Ella GCC Setup

fixes/modulenames_plus_common.patch

@@ -17,7 +17,7 @@ index eaf79f6d04..1be017f46e 100644
 @@ -614,8 +616,9 @@ def use_name(self):
              projection = self.conf.default_projections["all"]
 
-         name = self.spec.format(projection)
+         name = self.spec.format_path(projection)
 -        # Not everybody is working on linux...
 -        parts = name.split("/")
 +        # Not everybody is working on linux... so split on /

repo/packages/amdgromacs/package.py

@@ -4,6 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack.package import *
+from spack.util.prefix import Prefix
 
 class Amdgromacs(CMakePackage, ROCmPackage):
     """
@@ -13,19 +14,22 @@ class Amdgromacs(CMakePackage, ROCmPackage):
     homepage = "https://github.com/ROCmSoftwarePlatform/Gromacs"
     git = "https://github.com/ROCmSoftwarePlatform/Gromacs.git"
 
-    maintainers = ["cdipietrantonio"]
+    maintainers = ["cdipietrantonio","Ilkhom"]
 
     # Even though the branch is develop_2022_amd, the version string printed by gmx_mpi
     # is the following one:
     # GROMACS - gmx mdrun, 2023-dev-commit;ba2dd6f6d70 
-    version("2023", commit="ba2dd6f6d709cc4d4c1083024838e2082e72f3b1")
+    #version("2023", commit="ba2dd6f6d709cc4d4c1083024838e2082e72f3b1")
+    version("2023", commit="7bbbb2de208ac1a42c7144ac28ecc5fb0dc0dd4e")
     # version("2023", branch="develop_2023_amd")
 
     variant("openmp", default=True)
     # variant("plumed", default=False)
 
-    depends_on("fftw-api@3:")
-    depends_on("[email protected]:")
+#    depends_on("fftw-api@3:")
+    depends_on("cray-libsci")
+    depends_on("cray-fftw")
+#    depends_on("[email protected]:")
 #    depends_on("[email protected]", when="+plumed") # Plumed not supported at the moment
     depends_on("mpi")
     depends_on("hwloc")
@@ -36,25 +40,119 @@ class Amdgromacs(CMakePackage, ROCmPackage):
 #        plumed("patch", "-p", "-e", f"gromacs-{self.spec.version}", "-m", "shared")
 
     def cmake_args(self):
-        hipcc = self.spec["hip"].prefix.bin.hipcc
+#        hipcc = self.spec["hip"].prefix.bin.hipcc
         amdgpu_target = ",".join(self.spec.variants["amdgpu_target"].value)
 
+#        args = [
+#            "-D CMAKE_BUILD_TYPE=Release", "-D CMAKE_C_COMPILER=/opt/cray/pe/craype/2.7.20/bin/cc",
+#            "-D CMAKE_CXX_COMPILER=/opt/cray/pe/craype/2.7.20/bin/CC", "-D GMX_OPENMP=ON",
+#            "-D GMX_MPI=ON","-D GMX_GPU=HIP",
+#            f"-D CMAKE_HIP_ARCHITECTURES={amdgpu_target}", f"-D AMDGPU_TARGETS={amdgpu_target}",
+#            f"-D HIP_HIPCC_FLAGS='-O3 --amdgpu-target={amdgpu_target} --save-temps -I/opt/cray/pe/mpich/8.1.25/ofi/gnu/9.1/include'",
+#	        "-D GMX_GPU_USE_VKFFT=ON", "-D CMAKE_C_FLAGS='-Ofast'",
+#            "-D CMAKE_CXX_FLAGS='-Ofast'", 
+#            "-D GMX_SIMD=AVX2_256",
+#            "-D GMX_SIMD=AVX2_256", 
+#            "-D CMAKE_EXE_LINKER_FLAGS='-fopenmp'",
+#            "-D GMX_BUILD_FOR_COVERAGE=OFF",
+#            "-D GMX_EXTERNAL_LAPACK=ON", 
+#            "-D GMX_EXTERNAL_BLAS=ON",
+#            f"-D GMX_BLAS_USER=/opt/cray/pe/libsci/23.02.1.1/GNU/9.1/x86_64/lib/libsci_gnu.so",
+#            f"-D GMX_LAPACK_USER=/opt/cray/pe/libsci/23.02.1.1/GNU/9.1/x86_64/lib/libsci_gnu.so",
+#            "-D BUILD_SHARED_LIBS=OFF",
+#            "-D GMX_DOUBLE=OFF",
+#            f"-D CMAKE_CXX_LINK_FLAGS=-I/opt/cray/pe/mpich/8.1.25/ofi/gnu/9.1/include",
+#            f"-D HIP_CLANG_PARALLEL_BUILD_LINK_OPTIONS=-I/opt/cray/pe/mpich/8.1.25/ofi/gnu/9.1/include",
+#            "-D HIP_VERBOSE_BUILD=ON",
+#            "-D CMAKE_VERBOSE_MAKEFILE=ON"
+#        ]
+
         args = [
-            "-DBUILD_SHARED_LIBS=on", "-DMPI_C_LIB_NAMES=mpi",
-            "-DMPI_CXX_LIB_NAMES=mpi", f"-DMPI_mpi_LIBRARY={self.spec['mpi'].prefix.lib}/libmpi.so",
-            "-DGMX_BUILD_OWN_FFTW=OFF","-DGMX_BUILD_FOR_COVERAGE=off",
-            f"-DCMAKE_C_COMPILER={hipcc}", f"-DCMAKE_CXX_COMPILER={hipcc}",
-	        f"-DMPI_CXX_COMPILER={self.spec['mpi'].mpicxx}", f"-DMPI_C_COMPILER={self.spec['mpi'].mpicc}",
-            "-DGMX_MPI=on", "-DGMX_GPU=HIP",
-            self.define_from_variant("CMAKE_HIP_ARCHITECTURES", "amdgpu_target"),
-            "-DGMX_SIMD=AVX2_256", "-DREGRESSIONTEST_DOWNLOAD=OFF",
-            "-DGMX_GPU_USE_VKFFT=on",
-            f"-DHIP_HIPCC_FLAGS=-O3 --amdgpu-target={amdgpu_target} --save-temps",
-            "-DGMX_HWLOC=ON", "-DMPIEXEC=srun",
-		    "-DMPIEXEC_NUMPROC_FLAG=-n", 
+            "-DCMAKE_BUILD_TYPE=Release",
+            "-DCMAKE_C_COMPILER=cc",
+            "-DCMAKE_CXX_COMPILER=CC",
+            "-DGMX_OPENMP=ON",
+            "-DGMX_MPI=ON",
+            "-DGMX_GPU=HIP",
+            "-DCMAKE_HIP_ARCHITECTURES='gfx90a'",
+            "-DAMDGPU_TARGETS='gfx90a'",
+            "-DGPU_TARGETS='gfx90a'",
+            f"-D HIP_HIPCC_FLAGS='-O3 --amdgpu-target={amdgpu_target} --save-temps -I/opt/cray/pe/mpich/8.1.25/ofi/gnu/9.1/include'",
+            "-DGMX_GPU_USE_VKFFT=ON",
+            "-DCMAKE_C_FLAGS='-Ofast'",
+            "-DCMAKE_CXX_FLAGS='-Ofast'", 
+            "-DGMX_SIMD=AVX2_256",
+            "-DCMAKE_EXE_LINKER_FLAGS='-fopenmp'",
+            "-DGMX_BUILD_FOR_COVERAGE=OFF",
+            "-DGMX_EXTERNAL_LAPACK=ON",
+            "-DGMX_EXTERNAL_BLAS=ON",
+            f'-DGMX_BLAS_USER={self.spec["cray-libsci"].prefix}/lib/libsci_gnu.so',
+            f'-DGMX_LAPACK_USER={self.spec["cray-libsci"].prefix}/lib/libsci_gnu.so',
+            "-DBUILD_SHARED_LIBS=OFF",
+            "-DGMX_DOUBLE=OFF",
+            f'-D CMAKE_CXX_LINK_FLAGS=-I{self.spec["cray-mpich"].prefix}/include',
+            f'-D HIP_CLANG_PARALLEL_BUILD_LINK_OPTIONS=-I{self.spec["cray-mpich"].prefix}/include',
+            "-DHIP_VERBOSE_BUILD=ON",
+            "-DCMAKE_VERBOSE_MAKEFILE=ON"
         ]
 
+
+#            f"-DGMX_BLAS_USER=/opt/cray/pe/libsci/23.02.1.1/GNU/9.1/x86_64/lib/libsci_gnu.so",
+#            f"-DGMX_LAPACK_USER=/opt/cray/pe/libsci/23.02.1.1/GNU/9.1/x86_64/lib/libsci_gnu.so",
+#            f"-D HIP_CLANG_PARALLEL_BUILD_LINK_OPTIONS=-I/opt/cray/pe/mpich/8.1.25/ofi/gnu/9.1/include",
+
+#            "-DCMAKE_CXX_LINK_FLAGS=-I$CRAY_MPICH_PREFIX/include",
+#            "-DHIP_CLANG_PARALLEL_BUILD_LINK_OPTIONS=-I$CRAY_MPICH_PREFIX/include",
+#            "-DHIP_HIPCC_FLAGS='-O3 --amdgpu-target=gfx90a --save-temps -I$CRAY_MPICH_PREFIX/include'",
+
         if '+openmp' in self.spec:
             args.extend(["-DCMAKE_EXE_LINKER_FLAGS=-fopenmp", "-DGMX_OPENMP=ON"])
 
         return args
+
+    def get_paths(self):
+        rocm_spec = self.spec["hip"]
+        rocm_prefix = Prefix(rocm_spec.prefix)
+
+        paths = {
+            "hip-path": rocm_spec.prefix,
+            "rocm-path": rocm_spec.prefix,
+            "rocm-device-libs": rocm_spec.prefix, #rocm_prefix, #elf.spec["llvm-amdgpu"].prefix,
+            "llvm-amdgpu": rocm_prefix.llvm,
+            "hsa-rocr-dev": rocm_prefix.hsa,
+        }
+        paths["bitcode"] = paths["rocm-device-libs"].amdgcn.bitcode
+
+        return paths
+
+    def set_variables(self, env):
+        if self.spec.satisfies("+rocm"):
+            # Note: do not use self.spec[name] here, since not all dependencies
+            # have defined prefixes when hip is marked as external.
+            paths = self.get_paths()
+
+            # Used in hipcc, but only useful when hip is external, since only then
+            # there is a common prefix /opt/rocm-x.y.z.
+            env.set("ROCM_PATH", paths["rocm-path"])
+            # Just the prefix of hip (used in hipcc)
+            env.set("HIP_PATH", paths["hip-path"])
+            env.set("HIP_DEVICE_LIB_PATH", paths["bitcode"])
+            env.set("HIP_CLANG_PATH", paths["llvm-amdgpu"].bin)
+            env.set("HSA_PATH", paths["hsa-rocr-dev"])
+            env.set("DEVICE_LIB_PATH", paths["bitcode"])
+            env.set("LLVM_PATH", paths["llvm-amdgpu"])
+
+            env.append_path(
+                "HIPCC_COMPILE_FLAGS_APPEND",
+                "--rocm-path={0}".format(paths["rocm-path"]),
+                separator=" ",
+            )
+
+
+    def setup_build_environment(self, env):
+        if self.spec.satisfies("+rocm"):      
+            self.set_variables(env)
+
+    def setup_run_environment(self, env):
+        if self.spec.satisfies("+rocm"):
+            self.set_variables(env)    

repo/packages/ansys-fluids/package.py

@@ -72,8 +72,19 @@ def install(self, spec, prefix):
         tmp_install_path = os.environ['MYSCRATCH']+'/tmp'
         mkdirp('{0}/{1}'.format(self.stage.source_path, 'fluids_tmpdir'))
         mkdirp('{0}/{1}'.format(tmp_install_path, 'fluids'))
-        run_install = Executable("./INSTALL -silent -install_dir {0}/{1} -usetempdir {2}/{3}".format(tmp_install_path, 'fluids', self.stage.source_path, 'fluids_tmpdir'))
-        run_install()
+#       run_install = Executable("./INSTALL -silent -install_dir {0}/{1} -usetempdir {2}/{3}".format(tmp_install_path, 'fluids', self.stage.source_path, 'fluids_tmpdir'))
+        run_install = Executable("./INSTALL") # -silent -install_dir {0}/{1} -usetempdir {2}/{3}".format(tmp_install_path, 'fluids', self.stage.source_path, 'fluids_tmpdir'))
+        config_options = [
+                "-silent",
+                ]
+        config_options.append("-install_dir")
+        config_options.append("%s" % join_path(tmp_install_path, "fluids"))
+#                "-install_dir {0}/{1}".format(tmp_install_path, 'fluids', self.stage.source_path, 'fluids_tmpdir'),
+
+        config_options.append("-usetempdir")
+        config_options.append("%s" % join_path(self.stage.source_path, 'fluids_tmpdir'))
+
+        run_install(*config_options) 
         # change internal wrapper for launching fluent from mpirun to srun and also alter the platform using sed
         sed=which('sed')
         # find comments before start job and insert the new my_cdmline 

repo/packages/aoflagger/as.patch

@@ -0,0 +1,13 @@
+diff --git a/algorithms/antennaselector.h b/algorithms/antennaselector.h
+index 6353a4d..d8fad40 100644
+--- a/algorithms/antennaselector.h
++++ b/algorithms/antennaselector.h
+@@ -6,6 +6,8 @@ class DefaultStatistics;
+
+ #include <map>
+ #include <vector>
++#include <cstddef>
++using namespace std;
+
+ namespace rfiStrategy {
+

repo/packages/aoflagger/package.py

@@ -0,0 +1,26 @@
+from spack.patch import apply_patch
+import os
+
+PATCHFILE = os.path.join(os.path.dirname(os.path.abspath(__file__)), "as.patch")
+
+
+class Aoflagger(CMakePackage):
+    """RFI detector and quality analysis
+    for astronomical radio observations."""
+
+    maintainers("dipietrantonio")
+
+    version('3.4.0', git='https://gitlab.com/aroffringa/aoflagger.git', tag='v3.4.0', submodules=True)
+    version('3.2.0', git='https://gitlab.com/aroffringa/aoflagger.git', tag='v3.2.0', submodules=True)
+
+    depends_on('[email protected]:')
+    depends_on('[email protected]:')
+    depends_on('[email protected]: +test +system +date_time')
+    depends_on('libxml2')
+    depends_on('cfitsio')
+    depends_on('libpng')
+    depends_on('[email protected]: +cxx ~mpi api=v110')
+    depends_on('[email protected]:')
+    depends_on('cmake', type='build')
+
+    patch('as.patch', when='@3.2.0')

repo/packages/birli/package.py

@@ -0,0 +1,70 @@
+from spack.package import *
+
+class Birli(Package):
+    """A preprocessing pipeline for the Murchison Widefield Array"""
+
+    homepage = "https://github.com/MWATelescope/birli"
+    git = "https://github.com/MWATelescope/birli.git"
+
+    maintainers = ["d3v-null"]
+
+    version("main", branch="main")
+    version("0.15.1", tag="v0.15.1")
+    version("0.14.0", tag="v0.14.0")
+    version("0.13.0", tag="v0.13.0")
+    version("0.12.0", tag="v0.12.0")
+    version("0.10.0", tag="v0.10.0")
+
+    # unknown issue on setonix when enabled https://github.com/PawseySC/pawsey-spack-config/pull/280#issuecomment-2296128762
+    variant("cfitsio-static", default=False, description="Enable the fitsio_src feature of the fitsio-sys crate.")
+    variant("portable", default=True, description="Disable native CPU optimizations")
+
+    depends_on("[email protected]:", type="build")
+    depends_on("cmake", type="build")
+
+    # cfitsio > 4 introduces a breaking change, is incompatible with mwalib.
+    # default spack cfitsio does not give the +reentrant option
+    depends_on("[email protected] +reentrant")
+
+    depends_on("[email protected]:")
+    depends_on("erfa") # because of Marlu
+
+    test_requires_compiler = True
+
+    def setup_build_environment(self, env):
+        build_dir = self.stage.source_path
+        env.set('CARGO_HOME', f"{build_dir}/.cargo")
+        if self.spec.satisfies("+cfitsio-static"):
+            env.set('MWALIB_LINK_STATIC_CFITSIO', 1)
+        if self.spec.satisfies("~portable"):
+            env.append_flags("RUSTFLAGS", f"-C target-cpu=native")
+
+    def get_features(self):
+        features = []
+        if self.spec.satisfies('+cfitsio-static'):
+            features += ["cfitsio-static"]
+        return features
+
+    def get_cargo_args(self):
+        args = []
+        if (features:=self.get_features()):
+            args += [f"--features={','.join(features)}"]
+        # args += ["--verbose"] # for debugging
+        return args
+
+    def install(self, spec, prefix):
+        # os.system("env") # for debugging
+        cargo = Executable("cargo")
+        features = self.get_features()
+        cargo("install", "--path=.", "--locked", f"--root={prefix}", *self.get_cargo_args())
+
+    @run_after("install")
+    @on_package_attributes(run_tests=True)
+    def cargo_test(self):
+        cargo = Executable("cargo")
+        features = self.get_features()
+        cargo("test", "--release", "--lib", *self.get_cargo_args())
+
+    def setup_run_environment(self, env):
+        if not self.spec.satisfies("+cfitsio-static"):
+            env.prepend_path("LD_LIBRARY_PATH", self.spec["cfitsio"].prefix.lib)

repo/packages/blaspp/package.py

@@ -2,8 +2,8 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-#taken from spack/0.21.0
-
+# PAWSEY Additions
+# added 2023.11.05 version
 import os
 
 from spack.package import *
@@ -17,9 +17,9 @@ class Blaspp(CMakePackage, CudaPackage, ROCmPackage):
     homepage = "https://github.com/icl-utk-edu/blaspp"
     git = homepage
     url = "https://github.com/icl-utk-edu/blaspp/releases/download/v2023.01.00/blaspp-2023.01.00.tar.gz"
-    maintainers = ["teonnik", "Sely85", "G-Ragghianti", "mgates3"]
+    maintainers("teonnik", "Sely85", "G-Ragghianti", "mgates3")
 
-    version("master", branch="master")
+    version("2023.11.05", sha256="62dfc03ec07c0826e0466dc2c204b460caa929d53ad4f050cb132d92670be7ce")
     version(
         "2023.08.25", sha256="1d9c7227a6d8776944aa866592142b7b51c6e4ba5529d168eb8ae2b329c47401"
     )
@@ -47,11 +47,14 @@ class Blaspp(CMakePackage, CudaPackage, ROCmPackage):
 
     variant("openmp", default=True, description="Use OpenMP internally.")
     variant("shared", default=True, description="Build shared libraries")
+    variant("sycl", default=False, description="Build support for the SYCL backend")
 
     depends_on("[email protected]:", type="build")
     depends_on("blas")
     depends_on("llvm-openmp", when="%apple-clang +openmp")
     depends_on("rocblas", when="+rocm")
+    depends_on("intel-oneapi-mkl", when="+sycl")
+    depends_on("intel-oneapi-mkl threads=openmp", when="+sycl")
 
     # only supported with clingo solver: virtual dependency preferences
     # depends_on('openblas threads=openmp', when='+openmp ^openblas')
@@ -64,7 +67,13 @@ class Blaspp(CMakePackage, CudaPackage, ROCmPackage):
     conflicts(
         "+rocm", when="@:2020.10.02", msg="ROCm support requires BLAS++ 2021.04.00 or greater"
     )
-    conflicts("+rocm", when="+cuda", msg="BLAS++ can only support one GPU backend at a time")
+    backend_msg = "BLAS++ supports only one GPU backend at a time"
+    conflicts("+rocm", when="+cuda", msg=backend_msg)
+    conflicts("+rocm", when="+sycl", msg=backend_msg)
+    conflicts("+cuda", when="+sycl", msg=backend_msg)
+    conflicts("+sycl", when="@:2023.06.00", msg="SYCL support requires BLAS++ version 2023.08.25")
+
+    requires("%oneapi", when="+sycl", msg="blaspp+sycl must be compiled with %oneapi")
 
     def cmake_args(self):
         spec = self.spec
@@ -75,6 +84,8 @@ def cmake_args(self):
                 backend = "cuda"
             if "+rocm" in spec:
                 backend = "hip"
+            if "+sycl" in spec:
+                backend = "sycl"
             backend_config = "-Dgpu_backend=%s" % backend
 
         args = [