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 utils) #:select (target-64bit?))
  36   #:use-module (guix packages)
  37   #:use-module (gnu packages)
  38   #:use-module (gnu packages admin)
  39   #:use-module (gnu packages autotools)
  40   #:use-module (gnu packages base)
  41   #:use-module (gnu packages freeipmi)
  42   #:use-module (gnu packages linux)
  43   #:use-module (gnu packages mpi)
  44   #:use-module (gnu packages perl)
  45   #:use-module (gnu packages pkg-config)
  46   #:use-module (gnu packages python)
  47   #:use-module (gnu packages python-science)
  48   #:use-module (gnu packages python-xyz)
  49   #:use-module (gnu packages readline)
  50   #:use-module (gnu packages tcl)
  51   #:use-module (gnu packages tls)
  52   #:use-module (gnu packages web))
  53
  54 (define-public parallel
  55   (package
  56     (name "parallel")
  57     (version "20191222")
  58     (source
  59      (origin
  60       (method url-fetch)
  61       (uri (string-append "mirror://gnu/parallel/parallel-"
  62                           version ".tar.bz2"))
  63       (sha256
  64        (base32 "0xvw578440s9cc382n7z2l8npj30nwr6wwmkyxn2pj1pcszfjagy"))))
  65     (build-system gnu-build-system)
  66     (arguments
  67      `(#:phases
  68        (modify-phases %standard-phases
  69          (add-after 'unpack 'patch-bin-sh
  70            (lambda _
  71              (for-each
  72               (lambda (file)
  73                 (substitute* file
  74                   ;; Patch hard coded '/bin/sh' in the line ending in:
  75                   ;; $Global::shell = $ENV{'PARALLEL_SHELL'} ||
  76                   ;;  parent_shell($$) || $ENV{'SHELL'} || "/bin/sh";
  77                   (("/bin/sh\\\";\n$") (string-append (which "sh") "\";\n"))))
  78               (list "src/parallel" "src/sem"))
  79              #t))
  80          (add-after 'install 'wrap-program
  81            (lambda* (#:key inputs outputs #:allow-other-keys)
  82              (let ((out (assoc-ref outputs "out")))
  83                (wrap-program (string-append out "/bin/parallel")
  84                  `("PATH" ":" prefix
  85                    ,(map (lambda (input)
  86                            (string-append (assoc-ref inputs input) "/bin"))
  87                          '("perl"
  88                            "procps"))))
  89                #t)))
  90          (add-after 'wrap-program 'post-install-test
  91            (lambda* (#:key outputs #:allow-other-keys)
  92              (invoke (string-append
  93                       (assoc-ref outputs "out") "/bin/parallel")
  94                      "echo"
  95                      ":::" "1" "2" "3"))))))
  96     (inputs
  97      `(("perl" ,perl)
  98        ("procps" ,procps)))
  99     (home-page "https://www.gnu.org/software/parallel/")
 100     (synopsis "Build and execute command lines in parallel")
 101     (description
 102      "GNU Parallel is a tool for executing shell jobs in parallel using one
 103 or more computers.  Jobs can consist of single commands or of scripts
 104 and they are executed on lists of files, hosts, users or other items.")
 105     (license license:gpl3+)))
 106
 107 (define-public slurm
 108   (package
 109    (name "slurm")
 110    (version "19.05.3-2")
 111    (source (origin
 112             (method url-fetch)
 113             (uri (string-append
 114                   "https://download.schedmd.com/slurm/slurm-"
 115                   version ".tar.bz2"))
 116             (sha256
 117              (base32
 118               "0qj4blfymrd2ry2qmb58l3jbr4jwygc3adcfw7my27rippcijlyc"))
 119             (modules '((guix build utils)))
 120             (snippet
 121              '(begin
 122                 ;; According to
 123                 ;; <https://lists.gnu.org/archive/html/guix-devel/2016-02/msg00534.html>
 124                 ;; there are non-free bits under contribs/, though it's not
 125                 ;; clear which ones.  libpmi is clearly free (it used to be
 126                 ;; under src/api/), so remove all of contribs/ except
 127                 ;; contribs/pmi/.
 128                 (substitute* "configure.ac"
 129                   (("^[[:space:]]+contribs/(.*)$" all directory)
 130                    (if (and (string-prefix? "pmi" directory)
 131                             (not (string-prefix? "pmi2" directory)))
 132                        all
 133                        "")))
 134
 135                 (rename-file "contribs/pmi" "tmp-pmi")
 136                 (delete-file-recursively "contribs")
 137                 (mkdir "contribs")
 138                 (rename-file "tmp-pmi" "contribs/pmi")
 139                 #t))))
 140    ;; FIXME: More optional inputs could be added,
 141    ;; in particular mysql and gtk+.
 142    (inputs `(("expect" ,expect)
 143              ("freeipmi" ,freeipmi)
 144              ("hwloc" ,hwloc-2 "lib")
 145              ("json-c" ,json-c)
 146              ("linux-pam" , linux-pam)
 147              ("munge" ,munge)
 148              ("numactl" ,numactl)
 149              ("perl" ,perl)
 150              ("python" ,python-wrapper)
 151              ("readline" ,readline)))
 152    (native-inputs
 153     `(("autoconf" ,autoconf)
 154       ("pkg-config" ,pkg-config)))
 155    (build-system gnu-build-system)
 156    (arguments
 157     `(#:configure-flags
 158       (list "--enable-pam" "--sysconfdir=/etc/slurm"
 159             "--disable-static"
 160             (string-append "--with-freeipmi=" (assoc-ref %build-inputs "freeipmi"))
 161             (string-append "--with-hwloc=" (assoc-ref %build-inputs "hwloc"))
 162             (string-append "--with-json=" (assoc-ref %build-inputs "json-c"))
 163             (string-append "--with-munge=" (assoc-ref %build-inputs "munge"))
 164
 165             ;; 32-bit support is marked as deprecated and needs to be
 166             ;; explicitly enabled.
 167             ,@(if (target-64bit?) '() '("--enable-deprecated")))
 168       #:phases
 169       (modify-phases %standard-phases
 170         (add-after 'unpack 'autoconf
 171           (lambda _ (invoke "autoconf")))         ;configure.ac was patched
 172         (add-after 'install 'install-libpmi
 173           (lambda _
 174             ;; Open MPI expects libpmi to be provided by Slurm so install it.
 175             (invoke "make" "install" "-C" "contribs/pmi"))))))
 176    (home-page "https://slurm.schedmd.com/")
 177    (synopsis "Workload manager for cluster computing")
 178    (description
 179     "SLURM is a fault-tolerant and highly scalable cluster management and job
 180 scheduling system for large and small clusters.  It allocates access to
 181 resources (computer nodes) to users for some duration of time, provides a
 182 framework for starting, executing, and monitoring work (typically a parallel
 183 job) on a set of allocated nodes, and arbitrates contention for resources
 184 by managing a queue of pending work.")
 185    (license (list license:bsd-2       ; src/common/log.[ch], src/common/uthash
 186                   license:expat       ; slurm/pmi.h
 187                   license:isc         ; src/common/strlcpy.c
 188                   license:lgpl2.1+    ; hilbert.[ch], src/common/slurm_time.h
 189                   license:zlib        ; src/common/strnatcmp.c
 190                   license:gpl2+))))   ; the rest, often with OpenSSL exception
 191
 192 (define-public slurm-drmaa
 193   (package
 194     (name "slurm-drmaa")
 195     (version "1.0.7")
 196     (source (origin
 197               (method url-fetch)
 198               (uri "http://apps.man.poznan.pl/trac/slurm-drmaa/downloads/9")
 199               (file-name (string-append name "-" version ".tar.gz"))
 200               (sha256
 201                (base32
 202                 "0grw55hmny2mc4nc0y1arnvxd2k0dcdfn476kzs180fibjxgfw14"))))
 203     (build-system gnu-build-system)
 204     (inputs
 205      `(("slurm" ,slurm)))
 206     (native-inputs
 207      `(("which" ,which)))
 208     (home-page "http://apps.man.poznan.pl/trac/slurm-drmaa")
 209     (synopsis "Distributed resource management application API for SLURM")
 210     (description
 211      "PSNC DRMAA for Simple Linux Utility for Resource Management (SLURM) is
 212 an implementation of Open Grid Forum DRMAA 1.0 (Distributed Resource
 213 Management Application API) specification for submission and control of jobs
 214 to SLURM.  Using DRMAA, grid applications builders, portal developers and ISVs
 215 can use the same high-level API to link their software with different
 216 cluster/resource management systems.")
 217     (license license:gpl3+)))
 218
 219 (define-public python-slurm-magic
 220   (let ((commit "73dd1a2b85799f7dae4b3f1cd9027536eff0c4d7")
 221         (revision "0"))
 222     (package
 223       (name "python-slurm-magic")
 224       (version (git-version "0.0" revision commit))
 225       (home-page "https://github.com/NERSC/slurm-magic")
 226       (source (origin
 227                 (method git-fetch)
 228                 (uri (git-reference (url home-page)
 229                                     (commit commit)))
 230                 (sha256
 231                  (base32
 232                   "19pp2vs0wm8mx0arz9n6lw9wgyv70w9wyi4y6b91qc5j3bz5igfs"))
 233                 (file-name (git-file-name name version))))
 234       (build-system python-build-system)
 235       (arguments
 236        '(#:phases (modify-phases %standard-phases
 237                     (add-before 'build 'set-slurm-path
 238                       (lambda* (#:key inputs #:allow-other-keys)
 239                         ;; The '_execute' method tries to exec 'salloc'
 240                         ;; etc. from $PATH.  Record the absolute file name
 241                         ;; instead.
 242                         (let ((slurm (assoc-ref inputs "slurm")))
 243                           (substitute* "slurm_magic.py"
 244                             (("name = (.*)$" _ value)
 245                              (string-append "name = \""
 246                                             slurm "/bin/\" + "
 247                                             value "\n")))
 248                           #t))))))
 249       (inputs
 250        `(("slurm" ,slurm)))
 251       (propagated-inputs
 252        `(("python-ipython" ,python-ipython)
 253          ("python-pandas" ,python-pandas)))
 254       (synopsis "Control the SLURM batch scheduler from Jupyter Notebook")
 255       (description
 256        "This package implements Jupyter/IPython
 257 @uref{http://ipython.readthedocs.io/en/stable/interactive/magics.html, magic
 258 commands} for interacting with the SLURM workload manager.  SLURM magic simply
 259 wraps command-line executables and the commands themselves should look like
 260 their command-line counterparts.  Commands are spawned via @code{subprocess}
 261 and output captured in the notebook.  Whatever arguments are accepted by a
 262 SLURM command line executable are also accepted by the corresponding magic
 263 command---e.g., @code{%salloc}, @code{%sbatch}, etc.")
 264       (license license:bsd-3))))