cf163eecc5
In practice, one can only compiler for the Intel Data Center Max GPU via a SYCL build and the oneAPI compiler. This is unlikely to change, so we can be explicit about that.
687 lines
31 KiB
Python
687 lines
31 KiB
Python
# Copyright 2013-2023 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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import os
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import llnl.util.filesystem as fs
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from spack.package import *
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class Gromacs(CMakePackage, CudaPackage):
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"""GROMACS is a molecular dynamics package primarily designed for simulations
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of proteins, lipids and nucleic acids. It was originally developed in
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the Biophysical Chemistry department of University of Groningen, and is now
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maintained by contributors in universities and research centers across the world.
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GROMACS is one of the fastest and most popular software packages
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available and can run on CPUs as well as GPUs. It is free, open source
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released under the GNU Lesser General Public License. Before the version 4.6,
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GROMACS was released under the GNU General Public License.
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"""
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homepage = "https://www.gromacs.org"
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url = "https://ftp.gromacs.org/gromacs/gromacs-2022.2.tar.gz"
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list_url = "https://ftp.gromacs.org/gromacs"
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git = "https://gitlab.com/gromacs/gromacs.git"
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maintainers("danielahlin", "eirrgang", "junghans")
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version("main", branch="main")
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version("master", branch="main", deprecated=True)
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version("2023.3", sha256="4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb")
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version("2023.2", sha256="bce1480727e4b2bb900413b75d99a3266f3507877da4f5b2d491df798f9fcdae")
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version("2023.1", sha256="eef2bb4a6cb6314cf9da47f26df2a0d27af4bf7b3099723d43601073ab0a42f4")
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version("2023", sha256="ac92c6da72fbbcca414fd8a8d979e56ecf17c4c1cdabed2da5cfb4e7277b7ba8")
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version("2022.6", sha256="75d277138475679dd3e334e384a71516570cde767310476687f2a5b72333ea41")
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version("2022.5", sha256="083cc3c424bb93ffe86c12f952e3e5b4e6c9f6520de5338761f24b75e018c223")
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version("2022.4", sha256="c511be602ff29402065b50906841def98752639b92a95f1b0a1060d9b5e27297")
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version("2022.3", sha256="14cfb130ddaf8f759a3af643c04f5a0d0d32b09bc3448b16afa5b617f5e35dae")
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version("2022.2", sha256="656404f884d2fa2244c97d2a5b92af148d0dbea94ad13004724b3fcbf45e01bf")
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version("2022.1", sha256="85ddab5197d79524a702c4959c2c43be875e0fc471df3a35224939dce8512450")
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version("2022", sha256="fad60d606c02e6164018692c6c9f2c159a9130c2bf32e8c5f4f1b6ba2dda2b68")
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version("2021.7", sha256="4db7bbbfe5424de48373686ec0e8c5bfa7175d5cd74290ef1c1e840e6df67f06")
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version("2021.6", sha256="52df2c1d7586fd028d9397985c68bd6dd26e6e905ead382b7e6c473d087902c3")
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version("2021.5", sha256="eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6")
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version("2021.4", sha256="cb708a3e3e83abef5ba475fdb62ef8d42ce8868d68f52dafdb6702dc9742ba1d")
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version("2021.3", sha256="e109856ec444768dfbde41f3059e3123abdb8fe56ca33b1a83f31ed4575a1cc6")
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version("2021.2", sha256="d940d865ea91e78318043e71f229ce80d32b0dc578d64ee5aa2b1a4be801aadb")
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version("2021.1", sha256="bc1d0a75c134e1fb003202262fe10d3d32c59bbb40d714bc3e5015c71effe1e5")
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version("2021", sha256="efa78ab8409b0f5bf0fbca174fb8fbcf012815326b5c71a9d7c385cde9a8f87b")
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version("2020.7", sha256="744158d8f61b0d36ffe89ec934519b7e0981a7af438897740160da648d36c2f0")
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version("2020.6", sha256="d8bbe57ed3c9925a8cb99ecfe39e217f930bed47d5268a9e42b33da544bdb2ee")
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version("2020.5", sha256="7b6aff647f7c8ee1bf12204d02cef7c55f44402a73195bd5f42cf11850616478")
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version("2020.4", sha256="5519690321b5500c7951aaf53ff624042c3edd1a5f5d6dd1f2d802a3ecdbf4e6")
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version("2020.3", sha256="903183691132db14e55b011305db4b6f4901cc4912d2c56c131edfef18cc92a9")
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version("2020.2", sha256="7465e4cd616359d84489d919ec9e4b1aaf51f0a4296e693c249e83411b7bd2f3")
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version("2020.1", sha256="e1666558831a3951c02b81000842223698016922806a8ce152e8f616e29899cf")
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version("2020", sha256="477e56142b3dcd9cb61b8f67b24a55760b04d1655e8684f979a75a5eec40ba01")
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version("2019.6", sha256="bebe396dc0db11a9d4cc205abc13b50d88225617642508168a2195324f06a358")
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version("2019.5", sha256="438061a4a2d45bbb5cf5c3aadd6c6df32d2d77ce8c715f1c8ffe56156994083a")
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version("2019.4", sha256="ba4366eedfc8a1dbf6bddcef190be8cd75de53691133f305a7f9c296e5ca1867")
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version("2019.3", sha256="4211a598bf3b7aca2b14ad991448947da9032566f13239b1a05a2d4824357573")
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version("2019.2", sha256="bcbf5cc071926bc67baa5be6fb04f0986a2b107e1573e15fadcb7d7fc4fb9f7e")
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version("2019.1", sha256="b2c37ed2fcd0e64c4efcabdc8ee581143986527192e6e647a197c76d9c4583ec")
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version("2019", sha256="c5b281a5f0b5b4eeb1f4c7d4dc72f96985b566561ca28acc9c7c16f6ee110d0b")
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version("2018.8", sha256="776923415df4bc78869d7f387c834141fdcda930b2e75be979dc59ecfa6ebecf")
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version("2018.5", sha256="32261df6f7ec4149fc0508f9af416953d056e281590359838c1ed6644ba097b8")
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version("2018.4", sha256="6f2ee458c730994a8549d6b4f601ecfc9432731462f8bd4ffa35d330d9aaa891")
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version("2018.3", sha256="4423a49224972969c52af7b1f151579cea6ab52148d8d7cbae28c183520aa291")
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version("2018.2", sha256="4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857")
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version("2018.1", sha256="4d3533340499323fece83b4a2d4251fa856376f2426c541e00b8e6b4c0d705cd")
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version("2018", sha256="deb5d0b749a52a0c6083367b5f50a99e08003208d81954fb49e7009e1b1fd0e9")
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version("2016.6", sha256="bac0117d2cad21f9b94fe5b854fb9ae7435b098a6da4e732ee745f18e52473d7")
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version("2016.5", sha256="57db26c6d9af84710a1e0c47a1f5bf63a22641456448dcd2eeb556ebd14e0b7c")
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version("2016.4", sha256="4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264")
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version("2016.3", sha256="7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27")
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version("5.1.5", sha256="c25266abf07690ecad16ed3996899b1d489cbb1ef733a1befb3b5c75c91a703e")
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version("5.1.4", sha256="0f3793d8f1f0be747cf9ebb0b588fb2b2b5dc5acc32c3046a7bee2d2c03437bc")
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version("5.1.2", sha256="39d6f1d7ae8ba38cea6089da40676bfa4049a49903d21551abc030992a58f304")
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version("4.6.7", sha256="6afb1837e363192043de34b188ca3cf83db6bd189601f2001a1fc5b0b2a214d9")
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version("4.5.5", sha256="e0605e4810b0d552a8761fef5540c545beeaf85893f4a6e21df9905a33f871ba")
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variant(
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"mpi", default=True, description="Activate MPI support (disable for Thread-MPI support)"
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)
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variant("shared", default=True, description="Enables the build of shared libraries")
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variant(
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"double",
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default=False,
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description="Produces a double precision version of the executables",
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)
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variant(
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"cufftmp",
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default=False,
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when="@2022: +cuda+mpi",
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description="Enable multi-GPU FFT support with cuFFTMp",
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)
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variant(
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"heffte",
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default=False,
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when="@2021: +sycl+mpi",
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description="Enable multi-GPU FFT support with HeFFTe",
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)
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variant("opencl", default=False, description="Enable OpenCL support")
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variant("sycl", default=False, when="@2021:", description="Enable SYCL support")
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variant(
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"intel-data-center-gpu-max",
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default=False,
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when="@2022: +sycl",
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description="Enable support for Intel Data Center GPU Max",
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)
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variant("nosuffix", default=False, description="Disable default suffixes")
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variant(
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"build_type",
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default="Release",
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description="The build type to build",
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values=(
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"Debug",
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"Release",
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"RelWithDebInfo",
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"MinSizeRel",
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"Reference",
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"RelWithAssert",
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"Profile",
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),
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)
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variant(
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"nblib",
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default=True,
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when="@2021:",
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description="Build and install the NB-LIB C++ API for GROMACS",
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)
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variant(
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"gmxapi",
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default=True,
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when="@2019:",
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description="Build and install the gmxlib python API for GROMACS",
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)
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variant(
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"mdrun_only",
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default=False,
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description="Enables the build of a cut-down version"
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" of libgromacs and/or the mdrun program",
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)
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conflicts(
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"+mdrun_only", when="@2021:", msg="mdrun-only build option was removed for GROMACS 2021."
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)
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variant("openmp", default=True, description="Enables OpenMP at configure time")
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variant("openmp_max_threads", default="none", description="Max number of OpenMP threads")
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conflicts(
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"+openmp_max_threads", when="~openmp", msg="OpenMP is off but OpenMP Max threads is set"
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)
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variant(
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"sve",
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default=True,
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description="Enable SVE on aarch64 if available",
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when="target=neoverse_v1",
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)
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variant(
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"sve", default=True, description="Enable SVE on aarch64 if available", when="target=a64fx"
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)
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variant(
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"relaxed_double_precision",
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default=False,
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description="GMX_RELAXED_DOUBLE_PRECISION, use only for Fujitsu PRIMEHPC",
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)
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conflicts(
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"+relaxed_double_precision",
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when="@2021:",
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msg="GMX_RELAXED_DOUBLE_PRECISION option removed for GROMACS 2021.",
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)
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variant("hwloc", default=True, description="Use the hwloc portable hardware locality library")
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variant("cycle_subcounters", default=False, description="Enables cycle subcounters")
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variant("cp2k", default=False, description="CP2K QM/MM interface integration")
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conflicts(
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"+cp2k", when="@:2021", msg="CP2K QM/MM support have been introduced in GROMACS 2022"
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)
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conflicts("+shared", when="+cp2k", msg="Enabling CP2K requires static build")
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conflicts("%intel", when="@2022:", msg="GROMACS %intel support was removed in version 2022")
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conflicts("%gcc@:8", when="@2023:", msg="GROMACS requires GCC 9 or later since version 2023")
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conflicts(
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"^intel-oneapi-mkl@:2021.2",
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when="@2023:",
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msg="GROMACS requires oneMKL 2021.3 or later since version 2023",
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)
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depends_on("mpi", when="+mpi")
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# Plumed 2.9.0 needs Gromacs 2023, 2022.5, 2021.7, 2020.7
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# Plumed 2.8.3 needs Gromacs 2022.5, 2021.7, 2020.7, 2019.6
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# Plumed 2.8.2 needs Gromacs 2022.5, 2021.7, 2020.7, 2019.6
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# Plumed 2.8.1 needs Gromacs 2022.3, 2021.6, 2020.7, 2019.6
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# Plumed 2.8.0 needs Gromacs 2021.4, 2020.6, 2019.6
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# Plumed 2.7.6 needs Gromacs 2021.5, 2020.6, 2019.6
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# Plumed 2.7.5 needs Gromacs 2021.5, 2020.6, 2019.6
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# Plumed 2.7.4 needs Gromacs 2021.4, 2020.6, 2019.6
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# Plumed 2.7.3 needs Gromacs 2021.4, 2020.6, 2019.6
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# Plumed 2.7.2 needs Gromacs 2021, 2020.6, 2019.6
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# Plumed 2.7.1 needs Gromacs 2021, 2020.5, 2019.6
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# Plumed 2.7.0 needs Gromacs 2020.4, 2019.6
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# Plumed 2.6.6 needs Gromacs 2020.4, 2019.6, 2018.8
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# Plumed 2.6.5 needs Gromacs 2020.4, 2019.6, 2018.8
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# Plumed 2.6.4 needs Gromacs 2020.4, 2019.6, 2018.8
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# Plumed 2.6.3 needs Gromacs 2020.4, 2019.6, 2018.8
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# Plumed 2.6.2 needs Gromacs 2020.4, 2019.6, 2018.8
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# Plumed 2.6.1 needs Gromacs 2020.2, 2019.6, 2018.8
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# Plumed 2.6.0 needs Gromacs 2019.4, 2018.8
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# Plumed 2.5.7 needs Gromacs 2019.4, 2018.8, 2016.6
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# Plumed 2.5.6 needs Gromacs 2019.4, 2018.8, 2016.6
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# Plumed 2.5.5 needs Gromacs 2019.4, 2018.8, 2016.6
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# Plumed 2.5.4 needs Gromacs 2019.4, 2018.8, 2016.6
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# Plumed 2.5.3 needs Gromacs 2019.4, 2018.8, 2016.6
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# Plumed 2.5.2 needs Gromacs 2019.2, 2018.6, 2016.6
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# Plumed 2.5.1 needs Gromacs 2018.6, 2016.6
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# Plumed 2.5.0 needs Gromacs 2018.4, 2016.5
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# Above dependencies can be verified, and new versions added, by going to
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# https://github.com/plumed/plumed2/tree/v2.9.0/patches
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# and switching tags.
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plumed_patches = {
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"2023": "2.9.0",
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"2022.5": "2.8.2:2.9.0",
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"2022.3": "2.8.1",
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"2021.7": "2.8.2:2.9.0",
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"2021.6": "2.8.1",
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"2021.5": "2.7.5:2.7.6",
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"2021.4": "2.7.3:2.8.0",
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"2021": "2.7.1:2.7.2",
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"2020.7": "2.8.1:2.9.0",
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"2020.6": "2.7.2:2.8.0",
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"2020.5": "2.7.1",
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"2020.4": "2.6.2:2.7.0",
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"2020.2": "2.6.1",
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"2019.6": "2.6.1:2.8.3",
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"2019.4": "2.5.3:2.6.0",
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"2019.2": "2.5.2",
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"2018.8": "2.5.3:2.6",
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"2018.6": "2.5.1:2.5.2",
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"2018.4": "2.5.0",
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"2016.6": "2.5.1:2.5",
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"2016.5": "2.5.0",
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}
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variant(
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"plumed",
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default=False,
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description="Enable PLUMED support",
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when="@{0}".format(",".join(plumed_patches.keys())),
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)
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with when("+plumed"):
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depends_on("plumed+mpi", when="+mpi")
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depends_on("plumed~mpi", when="~mpi")
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for gmx_ver, plumed_vers in plumed_patches.items():
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depends_on("plumed@{0}".format(plumed_vers), when="@{0}+plumed".format(gmx_ver))
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variant(
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"intel_provided_gcc",
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default=False,
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description="Use this if Intel compiler is installed through spack."
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+ "The g++ location is written to icp{c,x}.cfg",
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)
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depends_on("fftw-api@3")
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depends_on("cmake@2.8.8:3", type="build")
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depends_on("cmake@3.4.3:3", type="build", when="@2018:")
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depends_on("cmake@3.9.6:3", type="build", when="@2020")
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depends_on("cmake@3.13.0:3", type="build", when="@2021")
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depends_on("cmake@3.16.3:3", type="build", when="@2022:")
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depends_on("cmake@3.18.4:3", type="build", when="@main")
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depends_on("cmake@3.16.0:3", type="build", when="%fj")
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depends_on("cuda", when="+cuda")
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depends_on("sycl", when="+sycl")
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depends_on("lapack")
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depends_on("blas")
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depends_on("gcc", when="%oneapi ~intel_provided_gcc")
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depends_on("gcc", when="%intel ~intel_provided_gcc")
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depends_on("hwloc@1.0:1", when="+hwloc@2016:2018")
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depends_on("hwloc", when="+hwloc@2019:")
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depends_on("cp2k@8.1:", when="+cp2k")
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depends_on("nvhpc", when="+cufftmp")
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depends_on("heffte", when="+heffte")
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requires(
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"%intel",
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"%oneapi",
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policy="one_of",
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when="+intel_provided_gcc",
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msg="Only attempt to find gcc libs for Intel compiler if Intel compiler is used.",
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)
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# If the Intel suite is used for Lapack, it must be used for fftw and vice-versa
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for _intel_pkg in INTEL_MATH_LIBRARIES:
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requires(f"^[virtuals=fftw-api] {_intel_pkg}", when=f"^[virtuals=lapack] {_intel_pkg}")
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requires(f"^[virtuals=lapack] {_intel_pkg}", when=f"^[virtuals=fftw-api] {_intel_pkg}")
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patch("gmxDetectCpu-cmake-3.14.patch", when="@2018:2019.3^cmake@3.14.0:")
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patch("gmxDetectSimd-cmake-3.14.patch", when="@5.0:2017^cmake@3.14.0:")
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# 2021.2 will always try to build tests (see https://gromacs.bioexcel.eu/t/compilation-failure-for-gromacs-2021-1-and-2021-2-with-cmake-3-20-2/2129)
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patch(
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"https://gitlab.com/gromacs/gromacs/-/commit/10262892e11a87fda0f59e633c89ed5ab1100509.diff",
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sha256="2c30d00404b76421c13866cc42afa5e63276f7926c862838751b158df8727b1b",
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when="@2021.1:2021.2",
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)
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filter_compiler_wrappers(
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"*.cmake", relative_root=os.path.join("share", "cmake", "gromacs_mpi")
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)
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filter_compiler_wrappers("*.cmake", relative_root=os.path.join("share", "cmake", "gromacs"))
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def patch(self):
|
|
# Otherwise build fails with GCC 11 (11.2)
|
|
if self.spec.satisfies("@2018:2020.6"):
|
|
filter_file(
|
|
"#include <vector>",
|
|
"#include <vector>\n#include <limits>",
|
|
"src/gromacs/awh/biasparams.h",
|
|
)
|
|
if self.spec.satisfies("@2018:2018.8"):
|
|
filter_file(
|
|
"#include <vector>",
|
|
"#include <vector>\n#include <limits>",
|
|
"src/gromacs/mdlib/minimize.cpp",
|
|
)
|
|
if self.spec.satisfies("@2019:2019.6,2020:2020.6"):
|
|
filter_file(
|
|
"#include <vector>",
|
|
"#include <vector>\n#include <limits>",
|
|
"src/gromacs/mdrun/minimize.cpp",
|
|
)
|
|
if self.spec.satisfies("@2020:2020.6"):
|
|
filter_file(
|
|
"#include <queue>",
|
|
"#include <queue>\n#include <limits>",
|
|
"src/gromacs/modularsimulator/modularsimulator.h",
|
|
)
|
|
# Ref: https://gitlab.com/gromacs/gromacs/-/merge_requests/3504
|
|
if self.spec.satisfies("@2023"):
|
|
filter_file(
|
|
" if (std::filesystem::equivalent(searchPath, buildBinPath))",
|
|
" if (std::error_code c; std::filesystem::equivalent(searchPath,"
|
|
" buildBinPath, c))",
|
|
"src/gromacs/commandline/cmdlineprogramcontext.cpp",
|
|
string=True,
|
|
)
|
|
|
|
if "+plumed" in self.spec:
|
|
self.spec["plumed"].package.apply_patch(self)
|
|
|
|
if self.spec.satisfies("%nvhpc"):
|
|
# Disable obsolete workaround
|
|
filter_file("ifdef __PGI", "if 0", "src/gromacs/fileio/xdrf.h")
|
|
|
|
if "+cuda" in self.spec:
|
|
# Upstream supports building of last two major versions of Gromacs.
|
|
# Older versions of Gromacs need to be patched to build with more recent
|
|
# versions of CUDA library.
|
|
|
|
# Hardware version 3.0 is supported up to CUDA 10.2 (Gromacs 4.6-2020.3
|
|
# needs to be patched, 2020.4 is handling it correctly)
|
|
|
|
if self.spec.satisfies("@4.6:2020.3^cuda@11:"):
|
|
filter_file(
|
|
r"-gencode;arch=compute_30,code=sm_30;?", "", "cmake/gmxManageNvccConfig.cmake"
|
|
)
|
|
filter_file(
|
|
r"-gencode;arch=compute_30,code=compute_30;?",
|
|
"",
|
|
"cmake/gmxManageNvccConfig.cmake",
|
|
)
|
|
|
|
# Hardware version 2.0 is supported up to CUDA 8 (Gromacs 4.6-2016.3
|
|
# needs to be patched, 2016.4 is handling it correctly, removed in 2019)
|
|
|
|
if self.spec.satisfies("@4.6:2016.3^cuda@9:"):
|
|
filter_file(
|
|
r"-gencode;arch=compute_20,code=sm_20;?", "", "cmake/gmxManageNvccConfig.cmake"
|
|
)
|
|
filter_file(
|
|
r"-gencode;arch=compute_20,code=compute_20;?",
|
|
"",
|
|
"cmake/gmxManageNvccConfig.cmake",
|
|
)
|
|
|
|
if self.spec.satisfies("@4.6:5.0^cuda@9:"):
|
|
filter_file(
|
|
r"-gencode;arch=compute_20,code=sm_21;?", "", "cmake/gmxManageNvccConfig.cmake"
|
|
)
|
|
|
|
|
|
class CMakeBuilder(spack.build_systems.cmake.CMakeBuilder):
|
|
@run_after("build")
|
|
def build_test_binaries(self):
|
|
"""Build the test binaries.
|
|
|
|
GROMACS usually excludes tests from the default build target, but building
|
|
the tests during spack's ``check`` phase takes a long time while producing
|
|
no visible output, even with ``--verbose``.
|
|
|
|
Here, we make sure the test binaries are built during the build phase
|
|
(as would normally be expected when configured with BUILD_TESTING)
|
|
when the ``--test`` flag is used.
|
|
|
|
Note: the GMX_DEVELOPER_BUILD option disables the EXCLUDE_FROM_ALL on the
|
|
test binaries, but the option incurs additional side effects that may
|
|
not be intended with ``--test``.
|
|
"""
|
|
if self.pkg.run_tests:
|
|
with fs.working_dir(self.build_directory):
|
|
make("tests")
|
|
|
|
def check(self):
|
|
"""Run the ``check`` target (skipping the ``test`` target).
|
|
|
|
Override the standard CMakeBuilder behavior. GROMACS has both `test`
|
|
and `check` targets, but we are only interested in the latter.
|
|
"""
|
|
with fs.working_dir(self.build_directory):
|
|
if self.generator == "Unix Makefiles":
|
|
make("check")
|
|
elif self.generator == "Ninja":
|
|
ninja("check")
|
|
|
|
def cmake_args(self):
|
|
options = []
|
|
# Warning: Use `define_from_variant()` with caution.
|
|
# GROMACS may use unexpected conventions for CMake variable values.
|
|
# For example: variables that accept boolean values like "OFF"
|
|
# may actually be STRING type, and undefined variables may trigger
|
|
# different defaults for dependent options than explicitly defined variables.
|
|
# `-DGMX_VAR=OFF` may not have the same meaning as `-DGMX_VAR=`.
|
|
# In other words, the mapping between package variants and the
|
|
# GMX CMake variables is often non-trivial.
|
|
|
|
if "+mpi" in self.spec:
|
|
options.append("-DGMX_MPI:BOOL=ON")
|
|
if self.pkg.version < Version("2020"):
|
|
# Ensures gmxapi builds properly
|
|
options.extend(
|
|
[
|
|
"-DCMAKE_C_COMPILER=%s" % self.spec["mpi"].mpicc,
|
|
"-DCMAKE_CXX_COMPILER=%s" % self.spec["mpi"].mpicxx,
|
|
"-DCMAKE_Fortran_COMPILER=%s" % self.spec["mpi"].mpifc,
|
|
]
|
|
)
|
|
elif self.pkg.version == Version("2021"):
|
|
# Work around https://gitlab.com/gromacs/gromacs/-/issues/3896
|
|
# Ensures gmxapi builds properly
|
|
options.extend(
|
|
[
|
|
"-DCMAKE_C_COMPILER=%s" % self.spec["mpi"].mpicc,
|
|
"-DCMAKE_CXX_COMPILER=%s" % self.spec["mpi"].mpicxx,
|
|
]
|
|
)
|
|
else:
|
|
options.extend(
|
|
[
|
|
"-DCMAKE_C_COMPILER=%s" % spack_cc,
|
|
"-DCMAKE_CXX_COMPILER=%s" % spack_cxx,
|
|
"-DMPI_C_COMPILER=%s" % self.spec["mpi"].mpicc,
|
|
"-DMPI_CXX_COMPILER=%s" % self.spec["mpi"].mpicxx,
|
|
]
|
|
)
|
|
else:
|
|
options.extend(
|
|
[
|
|
"-DCMAKE_C_COMPILER=%s" % spack_cc,
|
|
"-DCMAKE_CXX_COMPILER=%s" % spack_cxx,
|
|
"-DGMX_MPI:BOOL=OFF",
|
|
"-DGMX_THREAD_MPI:BOOL=ON",
|
|
]
|
|
)
|
|
|
|
if self.spec.satisfies("%aocc"):
|
|
options.append("-DCMAKE_CXX_FLAGS=--stdlib=libc++")
|
|
|
|
if self.spec.satisfies("@2020:"):
|
|
options.append("-DGMX_INSTALL_LEGACY_API=ON")
|
|
|
|
if self.spec.satisfies("%oneapi") or self.spec.satisfies("%intel"):
|
|
# If intel-oneapi-compilers was installed through spack the gcc is added to the
|
|
# configuration file.
|
|
if self.spec.satisfies("+intel_provided_gcc") and os.path.exists(
|
|
".".join([os.environ["SPACK_CXX"], "cfg"])
|
|
):
|
|
with open(".".join([os.environ["SPACK_CXX"], "cfg"]), "r") as f:
|
|
options.append("-DCMAKE_CXX_FLAGS={}".format(f.read()))
|
|
else:
|
|
options.append("-DGMX_GPLUSPLUS_PATH=%s/g++" % self.spec["gcc"].prefix.bin)
|
|
|
|
if "+double" in self.spec:
|
|
options.append("-DGMX_DOUBLE:BOOL=ON")
|
|
|
|
if "+nosuffix" in self.spec:
|
|
options.append("-DGMX_DEFAULT_SUFFIX:BOOL=OFF")
|
|
|
|
if "~shared" in self.spec:
|
|
options.append("-DBUILD_SHARED_LIBS:BOOL=OFF")
|
|
options.append("-DGMXAPI:BOOL=OFF")
|
|
|
|
if "+hwloc" in self.spec:
|
|
options.append("-DGMX_HWLOC:BOOL=ON")
|
|
else:
|
|
options.append("-DGMX_HWLOC:BOOL=OFF")
|
|
|
|
if self.pkg.version >= Version("2021"):
|
|
if "+cuda" in self.spec:
|
|
options.append("-DGMX_GPU:STRING=CUDA")
|
|
elif "+opencl" in self.spec:
|
|
options.append("-DGMX_GPU:STRING=OpenCL")
|
|
elif "+sycl" in self.spec:
|
|
options.append("-DGMX_GPU:STRING=SYCL")
|
|
else:
|
|
options.append("-DGMX_GPU:STRING=OFF")
|
|
else:
|
|
if "+cuda" in self.spec or "+opencl" in self.spec:
|
|
options.append("-DGMX_GPU:BOOL=ON")
|
|
if "+opencl" in self.spec:
|
|
options.append("-DGMX_USE_OPENCL=ON")
|
|
else:
|
|
options.append("-DGMX_GPU:BOOL=OFF")
|
|
|
|
if "+cuda" in self.spec:
|
|
options.append("-DCUDA_TOOLKIT_ROOT_DIR:STRING=" + self.spec["cuda"].prefix)
|
|
|
|
options.append("-DGMX_EXTERNAL_LAPACK:BOOL=ON")
|
|
if self.spec["lapack"].libs:
|
|
options.append("-DGMX_LAPACK_USER={0}".format(self.spec["lapack"].libs.joined(";")))
|
|
|
|
options.append("-DGMX_EXTERNAL_BLAS:BOOL=ON")
|
|
if self.spec["blas"].libs:
|
|
options.append("-DGMX_BLAS_USER={0}".format(self.spec["blas"].libs.joined(";")))
|
|
|
|
if "+cp2k" in self.spec:
|
|
options.append("-DGMX_CP2K:BOOL=ON")
|
|
options.append("-DCP2K_DIR:STRING={0}".format(self.spec["cp2k"].prefix))
|
|
|
|
if "+cufftmp" in self.spec:
|
|
options.append("-DGMX_USE_CUFFTMP=ON")
|
|
options.append(
|
|
f'-DcuFFTMp_ROOT={self.spec["nvhpc"].prefix}/Linux_{self.spec.target.family}'
|
|
+ f'/{self.spec["nvhpc"].version}/math_libs'
|
|
)
|
|
|
|
if "+heffte" in self.spec:
|
|
options.append("-DGMX_USE_HEFFTE=on")
|
|
options.append(f'-DHeffte_ROOT={self.spec["heffte"].prefix}')
|
|
|
|
if "+intel-data-center-gpu-max" in self.spec:
|
|
options.append("-DGMX_GPU_NB_CLUSTER_SIZE=8")
|
|
options.append("-DGMX_GPU_NB_NUM_CLUSTER_PER_CELL_X=1")
|
|
|
|
if "~nblib" in self.spec:
|
|
options.append("-DGMX_INSTALL_NBLIB_API=OFF")
|
|
if "~gmxapi" in self.spec:
|
|
options.append("-DGMXAPI=OFF")
|
|
|
|
# Activate SIMD based on properties of the target
|
|
target = self.spec.target
|
|
if target >= "zen4":
|
|
# AMD Family 17h (EPYC Genoa)
|
|
options.append("-DGMX_SIMD=AVX_512")
|
|
elif target >= "zen2":
|
|
# AMD Family 17h (EPYC Rome)
|
|
options.append("-DGMX_SIMD=AVX2_256")
|
|
elif target >= "zen":
|
|
# AMD Family 17h (EPYC Naples)
|
|
options.append("-DGMX_SIMD=AVX2_128")
|
|
elif target >= "bulldozer":
|
|
# AMD Family 15h
|
|
options.append("-DGMX_SIMD=AVX_128_FMA")
|
|
elif "vsx" in target:
|
|
# IBM Power 7 and beyond
|
|
if self.spec.satisfies("%nvhpc"):
|
|
options.append("-DGMX_SIMD=None")
|
|
else:
|
|
options.append("-DGMX_SIMD=IBM_VSX")
|
|
elif target.family == "aarch64":
|
|
# ARMv8
|
|
if self.spec.satisfies("%nvhpc"):
|
|
options.append("-DGMX_SIMD=None")
|
|
elif "sve" in target.features and "+sve" in self.spec:
|
|
options.append("-DGMX_SIMD=ARM_SVE")
|
|
else:
|
|
options.append("-DGMX_SIMD=ARM_NEON_ASIMD")
|
|
elif target == "mic_knl":
|
|
# Intel KNL
|
|
options.append("-DGMX_SIMD=AVX_512_KNL")
|
|
else:
|
|
# Other architectures
|
|
simd_features = [
|
|
("sse2", "SSE2"),
|
|
("sse4_1", "SSE4.1"),
|
|
("avx", "AVX_256"),
|
|
("axv128", "AVX2_128"),
|
|
("avx2", "AVX2_256"),
|
|
("avx512", "AVX_512"),
|
|
]
|
|
|
|
# Workaround NVIDIA compiler bug when avx512 is enabled
|
|
if self.spec.satisfies("%nvhpc") and ("avx512", "AVX_512") in simd_features:
|
|
simd_features.remove(("avx512", "AVX_512"))
|
|
|
|
feature_set = False
|
|
for feature, flag in reversed(simd_features):
|
|
if feature in target:
|
|
options.append("-DGMX_SIMD:STRING={0}".format(flag))
|
|
feature_set = True
|
|
break
|
|
|
|
# Fall back
|
|
if not feature_set:
|
|
options.append("-DGMX_SIMD:STRING=None")
|
|
|
|
# Use the 'rtdscp' assembly instruction only on
|
|
# appropriate architectures
|
|
options.append(self.define("GMX_USE_RDTSCP", str(target.family) in ("x86_64", "x86")))
|
|
|
|
if self.spec.satisfies("@:2020"):
|
|
options.append(self.define_from_variant("GMX_BUILD_MDRUN_ONLY", "mdrun_only"))
|
|
|
|
options.append(self.define_from_variant("GMX_OPENMP", "openmp"))
|
|
|
|
if self.spec.satisfies("@:2020"):
|
|
options.append(
|
|
self.define_from_variant(
|
|
"GMX_RELAXED_DOUBLE_PRECISION", "relaxed_double_precision"
|
|
)
|
|
)
|
|
|
|
if "+cycle_subcounters" in self.spec:
|
|
options.append("-DGMX_CYCLE_SUBCOUNTERS:BOOL=ON")
|
|
else:
|
|
options.append("-DGMX_CYCLE_SUBCOUNTERS:BOOL=OFF")
|
|
|
|
if "+openmp" in self.spec and self.spec.variants["openmp_max_threads"].value != "none":
|
|
options.append(
|
|
"-DGMX_OPENMP_MAX_THREADS=%s" % self.spec.variants["openmp_max_threads"].value
|
|
)
|
|
|
|
if self.spec["lapack"].name in INTEL_MATH_LIBRARIES:
|
|
# fftw-api@3 is provided by intel-mkl or intel-parllel-studio
|
|
# we use the mkl interface of gromacs
|
|
options.append("-DGMX_FFT_LIBRARY=mkl")
|
|
if self.spec.satisfies("@:2022"):
|
|
options.append(
|
|
"-DMKL_INCLUDE_DIR={0}".format(self.spec["mkl"].headers.directories[0])
|
|
)
|
|
# The 'blas' property provides a minimal set of libraries
|
|
# that is sufficient for fft. Using full mkl fails the cmake test
|
|
options.append("-DMKL_LIBRARIES={0}".format(self.spec["blas"].libs.joined(";")))
|
|
else:
|
|
# we rely on the fftw-api@3
|
|
options.append("-DGMX_FFT_LIBRARY=fftw3")
|
|
if "^amdfftw" in self.spec:
|
|
options.append("-DGMX_FFT_LIBRARY=fftw3")
|
|
options.append(
|
|
"-DFFTWF_INCLUDE_DIRS={0}".format(self.spec["amdfftw"].headers.directories[0])
|
|
)
|
|
options.append(
|
|
"-DFFTWF_LIBRARIES={0}".format(self.spec["amdfftw"].libs.joined(";"))
|
|
)
|
|
elif "^armpl-gcc" in self.spec:
|
|
options.append(
|
|
"-DFFTWF_INCLUDE_DIR={0}".format(self.spec["armpl-gcc"].headers.directories[0])
|
|
)
|
|
options.append(
|
|
"-DFFTWF_LIBRARY={0}".format(self.spec["armpl-gcc"].libs.joined(";"))
|
|
)
|
|
elif "^acfl" in self.spec:
|
|
options.append(
|
|
"-DFFTWF_INCLUDE_DIR={0}".format(self.spec["acfl"].headers.directories[0])
|
|
)
|
|
options.append("-DFFTWF_LIBRARY={0}".format(self.spec["acfl"].libs.joined(";")))
|
|
|
|
# Ensure that the GROMACS log files report how the code was patched
|
|
# during the build, so that any problems are easier to diagnose.
|
|
if "+plumed" in self.spec:
|
|
options.append("-DGMX_VERSION_STRING_OF_FORK=PLUMED-spack")
|
|
else:
|
|
options.append("-DGMX_VERSION_STRING_OF_FORK=spack")
|
|
return options
|