1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
|
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages parallel)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (gnu packages)
#:use-module (gnu packages admin)
#:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages freeipmi)
#:use-module (gnu packages linux)
#:use-module (gnu packages mpi)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages readline)
#:use-module (gnu packages tcl)
#:use-module (gnu packages tls)
#:use-module (gnu packages web))
(define-public parallel
(package
(name "parallel")
(version "20190522")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://gnu/parallel/parallel-"
version ".tar.bz2"))
(sha256
(base32 "0y3z9wybs3gak3zwgsby8r5gg6dwd3qlrkch0q4fn0i1j1jhmijv"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-bin-sh
(lambda _
(for-each
(lambda (file)
(substitute* file
;; Patch hard coded '/bin/sh' in the line ending in:
;; $Global::shell = $ENV{'PARALLEL_SHELL'} ||
;; parent_shell($$) || $ENV{'SHELL'} || "/bin/sh";
(("/bin/sh\\\";\n$") (string-append (which "sh") "\";\n"))))
(list "src/parallel" "src/sem"))
#t))
(add-after 'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(wrap-program (string-append out "/bin/parallel")
`("PATH" ":" prefix
,(map (lambda (input)
(string-append (assoc-ref inputs input) "/bin"))
'("perl"
"procps"))))
#t)))
(add-after 'wrap-program 'post-install-test
(lambda* (#:key outputs #:allow-other-keys)
(invoke (string-append
(assoc-ref outputs "out") "/bin/parallel")
"echo"
":::" "1" "2" "3"))))))
(inputs
`(("perl" ,perl)
("procps" ,procps)))
(home-page "https://www.gnu.org/software/parallel/")
(synopsis "Build and execute command lines in parallel")
(description
"GNU Parallel is a tool for executing shell jobs in parallel using one
or more computers. Jobs can consist of single commands or of scripts
and they are executed on lists of files, hosts, users or other items.")
(license license:gpl3+)))
(define-public slurm
(package
(name "slurm")
(version "17.11.3")
(source (origin
(method url-fetch)
(uri (string-append
"https://download.schedmd.com/slurm/slurm-"
version ".tar.bz2"))
(sha256
(base32
"1x3i6z03d9m46fvj1cslrapm1drvgyqch9pn4xf23kvbz4gkhaps"))
(modules '((guix build utils)))
(snippet
'(begin
(substitute* "configure.ac"
(("^[[:space:]]+contribs/.*$") ""))
(delete-file-recursively "contribs")
#t))))
;; FIXME: More optional inputs could be added,
;; in particular mysql and gtk+.
(inputs `(("expect" ,expect)
("freeipmi" ,freeipmi)
("hwloc" ,hwloc "lib")
("json-c" ,json-c)
("linux-pam" , linux-pam)
("munge" ,munge)
("numactl" ,numactl)
("openssl" ,openssl)
("perl" ,perl)
("python" ,python-wrapper)
("readline" ,readline)))
(native-inputs
`(("autoconf" ,autoconf)
("pkg-config" ,pkg-config)))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
(list "--enable-pam" "--sysconfdir=/etc/slurm"
(string-append "--with-freeipmi=" (assoc-ref %build-inputs "freeipmi"))
(string-append "--with-hwloc=" (assoc-ref %build-inputs "hwloc"))
(string-append "--with-json=" (assoc-ref %build-inputs "json-c"))
(string-append "--with-munge=" (assoc-ref %build-inputs "munge"))
(string-append "--with-ssl=" (assoc-ref %build-inputs "openssl")))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autoconf
(lambda _ (invoke "autoconf")))))) ; configure.ac was patched
(home-page "https://slurm.schedmd.com/")
(synopsis "Workload manager for cluster computing")
(description
"SLURM is a fault-tolerant and highly scalable cluster management and job
scheduling system for large and small clusters. It allocates access to
resources (computer nodes) to users for some duration of time, provides a
framework for starting, executing, and monitoring work (typically a parallel
job) on a set of allocated nodes, and arbitrates contention for resources
by managing a queue of pending work.")
(license (list license:bsd-2 ; src/common/log.[ch], src/common/uthash
license:expat ; slurm/pmi.h
license:isc ; src/common/strlcpy.c
license:lgpl2.1+ ; hilbert.[ch], src/common/slurm_time.h
license:zlib ; src/common/strnatcmp.c
license:gpl2+)))) ; the rest, often with OpenSSL exception
(define-public slurm-drmaa
(package
(name "slurm-drmaa")
(version "1.0.7")
(source (origin
(method url-fetch)
(uri "http://apps.man.poznan.pl/trac/slurm-drmaa/downloads/9")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0grw55hmny2mc4nc0y1arnvxd2k0dcdfn476kzs180fibjxgfw14"))))
(build-system gnu-build-system)
(inputs
`(("slurm" ,slurm)))
(native-inputs
`(("which" ,which)))
(home-page "http://apps.man.poznan.pl/trac/slurm-drmaa")
(synopsis "Distributed resource management application API for SLURM")
(description
"PSNC DRMAA for Simple Linux Utility for Resource Management (SLURM) is
an implementation of Open Grid Forum DRMAA 1.0 (Distributed Resource
Management Application API) specification for submission and control of jobs
to SLURM. Using DRMAA, grid applications builders, portal developers and ISVs
can use the same high-level API to link their software with different
cluster/resource management systems.")
(license license:gpl3+)))
(define-public python-slurm-magic
(let ((commit "73dd1a2b85799f7dae4b3f1cd9027536eff0c4d7")
(revision "0"))
(package
(name "python-slurm-magic")
(version (git-version "0.0" revision commit))
(home-page "https://github.com/NERSC/slurm-magic")
(source (origin
(method git-fetch)
(uri (git-reference (url home-page)
(commit commit)))
(sha256
(base32
"19pp2vs0wm8mx0arz9n6lw9wgyv70w9wyi4y6b91qc5j3bz5igfs"))
(file-name (git-file-name name version))))
(build-system python-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
(add-before 'build 'set-slurm-path
(lambda* (#:key inputs #:allow-other-keys)
;; The '_execute' method tries to exec 'salloc'
;; etc. from $PATH. Record the absolute file name
;; instead.
(let ((slurm (assoc-ref inputs "slurm")))
(substitute* "slurm_magic.py"
(("name = (.*)$" _ value)
(string-append "name = \""
slurm "/bin/\" + "
value "\n")))
#t))))))
(inputs
`(("slurm" ,slurm)))
(propagated-inputs
`(("python-ipython" ,python-ipython)
("python-pandas" ,python-pandas)))
(synopsis "Control the SLURM batch scheduler from Jupyter Notebook")
(description
"This package implements Jupyter/IPython
@uref{http://ipython.readthedocs.io/en/stable/interactive/magics.html, magic
commands} for interacting with the SLURM workload manager. SLURM magic simply
wraps command-line executables and the commands themselves should look like
their command-line counterparts. Commands are spawned via @code{subprocess}
and output captured in the notebook. Whatever arguments are accepted by a
SLURM command line executable are also accepted by the corresponding magic
command---e.g., @code{%salloc}, @code{%sbatch}, etc.")
(license license:bsd-3))))
|
