",
+        deprecated=True,
+    )
+    version(
+        "2020.5",
+        sha256="7b6aff647f7c8ee1bf12204d02cef7c55f44402a73195bd5f42cf11850616478",
+        deprecated=True,
+    )
+    version(
+        "2020.4",
+        sha256="5519690321b5500c7951aaf53ff624042c3edd1a5f5d6dd1f2d802a3ecdbf4e6",
+        deprecated=True,
+    )
+    version(
+        "2020.3",
+        sha256="903183691132db14e55b011305db4b6f4901cc4912d2c56c131edfef18cc92a9",
+        deprecated=True,
+    )
+    version(
+        "2020.2",
+        sha256="7465e4cd616359d84489d919ec9e4b1aaf51f0a4296e693c249e83411b7bd2f3",
+        deprecated=True,
+    )
+    version(
+        "2020.1",
+        sha256="e1666558831a3951c02b81000842223698016922806a8ce152e8f616e29899cf",
+        deprecated=True,
+    )
+    version(
+        "2020",
+        sha256="477e56142b3dcd9cb61b8f67b24a55760b04d1655e8684f979a75a5eec40ba01",
+        deprecated=True,
+    )
     version("2019.6", sha256="bebe396dc0db11a9d4cc205abc13b50d88225617642508168a2195324f06a358")
-    version("2019.5", sha256="438061a4a2d45bbb5cf5c3aadd6c6df32d2d77ce8c715f1c8ffe56156994083a")
-    version("2019.4", sha256="ba4366eedfc8a1dbf6bddcef190be8cd75de53691133f305a7f9c296e5ca1867")
-    version("2019.3", sha256="4211a598bf3b7aca2b14ad991448947da9032566f13239b1a05a2d4824357573")
-    version("2019.2", sha256="bcbf5cc071926bc67baa5be6fb04f0986a2b107e1573e15fadcb7d7fc4fb9f7e")
-    version("2019.1", sha256="b2c37ed2fcd0e64c4efcabdc8ee581143986527192e6e647a197c76d9c4583ec")
-    version("2019", sha256="c5b281a5f0b5b4eeb1f4c7d4dc72f96985b566561ca28acc9c7c16f6ee110d0b")
-    version("2018.8", sha256="776923415df4bc78869d7f387c834141fdcda930b2e75be979dc59ecfa6ebecf")
-    version("2018.5", sha256="32261df6f7ec4149fc0508f9af416953d056e281590359838c1ed6644ba097b8")
-    version("2018.4", sha256="6f2ee458c730994a8549d6b4f601ecfc9432731462f8bd4ffa35d330d9aaa891")
-    version("2018.3", sha256="4423a49224972969c52af7b1f151579cea6ab52148d8d7cbae28c183520aa291")
-    version("2018.2", sha256="4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857")
-    version("2018.1", sha256="4d3533340499323fece83b4a2d4251fa856376f2426c541e00b8e6b4c0d705cd")
-    version("2018", sha256="deb5d0b749a52a0c6083367b5f50a99e08003208d81954fb49e7009e1b1fd0e9")
-    version("2016.6", sha256="bac0117d2cad21f9b94fe5b854fb9ae7435b098a6da4e732ee745f18e52473d7")
-    version("2016.5", sha256="57db26c6d9af84710a1e0c47a1f5bf63a22641456448dcd2eeb556ebd14e0b7c")
-    version("2016.4", sha256="4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264")
-    version("2016.3", sha256="7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27")
-    version("5.1.5", sha256="c25266abf07690ecad16ed3996899b1d489cbb1ef733a1befb3b5c75c91a703e")
-    version("5.1.4", sha256="0f3793d8f1f0be747cf9ebb0b588fb2b2b5dc5acc32c3046a7bee2d2c03437bc")
-    version("5.1.2", sha256="39d6f1d7ae8ba38cea6089da40676bfa4049a49903d21551abc030992a58f304")
-    version("4.6.7", sha256="6afb1837e363192043de34b188ca3cf83db6bd189601f2001a1fc5b0b2a214d9")
-    version("4.5.5", sha256="e0605e4810b0d552a8761fef5540c545beeaf85893f4a6e21df9905a33f871ba")
+    version(
+        "2019.5",
+        sha256="438061a4a2d45bbb5cf5c3aadd6c6df32d2d77ce8c715f1c8ffe56156994083a",
+        deprecated=True,
+    )
+    version(
+        "2019.4",
+        sha256="ba4366eedfc8a1dbf6bddcef190be8cd75de53691133f305a7f9c296e5ca1867",
+        deprecated=True,
+    )
+    version(
+        "2019.3",
+        sha256="4211a598bf3b7aca2b14ad991448947da9032566f13239b1a05a2d4824357573",
+        deprecated=True,
+    )
+    version(
+        "2019.2",
+        sha256="bcbf5cc071926bc67baa5be6fb04f0986a2b107e1573e15fadcb7d7fc4fb9f7e",
+        deprecated=True,
+    )
+    version(
+        "2019.1",
+        sha256="b2c37ed2fcd0e64c4efcabdc8ee581143986527192e6e647a197c76d9c4583ec",
+        deprecated=True,
+    )
+    version(
+        "2019",
+        sha256="c5b281a5f0b5b4eeb1f4c7d4dc72f96985b566561ca28acc9c7c16f6ee110d0b",
+        deprecated=True,
+    )
+    version(
+        "2018.8",
+        sha256="776923415df4bc78869d7f387c834141fdcda930b2e75be979dc59ecfa6ebecf",
+        deprecated=True,
+    )
+    version(
+        "2018.5",
+        sha256="32261df6f7ec4149fc0508f9af416953d056e281590359838c1ed6644ba097b8",
+        deprecated=True,
+    )
+    version(
+        "2018.4",
+        sha256="6f2ee458c730994a8549d6b4f601ecfc9432731462f8bd4ffa35d330d9aaa891",
+        deprecated=True,
+    )
+    version(
+        "2018.3",
+        sha256="4423a49224972969c52af7b1f151579cea6ab52148d8d7cbae28c183520aa291",
+        deprecated=True,
+    )
+    version(
+        "2018.2",
+        sha256="4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857",
+        deprecated=True,
+    )
+    version(
+        "2018.1",
+        sha256="4d3533340499323fece83b4a2d4251fa856376f2426c541e00b8e6b4c0d705cd",
+        deprecated=True,
+    )
+    version(
+        "2018",
+        sha256="deb5d0b749a52a0c6083367b5f50a99e08003208d81954fb49e7009e1b1fd0e9",
+        deprecated=True,
+    )
+    version(
+        "2016.6",
+        sha256="bac0117d2cad21f9b94fe5b854fb9ae7435b098a6da4e732ee745f18e52473d7",
+        deprecated=True,
+    )
+    version(
+        "2016.5",
+        sha256="57db26c6d9af84710a1e0c47a1f5bf63a22641456448dcd2eeb556ebd14e0b7c",
+        deprecated=True,
+    )
+    version(
+        "2016.4",
+        sha256="4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264",
+        deprecated=True,
+    )
+    version(
+        "2016.3",
+        sha256="7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27",
+        deprecated=True,
+    )
+    version(
+        "5.1.5",
+        sha256="c25266abf07690ecad16ed3996899b1d489cbb1ef733a1befb3b5c75c91a703e",
+        deprecated=True,
+    )
+    version(
+        "5.1.4",
+        sha256="0f3793d8f1f0be747cf9ebb0b588fb2b2b5dc5acc32c3046a7bee2d2c03437bc",
+        deprecated=True,
+    )
+    version(
+        "5.1.2",
+        sha256="39d6f1d7ae8ba38cea6089da40676bfa4049a49903d21551abc030992a58f304",
+        deprecated=True,
+    )
+    version(
+        "4.6.7",
+        sha256="6afb1837e363192043de34b188ca3cf83db6bd189601f2001a1fc5b0b2a214d9",
+        deprecated=True,
+    )
+    version(
+        "4.5.5",
+        sha256="e0605e4810b0d552a8761fef5540c545beeaf85893f4a6e21df9905a33f871ba",
+        deprecated=True,
+    )
 
     depends_on("c", type="build")  # generated
     depends_on("cxx", type="build")  # generated
@@ -113,11 +283,22 @@ class Gromacs(CMakePackage, CudaPackage):
     variant(
         "heffte",
         default=False,
-        when="@2021: +sycl+mpi",
+        when="@2021: +mpi",
         description="Enable multi-GPU FFT support with HeFFTe",
     )
+    depends_on("heffte +cuda", when="+heffte +cuda")
+    depends_on("heffte +sycl", when="+heffte +sycl")
     variant("opencl", default=False, description="Enable OpenCL support")
-    variant("sycl", default=False, when="@2021: %clang", description="Enable SYCL support")
+    variant("sycl", default=False, when="@2021:", description="Enable SYCL support")
+    requires(
+        "^intel-oneapi-runtime",
+        "^hipsycl %clang",
+        policy="one_of",
+        when="+sycl",
+        msg="GROMACS SYCL support comes either from intel-oneapi-runtime or a "
+        + "package that provides the virtual package `sycl`, such as AdaptiveCpp "
+        + "plus a clang compiler.",
+    )
     variant(
         "intel-data-center-gpu-max",
         default=False,
@@ -627,7 +808,7 @@ def cmake_args(self):
             options.append("-DGMX_USE_ITT=on")
             options.append(
                 "-DITTNOTIFY_INCLUDE_DIR=%s"
-                % join_path(self.spec["intel-oneapi-vtune"].package.headers)
+                % self.spec["intel-oneapi-vtune"].package.headers.directories[0]
             )
 
         if self.spec.satisfies("~nblib"):

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

@@ -250,6 +250,9 @@ class Julia(MakefilePackage):
     depends_on("zlib-api")
     depends_on("zlib +shared +pic +optimize", when="^[virtuals=zlib-api] zlib")
 
+    # https://github.com/JuliaLang/julia/pull/45649#issuecomment-1192377430
+    conflicts("%gcc@12:", when="@:1.7")
+
     # Patches for julia
     patch("julia-1.6-system-libwhich-and-p7zip-symlink.patch", when="@1.6.0:1.6")
     patch("use-add-rpath.patch", when="@:1.8.0")

var/spack/repos/builtin/packages/ltr-retriever/package.py

@@ -3,8 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from os import symlink
-
 from spack.package import *
 
 
@@ -42,9 +40,7 @@ def install(self, spec, prefix):
                 "^TEsorter=.*$", "TEsorter={}".format(spec["py-tesorter"].prefix.bin), "paths"
             )
 
-        mkdirp(prefix.opt)
-        mkdirp(prefix.bin)
+        install_tree(".", prefix)
 
-        install_tree(".", prefix.opt.ltr_retriever)
-
-        symlink(prefix.opt.ltr_retriever.LTR_retriever, prefix.bin.LTR_retriever)
+    def setup_run_environment(self, env):
+        env.prepend_path("PATH", self.prefix)

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

@@ -58,8 +58,8 @@ class Openscenegraph(CMakePackage):
     )  # Qt windowing system was moved into separate osgQt project
     depends_on("qt@4:", when="@3.2:3.5.4")
     depends_on("qt@:4", when="@:3.1")
-    depends_on("libxinerama")
-    depends_on("libxrandr")
+    depends_on("libxinerama", when="platform=linux")
+    depends_on("libxrandr", when="platform=linux")
     depends_on("libpng")
     depends_on("jasper")
     depends_on("libtiff")

var/spack/repos/builtin/packages/r-rsamtools/package.py

@@ -58,3 +58,8 @@ class RRsamtools(RPackage):
 
     # this is not a listed dependency but is needed
     depends_on("curl")
+    depends_on("zlib-api")
+
+    def patch(self):
+        with working_dir("src"):
+            filter_file(r"(^PKG_LIBS=)(\$\(RHTSLIB_LIBS\))", "\\1\\2 -lz", "Makevars")

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

@@ -190,9 +190,6 @@ def edit(self, spec, prefix):
                                         spec["netcdf-fortran"].prefix
                                     )
                                 )
-                                libs_arg.append(
-                                    "-L{0}/lib -lhdf5_fortran -lhdf5".format(spec["hdf5"].prefix)
-                                )
 
                         if "+metis" in spec:
                             libs_arg.append("-L{0} -lmetis".format(self.spec["metis"].prefix.lib))