26d2356ad4
* genesis: New package. * fujitsu-ssl2: fix unit test error * genesis: Fix for comments and add test method * genesis: Fix for comments * genesis: Fix for comments
113 lines
4.2 KiB
Python
113 lines
4.2 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 Genesis(AutotoolsPackage, CudaPackage):
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"""GENESIS is a Molecular dynamics and modeling software
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for bimolecular systems such as proteins, lipids, glycans,
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and their complexes.
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"""
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homepage = "https://www.r-ccs.riken.jp/labs/cbrt/"
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url = "https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2020/09/genesis-1.5.1.tar.bz2"
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git = "https://github.com/genesis-release-r-ccs/genesis-2.0.git"
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version("master", branch="master")
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version(
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"1.5.1",
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sha256="62a453a573c36779484b4ffed2dfa56ea03dfe1308d631b33ef03f733259b3ac",
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url="https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2020/09/genesis-1.5.1.tar.bz2",
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)
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resource(
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when="@1.5.1",
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name="user_guide",
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url="https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2019/10/GENESIS-1.4.0.pdf",
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sha256="da2c3f8bfa1e93adb992d3cfce09fb45d8d447a94f9a4f884ac834ea7279b9c7",
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expand=False,
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placement="doc",
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)
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variant("openmp", default=True, description="Enable OpenMP.")
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variant("single", default=False, description="Enable single precision.")
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variant("hmdisk", default=False, description="Enable huge molecule on hard disk.")
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conflicts("%apple-clang", when="+openmp")
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depends_on("autoconf", type="build", when="@1.5.1 %fj")
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depends_on("autoconf", type="build", when="@master")
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depends_on("automake", type="build", when="@1.5.1 %fj")
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depends_on("automake", type="build", when="@master")
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depends_on("libtool", type="build", when="@1.5.1 %fj")
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depends_on("libtool", type="build", when="@master")
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depends_on("m4", type="build", when="@1.5.1 %fj")
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depends_on("m4", type="build", when="@master")
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depends_on("mpi", type=("build", "run"))
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depends_on("lapack")
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depends_on("python@2.6.9:2.8.0", type=("build", "run"), when="@master")
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patch("fj_compiler.patch", when="@master %fj")
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patch("fj_compiler_1.5.1.patch", when="@1.5.1 %fj")
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parallel = False
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@property
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def force_autoreconf(self):
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# Run autoreconf due to build system patch
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return self.spec.satisfies("@1.5.1 %fj")
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def configure_args(self):
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spec = self.spec
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options = []
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options.extend(self.enable_or_disable("openmp"))
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options.extend(self.enable_or_disable("single"))
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options.extend(self.enable_or_disable("hmdisk"))
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if "+cuda" in spec:
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options.append("--enable-gpu")
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options.append("--with-cuda=%s" % spec["cuda"].prefix)
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else:
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options.append("--disable-gpu")
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if spec.target == "a64fx" and self.spec.satisfies("@master %fj"):
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options.append("--host=Fugaku")
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return options
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def setup_build_environment(self, env):
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env.set("FC", self.spec["mpi"].mpifc, force=True)
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env.set("F77", self.spec["mpi"].mpif77, force=True)
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env.set("CC", self.spec["mpi"].mpicc, force=True)
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env.set("CXX", self.spec["mpi"].mpicxx, force=True)
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env.set("LAPACK_LIBS", self.spec["lapack"].libs.ld_flags)
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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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cuda_gencode = " ".join(self.cuda_flags(cuda_arch))
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env.set("NVCCFLAGS", cuda_gencode)
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def install(self, spec, prefix):
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make("install")
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install_tree("doc", prefix.share.doc)
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@run_after("install")
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def cache_test_sources(self):
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if self.spec.satisfies("@master"):
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self.cache_extra_test_sources(["tests"])
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def test(self):
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if self.spec.satisfies("@master"):
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exe_name = self.spec["python"].command.path
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test_name = join_path(
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self.install_test_root, "tests", "regression_test", "test.py"
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)
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bin_name = join_path(self.prefix.bin, "spdyn")
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opts = [
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test_name,
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self.spec["mpi"].prefix.bin.mpirun + " -np 8 " + bin_name,
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]
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env["OMP_NUM_THREADS"] = "1"
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self.run_test(exe_name, options=opts, expected="Passed 53 / 53")
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