603569e321
* Style: black 23, skip magic trailing commas * isort should use same line length as black * Fix unused import * Update version of black used in CI * Update new packages * Update new packages
82 lines
2.8 KiB
Python
82 lines
2.8 KiB
Python
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class Libbeagle(AutotoolsPackage, CudaPackage):
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"""Beagle performs genotype calling, genotype phasing, imputation of
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ungenotyped markers, and identity-by-descent segment detection."""
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homepage = "https://github.com/beagle-dev/beagle-lib"
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url = "https://github.com/beagle-dev/beagle-lib/archive/v3.1.2.tar.gz"
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version("3.1.2", sha256="dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275")
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version(
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"2.1.2",
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sha256="82ff13f4e7d7bffab6352e4551dfa13afabf82bff54ea5761d1fc1e78341d7de",
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url="https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz",
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)
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depends_on("autoconf", type="build")
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depends_on("automake", type="build")
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depends_on("libtool", type="build")
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depends_on("m4", type="build")
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depends_on("subversion", type="build")
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depends_on("pkgconfig", type="build")
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depends_on("java", type="build")
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depends_on("opencl", when="+opencl")
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cuda_arch_values = CudaPackage.cuda_arch_values
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variant("opencl", default=False, description="Include OpenCL (GPU) support")
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variant(
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"cuda_arch",
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description="CUDA architecture",
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default="none",
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values=("none",) + cuda_arch_values,
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multi=False,
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)
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conflicts("cuda_arch=none", when="+cuda", msg="must select a CUDA architecture")
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def patch(self):
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# update cuda architecture if necessary
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if "+cuda" in self.spec:
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cuda_arch = self.spec.variants["cuda_arch"].value
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archflag = "-arch=compute_{0}".format(cuda_arch)
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filter_file(
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"-arch compute_13", "", "libhmsbeagle/GPU/kernels/Makefile.am", string=True
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)
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filter_file(r'(NVCCFLAGS="-O3).*(")', r"\1 {0}\2".format(archflag), "configure.ac")
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# point CUDA_LIBS to libcuda.so
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filter_file(
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"-L$with_cuda/lib", "-L$with_cuda/lib64/stubs", "configure.ac", string=True
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)
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def autoreconf(self, spec, prefix):
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which("bash")("autogen.sh")
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def configure_args(self):
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args = [
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# Since spack will inject architecture flags turn off -march=native
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# when building libbeagle.
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"--disable-march-native"
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]
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if "+cuda" in self.spec:
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args.append("--with-cuda={0}".format(self.spec["cuda"].prefix))
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else:
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args.append("--without-cuda")
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if "+opencl" in self.spec:
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args.append("--with-opencl={0}".format(self.spec["opencl"].prefix))
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else:
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args.append("--without-opencl")
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return args
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