vtk: lzma patch for v9.0

1. libsci_cray.so is broken, as it fails to list `libdl.so` in
   DT_NEEDED.
2. cray compilers fail to build a different blas

lib/spack/spack/binary_distribution.py

@@ -2561,7 +2561,6 @@ def install_root_node(spec, unsigned=False, force=False, sha256=None):
     with spack.util.path.filter_padding():
         tty.msg('Installing "{0}" from a buildcache'.format(spec.format()))
         extract_tarball(spec, download_result, force)
-        spec.package.windows_establish_runtime_linkage()
         spack.hooks.post_install(spec, False)
         spack.store.STORE.db.add(spec, spack.store.STORE.layout)
 

lib/spack/spack/build_systems/cmake.py

@@ -108,6 +108,11 @@ def _conditional_cmake_defaults(pkg: spack.package_base.PackageBase, args: List[
     if _supports_compilation_databases(pkg):
         args.append(CMakeBuilder.define("CMAKE_EXPORT_COMPILE_COMMANDS", True))
 
+    # Enable MACOSX_RPATH by default when cmake_minimum_required < 3
+    # https://cmake.org/cmake/help/latest/policy/CMP0042.html
+    if pkg.spec.satisfies("platform=darwin") and cmake.satisfies("@3:"):
+        args.append(CMakeBuilder.define("CMAKE_POLICY_DEFAULT_CMP0042", "NEW"))
+
 
 def generator(*names: str, default: Optional[str] = None):
     """The build system generator to use.

lib/spack/spack/installer.py

@@ -488,7 +488,6 @@ def _process_binary_cache_tarball(
 
     with timer.measure("install"), spack.util.path.filter_padding():
         binary_distribution.extract_tarball(pkg.spec, download_result, force=False, timer=timer)
-        pkg.windows_establish_runtime_linkage()
 
         if hasattr(pkg, "_post_buildcache_install_hook"):
             pkg._post_buildcache_install_hook()

lib/spack/spack/util/executable.py

@@ -275,9 +275,9 @@ def streamify(arg, mode):
             long_msg = cmd_line_string + f"\n{result}"
             if fail_on_error:
                 raise ProcessTimeoutError(
-                    f"\nProcess timed out after {timeout}s"
-                    f"We expected the following command to run quickly but\
-it did not, please report this as an issue: {long_msg}",
+                    f"\nProcess timed out after {timeout}s. "
+                    "We expected the following command to run quickly but it did not, "
+                    f"please report this as an issue: {long_msg}",
                     long_message=long_msg,
                 ) from te
 

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

@@ -885,6 +885,7 @@ e4s-cray-rhel-generate:
   extends: [ ".generate-cray-rhel", ".e4s-cray-rhel" ]
 
 e4s-cray-rhel-build:
+  allow_failure: true  # libsci_cray.so broken, misses DT_NEEDED for libdl.so
   extends: [ ".build", ".e4s-cray-rhel" ]
   trigger:
     include:
@@ -907,6 +908,7 @@ e4s-cray-sles-generate:
   extends: [ ".generate-cray-sles", ".e4s-cray-sles" ]
 
 e4s-cray-sles-build:
+  allow_failure: true  # libsci_cray.so broken, misses DT_NEEDED for libdl.so
   extends: [ ".build", ".e4s-cray-sles" ]
   trigger:
     include:

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

@@ -6,7 +6,7 @@
 spack:
   view: false
   specs:
-  - vtk
+  - vtk~mpi
 
   cdash:
     build-group: Windows Visualization (Kitware)

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

@@ -0,0 +1,30 @@
+# 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 Cdi(AutotoolsPackage):
+    """
+    CDI is a C and Fortran Interface to access Climate and NWP model Data.
+    Supported data formats are GRIB, netCDF, SERVICE, EXTRA and IEG.
+    """
+
+    homepage = "https://code.mpimet.mpg.de/projects/cdi"
+    url = "https://code.mpimet.mpg.de/attachments/download/29309/cdi-2.4.0.tar.gz"
+
+    version("2.4.0", sha256="91fca015b04c6841b9eab8b49e7726d35e35b9ec4350922072ec6e9d5eb174ef")
+
+    variant(
+        "netcdf", default=True, description="This is needed to read/write NetCDF files with CDI"
+    )
+
+    depends_on("netcdf-c", when="+netcdf")
+
+    def configure_args(self):
+        args = []
+        if "+netcdf" in self.spec:
+            args.append("--with-netcdf=" + self.spec["netcdf-c"].prefix)
+        return args

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

@@ -14,7 +14,7 @@
 from spack.package import *
 
 
-def cmake_cache_entry(name, value, vtype=None):
+def cmake_cache_entry(name, value, vtype=None, force=False):
     """
     Helper that creates CMake cache entry strings used in
     'host-config' files.
@@ -24,7 +24,8 @@ def cmake_cache_entry(name, value, vtype=None):
             vtype = "BOOL"
         else:
             vtype = "PATH"
-    return 'set({0} "{1}" CACHE {2} "")\n\n'.format(name, value, vtype)
+    force_str = " FORCE" if force else ""
+    return 'set({0} "{1}" CACHE {2} ""{3})\n\n'.format(name, value, vtype, force_str)
 
 
 class Conduit(CMakePackage):
@@ -76,6 +77,8 @@ class Conduit(CMakePackage):
 
     maintainers("cyrush")
 
+    root_cmakelists_dir = "src"
+
     ###########################################################################
     # package variants
     ###########################################################################
@@ -121,6 +124,12 @@ class Conduit(CMakePackage):
     # package dependencies
     ###########################################################################
 
+    #######################
+    # BLT
+    #######################
+    depends_on("blt", type="build")
+    depends_on("blt@0.6.2:", type="build", when="@0.9:")
+
     #######################
     # CMake
     #######################
@@ -245,7 +254,7 @@ def url_for_version(self, version):
     def cmake_args(self):
         host_config = self._get_host_config_path(self.spec)
         options = []
-        options.extend(["-C", host_config, "../spack-src/src/"])
+        options.extend(["-C", host_config])
         return options
 
     @run_after("build")
@@ -255,6 +264,13 @@ def build_test(self):
             print("Running Conduit Unit Tests...")
             make("test")
 
+    # Copy the generated host-config to install directory for downstream use
+    @run_before("install")
+    def copy_host_config(self):
+        src = self._get_host_config_path(self.spec)
+        dst = join_path(self.spec.prefix, os.path.basename(src))
+        copy(src, dst)
+
     @run_after("install")
     @on_package_attributes(run_tests=True)
     def check_install(self):
@@ -291,7 +307,8 @@ def _get_host_config_path(self, spec):
         host_config_path = "{0}-{1}-{2}-conduit-{3}.cmake".format(
             socket.gethostname(), sys_type, spec.compiler, spec.dag_hash()
         )
-        dest_dir = spec.prefix
+
+        dest_dir = self.stage.source_path
         host_config_path = os.path.abspath(join_path(dest_dir, host_config_path))
         return host_config_path
 
@@ -392,15 +409,31 @@ def hostconfig(self):
         if fflags:
             cfg.write(cmake_cache_entry("CMAKE_Fortran_FLAGS", fflags))
 
+        # Add various rpath linker flags
+        rpaths = []
+        if self.compiler.extra_rpaths:
+            rpaths += self.compiler.extra_rpaths
+
+        # Note: This is not needed if we add `extra_rpaths` to this compiler spec case
         if (f_compiler is not None) and ("gfortran" in f_compiler) and ("clang" in cpp_compiler):
             libdir = os.path.join(os.path.dirname(os.path.dirname(f_compiler)), "lib")
-            flags = ""
             for _libpath in [libdir, libdir + "64"]:
                 if os.path.exists(_libpath):
-                    flags += " -Wl,-rpath,{0}".format(_libpath)
-            description = "Adds a missing libstdc++ rpath"
-            if flags:
-                cfg.write(cmake_cache_entry("BLT_EXE_LINKER_FLAGS", flags, description))
+                    rpaths.append(_libpath)
+
+        linkerflags = ""
+        for rpath in rpaths:
+            linkerflags += "-Wl,-rpath,{} ".format(rpath)
+        cfg.write(cmake_cache_entry("CMAKE_EXE_LINKER_FLAGS", linkerflags))
+        if spec.satisfies("+shared"):
+            cfg.write(cmake_cache_entry("CMAKE_SHARED_LINKER_FLAGS", linkerflags))
+        else:
+            cfg.write(cmake_cache_entry("CMAKE_STATIC_LINKER_FLAGS", linkerflags))
+
+        #######################
+        # BLT
+        #######################
+        cfg.write(cmake_cache_entry("BLT_SOURCE_DIR", spec["blt"].prefix))
 
         #######################
         # Examples/Utilities
@@ -436,7 +469,7 @@ def hostconfig(self):
             cfg.write(cmake_cache_entry("BLT_EXE_LINKER_FLAGS", flags))
             if spec.satisfies("+shared"):
                 flags = "${CMAKE_SHARED_LINKER_FLAGS} " + rpaths
-                cfg.write(cmake_cache_entry("CMAKE_SHARED_LINKER_FLAGS", flags))
+                cfg.write(cmake_cache_entry("CMAKE_SHARED_LINKER_FLAGS", flags, force=True))
 
         #######################
         # Python

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

@@ -33,6 +33,7 @@ class Gromacs(CMakePackage, CudaPackage):
 
     version("main", branch="main")
     version("master", branch="main", deprecated=True)
+    version("2024.3", sha256="bbda056ee59390be7d58d84c13a9ec0d4e3635617adf2eb747034922cba1f029")
     version("2024.2", sha256="802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b")
     version("2024.1", sha256="937d8f12a36fffbf2af7add71adbb5aa5c5537892d46c9a76afbecab1aa0aac7")
     version("2024", sha256="04d226d52066a8bc3a42e00d6213de737b4ec292e26703065924ff01956801e2")

var/spack/repos/builtin/packages/linaro-forge/package.py

@@ -22,7 +22,10 @@ class LinaroForge(Package):
     homepage = "https://www.linaroforge.com"
     maintainers("kenche-linaro")
 
-    if platform.machine() in ["aarch64", "arm64"]:
+    if platform.machine() == "aarch64":
+        version(
+            "24.0.4", sha256="d126e4690f7c9bf21e541721dac51dcee1f336a882211426bf98a15d80671e3d"
+        )
         version(
             "24.0.3", sha256="5030c5c23824963f82e94ed606e47cce802393fa4cb7757966818baa7012aa21"
         )
@@ -91,6 +94,9 @@ class LinaroForge(Package):
             "21.1.3", sha256="eecbc5686d60994c5468b2d7cd37bebe5d9ac0ba37bd1f98fbfc69b071db541e"
         )
     elif platform.machine() == "x86_64":
+        version(
+            "24.0.4", sha256="001e7b7cd796d8e807971b99a9ca233c24f8fcd6eee4e9b4bbb0ec8560d44f08"
+        )
         version(
             "24.0.3", sha256="1796559fb86220d5e17777215d3820f4b04aba271782276b81601d5065284526"
         )

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

@@ -84,9 +84,9 @@ def libs(self):
     def setup_run_environment(self, env):
         # Because MPI implementations provide compilers, they have to add to
         # their run environments the code to make the compilers available.
-        env.set("MPITRAMPOLINE_CC", self.compiler.cc_names[0])
-        env.set("MPITRAMPOLINE_CXX", self.compiler.cxx_names[0])
-        env.set("MPITRAMPOLINE_FC", self.compiler.fc_names[0])
+        env.set("MPITRAMPOLINE_CC", self.compiler.cc)
+        env.set("MPITRAMPOLINE_CXX", self.compiler.cxx)
+        env.set("MPITRAMPOLINE_FC", self.compiler.fc)
         env.set("MPICC", join_path(self.prefix.bin, "mpicc"))
         env.set("MPICXX", join_path(self.prefix.bin, "mpicxx"))
         env.set("MPIF77", join_path(self.prefix.bin, "mpifc"))

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

@@ -88,6 +88,7 @@ class Paraview(CMakePackage, CudaPackage, ROCmPackage):
     variant("adios2", default=False, description="Enable ADIOS2 support", when="@5.8:")
     variant("visitbridge", default=False, description="Enable VisItBridge support")
     variant("raytracing", default=False, description="Enable Raytracing support")
+    variant("cdi", default=False, description="Enable CDI support")
     variant(
         "openpmd",
         default=False,
@@ -234,6 +235,8 @@ class Paraview(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("openimagedenoise", when="+raytracing")
     depends_on("ospray +mpi", when="+raytracing +mpi")
 
+    depends_on("cdi", when="+cdi")
+
     depends_on("bzip2")
     depends_on("double-conversion")
     depends_on("expat")
@@ -706,6 +709,10 @@ def use_x11():
         cmake_args.append(self.define_from_variant("VTK_ENABLE_OSPRAY", "raytracing"))
         cmake_args.append(self.define_from_variant("VTKOSPRAY_ENABLE_DENOISER", "raytracing"))
 
+        # CDI
+        cmake_args.append(self.define_from_variant("PARAVIEW_PLUGIN_ENABLE_CDIReader", "cdi"))
+        cmake_args.append(self.define_from_variant("PARAVIEW_PLUGIN_AUTOLOAD_CDIReader", "cdi"))
+
         return cmake_args
 
     def test_smoke_test(self):

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

@@ -32,5 +32,8 @@ class PyGreenlet(PythonPackage):
     depends_on("c", type="build")  # generated
     depends_on("cxx", type="build")  # generated
 
-    depends_on("python", type=("build", "link", "run"))
+    with default_args(type=("build", "link", "run")):
+        depends_on("python")
+        depends_on("python@:3.11", when="@:2")
+
     depends_on("py-setuptools", type="build")

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

@@ -17,6 +17,7 @@ class PyMypy(PythonPackage):
 
     license("MIT AND PSF-2.0", checked_by="tgamblin")
 
+    version("1.11.2", sha256="7f9993ad3e0ffdc95c2a14b66dee63729f021968bff8ad911867579c65d13a79")
     version("1.11.1", sha256="f404a0b069709f18bbdb702eb3dcfe51910602995de00bd39cea3050b5772d08")
     version("1.10.1", sha256="1f8f492d7db9e3593ef42d4f115f04e556130f2819ad33ab84551403e97dd4c0")
     version("1.9.0", sha256="3cc5da0127e6a478cddd906068496a97a7618a21ce9b54bde5bf7e539c7af974")

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

@@ -20,6 +20,8 @@ class SpectrumMpi(BundlePackage):
 
     provides("mpi")
 
+    conflicts("platform=windows")
+
     executables = ["^ompi_info$"]
 
     @classmethod

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

@@ -204,25 +204,21 @@ def set_compiler_options(self, spec):
         #     ('CC', 'CXX' and 'FC')
         # 4 - if no -cc=<compiler> -cxx=<compiler> is passed tau is built with
         #     system compiler silently
-        # (regardless of what %<compiler> is used in the spec)
-        # 5 - On cray gnu compilers are not provied by self.compilers
-        #     Checking GCC_PATH will work if spack loads the gcc module
-        #
-        # In the following we give TAU what he expects and put compilers into
-        # PATH
-        compiler_path = os.path.dirname(self.compiler.cc)
-        if not compiler_path and self.compiler.cc_names[0] == "gcc":
-            compiler_path = os.environ.get("GCC_PATH", "")
-            if compiler_path:
-                compiler_path = compiler_path + "/bin/"
-        os.environ["PATH"] = ":".join([compiler_path, os.environ["PATH"]])
-        compiler_options = [
-            "-c++=%s" % os.path.basename(self.compiler.cxx),
-            "-cc=%s" % os.path.basename(self.compiler.cc),
-        ]
+        compiler_flags: Dict[str, str] = {
+            flag: os.path.basename(getattr(self.compiler, compiler))
+            for flag, compiler in (("-cc", "cc"), ("-c++", "cxx"), ("-fortran", "fc"))
+            if getattr(self.compiler, compiler)
+        }
 
-        if "+fortran" in spec and self.compiler.fc:
-            compiler_options.append("-fortran=%s" % os.path.basename(self.compiler.fc))
+        if "~fortran" in spec:
+            compiler_flags.pop("-fortran", None)
+
+        # tau does not understand `craycc`, `crayCC`, `crayftn`, strip off the `cray` prefix
+        for flag, value in compiler_flags.items():
+            if value.startswith("cray"):
+                compiler_flags[flag] = value[4:]
+
+        compiler_options = [f"{flag}={value}" for flag, value in compiler_flags.items()]
 
         ##########
 

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

@@ -128,6 +128,12 @@ class Vtk(CMakePackage):
 
     depends_on("xz")
     patch("vtk_find_liblzma.patch", when="@8.2")
+    patch(
+        "https://gitlab.kitware.com/vtk/vtk/-/commit/2100772c7840a712c61952afebe84ec4cae174eb.diff",
+        sha256="82a7d17535e732aa97e3cf895d8728f5fb42325a0cdae5befdb3a25bdb1615eb",
+        when="@9.0",
+    )
+
     patch("vtk_movie_link_ogg.patch", when="@8.2")
     patch("vtk_use_sqlite_name_vtk_expects.patch", when="@8.2")
     patch("vtk_proj_include_no_strict.patch", when="@9: platform=windows")