mirror of
https://github.com/cp2k/cp2k.git
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Spack: PLUMED 2.9.2 -> 2.10.0
This commit is contained in:
Matthias Krack
parent
93901f99c1
commit
bc61e0093c
2 changed files with 355 additions and 1 deletions
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@ -175,7 +175,7 @@ spack:
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- "openpmd-api@0.16.1"
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- "pace@2025.12.4"
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- "pexsi@2.0.0"
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- "plumed@2.9.2"
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- "plumed@2.10.0"
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- "py-torch@2.9.0"
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- "sirius@7.9.0"
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- "spfft@1.1.1"
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354
tools/spack/spack_repo/cp2k_dev/packages/plumed/package.py
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354
tools/spack/spack_repo/cp2k_dev/packages/plumed/package.py
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@ -0,0 +1,354 @@
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# Copyright Spack Project Developers. See 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 collections
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import os
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from pathlib import Path
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from spack_repo.builtin.build_systems.autotools import AutotoolsPackage
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from spack.package import *
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class Plumed(AutotoolsPackage):
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"""PLUMED is an open source library for free energy calculations in
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molecular systems which works together with some of the most popular
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molecular dynamics engines.
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Free energy calculations can be performed as a function of many order
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parameters with a particular focus on biological problems, using state
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of the art methods such as metadynamics, umbrella sampling and
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Jarzynski-equation based steered MD.
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The software, written in C++, can be easily interfaced with both fortran
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and C/C++ codes.
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"""
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homepage = "https://www.plumed.org/"
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url = "https://github.com/plumed/plumed2/archive/v2.7.4.tar.gz"
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git = "https://github.com/plumed/plumed2.git"
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maintainers("marcodelapierre")
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tags = ["e4s"]
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license("LGPL-3.0-or-later")
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version("master", branch="master")
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version("2.10.0", sha256="ca6410d47e91b4e0f953e1a8933f15b05c4681167611ab3b096ab121155f6879")
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version("2.9.2", sha256="301fbc958374f81d9b8c7a1eac73095f6dded52cce73ce33d64bdbebf51ac63d")
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version("2.9.1", sha256="e24563ad1eb657611918e0c978d9c5212340f128b4f1aa5efbd439a0b2e91b58")
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version("2.9.0", sha256="612d2387416b5f82dd8545709921440370e144fd46cef633654cf0ee43bac5f8")
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version("2.8.3", sha256="e98da486e252cdf290b0b5b2f3f021409ea0d2d775ab609a6ad68fc1ab143a3b")
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version("2.8.2", sha256="a2064bacba1dde36b05aaf351ba4b7e6d30a165b332b0a83b7a6db04b477be9f")
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version("2.8.1", sha256="f56bc9266c8a47241385c595717c2734a9b67148a7f4122b808bc0733710173e")
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version("2.8.0", sha256="8357eca6f280125037ad4e7c427f96f2af2f60ddfedce1a2e36e1e1cc3bff32b")
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version("2.7.6", sha256="9ca7b1e84bf2343a09a5b604222dd04aa0fc8b62a7cb82d1d68b795b6b189c06")
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version("2.7.5", sha256="39cb01108706df7ef71c7c315ddfc4306137f62ac72222b8582ab892221f7972")
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version("2.7.4", sha256="6f5dc16a753c71ed719f17f9cbb61642ab8e716fb7f77e22960dfa145c3b8211")
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version("2.7.3", sha256="aa1f6200c2ed351e40ce4391a9590f171532474b30f384feddfab10e36d7e08e")
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version("2.7.2", sha256="c9a31e68d6440828cf186ca43c9e11a5e5c7ad1c96b2b66ed5a5a141fc954373")
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version("2.7.1", sha256="cb8b5735d8dd61980fa6441f3dde3f33544240ae4177da0f529fb5abb355cd4a")
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version("2.7.0", sha256="14450ea566c25ac9bf71fd77bb9c0c95e9038462b5739c73a515be82e2011cd6")
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version("2.6.6", sha256="43a7bb410280141c020363671c685a759d4497b3db3eb3c04899264b51a26859")
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version("2.6.5", sha256="3b72587ba6fe72def46bcc7d917974123279879de7f8335acf542bba57865eed")
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version("2.6.4", sha256="53e49c0db6cc769d238834bea884e856f4e7bb8f71c9929e5584bd977113f03b")
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version("2.6.3", sha256="d05b9e4a4c1329fc932d5bdd04f20419be230f98159bdc012a91716461ab4a2f")
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version("2.6.2", sha256="bbc2ef0cb08d404513b8b737c72333b6656389e15effd6a0f9ace2a5758c9a4a")
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version("2.6.1", sha256="c1b3c397b2d971140aa240dde50e48a04ce78e3dedb02b6dca80fa53f8026e4e")
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version("2.6.0", sha256="3d57ae460607a49547ef38a52c4ac93493a3966857c352280a9c05f5dcdb1820")
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version("2.5.7", sha256="aa10d2879c3edeaef9d5a530fe8b05f67ecfbec2e9423e0f95701d0bc54826c7")
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version("2.5.6", sha256="1bc29b0274196fb553cdf7ba8ecb7a93a91d60a920d99863edbcd536d618ce8c")
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version("2.5.5", sha256="70faa9ff1938e286dc388cb793b39840953e5646855b684f48df1bc864b737e8")
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version("2.5.4", sha256="a1647e598191f261e75d06351e607475d395af481315052a4c28563ac9989a7f")
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version("2.5.3", sha256="543288be667dc4201fc461ecd2dd4878ddfbeac682d0c021c99ea8e501c7c9dc")
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version("2.5.2", sha256="85d10cc46e2e37c7719cf51c0931278f56c2c8f8a9d86188b2bf97c2535a2ab4")
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version("2.5.1", sha256="de309980dcfd6f6e0e70e138856f4bd9eb4d8a513906a5e6389f18a5af7f2eba")
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version("2.5.0", sha256="53e08187ec9f8af2326fa84407e34644a7c51d2af93034309fb70675eee5e4f7")
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# Variants. PLUMED by default builds a number of optional modules.
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# The ones listed here are not built by default for various reasons,
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# such as stability, lack of testing, or lack of demand.
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#
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# From 'configure --help' @2.3:
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# all/none/reset or : separated list such as
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# +crystallization:-bias default: reset
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#
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# Optional modules can be provided in two ways, via the `optional_modules` variant:
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# 1. Use a reference set of optional modules via `optional_modules` (recommended).
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# Allowed values are: `all`[default], `reset`.
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# 2. Pick any combination of specific optional modules (advanced).
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# Only the requested optional modules will be activated.
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# See list in variable `single_optional_modules` below.
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# This list comes from the Plumed manual, eg for 2.8:
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# https://www.plumed.org/doc-v2.8/user-doc/html/mymodules.html
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# These are implemented using multi-valued variants (`disjoint_sets`),
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# and the `conditional` option to handle version conflicts.
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single_optional_modules = (
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"adjmat",
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"analysis",
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conditional("annfunc", when="@2.6:"),
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"bias",
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"cltools",
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"colvar",
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"crystallization",
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"dimred",
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"drr",
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"eds",
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conditional("fisst", when="@2.7:"),
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"function",
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conditional("funnel", when="@2.7:"),
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"generic",
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"isdb",
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"logmfd",
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"manyrestraints",
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"mapping",
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conditional("maze", when="@2.6:"),
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"molfile",
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"multicolvar",
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conditional("opes", when="@2.7:"),
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conditional("pamm", when="optional_modules=adjmat"),
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"piv",
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conditional("s2cm", when="@2.8:"),
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conditional("sasa", when="@2.8:"),
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"secondarystructure",
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"setup",
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"vatom",
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"ves",
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conditional("xdrfile", when="@2.8:"),
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)
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variant(
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"optional_modules",
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values=disjoint_sets(("all",), ("reset",), single_optional_modules)
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.prohibit_empty_set()
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.with_default("all"),
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description="Activates optional modules: all, reset, or custom list (advanced)",
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)
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variant("shared", default=True, description="Builds shared libraries")
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variant("mpi", default=True, description="Activates MPI support")
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variant("gsl", default=True, description="Activates GSL support")
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variant(
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"arrayfire",
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default="none",
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values=("none", "cpu", "cuda", "opencl"),
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description="Activates FireArray support",
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)
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variant("pytorch", default=False, description="Activates PyTorch support", when="@2.9:")
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variant("metatomic", default=False, description="Activates metatomic support", when="@2.10:")
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depends_on("c", type="build") # generated
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depends_on("cxx", type="build") # generated
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depends_on("fortran", type="build") # generated
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# Dependencies. LAPACK and BLAS are recommended but not essential.
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depends_on("zlib-api")
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depends_on("blas")
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depends_on("lapack")
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depends_on("arrayfire", when="arrayfire=cpu")
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depends_on("arrayfire+cuda", when="arrayfire=cuda")
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depends_on("arrayfire+opencl", when="arrayfire=opencl")
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depends_on("mpi", when="+mpi")
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depends_on("gsl", when="+gsl")
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depends_on("autoconf", type="build")
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depends_on("automake", type="build")
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depends_on("libtool", type="build")
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depends_on("m4", type="build")
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depends_on("py-cython", type="build")
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depends_on("py-torch", when="+pytorch")
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conflicts("+metatomic ~pytorch", msg="metatomic support requires PyTorch")
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depends_on("libmetatomic-torch", when="+metatomic")
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# https://github.com/plumed/plumed2/issues/1256
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conflicts("^py-cython@3.1:", when="@:2.9.3")
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patch(
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"https://patch-diff.githubusercontent.com/raw/plumed/plumed2/pull/1313.patch?full_index=1",
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sha256="d4d2b6a178e4b38863f2acc9450ae27b4652368c369e96dd093bbdffaf811105",
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when="@2.10.0",
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)
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force_autoreconf = True
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parallel = True
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def apply_patch(self, other):
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# The name of MD engines differ slightly from the ones used in Spack
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format_strings = collections.defaultdict(lambda: "{0.name}-{0.version}")
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format_strings["espresso"] = "q{0.name}-{0.version}"
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format_strings["amber"] = "{0.name}{0.version}"
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get_md = lambda x: format_strings[x.name].format(x)
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# Get available patches
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plumed_patch = Executable(os.path.join(self.spec.prefix.bin, "plumed-patch"))
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out = plumed_patch("-q", "-l", output=str)
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available = out.split(":")[-1].split()
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# Check that `other` is among the patchable applications
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if get_md(other) not in available:
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msg = "{0.name}@{0.version} is not among the MD engine"
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msg += " that can be patched by {1.name}@{1.version}.\n"
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msg += "Supported engines are:\n"
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for x in available:
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msg += x + "\n"
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raise RuntimeError(msg.format(other, self.spec))
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# Call plumed-patch to patch executables
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target = format_strings[other.name].format(other)
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plumed_patch("-p", "-e", target)
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def setup_dependent_package(self, module, dependent_spec):
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# Make plumed visible from dependent packages
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module.plumed = self.command
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@property
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def plumed_inc(self):
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return os.path.join(self.prefix.lib, "plumed", "src", "lib", "Plumed.inc")
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@run_before("autoreconf")
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def filter_gslcblas(self):
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# This part is needed to avoid linking with gsl cblas
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# interface which will mask the cblas interface
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# provided by optimized libraries due to linking order
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filter_file("-lgslcblas", "", "configure.ac")
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def patch(self):
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# Ensure Spack's wrappers are used to compile the Python interface
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env = (
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'CC="{0}" LDSHARED="{0} -pthread -shared" '
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'CXX="{1}" LDCXXSHARED="{1} -pthread -shared"'.format(spack_cc, spack_cxx)
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)
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filter_file(
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"plumed_program_name=plumed",
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"{0} plumed_program_name=plumed".format(env),
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"src/lib/Makefile",
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"python/Makefile",
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)
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def configure_args(self):
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spec = self.spec
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# From plumed docs :
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# Also consider that this is different with respect to what some other
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# configure script does in that variables such as MPICXX are
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# completely ignored here. In case you work on a machine where CXX is
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# set to a serial compiler and MPICXX to a MPI compiler, to compile
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# with MPI you should use:
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#
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# > ./configure CXX="$MPICXX"
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# The configure.ac script may detect the wrong linker for
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# LD_RO which causes issues at link time. Here we work around
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# the issue saying we have no LD_RO executable.
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configure_opts = ["--disable-ld-r"]
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configure_opts.append("--disable-doc")
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# If using MPI then ensure the correct compiler wrapper is used.
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if "+mpi" in spec:
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configure_opts.extend(["--enable-mpi", "CXX={0}".format(spec["mpi"].mpicxx)])
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# If the MPI dependency is provided by the intel-oneapi-mpi package then the following
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# additional argument is required to allow it to build.
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if spec.satisfies("^[virtuals=mpi] intel-oneapi-mpi"):
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configure_opts.extend(["STATIC_LIBS=-mt_mpi"])
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enable_libmetatomic = self.spec.satisfies("+metatomic")
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enable_libtorch = self.spec.satisfies("+pytorch")
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extra_ldflags = []
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extra_libs = []
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extra_cppflags = []
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# Set flags to help find gsl
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if "+gsl" in spec:
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gsl_libs = spec["gsl"].libs
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blas_libs = spec["blas"].libs
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extra_ldflags.append((gsl_libs + blas_libs).search_flags)
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extra_libs.append((gsl_libs + blas_libs).link_flags)
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extra_cppflags.extend(
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[spec["gsl"].headers.include_flags, spec["blas"].headers.include_flags]
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)
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# Set flags to help with ArrayFire
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if "arrayfire=none" not in spec:
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libaf = "arrayfire:{0}".format(spec.variants["arrayfire"].value)
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extra_ldflags.append(spec[libaf].libs.search_flags)
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extra_libs.append(spec[libaf].libs.link_flags)
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extra_cppflags.append(spec[libaf].headers.include_flags)
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# Set flags to help with PyTorch
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if enable_libtorch:
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pytorch_path = Path(spec["py-torch"].package.cmake_prefix_paths[0]).parent.parent
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extra_ldflags.append(spec["py-torch"].libs.search_flags)
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extra_libs.append(spec["py-torch"].libs.link_flags)
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extra_ldflags.append(spec["python"].libs.search_flags)
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extra_libs.append(spec["python"].libs.link_flags)
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# Add include paths manually
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# Spack HeaderList.cpp_flags does not support include paths within include paths
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extra_cppflags.extend(
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[
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f"-I{pytorch_path / 'include'}",
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f"-I{pytorch_path / 'include' / 'torch' / 'csrc' / 'api' / 'include'}",
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spec["python"].headers.include_flags,
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]
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)
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if enable_libmetatomic:
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for libname in ["libmetatensor", "libmetatensor-torch", "libmetatomic-torch"]:
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extra_ldflags.append(spec[libname].libs.search_flags)
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extra_libs.append(spec[libname].libs.link_flags)
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extra_cppflags.append(spec[libname].headers.include_flags)
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if extra_ldflags:
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configure_opts.append("LDFLAGS={0}".format(" ".join(extra_ldflags)))
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if extra_libs:
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configure_opts.append("LIBS={0}".format(" ".join(extra_libs)))
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if extra_cppflags:
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configure_opts.append("CPPFLAGS={0}".format(" ".join(extra_cppflags)))
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# Additional arguments
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configure_opts.extend(
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[
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"--enable-shared={0}".format("yes" if "+shared" in spec else "no"),
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"--enable-gsl={0}".format("yes" if "+gsl" in spec else "no"),
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"--enable-af_cpu={0}".format("yes" if "arrayfire=cpu" in spec else "no"),
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"--enable-af_cuda={0}".format("yes" if "arrayfire=cuda" in spec else "no"),
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"--enable-af_ocl={0}".format("yes" if "arrayfire=ocl" in spec else "no"),
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"--enable-libtorch={0}".format("yes" if enable_libtorch else "no"),
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"--enable-libmetatomic={0}".format("yes" if enable_libmetatomic else "no"),
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]
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)
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# Construct list of optional modules
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optional_modules = spec.variants["optional_modules"].value
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# Predefined set of modules
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if "all" in optional_modules:
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selected_modules = "all"
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elif "reset" in optional_modules:
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selected_modules = "reset"
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# Custom set of modules
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else:
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# Ensure modules from variants
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if spec.satisfies("+pytorch") or sepec.satisfies("+metatomic"):
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optional_modules += ("pytorch",)
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if spec.satisfies("+libmetatomic"):
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optional_modules += ("metatomic",)
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selected_modules = "none"
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for mod in optional_modules:
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selected_modules += ":+{0}".format(mod)
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configure_opts.append("--enable-modules={0}".format(selected_modules))
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return configure_opts
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