py-proteus: New package

repos/spack_repo/builtin/packages/chrono/package.py

@@ -0,0 +1,149 @@
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+
+from spack_repo.builtin.build_systems.cmake import CMakePackage
+
+from spack.package import *
+
+
+class Chrono(CMakePackage):
+    """Project Chrono is an open-source multi-physics simulation engine for
+    rigid and flexible multibody dynamics, collision detection, granular
+    material, fluid-solid interaction and vehicle dynamics.
+
+    The ``+python`` variant additionally builds ``pychrono``, the SWIG-generated
+    Python module, which Chrono builds from the same tree rather than shipping
+    as a separate project.
+    """
+
+    homepage = "https://projectchrono.org/"
+    url = "https://github.com/projectchrono/chrono/archive/refs/tags/10.0.0.tar.gz"
+    git = "https://github.com/projectchrono/chrono.git"
+
+    maintainers("cekees")
+
+    license("BSD-3-Clause")
+
+    version("main", branch="main")
+    version("10.0.0", sha256="806e5e24a06f26bbd42344dd1f13d75e3214c9eb29901553574b9c87217d8722")
+
+    variant("python", default=False, description="Build the pychrono Python module")
+    variant("openmp", default=True, description="Enable OpenMP parallelism")
+    variant("shared", default=True, description="Build shared libraries")
+    variant("simd", default=False, description="Enable SIMD vectorization")
+
+    # Chrono compiles C as well as C++ (e.g. chrono_thirdparty/libstl/stlfile.c),
+    # so both must be declared -- omitting "c" fails at cmake time with
+    # "[spack cc]: Error: SPACK_CC_* variables not set".
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
+    depends_on("cmake@3.18:", type="build")
+
+    # Chrono's core headers include Eigen directly, so it is a link-time
+    # dependency of every consumer, not just a build-time one.
+    depends_on("eigen@3.3.0:")
+
+    # The Python module is generated with SWIG at build time
+    # (src/chrono_swig/chrono_python/CMakeLists.txt does find_package(SWIG)).
+    with when("+python"):
+        # NOT extends("python"): Chrono installs pychrono into
+        # share/chrono/python, never into site-packages -- verified on an actual
+        # install, whose prefix contains only include/ lib/ share/
+        # importer_blender/. extends() would promise spack a layout that does not
+        # exist. PYTHONPATH is set for this package and its dependents below,
+        # which is the same thing PETSc's own proteus build does
+        # (PYTHONPATH="$PREFIX/share/chrono/python").
+        depends_on("python@3.8:", type=("build", "run"))
+        depends_on("swig@4:", type="build")
+
+    depends_on("llvm-openmp", when="+openmp platform=darwin")
+
+    # ------------------------------------------------------------------
+    # ChClassFactory.h uses std::enable_if, std::is_polymorphic and
+    # std::is_abstract but includes only <cstdio> <string> <functional>
+    # <typeindex> <unordered_map> <memory>, relying on one of those to pull in
+    # <type_traits> transitively. libstdc++ and Apple's libc++ still do;
+    # newer libc++ (e.g. conda-forge's) does not, and Chrono_core then fails
+    # with 14 errors of the form
+    #
+    #   ChClassFactory.h:48:53: error: no member named 'is_polymorphic' in
+    #                                  namespace 'std'
+    #
+    # Belongs upstream in projectchrono/chrono; done here as a filter_file
+    # rather than a patch so it stays a no-op once upstream adds the include.
+    # ------------------------------------------------------------------
+    @run_before("cmake")
+    def add_missing_type_traits_include(self):
+        header = join_path(self.stage.source_path, "src", "chrono", "core", "ChClassFactory.h")
+        if not os.path.exists(header):
+            return
+        with open(header) as f:
+            if "#include <type_traits>" in f.read():
+                return
+        filter_file(r"^#include <cstdio>$", "#include <cstdio>\n#include <type_traits>", header)
+
+    def cmake_args(self):
+        args = [
+            self.define_from_variant("BUILD_SHARED_LIBS", "shared"),
+            self.define("BUILD_TESTING", False),
+            self.define("BUILD_DEMOS", False),
+            # Optional modules, each pulling dependencies Chrono does not need
+            # for multibody dynamics. Option names carry the CH_ prefix as of
+            # 10.0.0 (confirmed against the tag's own CMakeLists.txt).
+            self.define("CH_ENABLE_MODULE_CASCADE", False),
+            self.define("CH_ENABLE_MODULE_IRRLICHT", False),
+            self.define("CH_ENABLE_MODULE_MATLAB", False),
+            self.define("CH_ENABLE_MODULE_POSTPROCESS", False),
+            self.define("CH_ENABLE_MODULE_ROS", False),
+            self.define("CH_ENABLE_MODULE_VEHICLE", False),
+            self.define_from_variant("CH_ENABLE_MODULE_PYTHON", "python"),
+            self.define_from_variant("CH_ENABLE_OPENMP", "openmp"),
+            self.define_from_variant("CH_USE_SIMD", "simd"),
+            # Chrono appends CH_DEBUG_POSTFIX ("_d") to every library name in a
+            # Debug build, but consumers link the unsuffixed name. Force it
+            # empty so a Debug build keeps -g without renaming the libraries.
+            self.define("CH_DEBUG_POSTFIX", ""),
+        ]
+
+        if self.spec.satisfies("+python"):
+            # Chrono's find_package(Python3 ... COMPONENTS Development) has been
+            # observed to populate only Python3_EXECUTABLE, after which the SWIG
+            # module links without libpython and fails on every CPython symbol.
+            # Point CMake at the library and headers directly.
+            python = self.spec["python"]
+            args += [
+                self.define("Python3_EXECUTABLE", python.command.path),
+                self.define("Python3_INCLUDE_DIR", python.headers.directories[0]),
+                self.define("Python3_LIBRARY", python.libs[0]),
+            ]
+            if self.spec.satisfies("platform=darwin"):
+                # chrono_python's _core module target neither links -lpython nor
+                # passes -undefined dynamic_lookup. Unresolved symbols in a
+                # shared object are fine on Linux and resolve at dlopen time,
+                # but are a hard link error for a macOS bundle.
+                args.append(self.define("CMAKE_MODULE_LINKER_FLAGS", "-undefined dynamic_lookup"))
+
+        return args
+
+    # pychrono lives in share/chrono/python, so nothing finds it by default.
+    # Setting CH_INSTALL_PYTHON does not move it (tried against 10.0.0: the
+    # module still installed to share/chrono/python), so expose it explicitly --
+    # for this package's own run environment and for anything depending on it.
+    @property
+    def _pychrono_dir(self):
+        return join_path(self.prefix, "share", "chrono", "python")
+
+    def setup_run_environment(self, env):
+        if self.spec.satisfies("+python"):
+            env.prepend_path("PYTHONPATH", self._pychrono_dir)
+
+    def setup_dependent_build_environment(self, env, dependent_spec):
+        if self.spec.satisfies("+python"):
+            env.prepend_path("PYTHONPATH", self._pychrono_dir)
+
+    def setup_dependent_run_environment(self, env, dependent_spec):
+        if self.spec.satisfies("+python"):
+            env.prepend_path("PYTHONPATH", self._pychrono_dir)

repos/spack_repo/builtin/packages/openblas/package.py

@@ -647,7 +647,26 @@ def build(self, pkg: MakefilePackage, spec: Spec, prefix: Prefix) -> None:
         with working_dir(self.build_directory):
             # Due to the verbosity of the command line and number of object
             # files created, we suppress makefile command echoing via `-s`.
-            make("-s", *self.make_defs)
+            # Build the library targets only, ONE AT A TIME. A bare "make" is
+            # OpenBLAS's default "all" -- "libs netlib $(RELA) tests shared" -- so
+            # the test suite is built AND RUN by an ordinary install. That defeats
+            # the check_build/check_install hooks below, which are guarded by
+            # @on_package_attributes(run_tests=True) and are the intended opt-in,
+            # and it turns any test failure into a hard build failure: on macOS
+            # x86_64 (TARGET=SKYLAKEX NO_AVX512=1 DYNAMIC_ARCH=1) "TEST 1/125
+            # min:smin_negative" dies with "Bus error: 10" though the library
+            # itself builds cleanly.
+            #
+            # The invocations must stay SEPARATE. Passing "libs netlib shared" as
+            # three goals to one make lets them run concurrently, which races:
+            # "ar: libopenblas-r0.3.34.a: error reading zlatm5.o: file truncated"
+            # on linux-alderlake/gcc. That is the race this method's docstring is
+            # about, and the reason it overrides 'make all' in the first place.
+            #
+            # TEMPORARY: carried on this branch pending an upstream fix; drop it
+            # once spack/spack-packages takes the change.
+            for target in ("libs", "netlib", "shared"):
+                make("-s", target, *self.make_defs)
 
     def edit(self, pkg, spec, prefix):
         # https://github.com/spack/spack-packages/pull/5883#issuecomment-5189054355

repos/spack_repo/builtin/packages/petsc/package.py

@@ -136,6 +136,7 @@ class Petsc(Package, CudaPackage, ROCmPackage):
         when="+fortran",
         description="Activates support for superlu-dist (only parallel)",
     )
+    variant("superlu", default=False, description="Activates support for superlu (sequential)")
     variant("strumpack", default=False, description="Activates support for Strumpack")
     variant(
         "scalapack", default=False, when="+fortran", description="Activates support for Scalapack"
@@ -366,6 +367,11 @@ class Petsc(Package, CudaPackage, ROCmPackage):
     depends_on("mkl", when="+mkl-pardiso")
     depends_on("fftw+mpi", when="+fftw+mpi")
     depends_on("suite-sparse", when="+suite-sparse")
+    depends_on("superlu", when="+superlu")
+    conflicts(
+        "+superlu+int64",
+        msg="SuperLU has no support for 64-bit integers, use superlu-dist instead",
+    )
     depends_on("libx11", when="+X")
     depends_on("mpfr", when="+mpfr")
     depends_on("gmp", when="+mpfr")
@@ -549,6 +555,7 @@ def configure_options(self):
             ("kokkos", "kokkos", False, False),
             ("kokkos-kernels", "kokkos-kernels", False, False),
             ("superlu-dist", "superlu_dist", True, True),
+            "superlu",
             ("scotch", "ptscotch", True, True),
             (
                 "suite-sparse:umfpack,klu,cholmod,btf,ccolamd,colamd,camd,amd,"

repos/spack_repo/builtin/packages/pumi/package.py

@@ -33,6 +33,12 @@ class Pumi(CMakePackage):
     # scorec/core develop branch and we prefer not to expose spack users
     # to the added instability.
     version("master", submodules=True, branch="master")
+    version(
+        "4.2.1", submodules=True, commit="a40922de30f09af63a0251a0d53f95c6cadd9199"
+    )  # tag 4.2.1 (same commit as 4.2.0 -- retag only, includes the apfMDS.cc int/long fix)
+    version(
+        "4.1.0", submodules=True, commit="a8e3aef58bfe86790782c4ae5e5c1bb5f232ff30"
+    )  # tag 4.1.0
     version(
         "2.2.9", submodules=True, commit="f87525cae7597322edfb2ccf1c7d4437402d9481"
     )  # tag 2.2.9

repos/spack_repo/builtin/packages/py_proteus/package.py

@@ -0,0 +1,99 @@
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import glob
+import os
+
+from spack_repo.builtin.build_systems.python import PythonPackage
+
+from spack.package import *
+
+
+class PyProteus(PythonPackage):
+    """Proteus: Computational Methods and Simulation Toolkit. Python tools
+    for rapidly developing computer models and numerical methods"""
+
+    homepage = "http://proteustoolkit.org"
+    git = "https://github.com/cekees/proteus.git"
+
+    maintainers("cekees")
+
+    license("MIT")
+
+    version("main", branch="main")
+
+    variant("pumi", default=True, description="Enable PUMI mesh adaptation support")
+    variant("chrono", default=True, description="Enable Chrono modeling support")
+
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
+    depends_on("fortran", type="build")  # remove in future not a direct proteus dep
+    depends_on("python@3.9:", type=("build", "run"))
+    depends_on("py-setuptools@61:", type="build")
+    depends_on("py-cython@3:", type="build")
+    depends_on("py-pybind11@2.11:2", type="build")  # xtensor@0.27.1 *= overload issue
+    depends_on("py-numpy@1.25:", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-mpi4py", type=("build", "run"))
+    depends_on("py-petsc4py", type=("build", "run"))
+    depends_on("py-h5py+mpi", type=("build", "run"))
+    depends_on("mpi")
+    depends_on("petsc+mpi+hypre+superlu-dist+superlu")
+    depends_on("hdf5+mpi+hl")
+    depends_on("openblas")  # should relax to generic blas in future
+    depends_on("metis")  # through several dependencies
+    depends_on("superlu")
+    depends_on("triangle")  # shells out but has linked in past
+    depends_on("tetgen")  # shells out
+    depends_on("gmsh~fltk~med")  # shells out to the gmsh, no fltk/med needed
+    depends_on("ncurses")  # Fenton waves as text gui, generally not used
+    # run type matters: chrono exports PYTHONPATH for share/chrono/python
+    # (pychrono is not installed into site-packages) via
+    # setup_dependent_run_environment, which spack only applies to run deps.
+    depends_on("chrono+python", when="+chrono", type=("build", "link", "run"))
+    depends_on("pumi@4.2.1:+zoltan+shared", when="+pumi")  # <4.2.1 requires patch
+    depends_on("zoltan+parmetis~fortran", when="+pumi")
+    depends_on("parmetis")
+    depends_on("eigen@3.4")  # xtensor dep
+    depends_on("xtensor@0.26.0")
+    depends_on("xtensor-python@0.28.0:")
+    depends_on("xtl")
+
+    def _mpi_dir(self):
+        # try to find the right mpi.h as it's not always in self.spec["mpi"]
+        mpi_prefix = self.spec["mpi"].prefix
+        if os.path.isfile(os.path.join(mpi_prefix, "include", "mpi.h")):
+            return mpi_prefix
+        for candidate in glob.glob(os.path.join(mpi_prefix, "lib", "*", "mpich")):
+            if os.path.isfile(os.path.join(candidate, "include", "mpi.h")):
+                return candidate
+        for candidate in glob.glob(os.path.join(mpi_prefix, "lib", "*", "openmpi")):
+            if os.path.isfile(os.path.join(candidate, "include", "mpi.h")):
+                return candidate
+        return mpi_prefix
+
+    def setup_build_environment(self, env):
+        if self.spec.satisfies("~pumi"):
+            env.set("PROTEUS_SKIP_PUMI", "1")
+        if self.spec.satisfies("~chrono"):
+            env.set("PROTEUS_SKIP_CHRONO", "1")
+        env.set("PETSC_DIR", self.spec["petsc"].prefix)
+        env.set("MPI_DIR", self._mpi_dir())
+        env.set("HDF5_DIR", self.spec["hdf5"].prefix)
+        env.set("BLAS_DIR", self.spec["openblas"].prefix)
+        env.set("LAPACK_DIR", self.spec["openblas"].prefix)
+        env.set("SUPERLU_DIR", self.spec["superlu"].prefix)
+        env.set("NCURSES_DIR", self.spec["ncurses"].prefix)
+        env.set("METIS_DIR", self.spec["metis"].prefix)
+
+        if self.spec.satisfies("+pumi"):
+            env.set("SCOREC_DIR", self.spec["pumi"].prefix)
+            env.set("ZOLTAN_DIR", self.spec["zoltan"].prefix)
+            env.set("PARMETIS_DIR", self.spec["parmetis"].prefix)
+
+        if self.spec.satisfies("+chrono"):
+            env.set("CHRONO_DIR", self.spec["chrono"].prefix)
+
+        for dep in ("eigen", "xtensor", "xtensor-python", "xtl"):
+            env.prepend_path("CPATH", self.spec[dep].prefix.include)

repos/spack_repo/builtin/packages/triangle/package.py

@@ -23,11 +23,17 @@ class Triangle(Package):
 
     version("1.6", sha256="1766327add038495fa3499e9b7cc642179229750f7201b94f8e1b7bee76f8480")
 
-    depends_on("libx11", type="link")
+    depends_on("libx11", type=("build", "link"))
+    depends_on("xproto", type="build")
     depends_on("gmake", type="build")
 
     def install(self, spec, prefix):
-        make()
+        x11 = spec["libx11"].prefix
+        xproto = spec["xproto"].prefix
+        cswitches = "-O -std=gnu17 -I{0} -I{1} -L{2}".format(x11.include, xproto.include, x11.lib)
+        if not spec.satisfies("platform=darwin"):
+            cswitches = "-DLINUX " + cswitches
+        make("CSWITCHES=" + cswitches)
         mkdirp(prefix.bin)
 
         install("triangle", prefix.bin)

repos/spack_repo/builtin/packages/zoltan/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
 import re
 
 from spack_repo.builtin.build_systems.autotools import AutotoolsPackage
@@ -119,6 +120,11 @@ def configure_args(self):
                 # Although adding to config_libs _should_ suffice, it does not
                 # Add to ldflags as well
                 config_ldflags.append("-lgfortran")
+                gfortran_lib = Executable(self.compiler.fc)(
+                    "-print-file-name=libgfortran." + dso_suffix, output=str
+                ).strip()
+                if gfortran_lib and gfortran_lib != "libgfortran." + dso_suffix:
+                    config_ldflags.append("-L" + os.path.dirname(gfortran_lib))
             if spec.satisfies("%intel") or spec.satisfies("%oneapi"):
                 config_libs.append("-lifcore")
 
@@ -211,3 +217,10 @@ def solib_install(self):
         for lib_path in find(self.spec.prefix.lib, "lib*.a"):
             lib_shared_name = re.sub(r"\.a$", f".{dso_suffix}", lib_path)
             move(lib_path, lib_shared_name)
+            if dso_suffix == "dylib":
+                install_name_tool = which("install_name_tool", required=True)
+                install_name_tool(
+                    "-id",
+                    "@rpath/" + os.path.basename(lib_shared_name),
+                    lib_shared_name,
+                )