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# Copyright 2013-2019 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)
import glob
class Raxml(Package):
"""RAxML (Randomized Axelerated Maximum Likelihood) is a program for
sequential and parallel Maximum Likelihood based inference of large
phylogenetic trees.
"""
homepage = "https://sco.h-its.org/exelixis/web/software/raxml"
url = "https://github.com/stamatak/standard-RAxML/archive/v8.2.11.tar.gz"
version('8.2.11', '6bd5c4e1f93003ccf13c9b59a5d080ab')
variant('mpi', default=True, description='Enable MPI parallel support')
variant('pthreads', default=False, description='Enable pthreads version')
depends_on('mpi', when='+mpi')
patch('nox86.patch')
# Compiles with either GCC or ICC.
conflicts('%cce')
conflicts('%clang')
conflicts('%nag')
conflicts('%pgi')
conflicts('%xl')
conflicts('%xl_r')
# can't build multiple binaries in parallel without things breaking
parallel = False
def install(self, spec, prefix):
mkdirp(prefix.bin)
files = glob.iglob("Makefile.*")
for file in files:
makefile = FileFilter(file)
makefile.filter('gcc', spack_cc)
if spec.satisfies('+mpi'):
makefile.filter('mpicc', self.spec['mpi'].mpicc)
if spec.target.family == 'x86_64':
if spec.satisfies('+mpi +pthreads') and 'avx' in spec.target:
make('-f', 'Makefile.AVX.HYBRID.gcc')
install('raxmlHPC-HYBRID-AVX', prefix.bin)
if spec.satisfies('+mpi +pthreads') and 'sse3' in spec.target:
make('-f', 'Makefile.SSE3.HYBRID.gcc')
install('raxmlHPC-HYBRID-SSE3', prefix.bin)
if spec.satisfies('+mpi +pthreads'):
make('-f', 'Makefile.HYBRID.gcc')
install('raxmlHPC-HYBRID', prefix.bin)
if spec.satisfies('+mpi') and 'avx' in spec.target:
make('-f', 'Makefile.AVX.MPI.gcc')
install('raxmlHPC-MPI-AVX', prefix.bin)
if spec.satisfies('+mpi') and 'sse3' in spec.target:
make('-f', 'Makefile.SSE3.MPI.gcc')
install('raxmlHPC-MPI-SSE3', prefix.bin)
if spec.satisfies('+mpi'):
make('-f', 'Makefile.MPI.gcc')
install('raxmlHPC-MPI', prefix.bin)
if spec.satisfies('+pthreads') and 'avx' in spec.target:
make('-f', 'Makefile.AVX.PTHREADS.gcc')
install('raxmlHPC-PTHREADS-AVX', prefix.bin)
if spec.satisfies('+pthreads') and 'sse3' in spec.target:
make('-f', 'Makefile.SSE3.PTHREADS.gcc')
install('raxmlHPC-PTHREADS-SSE3', prefix.bin)
if spec.satisfies('+pthreads'):
make('-f', 'Makefile.PTHREADS.gcc')
install('raxmlHPC-PTHREADS', prefix.bin)
if 'sse3' in spec.target:
make('-f', 'Makefile.SSE3.gcc')
install('raxmlHPC-SSE3', prefix.bin)
if 'avx' in spec.target:
make('-f', 'Makefile.AVX.gcc')
install('raxmlHPC-AVX', prefix.bin)
make('-f', 'Makefile.gcc')
install('raxmlHPC', prefix.bin)
else:
if spec.satisfies('+mpi +pthreads'):
make('-f', 'Makefile.HYBRID.nox86.gcc')
install('raxmlHPC-HYBRID', prefix.bin)
if spec.satisfies('+mpi'):
make('-f', 'Makefile.MPI.nox86.gcc')
install('raxmlHPC-MPI', prefix.bin)
if spec.satisfies('+pthreads'):
make('-f', 'Makefile.PTHREADS.nox86.gcc')
install('raxmlHPC-PTHREADS', prefix.bin)
make('-f', 'Makefile.nox86.gcc')
install('raxmlHPC', prefix.bin)
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