c4d18b9e65
* gnu/packages/bioinformatics.scm (deeptools): Remove variable. * gnu/packages/efi.scm (efi_analyzer): Ditto. * gnu/packages/guile.scm (guile-2.2/bug-fix, guile-json): Ditto. * gnu/packages/image.scm (libjpeg): Ditto. * gnu/packages/kde.scm (kdevplatform): Ditto * gnu/packages/linphone.scm (linphoneqt): Ditto. * gnu/packages/maths.scm (blis-sandybridge, blis-haswell, blis-knl): Ditto. * gnu/packages/mpi.scm (hwloc-2.0): Ditto. * gnu/packages/music.scm (python-abjad, zlfo): Ditto. * gnu/packages/perl.scm (perl-base, perl-parent): Ditto. * gnu/packages/tryton.scm (python-trytond): Ditto. * gnu/packages/video.scm (gnome-mpv): Ditto. * tests/graph.scm: Use guile-json-1. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
537 lines
24 KiB
Scheme
537 lines
24 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 © 2014-2023 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, 2022 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2018–2022 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
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;;; Copyright © 2019, 2021 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 gexp)
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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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(package
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(name "hwloc")
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(version "1.11.13")
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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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"1j69p8a1pjpbpwn4w7l4dfxmaxxqikchjzqw1ncw05zmcmvlnjd4"))
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(patches (search-patches "hwloc-1-test-btrfs.patch"))))
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(properties
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;; Tell the 'generic-html' updater to monitor this URL for updates.
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`((release-monitoring-url
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. "https://www-lb.open-mpi.org/software/hwloc/current")))
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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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(append (list libx11 cairo ncurses expat)
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(if (target-arm32?) '() (list numactl))))
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(propagated-inputs
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;; hwloc.pc lists it in 'Requires.private'.
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(list libpciaccess))
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(native-inputs
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(list 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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(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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(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
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(string-append out "/share/man/man3"))))))))
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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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(package
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(inherit hwloc-1)
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(version "2.9.1")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://download.open-mpi.org/release/hwloc/v"
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(version-major+minor version)
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"/hwloc-" version ".tar.bz2"))
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(sha256
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(base32
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"17jr14a5ns5rpwvy28fy7xqagbvfprsz7wrsjgh5gx7y40d97i3w"))))
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;; libnuma is no longer needed.
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(inputs (modify-inputs (package-inputs hwloc-1)
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(delete "numactl")))
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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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(add-before 'check 'skip-tests-that-require-/sys
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(lambda _
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;; 'test-gather-topology.sh' requires /sys as of 2.9.0; skip it.
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(setenv "HWLOC_TEST_GATHER_TOPOLOGY" "0")))
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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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(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 "4.1.4")
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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 "03ckngrff1cl0l81vfvrfhp99rbgk7s0633kr1l468yibwbjx4cj"))
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(patches (search-patches "openmpi-mtl-priorities.patch"))))
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(properties
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;; Tell the 'generic-html' updater to monitor this URL for updates.
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`((release-monitoring-url
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. "https://www.open-mpi.org/software/ompi/current")))
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(build-system gnu-build-system)
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(inputs
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(let ((if-supported
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(lambda (package)
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(if (and (not (%current-target-system))
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(member (%current-system)
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(package-supported-systems package)))
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(list package)
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'()))))
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(append (list `(,hwloc-2 "lib")
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gfortran
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libfabric
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libevent
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opensm)
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(if-supported psm)
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(if-supported psm2)
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(if-supported ucx)
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(if-supported valgrind)
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(list rdma-core
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slurm)))) ;for PMI support (launching via "srun")
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(native-inputs
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(list pkg-config perl))
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(outputs '("out" "debug"))
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(arguments
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(list
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#:configure-flags #~`("--enable-mpi-ext=affinity" ;cr doesn't work
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"--with-sge"
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#$@(if (package? (this-package-input "valgrind"))
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#~("--enable-memchecker"
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"--with-valgrind")
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#~("--without-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 $prefix by default.
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"--enable-mpirun-prefix-by-default"
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;; InfiniBand support
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"--enable-openib-control-hdr-padding"
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"--enable-openib-dynamic-sl"
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"--enable-openib-udcm"
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"--enable-openib-rdmacm"
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"--enable-openib-rdmacm-ibaddr"
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;; Enable support for SLURM's Process Manager
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;; Interface (PMI).
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,(string-append "--with-pmi="
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#$(this-package-input "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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(search-input-directory inputs
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"/include/infiniband"))
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(setenv "CPLUS_INCLUDE_PATH"
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(search-input-directory inputs
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"/include/infiniband"))))
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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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(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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(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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(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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(define-public openmpi-c++
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(package/inherit openmpi
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(name "openmpi-c++")
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(outputs '("out"))
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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-cxx" #$flags))))
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(synopsis "C++ bindings for MPI")))
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;; TODO: javadoc files contain timestamps.
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(define-public java-openmpi
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(package/inherit openmpi
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(name "java-openmpi")
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(inputs
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`(("openmpi" ,openmpi)
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,@(package-inputs openmpi)))
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(native-inputs
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`(("jdk" ,openjdk11 "jdk")
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("zip" ,(@ (gnu packages compression) zip))
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,@(package-native-inputs openmpi)))
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(outputs '("out"))
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(arguments
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(cons*
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#:modules '((guix build gnu-build-system)
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((guix build ant-build-system) #:prefix ant:)
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(guix build utils))
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#:imported-modules `((guix build ant-build-system)
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,@%gnu-build-system-modules)
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(substitute-keyword-arguments (package-arguments openmpi)
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((#:configure-flags flags)
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#~(cons "--enable-mpi-java" #$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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(search-input-file inputs "/lib/libmpi.la")))))
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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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|
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(define-public openmpi-thread-multiple
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||
(package/inherit openmpi
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||
(name "openmpi-thread-multiple")
|
||
(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))))
|
||
(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
|
||
work correctly with all transports (such as @code{openib}), and the
|
||
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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|
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;;; Build phase to be used for packages that execute MPI code.
|
||
(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
|
||
;; be found in $PATH. Define this variable to placate Open MPI without
|
||
;; adding a dependency on OpenSSH (the agent isn't used anyway.)
|
||
(setenv "OMPI_MCA_plm_rsh_agent" (which "false"))
|
||
;; 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")
|
||
|
||
;; UCX sometimes outputs uninteresting warnings such as:
|
||
;;
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||
;; mpool.c:38 UCX WARN object 0x7ffff44fffc0 was not returned to mpool ucp_am_bufs
|
||
;;
|
||
;; These in turn leads to failures of test suites that capture and
|
||
;; compare stdout, such as that of 'hdf5-parallel-openmpi'. Thus, tell
|
||
;; UCX to not emit those warnings.
|
||
(setenv "UCX_LOG_LEVEL" "error")
|
||
|
||
;; Starting from 2.9.0, hwloc fails when /sys is unavailable:
|
||
;;
|
||
;; [hwloc/linux] failed to find sysfs cpu topology directory, aborting linux discovery.
|
||
;;
|
||
;; This in turn breaks Open MPI users. To work around it, define a fake
|
||
;; topology with 4 cores. That silently disables CPU binding, though
|
||
;; 'get_cpubind' will report there's no binding.
|
||
(setenv "HWLOC_SYNTHETIC" "4")
|
||
#t))
|
||
|
||
(define-public python-mpi4py
|
||
(package
|
||
(name "python-mpi4py")
|
||
(version "3.0.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "mpi4py" version))
|
||
(sha256
|
||
(base32 "07ssbhssv27rrjx1c5vd3vsr31vay5d8xcf4zh9yblcyidn72b81"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'mpi-setup
|
||
,%openmpi-setup)
|
||
(add-before 'check 'pre-check
|
||
(lambda _
|
||
;; Skip BaseTestSpawn class (causes error 'ompi_dpm_dyn_init()
|
||
;; failed --> Returned "Unreachable"' in chroot environment).
|
||
(substitute* "test/test_spawn.py"
|
||
(("unittest.skipMPI\\('openmpi\\(<3.0.0\\)'\\)")
|
||
"unittest.skipMPI('openmpi')"))
|
||
#t)))))
|
||
(inputs
|
||
(list openmpi))
|
||
(home-page "https://bitbucket.org/mpi4py/mpi4py/")
|
||
(synopsis "Python bindings for the Message Passing Interface standard")
|
||
(description "MPI for Python (mpi4py) provides bindings of the Message
|
||
Passing Interface (MPI) standard for the Python programming language, allowing
|
||
any Python program to exploit multiple processors.
|
||
|
||
mpi4py is constructed on top of the MPI-1/MPI-2 specification and provides an
|
||
object oriented interface which closely follows MPI-2 C++ bindings. It
|
||
supports point-to-point and collective communications of any picklable Python
|
||
object as well as optimized communications of Python objects (such as NumPy
|
||
arrays) that expose a buffer interface.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public mpich
|
||
(package
|
||
(name "mpich")
|
||
(version "3.3.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.mpich.org/static/downloads/"
|
||
version "/mpich-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1farz5zfx4cd0c3a0wb9pgfypzw0xxql1j1294z1sxslga1ziyjb"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(,zlib
|
||
(,hwloc-2 "lib")
|
||
,slurm
|
||
,@(if (and (not (%current-target-system))
|
||
(member (%current-system) (package-supported-systems ucx)))
|
||
(list ucx)
|
||
'())))
|
||
(native-inputs
|
||
(list perl which 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")))))
|
||
(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@ (.*)$" _
|
||
before after)
|
||
(string-append "pmpi_convenience_libs = "
|
||
before " " after)))))
|
||
(add-before 'configure 'define-gfortran-wrapper
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
;; 'configure' checks whether the Fortran compiler
|
||
;; allows argument type mismatch. Since gfortran >= 10
|
||
;; does not, provide a wrapper that passes
|
||
;; '-fallow-argument-mismatch' to get the desired
|
||
;; behavior.
|
||
(mkdir-p ".gfortran-wrapper/bin")
|
||
(call-with-output-file ".gfortran-wrapper/bin/gfortran"
|
||
(lambda (port)
|
||
(display (string-append "#!" (which "sh") "\n")
|
||
port)
|
||
(display
|
||
(string-append "exec \"" (which "gfortran")
|
||
"\" -fallow-argument-mismatch"
|
||
" \"$@\"\n")
|
||
port)
|
||
(chmod port #o755)))
|
||
|
||
(setenv "PATH"
|
||
(string-append (getcwd) "/"
|
||
".gfortran-wrapper/bin:"
|
||
(getenv "PATH"))))))))
|
||
(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)))
|