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# Copyright 2013-2023 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
from spack.package import *
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/v8.2.12.tar.gz"
license("GPL-3.0-or-later")
version("8.2.12", sha256="338f81b52b54e16090e193daf36c1d4baa9b902705cfdc7f4497e3e09718533b")
version("8.2.11", sha256="08cda74bf61b90eb09c229e39b1121c6d95caf182708e8745bd69d02848574d7")
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("%apple-clang")
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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