Commit | Line | Data |
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fb0e3709 | 1 | ;;; GNU Guix --- Functional package management for GNU |
41313ace | 2 | ;;; Copyright © 2014, 2015, 2018, 2019 Eric Bavier <bavier@member.fsf.org> |
b07712bf | 3 | ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org> |
29a7c98a | 4 | ;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net> |
37d6b097 | 5 | ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr> |
1f9bff41 | 6 | ;;; Copyright © 2017 Dave Love <fx@gnu.org> |
91298042 | 7 | ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> |
b9b53fb4 | 8 | ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> |
54fcd547 | 9 | ;;; Copyright © 2018 Paul Garlick <pgarlick@tourbillion-technology.com> |
e9823f9c | 10 | ;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net> |
fb0e3709 EB |
11 | ;;; |
12 | ;;; This file is part of GNU Guix. | |
13 | ;;; | |
14 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
15 | ;;; under the terms of the GNU General Public License as published by | |
16 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
17 | ;;; your option) any later version. | |
18 | ;;; | |
19 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
20 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
21 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
22 | ;;; GNU General Public License for more details. | |
23 | ;;; | |
24 | ;;; You should have received a copy of the GNU General Public License | |
25 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
26 | ||
27 | (define-module (gnu packages mpi) | |
28 | #:use-module (guix packages) | |
2b0d560a LC |
29 | #:use-module ((guix licenses) |
30 | #:hide (expat)) | |
fb0e3709 | 31 | #:use-module (guix download) |
29a7c98a | 32 | #:use-module (guix utils) |
fb0e3709 | 33 | #:use-module (guix build-system gnu) |
54fcd547 | 34 | #:use-module (guix build-system python) |
fb0e3709 | 35 | #:use-module (gnu packages) |
e9823f9c | 36 | #:use-module (gnu packages fabric-management) |
fb0e3709 | 37 | #:use-module (gnu packages gcc) |
fa5a2538 | 38 | #:use-module (gnu packages java) |
41313ace | 39 | #:use-module (gnu packages libevent) |
2b0d560a LC |
40 | #:use-module (gnu packages linux) |
41 | #:use-module (gnu packages pciutils) | |
42 | #:use-module (gnu packages xorg) | |
43 | #:use-module (gnu packages gtk) | |
44 | #:use-module (gnu packages xml) | |
38f0a2ba | 45 | #:use-module (gnu packages perl) |
2b0d560a | 46 | #:use-module (gnu packages ncurses) |
b07712bf | 47 | #:use-module (gnu packages parallel) |
2b0d560a | 48 | #:use-module (gnu packages pkg-config) |
91298042 | 49 | #:use-module (gnu packages valgrind) |
71e78931 | 50 | #:use-module (srfi srfi-1) |
91298042 | 51 | #:use-module (ice-9 match)) |
fb0e3709 | 52 | |
2b0d560a | 53 | (define-public hwloc |
71e78931 LC |
54 | ;; Note: For now we keep 1.x as the default because many packages have yet |
55 | ;; to migrate to 2.0. | |
2b0d560a LC |
56 | (package |
57 | (name "hwloc") | |
9dd50845 | 58 | (version "1.11.12") |
2b0d560a LC |
59 | (source (origin |
60 | (method url-fetch) | |
a2d0e200 | 61 | (uri (string-append "https://www.open-mpi.org/software/hwloc/v" |
ce7d9c98 EB |
62 | (version-major+minor version) |
63 | "/downloads/hwloc-" version ".tar.bz2")) | |
2b0d560a LC |
64 | (sha256 |
65 | (base32 | |
9dd50845 | 66 | "0za1b9lvrm3rhn0lrxja5f64r0aq1qs4m0pxn1ji2mbi8ndppyyx")))) |
2b0d560a | 67 | (build-system gnu-build-system) |
798b7678 LC |
68 | (outputs '("out" ;'lstopo' & co., depends on Cairo, libx11, etc. |
69 | "lib" ;small closure | |
70 | "debug")) | |
2b0d560a | 71 | (inputs |
5b527256 | 72 | `(("libx11" ,libx11) |
2b0d560a LC |
73 | ("cairo" ,cairo) |
74 | ("ncurses" ,ncurses) | |
37d6b097 AE |
75 | ("expat" ,expat) |
76 | ,@(if (not (string-prefix? "armhf" | |
77 | (or (%current-target-system) | |
78 | (%current-system)))) | |
79 | `(("numactl" ,numactl)) | |
80 | '()))) | |
c6e59259 LC |
81 | (propagated-inputs |
82 | ;; hwloc.pc lists it in 'Requires.private'. | |
83 | `(("libpciaccess" ,libpciaccess))) | |
2b0d560a LC |
84 | (native-inputs |
85 | `(("pkg-config" ,pkg-config))) | |
579f5c8a | 86 | (arguments |
7eb9f31c LC |
87 | `(#:configure-flags '("--localstatedir=/var") |
88 | #:phases | |
579f5c8a | 89 | (modify-phases %standard-phases |
10de06bd LC |
90 | (add-before 'check 'skip-linux-libnuma-test |
91 | (lambda _ | |
92 | ;; Arrange to skip 'tests/linux-libnuma', which fails on some | |
93 | ;; machines: <https://github.com/open-mpi/hwloc/issues/213>. | |
94 | (substitute* "tests/linux-libnuma.c" | |
95 | (("numa_available\\(\\)") | |
96 | "-1")) | |
97 | #t)) | |
798b7678 LC |
98 | (add-after 'install 'refine-libnuma |
99 | ;; Give -L arguments for libraries to avoid propagation | |
100 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
101 | (let ((out (assoc-ref outputs "lib")) | |
102 | (numa (assoc-ref inputs "numactl"))) | |
103 | (substitute* (map (lambda (f) (string-append out "/" f)) | |
104 | '("lib/pkgconfig/hwloc.pc" "lib/libhwloc.la")) | |
105 | (("-lnuma" lib) | |
106 | (string-append "-L" numa "/lib " lib)))))) | |
107 | (add-after 'install 'avoid-circular-references | |
108 | (lambda* (#:key outputs #:allow-other-keys) | |
109 | (let ((lib (assoc-ref outputs "lib"))) | |
110 | ;; Suppress the 'prefix=' and 'exec_prefix=' lines so that the | |
111 | ;; "lib" output doesn't refer to "out". | |
112 | (substitute* (string-append lib "/lib/pkgconfig/hwloc.pc") | |
113 | (("^.*prefix=.*$") | |
114 | "")) | |
115 | #t)))))) | |
a2d0e200 | 116 | (home-page "https://www.open-mpi.org/projects/hwloc/") |
2b0d560a LC |
117 | (synopsis "Abstraction of hardware architectures") |
118 | (description | |
119 | "hwloc provides a portable abstraction (across OS, | |
120 | versions, architectures, ...) of the hierarchical topology of modern | |
121 | architectures, including NUMA memory nodes, sockets, shared caches, cores and | |
122 | simultaneous multithreading. It also gathers various attributes such as cache | |
123 | and memory information. It primarily aims at helping high-performance | |
124 | computing applications with gathering information about the hardware so as to | |
125 | exploit it accordingly and efficiently. | |
126 | ||
127 | hwloc may display the topology in multiple convenient formats. It also offers | |
128 | a powerful programming interface to gather information about the hardware, | |
129 | bind processes, and much more.") | |
2b0d560a LC |
130 | (license bsd-3))) |
131 | ||
71e78931 LC |
132 | (define-public hwloc-2.0 |
133 | ;; Note: 2.0 isn't the default yet, see above. | |
134 | (package | |
135 | (inherit hwloc) | |
cb85742f | 136 | (version "2.0.3") |
71e78931 LC |
137 | (source (origin |
138 | (method url-fetch) | |
139 | (uri (string-append "https://www.open-mpi.org/software/hwloc/v" | |
140 | (version-major+minor version) | |
141 | "/downloads/hwloc-" version ".tar.bz2")) | |
142 | (sha256 | |
143 | (base32 | |
cb85742f | 144 | "09f7ajak8wv5issr0hw72vs3jkldc7crcc7z5fd34sspkvrsm4z3")))) |
71e78931 LC |
145 | |
146 | ;; libnuma is no longer needed. | |
10de06bd LC |
147 | (inputs (alist-delete "numactl" (package-inputs hwloc))) |
148 | (arguments | |
149 | (substitute-keyword-arguments (package-arguments hwloc) | |
150 | ((#:phases phases) | |
151 | `(modify-phases ,phases | |
152 | (replace 'skip-linux-libnuma-test | |
153 | (lambda _ | |
154 | ;; Arrange to skip 'tests/hwloc/linux-libnuma', which fails on | |
155 | ;; some machines: <https://github.com/open-mpi/hwloc/issues/213>. | |
156 | (substitute* "tests/hwloc/linux-libnuma.c" | |
157 | (("numa_available\\(\\)") | |
158 | "-1")) | |
159 | #t)))))))) | |
71e78931 | 160 | |
fb0e3709 EB |
161 | (define-public openmpi |
162 | (package | |
163 | (name "openmpi") | |
6e36c6ed | 164 | (version "4.0.1") |
fb0e3709 EB |
165 | (source |
166 | (origin | |
167 | (method url-fetch) | |
6876590f | 168 | (uri (string-append "https://www.open-mpi.org/software/ompi/v" |
29a7c98a | 169 | (version-major+minor version) |
fb0e3709 EB |
170 | "/downloads/openmpi-" version ".tar.bz2")) |
171 | (sha256 | |
6e36c6ed | 172 | (base32 "02cpzcp113gj5hb0j2xc0cqma2fn04i2i0bzf80r71120p9bdryc")))) |
fb0e3709 | 173 | (build-system gnu-build-system) |
5b527256 | 174 | (inputs |
798b7678 | 175 | `(("hwloc" ,hwloc "lib") |
19afbea1 | 176 | ("gfortran" ,gfortran) |
a0995702 | 177 | ("libfabric" ,libfabric) |
41313ace | 178 | ("libevent" ,libevent) |
e9823f9c | 179 | ("opensm" ,opensm) |
a560641a LC |
180 | ,@(if (and (not (%current-target-system)) |
181 | (member (%current-system) (package-supported-systems psm))) | |
182 | `(("psm" ,psm)) | |
183 | '()) | |
fbe1b85b LC |
184 | ,@(if (and (not (%current-target-system)) |
185 | (member (%current-system) (package-supported-systems psm2))) | |
186 | `(("psm2" ,psm2)) | |
187 | '()) | |
a0995702 | 188 | ("rdma-core" ,rdma-core) |
b07712bf LC |
189 | ("valgrind" ,valgrind) |
190 | ("slurm" ,slurm))) ;for PMI support (launching via "srun") | |
5b527256 | 191 | (native-inputs |
38f0a2ba EB |
192 | `(("pkg-config" ,pkg-config) |
193 | ("perl" ,perl))) | |
c971d9ef | 194 | (outputs '("out" "debug")) |
fb0e3709 | 195 | (arguments |
b08952f1 | 196 | `(#:configure-flags `("--enable-mpi-ext=affinity" ;cr doesn't work |
1691b4cd | 197 | "--enable-memchecker" |
efcacc17 | 198 | "--with-sge" |
41313ace EB |
199 | "--with-valgrind" |
200 | "--with-hwloc=external" | |
201 | "--with-libevent" | |
e9823f9c RW |
202 | |
203 | ;; InfiniBand support | |
204 | "--enable-openib-control-hdr-padding" | |
205 | "--enable-openib-dynamic-sl" | |
206 | "--enable-openib-udcm" | |
207 | "--enable-openib-rdmacm" | |
208 | "--enable-openib-rdmacm-ibaddr" | |
209 | ||
b07712bf LC |
210 | ;; Enable support for SLURM's Process Manager |
211 | ;; Interface (PMI). | |
212 | ,(string-append "--with-pmi=" | |
213 | (assoc-ref %build-inputs "slurm"))) | |
9474a4b3 | 214 | #:phases (modify-phases %standard-phases |
e9823f9c RW |
215 | ;; opensm is needed for InfiniBand support. |
216 | (add-after 'unpack 'find-opensm-headers | |
217 | (lambda* (#:key inputs #:allow-other-keys) | |
218 | (setenv "C_INCLUDE_PATH" | |
219 | (string-append (assoc-ref inputs "opensm") | |
220 | "/include/infiniband/:" | |
221 | (getenv "C_INCLUDE_PATH"))) | |
222 | (setenv "CPLUS_INCLUDE_PATH" | |
223 | (string-append (assoc-ref inputs "opensm") | |
224 | "/include/infiniband/:" | |
225 | (getenv "CPLUS_INCLUDE_PATH"))) | |
226 | #t)) | |
0d97d3cb | 227 | (add-before 'build 'remove-absolute |
0d97d3cb | 228 | (lambda _ |
a247fe7b DL |
229 | ;; Remove compiler absolute file names (OPAL_FC_ABSOLUTE |
230 | ;; etc.) to reduce the closure size. See | |
231 | ;; <https://lists.gnu.org/archive/html/guix-devel/2017-07/msg00388.html> | |
232 | ;; and | |
233 | ;; <https://www.mail-archive.com/users@lists.open-mpi.org//msg31397.html>. | |
0d97d3cb DL |
234 | (substitute* '("orte/tools/orte-info/param.c" |
235 | "oshmem/tools/oshmem_info/param.c" | |
236 | "ompi/tools/ompi_info/param.c") | |
237 | (("_ABSOLUTE") "")) | |
a247fe7b DL |
238 | ;; Avoid valgrind (which pulls in gdb etc.). |
239 | (substitute* | |
41313ace EB |
240 | '("./ompi/mca/io/romio321/src/io_romio321_component.c") |
241 | (("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS") | |
a247fe7b | 242 | "\"[elided to reduce closure]\"")) |
0d97d3cb | 243 | #t)) |
9474a4b3 EB |
244 | (add-before 'build 'scrub-timestamps ;reproducibility |
245 | (lambda _ | |
246 | (substitute* '("ompi/tools/ompi_info/param.c" | |
247 | "orte/tools/orte-info/param.c" | |
248 | "oshmem/tools/oshmem_info/param.c") | |
249 | ((".*(Built|Configured) on.*") "")) | |
250 | #t)) | |
251 | (add-after 'install 'remove-logs ;reproducibility | |
252 | (lambda* (#:key outputs #:allow-other-keys) | |
253 | (let ((out (assoc-ref outputs "out"))) | |
254 | (for-each delete-file (find-files out "config.log")) | |
255 | #t)))))) | |
fb0e3709 | 256 | (home-page "http://www.open-mpi.org") |
bb0f6d75 | 257 | (synopsis "MPI-3 implementation") |
fb0e3709 | 258 | (description |
bb0f6d75 | 259 | "The Open MPI Project is an MPI-3 implementation that is developed and |
8ede638c EB |
260 | maintained by a consortium of academic, research, and industry partners. Open |
261 | MPI is therefore able to combine the expertise, technologies, and resources | |
262 | from all across the High Performance Computing community in order to build the | |
263 | best MPI library available. Open MPI offers advantages for system and | |
264 | software vendors, application developers and computer science researchers.") | |
fb0e3709 EB |
265 | ;; See file://LICENSE |
266 | (license bsd-2))) | |
685bef2b | 267 | |
fa5a2538 RW |
268 | ;; TODO: javadoc files contain timestamps. |
269 | (define-public java-openmpi | |
270 | (package (inherit openmpi) | |
271 | (name "java-openmpi") | |
272 | (inputs | |
273 | `(("openmpi" ,openmpi) | |
274 | ,@(package-inputs openmpi))) | |
275 | (native-inputs | |
276 | `(("jdk" ,openjdk11 "jdk") | |
277 | ("zip" ,(@ (gnu packages compression) zip)) | |
278 | ,@(package-native-inputs openmpi))) | |
279 | (outputs '("out")) | |
280 | (arguments | |
281 | `(#:modules ((guix build gnu-build-system) | |
282 | ((guix build ant-build-system) #:prefix ant:) | |
283 | (guix build utils)) | |
284 | #:imported-modules ((guix build ant-build-system) | |
285 | (guix build syscalls) | |
286 | ,@%gnu-build-system-modules) | |
287 | ,@(substitute-keyword-arguments (package-arguments openmpi) | |
288 | ((#:configure-flags flags) | |
289 | `(cons "--enable-mpi-java" ,flags)) | |
290 | ((#:make-flags flags ''()) | |
291 | `(append '("-C" "ompi/mpi/java") | |
292 | ,flags)) | |
293 | ((#:phases phases) | |
294 | `(modify-phases ,phases | |
295 | ;; We could provide the location of the JDK in the configure | |
296 | ;; flags, but since the configure flags are embedded in the | |
297 | ;; info binaries that would leave a reference to the JDK in | |
298 | ;; the "out" output. To avoid this we set JAVA_HOME. | |
299 | (add-after 'unpack 'set-JAVA_HOME | |
300 | (lambda* (#:key inputs #:allow-other-keys) | |
301 | (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) | |
302 | #t)) | |
303 | (add-after 'unpack 'link-with-existing-mpi-libraries | |
304 | (lambda* (#:key inputs #:allow-other-keys) | |
305 | (substitute* "ompi/mpi/java/c/Makefile.in" | |
306 | (("\\$\\(top_builddir\\)/ompi/lib@OMPI_LIBMPI_NAME@.la") | |
307 | (string-append (assoc-ref inputs "openmpi") "/lib/libmpi.la"))) | |
308 | #t)) | |
309 | (add-after 'install 'strip-jar-timestamps | |
310 | (assoc-ref ant:%standard-phases 'strip-jar-timestamps))))))) | |
311 | (synopsis "Java bindings for MPI"))) | |
312 | ||
685bef2b DL |
313 | (define-public openmpi-thread-multiple |
314 | (package | |
315 | (inherit openmpi) | |
316 | (name "openmpi-thread-multiple") | |
317 | (arguments | |
318 | (substitute-keyword-arguments (package-arguments openmpi) | |
319 | ((#:configure-flags flags) | |
320 | `(cons "--enable-mpi-thread-multiple" ,flags)))) | |
321 | (description " This version of Open@tie{}MPI has an implementation of | |
322 | @code{MPI_Init_thread} that provides @code{MPI_THREAD_MULTIPLE}. This won't | |
323 | work correctly with all transports (such as @code{openib}), and the | |
324 | performance is generally worse than the vanilla @code{openmpi} package, which | |
325 | only provides @code{MPI_THREAD_FUNNELED}."))) | |
bbe46a4a EB |
326 | |
327 | ;;; Build phase to be used for packages that execute MPI code. | |
328 | (define-public %openmpi-setup | |
329 | '(lambda _ | |
330 | ;; By default, running the test suite would fail because 'ssh' could not | |
331 | ;; be found in $PATH. Define this variable to placate Open MPI without | |
332 | ;; adding a dependency on OpenSSH (the agent isn't used anyway.) | |
333 | (setenv "OMPI_MCA_plm_rsh_agent" (which "false")) | |
334 | ;; Allow oversubscription in case there are less physical cores available | |
335 | ;; in the build environment than the package wants while testing. | |
41313ace | 336 | (setenv "OMPI_MCA_rmaps_base_mapping_policy" "core:OVERSUBSCRIBE") |
bbe46a4a | 337 | #t)) |
54fcd547 PG |
338 | |
339 | (define-public python-mpi4py | |
340 | (package | |
341 | (name "python-mpi4py") | |
b49c8b9e | 342 | (version "3.0.1") |
54fcd547 PG |
343 | (source |
344 | (origin | |
345 | (method url-fetch) | |
346 | (uri (pypi-uri "mpi4py" version)) | |
347 | (sha256 | |
348 | (base32 | |
b49c8b9e | 349 | "0ld8rjmsjr0dklvj2g1gr3ax32sdq0xjxyh0cspknc1i36waajb5")))) |
54fcd547 PG |
350 | (build-system python-build-system) |
351 | (arguments | |
352 | `(#:phases | |
353 | (modify-phases %standard-phases | |
354 | (add-after 'build 'mpi-setup | |
355 | ,%openmpi-setup) | |
356 | (add-before 'check 'pre-check | |
357 | (lambda _ | |
358 | ;; Skip BaseTestSpawn class (causes error 'ompi_dpm_dyn_init() | |
359 | ;; failed --> Returned "Unreachable"' in chroot environment). | |
360 | (substitute* "test/test_spawn.py" | |
361 | (("unittest.skipMPI\\('openmpi\\(<3.0.0\\)'\\)") | |
362 | "unittest.skipMPI('openmpi')")) | |
363 | #t))))) | |
364 | (inputs | |
365 | `(("openmpi" ,openmpi))) | |
366 | (home-page "https://bitbucket.org/mpi4py/mpi4py/") | |
367 | (synopsis "Python bindings for the Message Passing Interface standard") | |
368 | (description "MPI for Python (mpi4py) provides bindings of the Message | |
369 | Passing Interface (MPI) standard for the Python programming language, allowing | |
370 | any Python program to exploit multiple processors. | |
371 | ||
372 | mpi4py is constructed on top of the MPI-1/MPI-2 specification and provides an | |
373 | object oriented interface which closely follows MPI-2 C++ bindings. It | |
374 | supports point-to-point and collective communications of any picklable Python | |
375 | object as well as optimized communications of Python objects (such as NumPy | |
376 | arrays) that expose a buffer interface.") | |
377 | (license bsd-3))) |