Creation of Beatnik package and associated updates to silo and cabana spack package (#40382)

* Added initial package for building Beatnik with spack

* Fixed github ID for Jason as a maintainer.

* Major revision of beatnik spack package to properly support GPU spack builds with CUDA (and ROCm, though that it untested)

* Marked that beatnik 1.0 will require cabana 0.6.0. We will wait for the cabana 0.6.0 release before we release beatnik

* Update to beatnik package spec to compile with hipcc when +rocm

* Updated spack package for cabana for version 0.6.0 and appropriate heffte dependency

* Updated beatnik package to require cabana 0.6.0

* More updates to cabana and beatnik to build with cabana 0.6.0

* Finish removing BLT dependence from beatnik

* More updates to beatnik package for compiling on cray systems

* Updated beatnik package for new cabana package

* Changes to silo package for new silo version

* Fixed version specs for heffte to be able to concretize and build

* Fixed spack style issues for beatnik and silo packages

* More spack formatting fixes to beatnik and silo

* Patrick adopting silo package as maintainer for now

* Should address final style changes to beatnik package spec

* Yet more style fixes.

* Perhaps this is the final style fixes? :)

* Minor fix to cabana package on required versions

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

@@ -0,0 +1,90 @@
+# Copyright 2013-2023 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 Beatnik(CMakePackage, CudaPackage, ROCmPackage):
+    """Fluid interface model solver based on Pandya and Shkoller's Z-Model formulation."""
+
+    homepage = "https://github.com/CUP-ECS/beatnik"
+    git = "https://github.com/CUP-ECS/beatnik.git"
+
+    maintainers("patrickb314", "JStewart28")
+
+    # Add proper versions and checksums here. Will add 1.0 when a proper SHA is available
+    # version("1.0", sha256="XXX")
+    version("develop", branch="develop")
+    version("main", branch="main")
+
+    # Variants are primarily backends to build on GPU systems and pass the right
+    # informtion to the packages we depend on
+    variant("cuda", default=False, description="Use CUDA support from subpackages")
+    variant("openmp", default=False, description="Use OpenMP support from subpackages")
+
+    # Dependencies for all Beatnik versions
+    depends_on("mpi")
+    depends_on("mpi +cuda", when="+cuda")
+    depends_on("mpi +rocm", when="+rocm")
+
+    # Kokkos dependencies
+    depends_on("kokkos @4:")
+    depends_on("kokkos +cuda +cuda_lambda +cuda_constexpr", when="+cuda")
+    depends_on("kokkos +rocm", when="+rocm")
+    depends_on("kokkos +wrapper", when="%gcc+cuda")
+
+    # Cabana dependencies
+    depends_on("cabana @0.6.0 +grid +heffte +silo +hdf5 +mpi")
+    depends_on("cabana +cuda", when="+cuda")
+    depends_on("cabana +rocm", when="+rocm")
+
+    # Silo dependencies
+    depends_on("silo @4.11:")
+    depends_on("silo @4.11.1:", when="%cce")  # Eariler silo versions have trouble cce
+
+    # Heffte dependencies - We always require FFTW so that there's a host
+    # backend even when we're compiling for GPUs
+    depends_on("heffte +fftw")
+    depends_on("heffte +cuda", when="+cuda")
+    depends_on("heffte +rocm", when="+rocm")
+
+    # If we're using CUDA or ROCM, require MPIs be GPU-aware
+    conflicts("mpich ~cuda", when="+cuda")
+    conflicts("mpich ~rocm", when="+rocm")
+    conflicts("openmpi ~cuda", when="+cuda")
+    conflicts("^intel-mpi")  # Heffte won't build with intel MPI because of needed C++ MPI support
+
+    # Propagate CUDA and AMD GPU targets to cabana
+    for cuda_arch in CudaPackage.cuda_arch_values:
+        depends_on("cabana cuda_arch=%s" % cuda_arch, when="+cuda cuda_arch=%s" % cuda_arch)
+    for amdgpu_value in ROCmPackage.amdgpu_targets:
+        depends_on(
+            "cabana +rocm amdgpu_target=%s" % amdgpu_value,
+            when="+rocm amdgpu_target=%s" % amdgpu_value,
+        )
+
+    # CMake specific build functions
+    def cmake_args(self):
+        args = []
+
+        # Use hipcc as the c compiler if we are compiling for rocm. Doing it this way
+        # keeps the wrapper insted of changeing CMAKE_CXX_COMPILER keeps the spack wrapper
+        # and the rpaths it sets for us from the underlying spec.
+        if "+rocm" in self.spec:
+            env["SPACK_CXX"] = self.spec["hip"].hipcc
+
+        # If we're building with cray mpich, we need to make sure we get the GTL library for
+        # gpu-aware MPI, since cabana and beatnik require it
+        if self.spec.satisfies("+rocm ^cray-mpich"):
+            gtl_dir = join_path(self.spec["cray-mpich"].prefix, "..", "..", "..", "gtl", "lib")
+            args.append(
+                "-DCMAKE_EXE_LINKER_FLAGS=-Wl,-rpath={0} -L{0} -lmpi_gtl_hsa".format(gtl_dir)
+            )
+        elif self.spec.satisfies("+cuda ^cray-mpich"):
+            gtl_dir = join_path(self.spec["cray-mpich"].prefix, "..", "..", "..", "gtl", "lib")
+            args.append(
+                "-DCMAKE_EXE_LINKER_FLAGS=-Wl,-rpath={0} -L{0} -lmpi_gtl_cuda".format(gtl_dir)
+            )
+        return args

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

@@ -12,7 +12,7 @@ class Cabana(CMakePackage, CudaPackage, ROCmPackage):
 
     homepage = "https://github.com/ECP-copa/Cabana"
     git = "https://github.com/ECP-copa/Cabana.git"
-    url = "https://github.com/ECP-copa/Cabana/archive/0.5.0.tar.gz"
+    url = "https://github.com/ECP-copa/Cabana/archive/0.6.0.tar.gz"
 
     maintainers("junghans", "streeve", "sslattery")
 
@@ -47,6 +47,7 @@ class Cabana(CMakePackage, CudaPackage, ROCmPackage):
 
     depends_on("cmake@3.9:", type="build", when="@:0.4.0")
     depends_on("cmake@3.16:", type="build", when="@0.5.0:")
+
     depends_on("googletest", type="test", when="+testing")
     _versions = {":0.2": "-legacy", "0.3:": "@3.1:", "0.4:": "@3.2:", "0.6:": "@3.7:"}
     for _version in _versions:
@@ -63,34 +64,50 @@ class Cabana(CMakePackage, CudaPackage, ROCmPackage):
                 _kk_spec = "kokkos{0}+{1}".format(_kk_version, _backend)
             depends_on(_kk_spec, when="@{0}+{1}".format(_version, _backend))
 
+    # Propagate cuda architectures down to Kokkos and optional submodules
     for arch in CudaPackage.cuda_arch_values:
         cuda_dep = "+cuda cuda_arch={0}".format(arch)
         depends_on("kokkos {0}".format(cuda_dep), when=cuda_dep)
+        depends_on("heffte {0}".format(cuda_dep), when="+heffte {0}".format(cuda_dep))
+        depends_on("arborx {0}".format(cuda_dep), when="+arborx {0}".format(cuda_dep))
+        depends_on("hypre {0}".format(cuda_dep), when="+hypre {0}".format(cuda_dep))
 
     for arch in ROCmPackage.amdgpu_targets:
         rocm_dep = "+rocm amdgpu_target={0}".format(arch)
         depends_on("kokkos {0}".format(rocm_dep), when=rocm_dep)
+        depends_on("heffte {0}".format(rocm_dep), when="+heffte {0}".format(rocm_dep))
+        depends_on("arborx {0}".format(rocm_dep), when="+arborx {0}".format(rocm_dep))
+        depends_on("hypre {0}".format(rocm_dep), when="+hypre {0}".format(rocm_dep))
 
     conflicts("+cuda", when="cuda_arch=none")
+    conflicts("+rocm", when="amdgpu_target=none")
+
     depends_on("kokkos+cuda_lambda", when="+cuda")
 
+    # Dependencies for subpackages
     depends_on("arborx", when="@0.3.0:+arborx")
     depends_on("hypre-cmake@2.22.0:", when="@0.4.0:+hypre")
     depends_on("hypre-cmake@2.22.1:", when="@0.5.0:+hypre")
-    # Previous heFFTe pinned at 2.x.0 because its cmakefiles can't roll forward
-    # compatibilty to later minor versions.
     depends_on("heffte@2.0.0", when="@0.4.0+heffte")
-    depends_on("heffte@2.1.0", when="@0.5.0:+heffte")
+    depends_on("heffte@2.1.0", when="@0.5.0+heffte")
     depends_on("heffte@2.3.0:", when="@0.6.0:+heffte")
     depends_on("silo", when="@0.5.0:+silo")
     depends_on("hdf5", when="@0.6.0:+hdf5")
     depends_on("mpi", when="+mpi")
 
+    # Cabana automatically builds HDF5 support with newer cmake versions
+    # in version 0.6.0. This is fixed post-0.6
+    conflicts("~hdf5", when="@0.6.0 ^cmake@:3.26")
+
+    # Cajita support requires MPI
     conflicts("+cajita ~mpi")
     conflicts("+grid ~mpi")
 
+    # Conflict variants only available in newer versions of cabana
     conflicts("+rocm", when="@:0.2.0")
     conflicts("+sycl", when="@:0.3.0")
+    conflicts("+silo", when="@:0.3.0")
+    conflicts("+hdf5", when="@:0.5.0")
 
     def cmake_args(self):
         options = [self.define_from_variant("BUILD_SHARED_LIBS", "shared")]

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

@@ -12,8 +12,21 @@ class Silo(AutotoolsPackage):
     data to binary, disk files."""
 
     homepage = "https://wci.llnl.gov/simulation/computer-codes/silo"
+    git = "https://github.com/LLNL/Silo.git"
     url = "https://wci.llnl.gov/sites/wci/files/2021-01/silo-4.10.2.tgz"
+    maintainers("patrickb314")
 
+    version(
+        "4.11.1",
+        preferred=True,
+        sha256="49eddc00304aa4a19074b099559edbdcaa3532c98df32f99aa62b9ec3ea7cee2",
+        url="https://github.com/LLNL/Silo/releases/download/4.11.1/silo-4.11.1.tar.xz",
+    )
+    version(
+        "4.11.1-bsd",
+        sha256="51ccfdf3c09dfc98c7858a0a6f08cc3b2a07ee3c4142ee6482ba7b24e314c2aa",
+        url="https://github.com/LLNL/Silo/releases/download/4.11.1/silo-4.11.1-bsd.tar.xz",
+    )
     version(
         "4.11",
         sha256="ab936c1f4fc158d9fdc4415965f7d9def7f4abeca596fe5a25bd8485654898ac",
@@ -68,19 +81,18 @@ class Silo(AutotoolsPackage):
     patch("H5FD_class_t-terminate.patch", when="@:4.10.2-bsd")
 
     # H5EPR_SEMI_COLON.patch was fixed in current dev
-    # patch("H5EPR_SEMI_COLON.patch", when="@:4.11-bsd")
+    patch("H5EPR_SEMI_COLON.patch", when="@:4.11-bsd")
-    patch("H5EPR_SEMI_COLON.patch")
 
     # Fix missing F77 init, fixed in 4.9
     patch("48-configure-f77.patch", when="@:4.8")
 
     # The previously used AX_CHECK_COMPILER_FLAGS macro was dropped from
     # autoconf-archive in 2011
-    patch("configure-AX_CHECK_COMPILE_FLAG.patch")
+    patch("configure-AX_CHECK_COMPILE_FLAG.patch", when="@:4.11-bsd")
 
     # API changes in hdf5-1.13 cause breakage
     # See https://github.com/LLNL/Silo/pull/260
-    patch("hdf5-113.patch", when="@4.11: +hdf5 ^hdf5@1.13:")
+    patch("hdf5-113.patch", when="@4.11:4.11-bsd +hdf5 ^hdf5@1.13:")
     conflicts("^hdf5@1.13:", when="@:4.10.2-bsd")
 
     # hzip and fpzip are not available in the BSD releases
@@ -88,10 +100,10 @@ class Silo(AutotoolsPackage):
     conflicts("+fpzip", when="@4.10.2-bsd,4.11-bsd")
 
     # zfp include missing
-    patch("zfp_error.patch", when="@4.11 +hdf5")
+    patch("zfp_error.patch", when="@4.11:4.11-bsd +hdf5")
 
     # use /usr/bin/env perl for portability
-    patch("mkinc-usr-bin-env-perl.patch")
+    patch("mkinc-usr-bin-env-perl.patch", when="@:4.11-bsd")
 
     def flag_handler(self, name, flags):
         spec = self.spec