305eefc062
* gnu/packages/mpi.scm (hwloc-1)[outputs]: Add "doc". [arguments]: Add 'move-man3-pages' phase.
500 lines
22 KiB
Scheme
500 lines
22 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2014, 2015, 2018, 2019 Eric Bavier <bavier@member.fsf.org>
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;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
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;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
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;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
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;;; Copyright © 2017 Dave Love <fx@gnu.org>
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;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
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;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages mpi)
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#:use-module (guix packages)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix download)
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#:use-module (guix utils)
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#:use-module (guix deprecation)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system python)
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#:use-module (gnu packages)
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#:use-module (gnu packages base)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages fabric-management)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages java)
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#:use-module (gnu packages libevent)
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#:use-module (gnu packages linux)
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#:use-module (gnu packages pciutils)
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#:use-module (gnu packages xorg)
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#:use-module (gnu packages gtk)
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#:use-module (gnu packages xml)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages ncurses)
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#:use-module (gnu packages parallel)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages valgrind)
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#:use-module (srfi srfi-1)
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#:use-module (ice-9 match))
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(define-public hwloc-1
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;; Note: For now we keep 1.x as the default because many packages have yet
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;; to migrate to 2.0.
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(package
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(name "hwloc")
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(version "1.11.12")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://www.open-mpi.org/software/hwloc/v"
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(version-major+minor version)
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"/downloads/hwloc-" version ".tar.bz2"))
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(sha256
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(base32
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"0za1b9lvrm3rhn0lrxja5f64r0aq1qs4m0pxn1ji2mbi8ndppyyx"))))
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(build-system gnu-build-system)
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(outputs '("out" ;'lstopo' & co., depends on Cairo, libx11, etc.
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"lib" ;small closure
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"doc" ;400+ section 3 man pages
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"debug"))
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(inputs
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`(("libx11" ,libx11)
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("cairo" ,cairo)
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("ncurses" ,ncurses)
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("expat" ,expat)
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,@(if (not (string-prefix? "armhf"
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(or (%current-target-system)
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(%current-system))))
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`(("numactl" ,numactl))
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'())))
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(propagated-inputs
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;; hwloc.pc lists it in 'Requires.private'.
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`(("libpciaccess" ,libpciaccess)))
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(native-inputs
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`(("pkg-config" ,pkg-config)))
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(arguments
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`(#:configure-flags '("--localstatedir=/var")
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#:phases
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(modify-phases %standard-phases
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(add-before 'check 'skip-linux-libnuma-test
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(lambda _
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;; Arrange to skip 'tests/linux-libnuma', which fails on some
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;; machines: <https://github.com/open-mpi/hwloc/issues/213>.
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(substitute* "tests/linux-libnuma.c"
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(("numa_available\\(\\)")
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"-1"))
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#t))
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(add-after 'install 'refine-libnuma
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;; Give -L arguments for libraries to avoid propagation
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "lib"))
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(numa (assoc-ref inputs "numactl")))
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(substitute* (map (lambda (f) (string-append out "/" f))
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'("lib/pkgconfig/hwloc.pc" "lib/libhwloc.la"))
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(("-lnuma" lib)
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(string-append "-L" numa "/lib " lib))))))
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(add-after 'install 'avoid-circular-references
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((lib (assoc-ref outputs "lib")))
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;; Suppress the 'prefix=' and 'exec_prefix=' lines so that the
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;; "lib" output doesn't refer to "out".
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(substitute* (string-append lib "/lib/pkgconfig/hwloc.pc")
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(("^.*prefix=.*$")
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""))
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#t)))
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(add-after 'install 'move-man3-pages
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(lambda* (#:key outputs #:allow-other-keys)
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;; Move section 3 man pages to the "doc" output.
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(let ((out (assoc-ref outputs "out"))
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(doc (assoc-ref outputs "doc")))
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(copy-recursively (string-append out "/share/man/man3")
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(string-append doc "/share/man/man3"))
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(delete-file-recursively (string-append out "/share/man/man3"))
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#t))))))
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(home-page "https://www.open-mpi.org/projects/hwloc/")
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(synopsis "Abstraction of hardware architectures")
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(description
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"hwloc provides a portable abstraction (across OS,
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versions, architectures, ...) of the hierarchical topology of modern
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architectures, including NUMA memory nodes, sockets, shared caches, cores and
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simultaneous multithreading. It also gathers various attributes such as cache
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and memory information. It primarily aims at helping high-performance
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computing applications with gathering information about the hardware so as to
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exploit it accordingly and efficiently.
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hwloc may display the topology in multiple convenient formats. It also offers
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a powerful programming interface to gather information about the hardware,
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bind processes, and much more.")
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(license license:bsd-3)))
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(define-public hwloc-2
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;; Note: 2.0 isn't the default yet, see above.
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(package
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(inherit hwloc-1)
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(version "2.2.0")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://www.open-mpi.org/software/hwloc/v"
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(version-major+minor version)
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"/downloads/hwloc-" version ".tar.bz2"))
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(sha256
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(base32
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"0li27a3lnmb77qxpijj0kpblz32wmqd3b386sypq8ar7vy9vhw5f"))))
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;; libnuma is no longer needed.
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(inputs (alist-delete "numactl" (package-inputs hwloc-1)))
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(arguments
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(substitute-keyword-arguments (package-arguments hwloc-1)
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((#:phases phases)
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`(modify-phases ,phases
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(replace 'skip-linux-libnuma-test
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(lambda _
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;; Arrange to skip 'tests/hwloc/linux-libnuma', which fails on
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;; some machines: <https://github.com/open-mpi/hwloc/issues/213>.
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(substitute* "tests/hwloc/linux-libnuma.c"
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(("numa_available\\(\\)")
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"-1"))
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#t))
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(add-before 'check 'skip-test-that-fails-on-qemu
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(lambda _
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;; Skip test that fails on emulated hardware due to QEMU bug:
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;; <https://bugs.gnu.org/40342>.
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(substitute* "tests/hwloc/hwloc_get_last_cpu_location.c"
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(("hwloc_topology_init" all)
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(string-append "exit (77);\n" all)))
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#t))))))))
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(define-deprecated hwloc-2.0 hwloc-2)
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(define-public hwloc
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;; The latest stable series of hwloc.
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hwloc-2)
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(define-public openmpi
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(package
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(name "openmpi")
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(version "4.0.5")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "https://www.open-mpi.org/software/ompi/v"
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(version-major+minor version)
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"/downloads/openmpi-" version ".tar.bz2"))
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(sha256
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(base32 "02f0r9d3xgs08svkmj8v7lzviyxqnkk4yd3z0wql550xnriki3y5"))
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(patches (search-patches "openmpi-mtl-priorities.patch"))))
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(build-system gnu-build-system)
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(inputs
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`(("hwloc" ,hwloc-2 "lib")
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("gfortran" ,gfortran)
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("libfabric" ,libfabric)
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("libevent" ,libevent)
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("opensm" ,opensm)
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,@(if (and (not (%current-target-system))
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(member (%current-system) (package-supported-systems psm)))
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`(("psm" ,psm))
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'())
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,@(if (and (not (%current-target-system))
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(member (%current-system) (package-supported-systems psm2)))
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`(("psm2" ,psm2))
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'())
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,@(if (and (not (%current-target-system))
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(member (%current-system) (package-supported-systems ucx)))
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`(("ucx" ,ucx))
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'())
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("rdma-core" ,rdma-core)
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("valgrind" ,valgrind)
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("slurm" ,slurm))) ;for PMI support (launching via "srun")
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(native-inputs
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`(("pkg-config" ,pkg-config)
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("perl" ,perl)))
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(outputs '("out" "debug"))
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(arguments
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`(#:configure-flags `("--enable-mpi-ext=affinity" ;cr doesn't work
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"--enable-memchecker"
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"--with-sge"
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"--with-valgrind"
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"--with-hwloc=external"
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"--with-libevent"
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;; Help 'orterun' and 'mpirun' find their tools
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;; under $prefix by default.
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"--enable-mpirun-prefix-by-default"
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;; InfiniBand support
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"--enable-openib-control-hdr-padding"
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"--enable-openib-dynamic-sl"
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"--enable-openib-udcm"
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"--enable-openib-rdmacm"
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"--enable-openib-rdmacm-ibaddr"
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;; Enable support for SLURM's Process Manager
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;; Interface (PMI).
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,(string-append "--with-pmi="
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(assoc-ref %build-inputs "slurm")))
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#:phases (modify-phases %standard-phases
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;; opensm is needed for InfiniBand support.
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(add-after 'unpack 'find-opensm-headers
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(lambda* (#:key inputs #:allow-other-keys)
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(setenv "C_INCLUDE_PATH"
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(string-append (assoc-ref inputs "opensm")
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"/include/infiniband"))
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(setenv "CPLUS_INCLUDE_PATH"
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(string-append (assoc-ref inputs "opensm")
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"/include/infiniband"))
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#t))
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(add-before 'build 'remove-absolute
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(lambda _
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;; Remove compiler absolute file names (OPAL_FC_ABSOLUTE
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;; etc.) to reduce the closure size. See
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;; <https://lists.gnu.org/archive/html/guix-devel/2017-07/msg00388.html>
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;; and
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;; <https://www.mail-archive.com/users@lists.open-mpi.org//msg31397.html>.
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(substitute* '("orte/tools/orte-info/param.c"
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"oshmem/tools/oshmem_info/param.c"
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"ompi/tools/ompi_info/param.c")
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(("_ABSOLUTE") ""))
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;; Avoid valgrind (which pulls in gdb etc.).
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(substitute*
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'("./ompi/mca/io/romio321/src/io_romio321_component.c")
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(("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS")
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"\"[elided to reduce closure]\""))
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#t))
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(add-before 'build 'scrub-timestamps ;reproducibility
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(lambda _
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(substitute* '("ompi/tools/ompi_info/param.c"
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"orte/tools/orte-info/param.c"
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"oshmem/tools/oshmem_info/param.c")
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((".*(Built|Configured) on.*") ""))
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#t))
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(add-after 'install 'remove-logs ;reproducibility
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out")))
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(for-each delete-file (find-files out "config.log"))
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#t))))))
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(home-page "https://www.open-mpi.org")
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(synopsis "MPI-3 implementation")
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(description
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"The Open MPI Project is an MPI-3 implementation that is developed and
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maintained by a consortium of academic, research, and industry partners. Open
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MPI is therefore able to combine the expertise, technologies, and resources
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from all across the High Performance Computing community in order to build the
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best MPI library available. Open MPI offers advantages for system and
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software vendors, application developers and computer science researchers.")
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;; See file://LICENSE
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(license license:bsd-2)))
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;; TODO: javadoc files contain timestamps.
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(define-public java-openmpi
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(package (inherit openmpi)
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(name "java-openmpi")
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(inputs
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`(("openmpi" ,openmpi)
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,@(package-inputs openmpi)))
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(native-inputs
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`(("jdk" ,openjdk11 "jdk")
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("zip" ,(@ (gnu packages compression) zip))
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,@(package-native-inputs openmpi)))
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(outputs '("out"))
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(arguments
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`(#:modules ((guix build gnu-build-system)
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((guix build ant-build-system) #:prefix ant:)
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(guix build utils))
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#:imported-modules ((guix build ant-build-system)
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(guix build syscalls)
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,@%gnu-build-system-modules)
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,@(substitute-keyword-arguments (package-arguments openmpi)
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((#:configure-flags flags)
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`(cons "--enable-mpi-java" ,flags))
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((#:make-flags flags ''())
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`(append '("-C" "ompi/mpi/java")
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,flags))
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((#:phases phases)
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`(modify-phases ,phases
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;; We could provide the location of the JDK in the configure
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;; flags, but since the configure flags are embedded in the
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;; info binaries that would leave a reference to the JDK in
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;; the "out" output. To avoid this we set JAVA_HOME.
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(add-after 'unpack 'set-JAVA_HOME
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(lambda* (#:key inputs #:allow-other-keys)
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(setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
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#t))
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(add-after 'unpack 'link-with-existing-mpi-libraries
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "ompi/mpi/java/c/Makefile.in"
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(("\\$\\(top_builddir\\)/ompi/lib@OMPI_LIBMPI_NAME@.la")
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(string-append (assoc-ref inputs "openmpi") "/lib/libmpi.la")))
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#t))
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(add-after 'install 'strip-jar-timestamps
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(assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))))
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(synopsis "Java bindings for MPI")))
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(define-public openmpi-thread-multiple
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(package
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(inherit openmpi)
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(name "openmpi-thread-multiple")
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(arguments
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(substitute-keyword-arguments (package-arguments openmpi)
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((#:configure-flags flags)
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`(cons "--enable-mpi-thread-multiple" ,flags))))
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(description " This version of Open@tie{}MPI has an implementation of
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@code{MPI_Init_thread} that provides @code{MPI_THREAD_MULTIPLE}. This won't
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work correctly with all transports (such as @code{openib}), and the
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performance is generally worse than the vanilla @code{openmpi} package, which
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only provides @code{MPI_THREAD_FUNNELED}.")))
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;;; Build phase to be used for packages that execute MPI code.
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(define-public %openmpi-setup
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'(lambda _
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;; By default, running the test suite would fail because 'ssh' could not
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;; be found in $PATH. Define this variable to placate Open MPI without
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;; adding a dependency on OpenSSH (the agent isn't used anyway.)
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(setenv "OMPI_MCA_plm_rsh_agent" (which "false"))
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;; Allow oversubscription in case there are less physical cores available
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;; in the build environment than the package wants while testing.
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(setenv "OMPI_MCA_rmaps_base_mapping_policy" "core:OVERSUBSCRIBE")
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;; UCX sometimes outputs uninteresting warnings such as:
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;;
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;; mpool.c:38 UCX WARN object 0x7ffff44fffc0 was not returned to mpool ucp_am_bufs
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;;
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;; These in turn leads to failures of test suites that capture and
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;; compare stdout, such as that of 'hdf5-parallel-openmpi'. Thus, tell
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;; UCX to not emit those warnings.
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(setenv "UCX_LOG_LEVEL" "error")
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#t))
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(define-public python-mpi4py
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(package
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(name "python-mpi4py")
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(version "3.0.3")
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(source
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|
(origin
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(method url-fetch)
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(uri (pypi-uri "mpi4py" version))
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(sha256
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(base32 "07ssbhssv27rrjx1c5vd3vsr31vay5d8xcf4zh9yblcyidn72b81"))))
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(build-system python-build-system)
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|
(arguments
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`(#:phases
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|
(modify-phases %standard-phases
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|
(add-after 'build 'mpi-setup
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|
,%openmpi-setup)
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|
(add-before 'check 'pre-check
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|
(lambda _
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;; Skip BaseTestSpawn class (causes error 'ompi_dpm_dyn_init()
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;; failed --> Returned "Unreachable"' in chroot environment).
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(substitute* "test/test_spawn.py"
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(("unittest.skipMPI\\('openmpi\\(<3.0.0\\)'\\)")
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"unittest.skipMPI('openmpi')"))
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#t)))))
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(inputs
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`(("openmpi" ,openmpi)))
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(home-page "https://bitbucket.org/mpi4py/mpi4py/")
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(synopsis "Python bindings for the Message Passing Interface standard")
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(description "MPI for Python (mpi4py) provides bindings of the Message
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Passing Interface (MPI) standard for the Python programming language, allowing
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any Python program to exploit multiple processors.
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mpi4py is constructed on top of the MPI-1/MPI-2 specification and provides an
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object oriented interface which closely follows MPI-2 C++ bindings. It
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supports point-to-point and collective communications of any picklable Python
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object as well as optimized communications of Python objects (such as NumPy
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arrays) that expose a buffer interface.")
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(license license:bsd-3)))
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(define-public mpich
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(package
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(name "mpich")
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(version "3.3.2")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://www.mpich.org/static/downloads/"
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version "/mpich-" version ".tar.gz"))
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(sha256
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(base32
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|
"1farz5zfx4cd0c3a0wb9pgfypzw0xxql1j1294z1sxslga1ziyjb"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("zlib" ,zlib)
|
|
("hwloc" ,hwloc-2 "lib")
|
|
("slurm" ,slurm)
|
|
,@(if (and (not (%current-target-system))
|
|
(member (%current-system) (package-supported-systems ucx)))
|
|
`(("ucx" ,ucx))
|
|
'())))
|
|
(native-inputs
|
|
`(("perl" ,perl)
|
|
("which" ,which)
|
|
("gfortran" ,gfortran)))
|
|
(outputs '("out" "debug"))
|
|
(arguments
|
|
`(#:configure-flags
|
|
(list "--disable-silent-rules" ;let's see what's happening
|
|
"--enable-debuginfo"
|
|
|
|
;; Default to "ch4", as will be the case in 3.4. It also works
|
|
;; around issues when running test suites of packages that use
|
|
;; MPICH: <https://issues.guix.gnu.org/39588#15>.
|
|
"--with-device=ch4:ucx" ; --with-device=ch4:ofi segfaults in tests
|
|
|
|
(string-append "--with-hwloc-prefix="
|
|
(assoc-ref %build-inputs "hwloc"))
|
|
|
|
,@(if (assoc "ucx" (package-inputs this-package))
|
|
`((string-append "--with-ucx="
|
|
(assoc-ref %build-inputs "ucx")))
|
|
'()))
|
|
|
|
#:phases (modify-phases %standard-phases
|
|
(add-after 'unpack 'patch-sources
|
|
(lambda _
|
|
(substitute* "./maint/gen_subcfg_m4"
|
|
(("/usr/bin/env") (which "env")))
|
|
(substitute* "src/glue/romio/all_romio_symbols"
|
|
(("/usr/bin/env") (which "env")))
|
|
(substitute* (find-files "." "buildiface")
|
|
(("/usr/bin/env") (which "env")))
|
|
(substitute* "maint/extracterrmsgs"
|
|
(("/usr/bin/env") (which "env")))
|
|
(substitute* (find-files "." "f77tof90")
|
|
(("/usr/bin/env") (which "env")))
|
|
(substitute* (find-files "." "\\.sh$")
|
|
(("/bin/sh") (which "sh")))
|
|
#t))
|
|
(add-before 'configure 'fix-makefile
|
|
(lambda _
|
|
;; Remove "@hwloclib@" from 'pmpi_convenience_libs'.
|
|
;; This fixes "No rule to make target '-lhwloc', needed
|
|
;; by 'lib/libmpi.la'".
|
|
(substitute* "Makefile.in"
|
|
(("^pmpi_convenience_libs = (.*) @hwloclib@ (.*)$" _
|
|
before after)
|
|
(string-append "pmpi_convenience_libs = "
|
|
before " " after)))
|
|
#t)))))
|
|
(home-page "https://www.mpich.org/")
|
|
(synopsis "Implementation of the Message Passing Interface (MPI)")
|
|
(description
|
|
"MPICH is a high-performance and portable implementation of the Message
|
|
Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3). MPICH provides an
|
|
MPI implementation that efficiently supports different computation and
|
|
communication platforms including commodity clusters, high-speed networks (10
|
|
Gigabit Ethernet, InfiniBand, Myrinet, Quadrics), and proprietary high-end
|
|
computing systems (Blue Gene, Cray). It enables research in MPI through a
|
|
modular framework for other derived implementations.")
|
|
(license license:bsd-2)))
|