gnu/packages/parallel.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2013, 2014, 2020 Eric Bavier <bavier@posteo.net>
   3 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
   4 ;;; Copyright © 2015, 2016, 2017, 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
   5 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
   6 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
   7 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
   8 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
   9 ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
  10 ;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
  11 ;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
  12 ;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
  13 ;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
  14 ;;;
  15 ;;; This file is part of GNU Guix.
  16 ;;;
  17 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  18 ;;; under the terms of the GNU General Public License as published by
  19 ;;; the Free Software Foundation; either version 3 of the License, or (at
  20 ;;; your option) any later version.
  21 ;;;
  22 ;;; GNU Guix is distributed in the hope that it will be useful, but
  23 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  24 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  25 ;;; GNU General Public License for more details.
  26 ;;;
  27 ;;; You should have received a copy of the GNU General Public License
  28 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  29
  30 (define-module (gnu packages parallel)
  31   #:use-module (guix download)
  32   #:use-module (guix git-download)
  33   #:use-module (guix build-system gnu)
  34   #:use-module (guix build-system python)
  35   #:use-module ((guix licenses) #:prefix license:)
  36   #:use-module ((guix utils) #:select (target-64bit?))
  37   #:use-module (guix packages)
  38   #:use-module (gnu packages)
  39   #:use-module (gnu packages admin)
  40   #:use-module (gnu packages autotools)
  41   #:use-module (gnu packages base)
  42   #:use-module (gnu packages freeipmi)
  43   #:use-module (gnu packages linux)
  44   #:use-module (gnu packages mpi)
  45   #:use-module (gnu packages perl)
  46   #:use-module (gnu packages pkg-config)
  47   #:use-module (gnu packages python)
  48   #:use-module (gnu packages python-science)
  49   #:use-module (gnu packages python-xyz)
  50   #:use-module (gnu packages readline)
  51   #:use-module (gnu packages tcl)
  52   #:use-module (gnu packages tls)
  53   #:use-module (gnu packages web))
  54
  55 (define-public parallel
  56   (package
  57     (name "parallel")
  58     (version "20200822")
  59     (source
  60      (origin
  61       (method url-fetch)
  62       (uri (string-append "mirror://gnu/parallel/parallel-"
  63                           version ".tar.bz2"))
  64       (sha256
  65        (base32 "02dy46g6f05p7s2qs8h6yg20p1zl3flxxf77n5jw74l3h1m24m4n"))))
  66     (build-system gnu-build-system)
  67     (arguments
  68      `(#:phases
  69        (modify-phases %standard-phases
  70          (add-after 'unpack 'patch-bin-sh
  71            (lambda _
  72              (for-each
  73               (lambda (file)
  74                 (substitute* file
  75                   ;; Patch hard coded '/bin/sh' in the line ending in:
  76                   ;; $Global::shell = $ENV{'PARALLEL_SHELL'} ||
  77                   ;;  parent_shell($$) || $ENV{'SHELL'} || "/bin/sh";
  78                   (("/bin/sh\\\";\n$") (string-append (which "sh") "\";\n"))))
  79               (list "src/parallel" "src/sem"))
  80              #t))
  81          (add-after 'install 'wrap-program
  82            (lambda* (#:key inputs outputs #:allow-other-keys)
  83              (let ((out (assoc-ref outputs "out")))
  84                (wrap-program (string-append out "/bin/parallel")
  85                  `("PATH" ":" prefix
  86                    ,(map (lambda (input)
  87                            (string-append (assoc-ref inputs input) "/bin"))
  88                          '("perl"
  89                            "procps"))))
  90                #t)))
  91          (add-after 'wrap-program 'post-install-test
  92            (lambda* (#:key outputs #:allow-other-keys)
  93              (invoke (string-append
  94                       (assoc-ref outputs "out") "/bin/parallel")
  95                      "echo"
  96                      ":::" "1" "2" "3"))))))
  97     (inputs
  98      `(("perl" ,perl)
  99        ("procps" ,procps)))
 100     (home-page "https://www.gnu.org/software/parallel/")
 101     (synopsis "Build and execute command lines in parallel")
 102     (description
 103      "GNU Parallel is a tool for executing shell jobs in parallel using one
 104 or more computers.  Jobs can consist of single commands or of scripts
 105 and they are executed on lists of files, hosts, users or other items.")
 106     (license license:gpl3+)))
 107
 108 (define-public slurm
 109   (package
 110    (name "slurm")
 111    (version "19.05.3-2")
 112    (source (origin
 113             (method url-fetch)
 114             (uri (string-append
 115                   "https://download.schedmd.com/slurm/slurm-"
 116                   version ".tar.bz2"))
 117             (sha256
 118              (base32
 119               "0qj4blfymrd2ry2qmb58l3jbr4jwygc3adcfw7my27rippcijlyc"))
 120             (modules '((guix build utils)))
 121             (snippet
 122              '(begin
 123                 ;; According to
 124                 ;; <https://lists.gnu.org/archive/html/guix-devel/2016-02/msg00534.html>
 125                 ;; there are non-free bits under contribs/, though it's not
 126                 ;; clear which ones.  libpmi is clearly free (it used to be
 127                 ;; under src/api/), so remove all of contribs/ except
 128                 ;; contribs/pmi/.
 129                 (substitute* "configure.ac"
 130                   (("^[[:space:]]+contribs/(.*)$" all directory)
 131                    (if (and (string-prefix? "pmi" directory)
 132                             (not (string-prefix? "pmi2" directory)))
 133                        all
 134                        "")))
 135
 136                 (rename-file "contribs/pmi" "tmp-pmi")
 137                 (delete-file-recursively "contribs")
 138                 (mkdir "contribs")
 139                 (rename-file "tmp-pmi" "contribs/pmi")
 140                 #t))))
 141    ;; FIXME: More optional inputs could be added,
 142    ;; in particular mysql and gtk+.
 143    (inputs `(("expect" ,expect)
 144              ("freeipmi" ,freeipmi)
 145              ("hwloc" ,hwloc-2 "lib")
 146              ("json-c" ,json-c)
 147              ("linux-pam" , linux-pam)
 148              ("munge" ,munge)
 149              ("numactl" ,numactl)
 150              ("perl" ,perl)
 151              ("python" ,python-wrapper)
 152              ("readline" ,readline)))
 153    (native-inputs
 154     `(("autoconf" ,autoconf)
 155       ("pkg-config" ,pkg-config)))
 156    (build-system gnu-build-system)
 157    (arguments
 158     `(#:configure-flags
 159       (list "--enable-pam" "--sysconfdir=/etc/slurm"
 160             "--disable-static"
 161             (string-append "--with-freeipmi=" (assoc-ref %build-inputs "freeipmi"))
 162             (string-append "--with-hwloc=" (assoc-ref %build-inputs "hwloc"))
 163             (string-append "--with-json=" (assoc-ref %build-inputs "json-c"))
 164             (string-append "--with-munge=" (assoc-ref %build-inputs "munge"))
 165
 166             ;; 32-bit support is marked as deprecated and needs to be
 167             ;; explicitly enabled.
 168             ,@(if (target-64bit?) '() '("--enable-deprecated")))
 169       #:phases
 170       (modify-phases %standard-phases
 171         (add-after 'unpack 'autoconf
 172           (lambda _ (invoke "autoconf")))         ;configure.ac was patched
 173         (add-after 'install 'install-libpmi
 174           (lambda _
 175             ;; Open MPI expects libpmi to be provided by Slurm so install it.
 176             (invoke "make" "install" "-C" "contribs/pmi"))))))
 177    (home-page "https://slurm.schedmd.com/")
 178    (synopsis "Workload manager for cluster computing")
 179    (description
 180     "SLURM is a fault-tolerant and highly scalable cluster management and job
 181 scheduling system for large and small clusters.  It allocates access to
 182 resources (computer nodes) to users for some duration of time, provides a
 183 framework for starting, executing, and monitoring work (typically a parallel
 184 job) on a set of allocated nodes, and arbitrates contention for resources
 185 by managing a queue of pending work.")
 186    (license (list license:bsd-2       ; src/common/log.[ch], src/common/uthash
 187                   license:expat       ; slurm/pmi.h
 188                   license:isc         ; src/common/strlcpy.c
 189                   license:lgpl2.1+    ; hilbert.[ch], src/common/slurm_time.h
 190                   license:zlib        ; src/common/strnatcmp.c
 191                   license:gpl2+))))   ; the rest, often with OpenSSL exception
 192
 193 (define-public slurm-drmaa
 194   (package
 195     (name "slurm-drmaa")
 196     (version "1.1.1")
 197     (source (origin
 198               (method url-fetch)
 199               (uri (string-append
 200                     "https://github.com/natefoo/slurm-drmaa/releases/download/"
 201                     version "/slurm-drmaa-" version ".tar.gz"))
 202               (sha256
 203                (base32
 204                 "19r4cm88pcpm3wli4cc61zq7354pg67cg866f3a430p15hm1knrn"))))
 205     (build-system gnu-build-system)
 206     (arguments `(#:tests? #f)) ; The tests require "bats".
 207     (inputs
 208      `(("slurm" ,slurm)))
 209     (native-inputs
 210      `(("which" ,which)))
 211     (home-page "https://github.com/natefoo/slurm-drmaa")
 212     (synopsis "Distributed resource management application API for SLURM")
 213     (description
 214      "PSNC DRMAA for Simple Linux Utility for Resource Management (SLURM) is
 215 an implementation of Open Grid Forum DRMAA 1.0 (Distributed Resource
 216 Management Application API) specification for submission and control of jobs
 217 to SLURM.  Using DRMAA, grid applications builders, portal developers and ISVs
 218 can use the same high-level API to link their software with different
 219 cluster/resource management systems.")
 220     (license license:gpl3+)))
 221
 222 (define-public python-slurm-magic
 223   (let ((commit "73dd1a2b85799f7dae4b3f1cd9027536eff0c4d7")
 224         (revision "0"))
 225     (package
 226       (name "python-slurm-magic")
 227       (version (git-version "0.0" revision commit))
 228       (home-page "https://github.com/NERSC/slurm-magic")
 229       (source (origin
 230                 (method git-fetch)
 231                 (uri (git-reference (url home-page)
 232                                     (commit commit)))
 233                 (sha256
 234                  (base32
 235                   "19pp2vs0wm8mx0arz9n6lw9wgyv70w9wyi4y6b91qc5j3bz5igfs"))
 236                 (file-name (git-file-name name version))))
 237       (build-system python-build-system)
 238       (arguments
 239        '(#:phases (modify-phases %standard-phases
 240                     (add-before 'build 'set-slurm-path
 241                       (lambda* (#:key inputs #:allow-other-keys)
 242                         ;; The '_execute' method tries to exec 'salloc'
 243                         ;; etc. from $PATH.  Record the absolute file name
 244                         ;; instead.
 245                         (let ((slurm (assoc-ref inputs "slurm")))
 246                           (substitute* "slurm_magic.py"
 247                             (("name = (.*)$" _ value)
 248                              (string-append "name = \""
 249                                             slurm "/bin/\" + "
 250                                             value "\n")))
 251                           #t))))))
 252       (inputs
 253        `(("slurm" ,slurm)))
 254       (propagated-inputs
 255        `(("python-ipython" ,python-ipython)
 256          ("python-pandas" ,python-pandas)))
 257       (synopsis "Control the SLURM batch scheduler from Jupyter Notebook")
 258       (description
 259        "This package implements Jupyter/IPython
 260 @uref{http://ipython.readthedocs.io/en/stable/interactive/magics.html, magic
 261 commands} for interacting with the SLURM workload manager.  SLURM magic simply
 262 wraps command-line executables and the commands themselves should look like
 263 their command-line counterparts.  Commands are spawned via @code{subprocess}
 264 and output captured in the notebook.  Whatever arguments are accepted by a
 265 SLURM command line executable are also accepted by the corresponding magic
 266 command---e.g., @code{%salloc}, @code{%sbatch}, etc.")
 267       (license license:bsd-3))))