a8ccb8e116
- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
`spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
for oneapi.py
70 lines
2.5 KiB
Python
70 lines
2.5 KiB
Python
# Copyright 2013-2021 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 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('2.1.2', 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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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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cuda_arch_values = CudaPackage.cuda_arch_values
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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',
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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('-arch compute_13', '',
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'libhmsbeagle/GPU/kernels/Makefile.am',
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string=True)
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filter_file(r'(NVCCFLAGS="-O3).*(")',
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r'\1 {0}\2'.format(archflag), 'configure.ac')
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# point CUDA_LIBS to libcuda.so
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filter_file('-L$with_cuda/lib', '-L$with_cuda/lib64/stubs',
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'configure.ac', string=True)
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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=%s' % self.spec['cuda'].prefix)
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else:
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args.append('--without-cuda')
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return args
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