gnu/packages/parallel.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2013, 2014 Eric Bavier <bavier@member.fsf.org>
   3 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
   4 ;;; Copyright © 2015, 2016, 2017, 2018 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 Tobias Geerinckx-Rice <me@tobias.gr>
  11 ;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
  12 ;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
  13 ;;;
  14 ;;; This file is part of GNU Guix.
  15 ;;;
  16 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  17 ;;; under the terms of the GNU General Public License as published by
  18 ;;; the Free Software Foundation; either version 3 of the License, or (at
  19 ;;; your option) any later version.
  20 ;;;
  21 ;;; GNU Guix is distributed in the hope that it will be useful, but
  22 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  23 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  24 ;;; GNU General Public License for more details.
  25 ;;;
  26 ;;; You should have received a copy of the GNU General Public License
  27 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  28
  29 (define-module (gnu packages parallel)
  30   #:use-module (guix download)
  31   #:use-module (guix git-download)
  32   #:use-module (guix build-system gnu)
  33   #:use-module (guix build-system python)
  34   #:use-module ((guix licenses) #:prefix license:)
  35   #:use-module (guix packages)
  36   #:use-module (gnu packages)
  37   #:use-module (gnu packages admin)
  38   #:use-module (gnu packages autotools)
  39   #:use-module (gnu packages base)
  40   #:use-module (gnu packages freeipmi)
  41   #:use-module (gnu packages linux)
  42   #:use-module (gnu packages mpi)
  43   #:use-module (gnu packages perl)
  44   #:use-module (gnu packages pkg-config)
  45   #:use-module (gnu packages python)
  46   #:use-module (gnu packages python-xyz)
  47   #:use-module (gnu packages readline)
  48   #:use-module (gnu packages tcl)
  49   #:use-module (gnu packages tls)
  50   #:use-module (gnu packages web))
  51
  52 (define-public parallel
  53   (package
  54     (name "parallel")
  55     (version "20191022")
  56     (source
  57      (origin
  58       (method url-fetch)
  59       (uri (string-append "mirror://gnu/parallel/parallel-"
  60                           version ".tar.bz2"))
  61       (sha256
  62        (base32 "1a89x5ix9kls1abj8zkgxdf3g3s5phzb83xcd4cwpz4szfjfw6v4"))))
  63     (build-system gnu-build-system)
  64     (arguments
  65      `(#:phases
  66        (modify-phases %standard-phases
  67          (add-after 'unpack 'patch-bin-sh
  68            (lambda _
  69              (for-each
  70               (lambda (file)
  71                 (substitute* file
  72                   ;; Patch hard coded '/bin/sh' in the line ending in:
  73                   ;; $Global::shell = $ENV{'PARALLEL_SHELL'} ||
  74                   ;;  parent_shell($$) || $ENV{'SHELL'} || "/bin/sh";
  75                   (("/bin/sh\\\";\n$") (string-append (which "sh") "\";\n"))))
  76               (list "src/parallel" "src/sem"))
  77              #t))
  78          (add-after 'install 'wrap-program
  79            (lambda* (#:key inputs outputs #:allow-other-keys)
  80              (let ((out (assoc-ref outputs "out")))
  81                (wrap-program (string-append out "/bin/parallel")
  82                  `("PATH" ":" prefix
  83                    ,(map (lambda (input)
  84                            (string-append (assoc-ref inputs input) "/bin"))
  85                          '("perl"
  86                            "procps"))))
  87                #t)))
  88          (add-after 'wrap-program 'post-install-test
  89            (lambda* (#:key outputs #:allow-other-keys)
  90              (invoke (string-append
  91                       (assoc-ref outputs "out") "/bin/parallel")
  92                      "echo"
  93                      ":::" "1" "2" "3"))))))
  94     (inputs
  95      `(("perl" ,perl)
  96        ("procps" ,procps)))
  97     (home-page "https://www.gnu.org/software/parallel/")
  98     (synopsis "Build and execute command lines in parallel")
  99     (description
 100      "GNU Parallel is a tool for executing shell jobs in parallel using one
 101 or more computers.  Jobs can consist of single commands or of scripts
 102 and they are executed on lists of files, hosts, users or other items.")
 103     (license license:gpl3+)))
 104
 105 (define-public slurm
 106   (package
 107    (name "slurm")
 108    (version "17.11.3")
 109    (source (origin
 110             (method url-fetch)
 111             (uri (string-append
 112                   "https://download.schedmd.com/slurm/slurm-"
 113                   version ".tar.bz2"))
 114             (sha256
 115              (base32
 116               "1x3i6z03d9m46fvj1cslrapm1drvgyqch9pn4xf23kvbz4gkhaps"))
 117             (modules '((guix build utils)))
 118             (snippet
 119              '(begin
 120                 (substitute* "configure.ac"
 121                   (("^[[:space:]]+contribs/.*$") ""))
 122                 (delete-file-recursively "contribs")
 123                 #t))))
 124    ;; FIXME: More optional inputs could be added,
 125    ;; in particular mysql and gtk+.
 126    (inputs `(("expect" ,expect)
 127              ("freeipmi" ,freeipmi)
 128              ("hwloc" ,hwloc "lib")
 129              ("json-c" ,json-c)
 130              ("linux-pam" , linux-pam)
 131              ("munge" ,munge)
 132              ("numactl" ,numactl)
 133              ("openssl" ,openssl)
 134              ("perl" ,perl)
 135              ("python" ,python-wrapper)
 136              ("readline" ,readline)))
 137    (native-inputs
 138     `(("autoconf" ,autoconf)
 139       ("pkg-config" ,pkg-config)))
 140    (build-system gnu-build-system)
 141    (arguments
 142     `(#:configure-flags
 143       (list "--enable-pam" "--sysconfdir=/etc/slurm"
 144             (string-append "--with-freeipmi=" (assoc-ref %build-inputs "freeipmi"))
 145             (string-append "--with-hwloc=" (assoc-ref %build-inputs "hwloc"))
 146             (string-append "--with-json=" (assoc-ref %build-inputs "json-c"))
 147             (string-append "--with-munge=" (assoc-ref %build-inputs "munge"))
 148             (string-append "--with-ssl=" (assoc-ref %build-inputs "openssl")))
 149       #:phases
 150       (modify-phases %standard-phases
 151         (add-after 'unpack 'autoconf
 152           (lambda _ (invoke "autoconf")))))) ; configure.ac was patched
 153    (home-page "https://slurm.schedmd.com/")
 154    (synopsis "Workload manager for cluster computing")
 155    (description
 156     "SLURM is a fault-tolerant and highly scalable cluster management and job
 157 scheduling system for large and small clusters.  It allocates access to
 158 resources (computer nodes) to users for some duration of time, provides a
 159 framework for starting, executing, and monitoring work (typically a parallel
 160 job) on a set of allocated nodes, and arbitrates contention for resources
 161 by managing a queue of pending work.")
 162    (license (list license:bsd-2       ; src/common/log.[ch], src/common/uthash
 163                   license:expat       ; slurm/pmi.h
 164                   license:isc         ; src/common/strlcpy.c
 165                   license:lgpl2.1+    ; hilbert.[ch], src/common/slurm_time.h
 166                   license:zlib        ; src/common/strnatcmp.c
 167                   license:gpl2+))))   ; the rest, often with OpenSSL exception
 168
 169 (define-public slurm-drmaa
 170   (package
 171     (name "slurm-drmaa")
 172     (version "1.0.7")
 173     (source (origin
 174               (method url-fetch)
 175               (uri "http://apps.man.poznan.pl/trac/slurm-drmaa/downloads/9")
 176               (file-name (string-append name "-" version ".tar.gz"))
 177               (sha256
 178                (base32
 179                 "0grw55hmny2mc4nc0y1arnvxd2k0dcdfn476kzs180fibjxgfw14"))))
 180     (build-system gnu-build-system)
 181     (inputs
 182      `(("slurm" ,slurm)))
 183     (native-inputs
 184      `(("which" ,which)))
 185     (home-page "http://apps.man.poznan.pl/trac/slurm-drmaa")
 186     (synopsis "Distributed resource management application API for SLURM")
 187     (description
 188      "PSNC DRMAA for Simple Linux Utility for Resource Management (SLURM) is
 189 an implementation of Open Grid Forum DRMAA 1.0 (Distributed Resource
 190 Management Application API) specification for submission and control of jobs
 191 to SLURM.  Using DRMAA, grid applications builders, portal developers and ISVs
 192 can use the same high-level API to link their software with different
 193 cluster/resource management systems.")
 194     (license license:gpl3+)))
 195
 196 (define-public python-slurm-magic
 197   (let ((commit "73dd1a2b85799f7dae4b3f1cd9027536eff0c4d7")
 198         (revision "0"))
 199     (package
 200       (name "python-slurm-magic")
 201       (version (git-version "0.0" revision commit))
 202       (home-page "https://github.com/NERSC/slurm-magic")
 203       (source (origin
 204                 (method git-fetch)
 205                 (uri (git-reference (url home-page)
 206                                     (commit commit)))
 207                 (sha256
 208                  (base32
 209                   "19pp2vs0wm8mx0arz9n6lw9wgyv70w9wyi4y6b91qc5j3bz5igfs"))
 210                 (file-name (git-file-name name version))))
 211       (build-system python-build-system)
 212       (arguments
 213        '(#:phases (modify-phases %standard-phases
 214                     (add-before 'build 'set-slurm-path
 215                       (lambda* (#:key inputs #:allow-other-keys)
 216                         ;; The '_execute' method tries to exec 'salloc'
 217                         ;; etc. from $PATH.  Record the absolute file name
 218                         ;; instead.
 219                         (let ((slurm (assoc-ref inputs "slurm")))
 220                           (substitute* "slurm_magic.py"
 221                             (("name = (.*)$" _ value)
 222                              (string-append "name = \""
 223                                             slurm "/bin/\" + "
 224                                             value "\n")))
 225                           #t))))))
 226       (inputs
 227        `(("slurm" ,slurm)))
 228       (propagated-inputs
 229        `(("python-ipython" ,python-ipython)
 230          ("python-pandas" ,python-pandas)))
 231       (synopsis "Control the SLURM batch scheduler from Jupyter Notebook")
 232       (description
 233        "This package implements Jupyter/IPython
 234 @uref{http://ipython.readthedocs.io/en/stable/interactive/magics.html, magic
 235 commands} for interacting with the SLURM workload manager.  SLURM magic simply
 236 wraps command-line executables and the commands themselves should look like
 237 their command-line counterparts.  Commands are spawned via @code{subprocess}
 238 and output captured in the notebook.  Whatever arguments are accepted by a
 239 SLURM command line executable are also accepted by the corresponding magic
 240 command---e.g., @code{%salloc}, @code{%sbatch}, etc.")
 241       (license license:bsd-3))))