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# Copyright 2013-2022 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)
from spack import *
class Genesis(AutotoolsPackage, CudaPackage):
"""GENESIS is a Molecular dynamics and modeling software
for bimolecular systems such as proteins, lipids, glycans,
and their complexes.
"""
homepage = "https://www.r-ccs.riken.jp/labs/cbrt/"
url = "https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2020/09/genesis-1.5.1.tar.bz2"
git = "https://github.com/genesis-release-r-ccs/genesis-2.0.git"
version("master", branch="master")
version(
"1.6.0",
sha256="d0185a5464ed4231f6ee81f6dcaa15935a99fa30b96658d2b7c25d7fbc5b38e9",
url="https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2020/12/genesis-1.6.0.tar.bz2",
)
version(
"1.5.1",
sha256="62a453a573c36779484b4ffed2dfa56ea03dfe1308d631b33ef03f733259b3ac",
url="https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2020/09/genesis-1.5.1.tar.bz2",
)
resource(
when="@1.6.0",
name="user_guide",
url="https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2020/12/GENESIS-1.6.0.pdf",
sha256="4a6d54eb8f66edde57a4099cdac40cc8e0e2fd6bdb84946da6bf2b3ed84a4ba1",
expand=False,
placement="doc",
)
resource(
when="@1.5.1",
name="user_guide",
url="https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2019/10/GENESIS-1.4.0.pdf",
sha256="da2c3f8bfa1e93adb992d3cfce09fb45d8d447a94f9a4f884ac834ea7279b9c7",
expand=False,
placement="doc",
)
variant("openmp", default=True, description="Enable OpenMP.")
variant("single", default=False, description="Enable single precision.")
variant("hmdisk", default=False, description="Enable huge molecule on hard disk.")
conflicts("%apple-clang", when="+openmp")
depends_on("autoconf", type="build", when="@1.5.1 %fj")
depends_on("autoconf", type="build", when="@master")
depends_on("automake", type="build", when="@1.5.1 %fj")
depends_on("automake", type="build", when="@master")
depends_on("libtool", type="build", when="@1.5.1 %fj")
depends_on("libtool", type="build", when="@master")
depends_on("m4", type="build", when="@1.5.1 %fj")
depends_on("m4", type="build", when="@master")
depends_on("mpi", type=("build", "run"))
depends_on("lapack")
depends_on("python@2.6.9:2.8.0", type=("build", "run"), when="@master")
patch("fj_compiler.patch", when="@master %fj")
patch("fj_compiler_1.5.1.patch", when="@1.5.1 %fj")
parallel = False
@property
def force_autoreconf(self):
# Run autoreconf due to build system patch
return self.spec.satisfies("@1.5.1 %fj")
def configure_args(self):
spec = self.spec
options = []
options.extend(self.enable_or_disable("openmp"))
options.extend(self.enable_or_disable("single"))
options.extend(self.enable_or_disable("hmdisk"))
if "+cuda" in spec:
options.append("--enable-gpu")
options.append("--with-cuda=%s" % spec["cuda"].prefix)
else:
options.append("--disable-gpu")
if spec.target == "a64fx" and self.spec.satisfies("@master %fj"):
options.append("--host=Fugaku")
return options
def setup_build_environment(self, env):
env.set("FC", self.spec["mpi"].mpifc, force=True)
env.set("F77", self.spec["mpi"].mpif77, force=True)
env.set("CC", self.spec["mpi"].mpicc, force=True)
env.set("CXX", self.spec["mpi"].mpicxx, force=True)
env.set("LAPACK_LIBS", self.spec["lapack"].libs.ld_flags)
if "+cuda" in self.spec:
cuda_arch = self.spec.variants["cuda_arch"].value
cuda_gencode = " ".join(self.cuda_flags(cuda_arch))
env.set("NVCCFLAGS", cuda_gencode)
def install(self, spec, prefix):
make("install")
install_tree("doc", prefix.share.doc)
@property
def cached_tests_work_dir(self):
"""The working directory for cached test sources."""
return join_path(self.test_suite.current_test_cache_dir,
"tests")
@run_after("install")
def cache_test_sources(self):
"""Copy test files after the package is installed for test()."""
if self.spec.satisfies("@master"):
self.cache_extra_test_sources(["tests"])
def test(self):
"""Perform stand-alone/smoke tests using installed package."""
if not self.spec.satisfies("@master"):
print('Skipping: Tests are only available for the master branch')
return
test_name = join_path(
self.cached_tests_work_dir, "regression_test", "test.py"
)
bin_name = join_path(self.prefix.bin, "spdyn")
opts = [
test_name,
self.spec["mpi"].prefix.bin.mpirun + " -np 8 " + bin_name,
]
env["OMP_NUM_THREADS"] = "1"
self.run_test(
self.spec["python"].command.path,
options=opts,
expected="Passed 53 / 53",
purpose="test: running regression test",
work_dir=self.cached_tests_work_dir
)
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