Commit | Line | Data |
---|---|---|
fb0e3709 | 1 | ;;; GNU Guix --- Functional package management for GNU |
41313ace | 2 | ;;; Copyright © 2014, 2015, 2018, 2019 Eric Bavier <bavier@member.fsf.org> |
1a1d0fe5 | 3 | ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 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> |
9dd7082c | 8 | ;;; Copyright © 2018, 2019, 2020 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) | |
15e62623 | 29 | #:use-module ((guix licenses) #:prefix license:) |
fb0e3709 | 30 | #:use-module (guix download) |
29a7c98a | 31 | #:use-module (guix utils) |
8c8e1089 | 32 | #:use-module (guix deprecation) |
fb0e3709 | 33 | #:use-module (guix build-system gnu) |
54fcd547 | 34 | #:use-module (guix build-system python) |
fb0e3709 | 35 | #:use-module (gnu packages) |
c70261bf MB |
36 | #:use-module (gnu packages base) |
37 | #:use-module (gnu packages compression) | |
e9823f9c | 38 | #:use-module (gnu packages fabric-management) |
fb0e3709 | 39 | #:use-module (gnu packages gcc) |
fa5a2538 | 40 | #:use-module (gnu packages java) |
41313ace | 41 | #:use-module (gnu packages libevent) |
2b0d560a LC |
42 | #:use-module (gnu packages linux) |
43 | #:use-module (gnu packages pciutils) | |
44 | #:use-module (gnu packages xorg) | |
45 | #:use-module (gnu packages gtk) | |
46 | #:use-module (gnu packages xml) | |
38f0a2ba | 47 | #:use-module (gnu packages perl) |
2b0d560a | 48 | #:use-module (gnu packages ncurses) |
b07712bf | 49 | #:use-module (gnu packages parallel) |
2b0d560a | 50 | #:use-module (gnu packages pkg-config) |
91298042 | 51 | #:use-module (gnu packages valgrind) |
71e78931 | 52 | #:use-module (srfi srfi-1) |
91298042 | 53 | #:use-module (ice-9 match)) |
fb0e3709 | 54 | |
8ec7ca22 | 55 | (define-public hwloc-1 |
71e78931 LC |
56 | ;; Note: For now we keep 1.x as the default because many packages have yet |
57 | ;; to migrate to 2.0. | |
2b0d560a LC |
58 | (package |
59 | (name "hwloc") | |
9dd50845 | 60 | (version "1.11.12") |
2b0d560a LC |
61 | (source (origin |
62 | (method url-fetch) | |
a2d0e200 | 63 | (uri (string-append "https://www.open-mpi.org/software/hwloc/v" |
ce7d9c98 EB |
64 | (version-major+minor version) |
65 | "/downloads/hwloc-" version ".tar.bz2")) | |
2b0d560a LC |
66 | (sha256 |
67 | (base32 | |
9dd50845 | 68 | "0za1b9lvrm3rhn0lrxja5f64r0aq1qs4m0pxn1ji2mbi8ndppyyx")))) |
fe96f641 LC |
69 | |
70 | (properties | |
71 | ;; Tell the 'generic-html' updater to monitor this URL for updates. | |
72 | `((release-monitoring-url | |
73 | . "https://www-lb.open-mpi.org/software/hwloc/current"))) | |
74 | ||
2b0d560a | 75 | (build-system gnu-build-system) |
798b7678 LC |
76 | (outputs '("out" ;'lstopo' & co., depends on Cairo, libx11, etc. |
77 | "lib" ;small closure | |
305eefc0 | 78 | "doc" ;400+ section 3 man pages |
798b7678 | 79 | "debug")) |
2b0d560a | 80 | (inputs |
5b527256 | 81 | `(("libx11" ,libx11) |
2b0d560a LC |
82 | ("cairo" ,cairo) |
83 | ("ncurses" ,ncurses) | |
37d6b097 AE |
84 | ("expat" ,expat) |
85 | ,@(if (not (string-prefix? "armhf" | |
86 | (or (%current-target-system) | |
87 | (%current-system)))) | |
88 | `(("numactl" ,numactl)) | |
89 | '()))) | |
c6e59259 LC |
90 | (propagated-inputs |
91 | ;; hwloc.pc lists it in 'Requires.private'. | |
92 | `(("libpciaccess" ,libpciaccess))) | |
2b0d560a LC |
93 | (native-inputs |
94 | `(("pkg-config" ,pkg-config))) | |
579f5c8a | 95 | (arguments |
7eb9f31c LC |
96 | `(#:configure-flags '("--localstatedir=/var") |
97 | #:phases | |
579f5c8a | 98 | (modify-phases %standard-phases |
10de06bd LC |
99 | (add-before 'check 'skip-linux-libnuma-test |
100 | (lambda _ | |
101 | ;; Arrange to skip 'tests/linux-libnuma', which fails on some | |
102 | ;; machines: <https://github.com/open-mpi/hwloc/issues/213>. | |
103 | (substitute* "tests/linux-libnuma.c" | |
104 | (("numa_available\\(\\)") | |
105 | "-1")) | |
106 | #t)) | |
798b7678 LC |
107 | (add-after 'install 'refine-libnuma |
108 | ;; Give -L arguments for libraries to avoid propagation | |
109 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
110 | (let ((out (assoc-ref outputs "lib")) | |
111 | (numa (assoc-ref inputs "numactl"))) | |
112 | (substitute* (map (lambda (f) (string-append out "/" f)) | |
113 | '("lib/pkgconfig/hwloc.pc" "lib/libhwloc.la")) | |
114 | (("-lnuma" lib) | |
115 | (string-append "-L" numa "/lib " lib)))))) | |
116 | (add-after 'install 'avoid-circular-references | |
117 | (lambda* (#:key outputs #:allow-other-keys) | |
118 | (let ((lib (assoc-ref outputs "lib"))) | |
119 | ;; Suppress the 'prefix=' and 'exec_prefix=' lines so that the | |
120 | ;; "lib" output doesn't refer to "out". | |
121 | (substitute* (string-append lib "/lib/pkgconfig/hwloc.pc") | |
122 | (("^.*prefix=.*$") | |
123 | "")) | |
305eefc0 LC |
124 | #t))) |
125 | (add-after 'install 'move-man3-pages | |
126 | (lambda* (#:key outputs #:allow-other-keys) | |
127 | ;; Move section 3 man pages to the "doc" output. | |
128 | (let ((out (assoc-ref outputs "out")) | |
129 | (doc (assoc-ref outputs "doc"))) | |
130 | (copy-recursively (string-append out "/share/man/man3") | |
131 | (string-append doc "/share/man/man3")) | |
132 | (delete-file-recursively (string-append out "/share/man/man3")) | |
798b7678 | 133 | #t)))))) |
a2d0e200 | 134 | (home-page "https://www.open-mpi.org/projects/hwloc/") |
2b0d560a LC |
135 | (synopsis "Abstraction of hardware architectures") |
136 | (description | |
137 | "hwloc provides a portable abstraction (across OS, | |
138 | versions, architectures, ...) of the hierarchical topology of modern | |
139 | architectures, including NUMA memory nodes, sockets, shared caches, cores and | |
140 | simultaneous multithreading. It also gathers various attributes such as cache | |
141 | and memory information. It primarily aims at helping high-performance | |
142 | computing applications with gathering information about the hardware so as to | |
143 | exploit it accordingly and efficiently. | |
144 | ||
145 | hwloc may display the topology in multiple convenient formats. It also offers | |
146 | a powerful programming interface to gather information about the hardware, | |
147 | bind processes, and much more.") | |
15e62623 | 148 | (license license:bsd-3))) |
2b0d560a | 149 | |
8c8e1089 | 150 | (define-public hwloc-2 |
1a1d0fe5 | 151 | ;; Note: 2.x isn't the default yet, see above. |
71e78931 | 152 | (package |
8ec7ca22 | 153 | (inherit hwloc-1) |
1a1d0fe5 | 154 | (version "2.4.1") |
71e78931 LC |
155 | (source (origin |
156 | (method url-fetch) | |
1a1d0fe5 | 157 | (uri (string-append "https://download.open-mpi.org/release/hwloc/v" |
71e78931 | 158 | (version-major+minor version) |
1a1d0fe5 | 159 | "/hwloc-" version ".tar.bz2")) |
71e78931 LC |
160 | (sha256 |
161 | (base32 | |
1a1d0fe5 | 162 | "0qyywmyns2jf3is3axrwmffvdd7ji7liy5axp650q4i6kzk2291r")))) |
71e78931 LC |
163 | |
164 | ;; libnuma is no longer needed. | |
0d8a8234 | 165 | (inputs (alist-delete "numactl" (package-inputs hwloc-1))) |
10de06bd | 166 | (arguments |
0d8a8234 | 167 | (substitute-keyword-arguments (package-arguments hwloc-1) |
10de06bd LC |
168 | ((#:phases phases) |
169 | `(modify-phases ,phases | |
170 | (replace 'skip-linux-libnuma-test | |
171 | (lambda _ | |
172 | ;; Arrange to skip 'tests/hwloc/linux-libnuma', which fails on | |
173 | ;; some machines: <https://github.com/open-mpi/hwloc/issues/213>. | |
174 | (substitute* "tests/hwloc/linux-libnuma.c" | |
175 | (("numa_available\\(\\)") | |
176 | "-1")) | |
8db4e704 LC |
177 | #t)) |
178 | (add-before 'check 'skip-test-that-fails-on-qemu | |
179 | (lambda _ | |
180 | ;; Skip test that fails on emulated hardware due to QEMU bug: | |
181 | ;; <https://bugs.gnu.org/40342>. | |
182 | (substitute* "tests/hwloc/hwloc_get_last_cpu_location.c" | |
183 | (("hwloc_topology_init" all) | |
184 | (string-append "exit (77);\n" all))) | |
10de06bd | 185 | #t)))))))) |
71e78931 | 186 | |
9b65dea8 | 187 | (define-deprecated hwloc-2.0 hwloc-2) |
8c8e1089 | 188 | |
8ec7ca22 LC |
189 | (define-public hwloc |
190 | ;; The latest stable series of hwloc. | |
191 | hwloc-2) | |
192 | ||
fb0e3709 EB |
193 | (define-public openmpi |
194 | (package | |
195 | (name "openmpi") | |
ee218032 | 196 | (version "4.1.0") |
fb0e3709 EB |
197 | (source |
198 | (origin | |
199 | (method url-fetch) | |
6876590f | 200 | (uri (string-append "https://www.open-mpi.org/software/ompi/v" |
29a7c98a | 201 | (version-major+minor version) |
fb0e3709 EB |
202 | "/downloads/openmpi-" version ".tar.bz2")) |
203 | (sha256 | |
ee218032 | 204 | (base32 "1dfmkyilgml9w9s5p0jmfj3xcdwdccwqbjw5iim9p0chf2vnz1kk")) |
68ac34e1 | 205 | (patches (search-patches "openmpi-mtl-priorities.patch")))) |
14aa86e5 LC |
206 | |
207 | (properties | |
208 | ;; Tell the 'generic-html' updater to monitor this URL for updates. | |
209 | `((release-monitoring-url | |
210 | . "https://www.open-mpi.org/software/ompi/current"))) | |
211 | ||
fb0e3709 | 212 | (build-system gnu-build-system) |
5b527256 | 213 | (inputs |
58a536bb | 214 | `(("hwloc" ,hwloc-2 "lib") |
19afbea1 | 215 | ("gfortran" ,gfortran) |
a0995702 | 216 | ("libfabric" ,libfabric) |
41313ace | 217 | ("libevent" ,libevent) |
e9823f9c | 218 | ("opensm" ,opensm) |
a560641a LC |
219 | ,@(if (and (not (%current-target-system)) |
220 | (member (%current-system) (package-supported-systems psm))) | |
221 | `(("psm" ,psm)) | |
222 | '()) | |
fbe1b85b LC |
223 | ,@(if (and (not (%current-target-system)) |
224 | (member (%current-system) (package-supported-systems psm2))) | |
225 | `(("psm2" ,psm2)) | |
226 | '()) | |
8ba94edd | 227 | ,@(if (and (not (%current-target-system)) |
96a469f1 | 228 | (member (%current-system) (package-supported-systems ucx))) |
8ba94edd LC |
229 | `(("ucx" ,ucx)) |
230 | '()) | |
a0995702 | 231 | ("rdma-core" ,rdma-core) |
b07712bf LC |
232 | ("valgrind" ,valgrind) |
233 | ("slurm" ,slurm))) ;for PMI support (launching via "srun") | |
5b527256 | 234 | (native-inputs |
38f0a2ba EB |
235 | `(("pkg-config" ,pkg-config) |
236 | ("perl" ,perl))) | |
c971d9ef | 237 | (outputs '("out" "debug")) |
fb0e3709 | 238 | (arguments |
b08952f1 | 239 | `(#:configure-flags `("--enable-mpi-ext=affinity" ;cr doesn't work |
1691b4cd | 240 | "--enable-memchecker" |
efcacc17 | 241 | "--with-sge" |
41313ace EB |
242 | "--with-valgrind" |
243 | "--with-hwloc=external" | |
244 | "--with-libevent" | |
e9823f9c | 245 | |
215b49a8 LC |
246 | ;; Help 'orterun' and 'mpirun' find their tools |
247 | ;; under $prefix by default. | |
248 | "--enable-mpirun-prefix-by-default" | |
249 | ||
e9823f9c RW |
250 | ;; InfiniBand support |
251 | "--enable-openib-control-hdr-padding" | |
252 | "--enable-openib-dynamic-sl" | |
253 | "--enable-openib-udcm" | |
254 | "--enable-openib-rdmacm" | |
255 | "--enable-openib-rdmacm-ibaddr" | |
256 | ||
b07712bf LC |
257 | ;; Enable support for SLURM's Process Manager |
258 | ;; Interface (PMI). | |
259 | ,(string-append "--with-pmi=" | |
260 | (assoc-ref %build-inputs "slurm"))) | |
9474a4b3 | 261 | #:phases (modify-phases %standard-phases |
e9823f9c RW |
262 | ;; opensm is needed for InfiniBand support. |
263 | (add-after 'unpack 'find-opensm-headers | |
264 | (lambda* (#:key inputs #:allow-other-keys) | |
265 | (setenv "C_INCLUDE_PATH" | |
266 | (string-append (assoc-ref inputs "opensm") | |
97149c57 | 267 | "/include/infiniband")) |
e9823f9c RW |
268 | (setenv "CPLUS_INCLUDE_PATH" |
269 | (string-append (assoc-ref inputs "opensm") | |
97149c57 | 270 | "/include/infiniband")) |
e9823f9c | 271 | #t)) |
0d97d3cb | 272 | (add-before 'build 'remove-absolute |
0d97d3cb | 273 | (lambda _ |
a247fe7b DL |
274 | ;; Remove compiler absolute file names (OPAL_FC_ABSOLUTE |
275 | ;; etc.) to reduce the closure size. See | |
276 | ;; <https://lists.gnu.org/archive/html/guix-devel/2017-07/msg00388.html> | |
277 | ;; and | |
278 | ;; <https://www.mail-archive.com/users@lists.open-mpi.org//msg31397.html>. | |
0d97d3cb DL |
279 | (substitute* '("orte/tools/orte-info/param.c" |
280 | "oshmem/tools/oshmem_info/param.c" | |
281 | "ompi/tools/ompi_info/param.c") | |
282 | (("_ABSOLUTE") "")) | |
a247fe7b DL |
283 | ;; Avoid valgrind (which pulls in gdb etc.). |
284 | (substitute* | |
41313ace EB |
285 | '("./ompi/mca/io/romio321/src/io_romio321_component.c") |
286 | (("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS") | |
a247fe7b | 287 | "\"[elided to reduce closure]\"")) |
0d97d3cb | 288 | #t)) |
9474a4b3 EB |
289 | (add-before 'build 'scrub-timestamps ;reproducibility |
290 | (lambda _ | |
291 | (substitute* '("ompi/tools/ompi_info/param.c" | |
292 | "orte/tools/orte-info/param.c" | |
293 | "oshmem/tools/oshmem_info/param.c") | |
294 | ((".*(Built|Configured) on.*") "")) | |
295 | #t)) | |
296 | (add-after 'install 'remove-logs ;reproducibility | |
297 | (lambda* (#:key outputs #:allow-other-keys) | |
298 | (let ((out (assoc-ref outputs "out"))) | |
299 | (for-each delete-file (find-files out "config.log")) | |
300 | #t)))))) | |
f9a69e9b | 301 | (home-page "https://www.open-mpi.org") |
bb0f6d75 | 302 | (synopsis "MPI-3 implementation") |
fb0e3709 | 303 | (description |
bb0f6d75 | 304 | "The Open MPI Project is an MPI-3 implementation that is developed and |
8ede638c EB |
305 | maintained by a consortium of academic, research, and industry partners. Open |
306 | MPI is therefore able to combine the expertise, technologies, and resources | |
307 | from all across the High Performance Computing community in order to build the | |
308 | best MPI library available. Open MPI offers advantages for system and | |
309 | software vendors, application developers and computer science researchers.") | |
fb0e3709 | 310 | ;; See file://LICENSE |
15e62623 | 311 | (license license:bsd-2))) |
685bef2b | 312 | |
fa5a2538 RW |
313 | ;; TODO: javadoc files contain timestamps. |
314 | (define-public java-openmpi | |
1a265842 | 315 | (package/inherit openmpi |
fa5a2538 RW |
316 | (name "java-openmpi") |
317 | (inputs | |
318 | `(("openmpi" ,openmpi) | |
319 | ,@(package-inputs openmpi))) | |
320 | (native-inputs | |
321 | `(("jdk" ,openjdk11 "jdk") | |
322 | ("zip" ,(@ (gnu packages compression) zip)) | |
323 | ,@(package-native-inputs openmpi))) | |
324 | (outputs '("out")) | |
325 | (arguments | |
326 | `(#:modules ((guix build gnu-build-system) | |
327 | ((guix build ant-build-system) #:prefix ant:) | |
328 | (guix build utils)) | |
329 | #:imported-modules ((guix build ant-build-system) | |
330 | (guix build syscalls) | |
331 | ,@%gnu-build-system-modules) | |
332 | ,@(substitute-keyword-arguments (package-arguments openmpi) | |
333 | ((#:configure-flags flags) | |
334 | `(cons "--enable-mpi-java" ,flags)) | |
335 | ((#:make-flags flags ''()) | |
336 | `(append '("-C" "ompi/mpi/java") | |
337 | ,flags)) | |
338 | ((#:phases phases) | |
339 | `(modify-phases ,phases | |
340 | ;; We could provide the location of the JDK in the configure | |
341 | ;; flags, but since the configure flags are embedded in the | |
342 | ;; info binaries that would leave a reference to the JDK in | |
343 | ;; the "out" output. To avoid this we set JAVA_HOME. | |
344 | (add-after 'unpack 'set-JAVA_HOME | |
345 | (lambda* (#:key inputs #:allow-other-keys) | |
346 | (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) | |
347 | #t)) | |
348 | (add-after 'unpack 'link-with-existing-mpi-libraries | |
349 | (lambda* (#:key inputs #:allow-other-keys) | |
350 | (substitute* "ompi/mpi/java/c/Makefile.in" | |
351 | (("\\$\\(top_builddir\\)/ompi/lib@OMPI_LIBMPI_NAME@.la") | |
352 | (string-append (assoc-ref inputs "openmpi") "/lib/libmpi.la"))) | |
353 | #t)) | |
354 | (add-after 'install 'strip-jar-timestamps | |
355 | (assoc-ref ant:%standard-phases 'strip-jar-timestamps))))))) | |
356 | (synopsis "Java bindings for MPI"))) | |
357 | ||
685bef2b | 358 | (define-public openmpi-thread-multiple |
1a265842 | 359 | (package/inherit openmpi |
685bef2b DL |
360 | (name "openmpi-thread-multiple") |
361 | (arguments | |
362 | (substitute-keyword-arguments (package-arguments openmpi) | |
363 | ((#:configure-flags flags) | |
364 | `(cons "--enable-mpi-thread-multiple" ,flags)))) | |
365 | (description " This version of Open@tie{}MPI has an implementation of | |
366 | @code{MPI_Init_thread} that provides @code{MPI_THREAD_MULTIPLE}. This won't | |
367 | work correctly with all transports (such as @code{openib}), and the | |
368 | performance is generally worse than the vanilla @code{openmpi} package, which | |
369 | only provides @code{MPI_THREAD_FUNNELED}."))) | |
bbe46a4a EB |
370 | |
371 | ;;; Build phase to be used for packages that execute MPI code. | |
372 | (define-public %openmpi-setup | |
373 | '(lambda _ | |
374 | ;; By default, running the test suite would fail because 'ssh' could not | |
375 | ;; be found in $PATH. Define this variable to placate Open MPI without | |
376 | ;; adding a dependency on OpenSSH (the agent isn't used anyway.) | |
377 | (setenv "OMPI_MCA_plm_rsh_agent" (which "false")) | |
378 | ;; Allow oversubscription in case there are less physical cores available | |
379 | ;; in the build environment than the package wants while testing. | |
41313ace | 380 | (setenv "OMPI_MCA_rmaps_base_mapping_policy" "core:OVERSUBSCRIBE") |
b1077c22 LC |
381 | |
382 | ;; UCX sometimes outputs uninteresting warnings such as: | |
383 | ;; | |
384 | ;; mpool.c:38 UCX WARN object 0x7ffff44fffc0 was not returned to mpool ucp_am_bufs | |
385 | ;; | |
386 | ;; These in turn leads to failures of test suites that capture and | |
387 | ;; compare stdout, such as that of 'hdf5-parallel-openmpi'. Thus, tell | |
388 | ;; UCX to not emit those warnings. | |
389 | (setenv "UCX_LOG_LEVEL" "error") | |
bbe46a4a | 390 | #t)) |
54fcd547 PG |
391 | |
392 | (define-public python-mpi4py | |
393 | (package | |
394 | (name "python-mpi4py") | |
fe390200 | 395 | (version "3.0.3") |
54fcd547 | 396 | (source |
fe390200 TGR |
397 | (origin |
398 | (method url-fetch) | |
399 | (uri (pypi-uri "mpi4py" version)) | |
400 | (sha256 | |
401 | (base32 "07ssbhssv27rrjx1c5vd3vsr31vay5d8xcf4zh9yblcyidn72b81")))) | |
54fcd547 PG |
402 | (build-system python-build-system) |
403 | (arguments | |
404 | `(#:phases | |
405 | (modify-phases %standard-phases | |
406 | (add-after 'build 'mpi-setup | |
407 | ,%openmpi-setup) | |
408 | (add-before 'check 'pre-check | |
409 | (lambda _ | |
410 | ;; Skip BaseTestSpawn class (causes error 'ompi_dpm_dyn_init() | |
411 | ;; failed --> Returned "Unreachable"' in chroot environment). | |
412 | (substitute* "test/test_spawn.py" | |
413 | (("unittest.skipMPI\\('openmpi\\(<3.0.0\\)'\\)") | |
414 | "unittest.skipMPI('openmpi')")) | |
415 | #t))))) | |
416 | (inputs | |
417 | `(("openmpi" ,openmpi))) | |
418 | (home-page "https://bitbucket.org/mpi4py/mpi4py/") | |
419 | (synopsis "Python bindings for the Message Passing Interface standard") | |
420 | (description "MPI for Python (mpi4py) provides bindings of the Message | |
421 | Passing Interface (MPI) standard for the Python programming language, allowing | |
422 | any Python program to exploit multiple processors. | |
423 | ||
424 | mpi4py is constructed on top of the MPI-1/MPI-2 specification and provides an | |
425 | object oriented interface which closely follows MPI-2 C++ bindings. It | |
426 | supports point-to-point and collective communications of any picklable Python | |
427 | object as well as optimized communications of Python objects (such as NumPy | |
428 | arrays) that expose a buffer interface.") | |
15e62623 | 429 | (license license:bsd-3))) |
c70261bf MB |
430 | |
431 | (define-public mpich | |
432 | (package | |
433 | (name "mpich") | |
434 | (version "3.3.2") | |
435 | (source (origin | |
436 | (method url-fetch) | |
437 | (uri (string-append "http://www.mpich.org/static/downloads/" | |
438 | version "/mpich-" version ".tar.gz")) | |
439 | (sha256 | |
440 | (base32 | |
441 | "1farz5zfx4cd0c3a0wb9pgfypzw0xxql1j1294z1sxslga1ziyjb")))) | |
442 | (build-system gnu-build-system) | |
443 | (inputs | |
444 | `(("zlib" ,zlib) | |
445 | ("hwloc" ,hwloc-2 "lib") | |
446 | ("slurm" ,slurm) | |
447 | ,@(if (and (not (%current-target-system)) | |
448 | (member (%current-system) (package-supported-systems ucx))) | |
449 | `(("ucx" ,ucx)) | |
450 | '()))) | |
451 | (native-inputs | |
452 | `(("perl" ,perl) | |
453 | ("which" ,which) | |
454 | ("gfortran" ,gfortran))) | |
455 | (outputs '("out" "debug")) | |
456 | (arguments | |
457 | `(#:configure-flags | |
458 | (list "--disable-silent-rules" ;let's see what's happening | |
459 | "--enable-debuginfo" | |
c73496f4 LC |
460 | |
461 | ;; Default to "ch4", as will be the case in 3.4. It also works | |
462 | ;; around issues when running test suites of packages that use | |
463 | ;; MPICH: <https://issues.guix.gnu.org/39588#15>. | |
464 | "--with-device=ch4:ucx" ; --with-device=ch4:ofi segfaults in tests | |
465 | ||
c70261bf MB |
466 | (string-append "--with-hwloc-prefix=" |
467 | (assoc-ref %build-inputs "hwloc")) | |
468 | ||
469 | ,@(if (assoc "ucx" (package-inputs this-package)) | |
470 | `((string-append "--with-ucx=" | |
471 | (assoc-ref %build-inputs "ucx"))) | |
472 | '())) | |
473 | ||
474 | #:phases (modify-phases %standard-phases | |
475 | (add-after 'unpack 'patch-sources | |
476 | (lambda _ | |
477 | (substitute* "./maint/gen_subcfg_m4" | |
478 | (("/usr/bin/env") (which "env"))) | |
479 | (substitute* "src/glue/romio/all_romio_symbols" | |
480 | (("/usr/bin/env") (which "env"))) | |
481 | (substitute* (find-files "." "buildiface") | |
482 | (("/usr/bin/env") (which "env"))) | |
483 | (substitute* "maint/extracterrmsgs" | |
484 | (("/usr/bin/env") (which "env"))) | |
485 | (substitute* (find-files "." "f77tof90") | |
486 | (("/usr/bin/env") (which "env"))) | |
487 | (substitute* (find-files "." "\\.sh$") | |
488 | (("/bin/sh") (which "sh"))) | |
489 | #t)) | |
490 | (add-before 'configure 'fix-makefile | |
491 | (lambda _ | |
492 | ;; Remove "@hwloclib@" from 'pmpi_convenience_libs'. | |
493 | ;; This fixes "No rule to make target '-lhwloc', needed | |
494 | ;; by 'lib/libmpi.la'". | |
495 | (substitute* "Makefile.in" | |
496 | (("^pmpi_convenience_libs = (.*) @hwloclib@ (.*)$" _ | |
497 | before after) | |
498 | (string-append "pmpi_convenience_libs = " | |
499 | before " " after))) | |
500 | #t))))) | |
501 | (home-page "https://www.mpich.org/") | |
502 | (synopsis "Implementation of the Message Passing Interface (MPI)") | |
503 | (description | |
504 | "MPICH is a high-performance and portable implementation of the Message | |
505 | Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3). MPICH provides an | |
506 | MPI implementation that efficiently supports different computation and | |
507 | communication platforms including commodity clusters, high-speed networks (10 | |
508 | Gigabit Ethernet, InfiniBand, Myrinet, Quadrics), and proprietary high-end | |
509 | computing systems (Blue Gene, Cray). It enables research in MPI through a | |
510 | modular framework for other derived implementations.") | |
15e62623 | 511 | (license license:bsd-2))) |