45af7b8923
* gnu/packages/parallel.scm (parallel): Update to 20230822. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
554 lines
23 KiB
Scheme
554 lines
23 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2013, 2014, 2020 Eric Bavier <bavier@posteo.net>
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;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
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;;; Copyright © 2015-2018, 2020-2023 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
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;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
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;;; Copyright © 2016, 2020, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
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;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
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;;; Copyright © 2018–2022 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
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;;; Copyright © 2019-2022 Ludovic Courtès <ludo@gnu.org>
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;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
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;;; Copyright © 2021 Stefan Reichör <stefan@xsteve.at>
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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 parallel)
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#:use-module (guix download)
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#:use-module (guix git-download)
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#:use-module (guix build-system cmake)
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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 ((guix licenses) #:prefix license:)
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#:use-module ((guix utils) #:select (target-64bit?))
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#:use-module (guix packages)
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#:use-module (guix utils)
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#:use-module (guix gexp)
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#:use-module (gnu packages)
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#:use-module (gnu packages admin)
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#:use-module (gnu packages autotools)
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#:use-module (gnu packages base)
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#:use-module (gnu packages bash)
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#:use-module (gnu packages check)
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#:use-module (gnu packages documentation)
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#:use-module (gnu packages flex)
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#:use-module (gnu packages freeipmi)
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#:use-module (gnu packages linux)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages mpi)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-science)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages readline)
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#:use-module (gnu packages tcl)
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#:use-module (gnu packages tls)
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#:use-module (gnu packages web))
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(define-public parallel
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(package
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(name "parallel")
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(version "20230822")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "mirror://gnu/parallel/parallel-"
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version ".tar.bz2"))
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(sha256
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(base32 "0ppwdgp9j7r0a5l5zb0mla70jq24wmy1n33b5naw44y1lfclanab"))
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(snippet
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'(begin
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(use-modules (guix build utils))
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;; Delete pre-generated manpages and documents.
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;; TODO: generate rst files.
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;; parallel_cheat_bw.pdf uses libreoffice to be generated.
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(rename-file "src/parallel_cheat_bw.pdf"
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"src/parallel_cheat_bw.pdf-keep")
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(for-each delete-file (find-files "src" "\\.(1|7|html|pdf)$"))
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(rename-file "src/parallel_cheat_bw.pdf-keep"
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"src/parallel_cheat_bw.pdf")))))
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(build-system gnu-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 'unpack 'patch-bin-sh
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(lambda _
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(for-each
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(lambda (file)
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(substitute* file
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;; Patch hard coded '/bin/sh' in the line ending in:
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;; $Global::shell = $ENV{'PARALLEL_SHELL'} ||
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;; parent_shell($$) || $ENV{'SHELL'} || "/bin/sh";
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(("/bin/sh\\\";\n$") (string-append (which "sh") "\";\n"))))
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(list "src/parallel" "src/sem"))))
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(add-before 'install 'add-install-to-path
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(lambda* (#:key outputs #:allow-other-keys)
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(setenv "PATH" (string-append (getenv "PATH") ":"
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(assoc-ref outputs "out") "/bin"))))
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(add-after 'install 'wrap-program
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out")))
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(wrap-program (string-append out "/bin/parallel")
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`("PATH" ":" prefix
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,(map (lambda (input)
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(string-append (assoc-ref inputs input) "/bin"))
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'("perl"
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"procps")))))))
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(add-after 'wrap-program 'post-install-test
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(lambda* (#:key outputs #:allow-other-keys)
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(invoke (string-append
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(assoc-ref outputs "out") "/bin/parallel")
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"echo"
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":::" "1" "2" "3"))))))
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(native-inputs
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(list perl pod2pdf))
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(inputs
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(list bash-minimal perl procps))
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(home-page "https://www.gnu.org/software/parallel/")
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(synopsis "Build and execute command lines in parallel")
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(description
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"GNU Parallel is a tool for executing shell jobs in parallel using one
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or more computers. Jobs can consist of single commands or of scripts
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and they are executed on lists of files, hosts, users or other items.")
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(license license:gpl3+)))
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(define-public xe
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(package
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(name "xe")
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(version "0.11")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/leahneukirchen/xe")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "04jr8f6jcijr0bsmn8ajm0aj35qh9my3xjsaq64h8lwg5bpyn29x"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f
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#:make-flags (list (string-append "CC=" ,(cc-for-target))
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(string-append "PREFIX=" %output))
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#:phases (modify-phases %standard-phases
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(delete 'configure))))
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(synopsis "Execute a command for every argument")
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(description
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"The xe utility constructs command lines from specified arguments,
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combining some of the best features of xargs(1) and apply(1). Parallel
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execution is also possible.")
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(home-page "https://github.com/leahneukirchen/xe")
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(license license:public-domain)))
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(define-public xjobs
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(package
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(name "xjobs")
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(version "20200726")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"http://www.maier-komor.de/xjobs/xjobs-"
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version ".tgz"))
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(sha256
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(base32
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"0ay6gn43pnm7r1jamwgpycl67bjg5n87ncl27jb01w2x6x70z0i3"))))
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(build-system gnu-build-system)
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(arguments `(#:tests? #f)) ;; No tests
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(native-inputs
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(list flex which))
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(home-page "https://www.maier-komor.de/xjobs.html")
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(properties `((release-monitoring-url . ,home-page)))
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(synopsis
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"Parallel execution of jobs with several useful options")
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(description
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"xjobs reads job descriptions line by line and executes them in
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parallel. It limits the number of parallel executing jobs and starts new jobs
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when jobs finish.")
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(license license:gpl2+)))
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(define-public slurm
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(package
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(name "slurm")
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(version "22.05.1")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"https://download.schedmd.com/slurm/slurm-"
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version ".tar.bz2"))
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(sha256
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(base32
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"0f3hhlki8g7slllsnyj1qikbsvr62i0hig85lcdcfnmsagzlhbyi"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; According to
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;; <https://lists.gnu.org/archive/html/guix-devel/2016-02/msg00534.html>
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;; there are non-free bits under contribs/, though it's not
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;; clear which ones. libpmi is clearly free (it used to be
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;; under src/api/) and so is pmi2 (lax non-copyleft
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;; license), so remove all of contribs/ except pmi and pmi2.
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(substitute* "configure.ac"
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(("^[[:space:]]+contribs/(.*)$" all directory)
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(if (string-prefix? "pmi" directory)
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all
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"")))
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(rename-file "contribs/pmi" "tmp-pmi")
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(rename-file "contribs/pmi2" "tmp-pmi2")
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(delete-file-recursively "contribs")
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(mkdir "contribs")
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(rename-file "tmp-pmi" "contribs/pmi")
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(rename-file "tmp-pmi2" "contribs/pmi2")))))
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;; FIXME: More optional inputs could be added,
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;; in particular mysql and gtk+.
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(inputs (list freeipmi
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`(,hwloc-2 "lib")
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json-c
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linux-pam
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munge
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numactl
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readline))
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(native-inputs
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(list autoconf expect perl pkg-config python-wrapper))
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(build-system gnu-build-system)
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(arguments
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(list #:configure-flags
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#~(list "--enable-pam" "--sysconfdir=/etc/slurm"
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"--disable-static"
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(string-append "--with-freeipmi=" #$(this-package-input "freeipmi"))
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(string-append "--with-hwloc="
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(ungexp (this-package-input "hwloc") "lib"))
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(string-append "--with-json=" #$(this-package-input "json-c"))
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(string-append "--with-munge=" #$(this-package-input "munge"))
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;; 32-bit support is marked as deprecated and needs to be
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;; explicitly enabled.
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#$@(if (target-64bit?) '() '("--enable-deprecated")))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'patch-plugin-linker-flags
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(lambda _
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(substitute* (find-files "src/plugins/" "Makefile.in")
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(("_la_LDFLAGS = ")
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"_la_LDFLAGS = ../../../api/libslurm.la "))))
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(add-after 'patch-plugin-linker-flags 'autoconf
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(lambda _ (invoke "autoconf"))) ;configure.ac was patched
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(add-after 'install 'install-libpmi
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(lambda _
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;; Open MPI expects libpmi to be provided by Slurm so install it.
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(invoke "make" "install" "-C" "contribs/pmi")
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;; Others expect pmi2.
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(invoke "make" "install" "-C" "contribs/pmi2"))))))
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(home-page "https://slurm.schedmd.com/")
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(synopsis "Workload manager for cluster computing")
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(description
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"SLURM is a fault-tolerant and highly scalable cluster management and job
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scheduling system for large and small clusters. It allocates access to
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resources (computer nodes) to users for some duration of time, provides a
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framework for starting, executing, and monitoring work (typically a parallel
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job) on a set of allocated nodes, and arbitrates contention for resources
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by managing a queue of pending work.")
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(license (list license:bsd-2 ; src/common/log.[ch], src/common/uthash
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license:expat ; slurm/pmi.h
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license:isc ; src/common/strlcpy.c
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license:lgpl2.1+ ; hilbert.[ch], src/common/slurm_time.h
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license:zlib ; src/common/strnatcmp.c
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(license:non-copyleft ;contribs/pmi2, Argonne Natl. Lab.
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"https://github.com/SchedMD/slurm/blob/master/contribs/pmi2/COPYRIGHT")
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license:gpl2+)))) ; the rest, often with OpenSSL exception
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;; The SLURM client/daemon protocol and file format changes from time to time
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;; in incompatible ways, as noted in
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;; <https://slurm.schedmd.com/troubleshoot.html#network>. Thus, keep older
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;; releases here. See also <https://issues.guix.gnu.org/44387>.
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;; As noted in the link, YY.MM is the release scheme, and the 'maintenance'
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;; digit does not introduce incompatibilities.
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(define-public slurm-21.08
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(package
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(inherit slurm)
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(version "21.08.8")
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(source (origin
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(inherit (package-source slurm))
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(method url-fetch)
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(uri (string-append
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"https://download.schedmd.com/slurm/slurm-"
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version ".tar.bz2"))
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(sha256
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(base32
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"1sjln54idc9rhg8f2nvm38sgs6fncncyzslas8ixy65pqz2hphbf"))))))
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(define-public slurm-20.11
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(package
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(inherit slurm)
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(version "20.11.9")
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(source (origin
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(inherit (package-source slurm))
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(method url-fetch)
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(uri (string-append
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"https://download.schedmd.com/slurm/slurm-"
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version ".tar.bz2"))
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(sha256
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(base32
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"0xq2d6dm285y541dyg1h66z7svsisrq8c81ag0f601xz1cn3mq9m"))))))
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(define-public slurm-20.02
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(package
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(inherit slurm)
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(version "20.02.6-1")
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(source (origin
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(inherit (package-source slurm))
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(method url-fetch)
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(uri (string-append
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"https://download.schedmd.com/slurm/slurm-"
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version ".tar.bz2"))
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(sha256
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(base32
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"0qj4blfymrd2ry2qmb58l3jbr4jwygc3adcfw7my27rippcijlyc"))))
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(arguments
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(substitute-keyword-arguments (package-arguments slurm)
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((#:configure-flags flags ''())
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#~(append '("CFLAGS=-O2 -g -fcommon" "LDFLAGS=-fcommon")
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#$flags))))))
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(define-public slurm-19.05
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(package
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(inherit slurm-20.02)
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(version "19.05.8")
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(source (origin
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(inherit (package-source slurm))
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(method url-fetch)
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(uri (string-append
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"https://download.schedmd.com/slurm/slurm-"
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version ".tar.bz2"))
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(sha256
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(base32
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"10c9j4a9a6d4ibpf75006mn03p8xgpaprc247x2idakysjf2fw43"))))))
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;; Same as Debian 10
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(define-public slurm-18.08
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(package
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(inherit slurm-20.02)
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(version "18.08.9")
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(source
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(origin
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(inherit (package-source slurm))
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(uri (string-append
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"https://download.schedmd.com/slurm/slurm-"
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version ".tar.bz2"))
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(sha256
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(base32
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"1bgrpz75m7l4xhirsd0fvnkzlkrl8v2qpmjcz60barc5qm2kn457"))))))
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(define-public slurm-drmaa
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(package
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(name "slurm-drmaa")
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(version "1.1.3")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"https://github.com/natefoo/slurm-drmaa/releases/download/"
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version "/slurm-drmaa-" version ".tar.gz"))
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(sha256
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(base32
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"1fn3p4wjj0sgvx0isy3hiwi35vhxa2n2ksq5cn9sq2hg7yyb2phl"))))
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(build-system gnu-build-system)
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(arguments `(#:tests? #f)) ; The tests require "bats".
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(inputs
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||
(list slurm))
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||
(native-inputs
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||
(list which))
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||
(home-page "https://github.com/natefoo/slurm-drmaa")
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||
(synopsis "Distributed resource management application API for SLURM")
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||
(description
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||
"PSNC DRMAA for Simple Linux Utility for Resource Management (SLURM) is
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an implementation of Open Grid Forum DRMAA 1.0 (Distributed Resource
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Management Application API) specification for submission and control of jobs
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to SLURM. Using DRMAA, grid applications builders, portal developers and ISVs
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can use the same high-level API to link their software with different
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cluster/resource management systems.")
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(license license:gpl3+)))
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(define-public python-slurm-magic
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(let ((commit "73dd1a2b85799f7dae4b3f1cd9027536eff0c4d7")
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(revision "0"))
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||
(package
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||
(name "python-slurm-magic")
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||
(version (git-version "0.0" revision commit))
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||
(home-page "https://github.com/NERSC/slurm-magic")
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||
(source (origin
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||
(method git-fetch)
|
||
(uri (git-reference (url home-page)
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||
(commit commit)))
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||
(sha256
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||
(base32
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||
"19pp2vs0wm8mx0arz9n6lw9wgyv70w9wyi4y6b91qc5j3bz5igfs"))
|
||
(file-name (git-file-name name version))))
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(build-system python-build-system)
|
||
(arguments
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||
'(#:phases (modify-phases %standard-phases
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||
(add-before 'build 'set-slurm-path
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||
(lambda* (#:key inputs #:allow-other-keys)
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;; The '_execute' method tries to exec 'salloc'
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;; etc. from $PATH. Record the absolute file name
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;; instead.
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(let ((slurm (assoc-ref inputs "slurm")))
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(substitute* "slurm_magic.py"
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||
(("name = (.*)$" _ value)
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(string-append "name = \""
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slurm "/bin/\" + "
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value "\n")))
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#t))))))
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(inputs
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||
(list slurm))
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(propagated-inputs
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(list python-ipython python-pandas))
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(synopsis "Control the SLURM batch scheduler from Jupyter Notebook")
|
||
(description
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||
"This package implements Jupyter/IPython
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@uref{http://ipython.readthedocs.io/en/stable/interactive/magics.html, magic
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commands} for interacting with the SLURM workload manager. SLURM magic simply
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wraps command-line executables and the commands themselves should look like
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their command-line counterparts. Commands are spawned via @code{subprocess}
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and output captured in the notebook. Whatever arguments are accepted by a
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SLURM command line executable are also accepted by the corresponding magic
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command---e.g., @code{%salloc}, @code{%sbatch}, etc.")
|
||
(license license:bsd-3))))
|
||
|
||
(define-public pthreadpool
|
||
;; This repository has only one tag, 0.1, which is older than what users
|
||
;; such as XNNPACK expect.
|
||
(let ((commit "1787867f6183f056420e532eec640cba25efafea")
|
||
(version "0.1")
|
||
(revision "1"))
|
||
(package
|
||
(name "pthreadpool")
|
||
(version (git-version version revision commit))
|
||
(home-page "https://github.com/Maratyszcza/pthreadpool")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url home-page) (commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"02hdvxfn5krw8zivkgjx3b4rk9p02yr4mpdjlp75lsv6z1xf5yrx"))
|
||
(patches (search-patches "pthreadpool-system-libraries.patch"))))
|
||
(build-system cmake-build-system)
|
||
(arguments '(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")))
|
||
(inputs
|
||
(list googletest googlebenchmark fxdiv))
|
||
(synopsis "Efficient thread pool implementation")
|
||
(description
|
||
"The pthreadpool library implements an efficient and portable thread
|
||
pool, similar to those implemented by OpenMP run-time support libraries for
|
||
constructs such as @code{#pragma omp parallel for}, with additional
|
||
features.")
|
||
(license license:bsd-2))))
|
||
|
||
(define-public cpuinfo
|
||
;; There's currently no tag on this repo.
|
||
(let ((version "0.0")
|
||
(revision "2")
|
||
(commit "53298db833c5c5a1598639e9b47cc1a602bbac26"))
|
||
(package
|
||
(name "cpuinfo")
|
||
(version (git-version version revision commit))
|
||
(home-page "https://github.com/pytorch/cpuinfo")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url home-page) (commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"01kfgxya2w32dz9bd3qm3i2d6nffw0qfyql11rxl7d3g830brj5k"))
|
||
(patches (search-patches "cpuinfo-system-libraries.patch"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
(list
|
||
#:configure-flags '(list "-DBUILD_SHARED_LIBS=ON")
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-after 'unpack 'skip-bad-test
|
||
(lambda _
|
||
(substitute* "test/init.cc"
|
||
(("TEST\\(CORE, known_uarch\\) \\{" m)
|
||
(string-append m "\
|
||
GTEST_SKIP() << \"See https://github.com/pytorch/cpuinfo/issues/132\";"))))))))
|
||
(inputs
|
||
(list googletest googlebenchmark))
|
||
(synopsis "C/C++ library to obtain information about the CPU")
|
||
(description
|
||
"The cpuinfo library provides a C/C++ and a command-line interface to
|
||
obtain information about the CPU being used: supported instruction set,
|
||
processor name, cache information, and topology information.")
|
||
(license license:bsd-2))))
|
||
|
||
(define-public clog
|
||
(package
|
||
(inherit cpuinfo) ;distributed with cpuinfo but not built by it
|
||
(name "clog")
|
||
(source (origin
|
||
(inherit (package-source cpuinfo))
|
||
(patches (search-patches "clog-fix-shared-build.patch"))))
|
||
(arguments
|
||
(list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")
|
||
#:phases #~(modify-phases %standard-phases
|
||
(add-after 'unpack 'chdir
|
||
(lambda _
|
||
(chdir "deps/clog"))))))
|
||
(native-inputs (list googletest))
|
||
(inputs '())
|
||
(synopsis "C-style logging library based on printf")
|
||
(description
|
||
"This package provides a C-style library for logging errors,
|
||
warnings, information notes, and debug information. Its features are:
|
||
@itemize
|
||
@item printf-style interface for formatting variadic parameters.
|
||
@item Separate functions for logging errors, warnings, information notes, and
|
||
debug information.
|
||
@item Independent logging settings for different modules.
|
||
@item Logging to logcat on Android and stderr/stdout on other platforms.
|
||
@item Compatible with C99 and C++.
|
||
@item Covered with unit tests.
|
||
@end itemize")))
|
||
|
||
(define-public psimd
|
||
;; There is currently no tag in this repo.
|
||
(let ((commit "072586a71b55b7f8c584153d223e95687148a900")
|
||
(version "0.0")
|
||
(revision "1"))
|
||
(package
|
||
(name "psimd")
|
||
(version (git-version version revision commit))
|
||
(home-page "https://github.com/Maratyszcza/Psimd")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url home-page) (commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"16mslhvqs0gpqbg7kkq566a8gkn58cgjpqca8ljj9qcv5mk9apwm"))))
|
||
(build-system cmake-build-system)
|
||
(arguments '(#:tests? #f)) ;there are no tests
|
||
(synopsis "Portable 128-bit SIMD intrinsics")
|
||
(description
|
||
"This header-only C++ library provides a portable interface to
|
||
single-instruction multiple-data (SIMD) intrinsics.")
|
||
(license license:expat))))
|