Commit | Line | Data |
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e3aaefe7 | 1 | ;;; GNU Guix --- Functional package management for GNU |
552f5c00 | 2 | ;;; Copyright © 2013, 2014 Eric Bavier <bavier@member.fsf.org> |
ff03ef0b | 3 | ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org> |
de596e99 | 4 | ;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il> |
552f5c00 PP |
5 | ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> |
6 | ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr> | |
524eee02 | 7 | ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net> |
47bc991f | 8 | ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> |
035ee04b | 9 | ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com> |
d4c95a23 | 10 | ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> |
4e7950fd | 11 | ;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org> |
0c212811 | 12 | ;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org> |
e3aaefe7 EB |
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) | |
552f5c00 | 30 | #:use-module (guix download) |
0c212811 LC |
31 | #:use-module (guix git-download) |
32 | #:use-module (guix build-system gnu) | |
33 | #:use-module (guix build-system python) | |
552f5c00 | 34 | #:use-module ((guix licenses) #:prefix license:) |
bead6dcb | 35 | #:use-module ((guix utils) #:select (target-64bit?)) |
552f5c00 | 36 | #:use-module (guix packages) |
e3aaefe7 | 37 | #:use-module (gnu packages) |
552f5c00 PP |
38 | #:use-module (gnu packages admin) |
39 | #:use-module (gnu packages autotools) | |
524eee02 | 40 | #:use-module (gnu packages base) |
552f5c00 PP |
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) | |
312ec128 | 47 | #:use-module (gnu packages python-science) |
0c212811 | 48 | #:use-module (gnu packages python-xyz) |
552f5c00 PP |
49 | #:use-module (gnu packages readline) |
50 | #:use-module (gnu packages tcl) | |
51 | #:use-module (gnu packages tls) | |
52 | #:use-module (gnu packages web)) | |
e3aaefe7 EB |
53 | |
54 | (define-public parallel | |
55 | (package | |
56 | (name "parallel") | |
026a0ba9 | 57 | (version "20191222") |
e3aaefe7 EB |
58 | (source |
59 | (origin | |
60 | (method url-fetch) | |
61 | (uri (string-append "mirror://gnu/parallel/parallel-" | |
62 | version ".tar.bz2")) | |
63 | (sha256 | |
026a0ba9 | 64 | (base32 "0xvw578440s9cc382n7z2l8npj30nwr6wwmkyxn2pj1pcszfjagy")))) |
e3aaefe7 | 65 | (build-system gnu-build-system) |
47bc991f BW |
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 | |
2c36baa5 | 74 | ;; Patch hard coded '/bin/sh' in the line ending in: |
47bc991f BW |
75 | ;; $Global::shell = $ENV{'PARALLEL_SHELL'} || |
76 | ;; parent_shell($$) || $ENV{'SHELL'} || "/bin/sh"; | |
4e7950fd | 77 | (("/bin/sh\\\";\n$") (string-append (which "sh") "\";\n")))) |
fccab993 EF |
78 | (list "src/parallel" "src/sem")) |
79 | #t)) | |
4e7950fd CL |
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 | |
47bc991f | 91 | (lambda* (#:key outputs #:allow-other-keys) |
28b0b21e TGR |
92 | (invoke (string-append |
93 | (assoc-ref outputs "out") "/bin/parallel") | |
94 | "echo" | |
95 | ":::" "1" "2" "3")))))) | |
47bc991f | 96 | (inputs |
5ca5ab8b | 97 | `(("perl" ,perl) |
47bc991f | 98 | ("procps" ,procps))) |
fccab993 | 99 | (home-page "https://www.gnu.org/software/parallel/") |
e3aaefe7 EB |
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.") | |
552f5c00 PP |
105 | (license license:gpl3+))) |
106 | ||
107 | (define-public slurm | |
108 | (package | |
109 | (name "slurm") | |
7c96befa | 110 | (version "19.05.3-2") |
552f5c00 PP |
111 | (source (origin |
112 | (method url-fetch) | |
113 | (uri (string-append | |
ea1f073d LF |
114 | "https://download.schedmd.com/slurm/slurm-" |
115 | version ".tar.bz2")) | |
552f5c00 PP |
116 | (sha256 |
117 | (base32 | |
7c96befa | 118 | "0qj4blfymrd2ry2qmb58l3jbr4jwygc3adcfw7my27rippcijlyc")) |
552f5c00 PP |
119 | (modules '((guix build utils))) |
120 | (snippet | |
121 | '(begin | |
7c96befa LC |
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/. | |
4ff22ec3 | 128 | (substitute* "configure.ac" |
7c96befa LC |
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") | |
552f5c00 | 136 | (delete-file-recursively "contribs") |
7c96befa LC |
137 | (mkdir "contribs") |
138 | (rename-file "tmp-pmi" "contribs/pmi") | |
552f5c00 PP |
139 | #t)))) |
140 | ;; FIXME: More optional inputs could be added, | |
141 | ;; in particular mysql and gtk+. | |
142 | (inputs `(("expect" ,expect) | |
143 | ("freeipmi" ,freeipmi) | |
58a536bb | 144 | ("hwloc" ,hwloc-2 "lib") |
552f5c00 PP |
145 | ("json-c" ,json-c) |
146 | ("linux-pam" , linux-pam) | |
147 | ("munge" ,munge) | |
148 | ("numactl" ,numactl) | |
552f5c00 PP |
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 | |
e31ece97 | 158 | (list "--enable-pam" "--sysconfdir=/etc/slurm" |
52cd164a | 159 | "--disable-static" |
552f5c00 PP |
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")) | |
bead6dcb LC |
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"))) | |
552f5c00 PP |
168 | #:phases |
169 | (modify-phases %standard-phases | |
4ff22ec3 | 170 | (add-after 'unpack 'autoconf |
7c96befa LC |
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")))))) | |
91257587 | 176 | (home-page "https://slurm.schedmd.com/") |
552f5c00 PP |
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.") | |
70260b33 TGR |
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 | |
524eee02 RW |
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+))) | |
0c212811 LC |
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)))) |