From 74172fb9d2cd85c74c2cf72a206f6bdfa27137f9 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Fri, 10 Nov 2023 14:56:04 +0100 Subject: [PATCH] gromacs et al: fix ^mkl pattern (#41002) The ^mkl pattern was used to refer to three packages even though none of software using it was depending on "mkl". This pattern, which follows Hyrum's law, is now being removed in favor of a more explicit one. In this PR gromacs, abinit, lammps, and quantum-espresso are modified. Intel packages are also modified to provide "lapack" and "blas" together. --- lib/spack/spack/build_systems/oneapi.py | 7 +++++-- lib/spack/spack/package.py | 1 + var/spack/repos/builtin/packages/abinit/package.py | 14 ++++++++++---- .../repos/builtin/packages/gromacs/package.py | 7 ++++++- .../repos/builtin/packages/intel-mkl/package.py | 3 +-- .../builtin/packages/intel-oneapi-mkl/package.py | 3 +-- .../packages/intel-parallel-studio/package.py | 3 +-- var/spack/repos/builtin/packages/lammps/package.py | 2 +- .../builtin/packages/quantum-espresso/package.py | 12 +++++++++--- var/spack/repos/builtin/packages/r/package.py | 2 +- 10 files changed, 36 insertions(+), 18 deletions(-) diff --git a/lib/spack/spack/build_systems/oneapi.py b/lib/spack/spack/build_systems/oneapi.py index 1961eb312c..4c432c0cac 100644 --- a/lib/spack/spack/build_systems/oneapi.py +++ b/lib/spack/spack/build_systems/oneapi.py @@ -9,11 +9,10 @@ import shutil from os.path import basename, dirname, isdir -from llnl.util.filesystem import find_headers, find_libraries, join_path +from llnl.util.filesystem import find_headers, find_libraries, join_path, mkdirp from llnl.util.link_tree import LinkTree from spack.directives import conflicts, variant -from spack.package import mkdirp from spack.util.environment import EnvironmentModifications from spack.util.executable import Executable @@ -212,3 +211,7 @@ def link_flags(self): @property def ld_flags(self): return "{0} {1}".format(self.search_flags, self.link_flags) + + +#: Tuple of Intel math libraries, exported to packages +INTEL_MATH_LIBRARIES = ("intel-mkl", "intel-oneapi-mkl", "intel-parallel-studio") diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index c537a7103a..16b1216acb 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -49,6 +49,7 @@ from spack.build_systems.nmake import NMakePackage from spack.build_systems.octave import OctavePackage from spack.build_systems.oneapi import ( + INTEL_MATH_LIBRARIES, IntelOneApiLibraryPackage, IntelOneApiPackage, IntelOneApiStaticLibraryList, diff --git a/var/spack/repos/builtin/packages/abinit/package.py b/var/spack/repos/builtin/packages/abinit/package.py index a343bf69d7..9f0938daf1 100644 --- a/var/spack/repos/builtin/packages/abinit/package.py +++ b/var/spack/repos/builtin/packages/abinit/package.py @@ -85,6 +85,11 @@ class Abinit(AutotoolsPackage): # libxml2 depends_on("libxml2", when="@9:+libxml2") + # If the Intel suite is used for Lapack, it must be used for fftw and vice-versa + for _intel_pkg in INTEL_MATH_LIBRARIES: + requires(f"^[virtuals=fftw-api] {_intel_pkg}", when=f"^[virtuals=lapack] {_intel_pkg}") + requires(f"^[virtuals=lapack] {_intel_pkg}", when=f"^[virtuals=fftw-api] {_intel_pkg}") + # Cannot ask for +scalapack if it does not depend on MPI conflicts("+scalapack", when="~mpi") @@ -186,7 +191,8 @@ def configure_args(self): # BLAS/LAPACK/SCALAPACK-ELPA linalg = spec["lapack"].libs + spec["blas"].libs - if "^mkl" in spec: + is_using_intel_libraries = spec["lapack"].name in INTEL_MATH_LIBRARIES + if is_using_intel_libraries: linalg_flavor = "mkl" elif "@9:" in spec and "^openblas" in spec: linalg_flavor = "openblas" @@ -207,7 +213,7 @@ def configure_args(self): oapp(f"--with-linalg-flavor={linalg_flavor}") - if "^mkl" in spec: + if is_using_intel_libraries: fftflavor = "dfti" else: if "+openmp" in spec: @@ -218,7 +224,7 @@ def configure_args(self): oapp(f"--with-fft-flavor={fftflavor}") if "@:8" in spec: - if "^mkl" in spec: + if is_using_intel_libraries: oapp(f"--with-fft-incs={spec['fftw-api'].headers.cpp_flags}") oapp(f"--with-fft-libs={spec['fftw-api'].libs.ld_flags}") else: @@ -229,7 +235,7 @@ def configure_args(self): ] ) else: - if "^mkl" in spec: + if is_using_intel_libraries: options.extend( [ f"FFT_CPPFLAGS={spec['fftw-api'].headers.cpp_flags}", diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py index 7a4147a6ee..66c594c71e 100644 --- a/var/spack/repos/builtin/packages/gromacs/package.py +++ b/var/spack/repos/builtin/packages/gromacs/package.py @@ -263,6 +263,11 @@ class Gromacs(CMakePackage, CudaPackage): msg="Only attempt to find gcc libs for Intel compiler if Intel compiler is used.", ) + # If the Intel suite is used for Lapack, it must be used for fftw and vice-versa + for _intel_pkg in INTEL_MATH_LIBRARIES: + requires(f"^[virtuals=fftw-api] {_intel_pkg}", when=f"^[virtuals=lapack] {_intel_pkg}") + requires(f"^[virtuals=lapack] {_intel_pkg}", when=f"^[virtuals=fftw-api] {_intel_pkg}") + patch("gmxDetectCpu-cmake-3.14.patch", when="@2018:2019.3^cmake@3.14.0:") patch("gmxDetectSimd-cmake-3.14.patch", when="@5.0:2017^cmake@3.14.0:") # 2021.2 will always try to build tests (see https://gromacs.bioexcel.eu/t/compilation-failure-for-gromacs-2021-1-and-2021-2-with-cmake-3-20-2/2129) @@ -594,7 +599,7 @@ def cmake_args(self): "-DGMX_OPENMP_MAX_THREADS=%s" % self.spec.variants["openmp_max_threads"].value ) - if "^mkl" in self.spec: + if self.spec["lapack"].name in INTEL_MATH_LIBRARIES: # fftw-api@3 is provided by intel-mkl or intel-parllel-studio # we use the mkl interface of gromacs options.append("-DGMX_FFT_LIBRARY=mkl") diff --git a/var/spack/repos/builtin/packages/intel-mkl/package.py b/var/spack/repos/builtin/packages/intel-mkl/package.py index 7dd8ab4122..c66235f382 100644 --- a/var/spack/repos/builtin/packages/intel-mkl/package.py +++ b/var/spack/repos/builtin/packages/intel-mkl/package.py @@ -153,8 +153,7 @@ class IntelMkl(IntelPackage): multi=False, ) - provides("blas") - provides("lapack") + provides("blas", "lapack") provides("lapack@3.9.0", when="@2020.4") provides("lapack@3.7.0", when="@11.3") provides("scalapack") diff --git a/var/spack/repos/builtin/packages/intel-oneapi-mkl/package.py b/var/spack/repos/builtin/packages/intel-oneapi-mkl/package.py index 1d80c52f62..db3fdd6d7e 100644 --- a/var/spack/repos/builtin/packages/intel-oneapi-mkl/package.py +++ b/var/spack/repos/builtin/packages/intel-oneapi-mkl/package.py @@ -126,8 +126,7 @@ class IntelOneapiMkl(IntelOneApiLibraryPackage): provides("fftw-api@3") provides("scalapack", when="+cluster") provides("mkl") - provides("lapack") - provides("blas") + provides("lapack", "blas") @property def component_dir(self): diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py index 84810bacfa..50e7021de8 100644 --- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py +++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py @@ -536,8 +536,7 @@ class IntelParallelStudio(IntelPackage): provides("ipp", when="+ipp") provides("mkl", when="+mkl") - provides("blas", when="+mkl") - provides("lapack", when="+mkl") + provides("blas", "lapack", when="+mkl") provides("scalapack", when="+mkl") provides("fftw-api@3", when="+mkl@professional.2017:") diff --git a/var/spack/repos/builtin/packages/lammps/package.py b/var/spack/repos/builtin/packages/lammps/package.py index a44c7bd603..b2d3d11133 100644 --- a/var/spack/repos/builtin/packages/lammps/package.py +++ b/var/spack/repos/builtin/packages/lammps/package.py @@ -791,7 +791,7 @@ def cmake_args(self): # FFTW libraries are available and enable them by default. if "^fftw" in spec or "^cray-fftw" in spec or "^amdfftw" in spec: args.append(self.define("FFT", "FFTW3")) - elif "^mkl" in spec: + elif spec["fftw-api"].name in INTEL_MATH_LIBRARIES: args.append(self.define("FFT", "MKL")) elif "^armpl-gcc" in spec or "^acfl" in spec: args.append(self.define("FFT", "FFTW3")) diff --git a/var/spack/repos/builtin/packages/quantum-espresso/package.py b/var/spack/repos/builtin/packages/quantum-espresso/package.py index 4d41903cd6..40c036320d 100644 --- a/var/spack/repos/builtin/packages/quantum-espresso/package.py +++ b/var/spack/repos/builtin/packages/quantum-espresso/package.py @@ -242,6 +242,11 @@ class QuantumEspresso(CMakePackage, Package): depends_on("git@2.13:", type="build") depends_on("m4", type="build") + # If the Intel suite is used for Lapack, it must be used for fftw and vice-versa + for _intel_pkg in INTEL_MATH_LIBRARIES: + requires(f"^[virtuals=fftw-api] {_intel_pkg}", when=f"^[virtuals=lapack] {_intel_pkg}") + requires(f"^[virtuals=lapack] {_intel_pkg}", when=f"^[virtuals=fftw-api] {_intel_pkg}") + # CONFLICTS SECTION # Omitted for now due to concretizer bug # MKL with 64-bit integers not supported. @@ -489,7 +494,8 @@ def install(self, pkg, spec, prefix): # you need to pass it in the FFTW_INCLUDE and FFT_LIBS directory. # QE supports an internal FFTW2, but only an external FFTW3 interface. - if "^mkl" in spec: + is_using_intel_libraries = spec["lapack"].name in INTEL_MATH_LIBRARIES + if is_using_intel_libraries: # A seperate FFT library is not needed when linking against MKL options.append("FFTW_INCLUDE={0}".format(join_path(env["MKLROOT"], "include/fftw"))) if "^fftw@3:" in spec: @@ -531,11 +537,11 @@ def install(self, pkg, spec, prefix): if spec.satisfies("@:6.4"): # set even if MKL is selected options.append("BLAS_LIBS={0}".format(lapack_blas.ld_flags)) else: # behavior changed at 6.5 and later - if not spec.satisfies("^mkl"): + if not is_using_intel_libraries: options.append("BLAS_LIBS={0}".format(lapack_blas.ld_flags)) if "+scalapack" in spec: - if "^mkl" in spec: + if is_using_intel_libraries: if "^openmpi" in spec: scalapack_option = "yes" else: # mpich, intel-mpi diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py index dfe397ca2c..7232a7e6c1 100644 --- a/var/spack/repos/builtin/packages/r/package.py +++ b/var/spack/repos/builtin/packages/r/package.py @@ -137,7 +137,7 @@ def configure_args(self): ] if "+external-lapack" in spec: - if "^mkl" in spec and "gfortran" in self.compiler.fc: + if spec["lapack"].name in INTEL_MATH_LIBRARIES and "gfortran" in self.compiler.fc: mkl_re = re.compile(r"(mkl_)intel(_i?lp64\b)") config_args.extend( [