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, 2021 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, 2020 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, 2020 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 "20201222")
  59     (source
  60      (origin
  61       (method url-fetch)
  62       (uri (string-append "mirror://gnu/parallel/parallel-"
  63                           version ".tar.bz2"))
  64       (sha256
  65        (base32 "13kxg2vmy20ciiv1gp96g33bmvma1nh5d66jdix1fqj6xjaizr5n"))))
  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 "20.11.2")
 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               "15h2vs58apgdz02ijgr46090vjyaa81qcm76mm6fxlvkkfd4pyxp"))
 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 `(("freeipmi" ,freeipmi)
 144              ("hwloc" ,hwloc-2 "lib")
 145              ("json-c" ,json-c)
 146              ("linux-pam" , linux-pam)
 147              ("munge" ,munge)
 148              ("numactl" ,numactl)
 149              ("readline" ,readline)))
 150    (native-inputs
 151     `(("autoconf" ,autoconf)
 152       ("expect" ,expect)
 153       ("perl" ,perl)
 154       ("pkg-config" ,pkg-config)
 155       ("python" ,python-wrapper)))
 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 ;; The SLURM client/daemon protocol and file format changes from time to time
 194 ;; in incompatible ways, as noted in
 195 ;; <https://slurm.schedmd.com/troubleshoot.html#network>.  Thus, keep older
 196 ;; releases here.  See also <https://issues.guix.gnu.org/44387>.
 197
 198 (define-public slurm-20.02
 199   (package
 200     (inherit slurm)
 201     (version "20.02.6-1")
 202     (source (origin
 203               (inherit (package-source slurm))
 204               (method url-fetch)
 205               (uri (string-append
 206                     "https://download.schedmd.com/slurm/slurm-"
 207                     version ".tar.bz2"))
 208               (sha256
 209                (base32
 210                 "0qj4blfymrd2ry2qmb58l3jbr4jwygc3adcfw7my27rippcijlyc"))))))
 211
 212
 213 (define-public slurm-19.05
 214   (package
 215     (inherit slurm)
 216     (version "19.05.3-2")
 217     (source (origin
 218               (inherit (package-source slurm))
 219               (method url-fetch)
 220               (uri (string-append
 221                     "https://download.schedmd.com/slurm/slurm-"
 222                     version ".tar.bz2"))
 223               (sha256
 224                (base32
 225                 "0qj4blfymrd2ry2qmb58l3jbr4jwygc3adcfw7my27rippcijlyc"))))))
 226
 227 ;; Same as Debian 10
 228 (define-public slurm-18.08
 229   (package
 230     (inherit slurm)
 231     (version "18.08.5-2")
 232     (source
 233       (origin
 234         (inherit (package-source slurm))
 235         (uri (string-append
 236                "https://download.schedmd.com/slurm/slurm-"
 237                version ".tar.bz2"))
 238         (sha256
 239          (base32
 240           "0xrj12nmkhvhzi7cyh4yvdm8qa51ji3j82mgpq7sx87g30f9spn4"))))))
 241
 242 (define-public slurm-drmaa
 243   (package
 244     (name "slurm-drmaa")
 245     (version "1.1.1")
 246     (source (origin
 247               (method url-fetch)
 248               (uri (string-append
 249                     "https://github.com/natefoo/slurm-drmaa/releases/download/"
 250                     version "/slurm-drmaa-" version ".tar.gz"))
 251               (sha256
 252                (base32
 253                 "19r4cm88pcpm3wli4cc61zq7354pg67cg866f3a430p15hm1knrn"))))
 254     (build-system gnu-build-system)
 255     (arguments `(#:tests? #f)) ; The tests require "bats".
 256     (inputs
 257      `(("slurm" ,slurm)))
 258     (native-inputs
 259      `(("which" ,which)))
 260     (home-page "https://github.com/natefoo/slurm-drmaa")
 261     (synopsis "Distributed resource management application API for SLURM")
 262     (description
 263      "PSNC DRMAA for Simple Linux Utility for Resource Management (SLURM) is
 264 an implementation of Open Grid Forum DRMAA 1.0 (Distributed Resource
 265 Management Application API) specification for submission and control of jobs
 266 to SLURM.  Using DRMAA, grid applications builders, portal developers and ISVs
 267 can use the same high-level API to link their software with different
 268 cluster/resource management systems.")
 269     (license license:gpl3+)))
 270
 271 (define-public python-slurm-magic
 272   (let ((commit "73dd1a2b85799f7dae4b3f1cd9027536eff0c4d7")
 273         (revision "0"))
 274     (package
 275       (name "python-slurm-magic")
 276       (version (git-version "0.0" revision commit))
 277       (home-page "https://github.com/NERSC/slurm-magic")
 278       (source (origin
 279                 (method git-fetch)
 280                 (uri (git-reference (url home-page)
 281                                     (commit commit)))
 282                 (sha256
 283                  (base32
 284                   "19pp2vs0wm8mx0arz9n6lw9wgyv70w9wyi4y6b91qc5j3bz5igfs"))
 285                 (file-name (git-file-name name version))))
 286       (build-system python-build-system)
 287       (arguments
 288        '(#:phases (modify-phases %standard-phases
 289                     (add-before 'build 'set-slurm-path
 290                       (lambda* (#:key inputs #:allow-other-keys)
 291                         ;; The '_execute' method tries to exec 'salloc'
 292                         ;; etc. from $PATH.  Record the absolute file name
 293                         ;; instead.
 294                         (let ((slurm (assoc-ref inputs "slurm")))
 295                           (substitute* "slurm_magic.py"
 296                             (("name = (.*)$" _ value)
 297                              (string-append "name = \""
 298                                             slurm "/bin/\" + "
 299                                             value "\n")))
 300                           #t))))))
 301       (inputs
 302        `(("slurm" ,slurm)))
 303       (propagated-inputs
 304        `(("python-ipython" ,python-ipython)
 305          ("python-pandas" ,python-pandas)))
 306       (synopsis "Control the SLURM batch scheduler from Jupyter Notebook")
 307       (description
 308        "This package implements Jupyter/IPython
 309 @uref{http://ipython.readthedocs.io/en/stable/interactive/magics.html, magic
 310 commands} for interacting with the SLURM workload manager.  SLURM magic simply
 311 wraps command-line executables and the commands themselves should look like
 312 their command-line counterparts.  Commands are spawned via @code{subprocess}
 313 and output captured in the notebook.  Whatever arguments are accepted by a
 314 SLURM command line executable are also accepted by the corresponding magic
 315 command---e.g., @code{%salloc}, @code{%sbatch}, etc.")
 316       (license license:bsd-3))))