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> |
fe390200 | 8 | ;;; Copyright © 2018, 2019 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) |
8c8e1089 | 33 | #:use-module (guix deprecation) |
fb0e3709 | 34 | #:use-module (guix build-system gnu) |
54fcd547 | 35 | #:use-module (guix build-system python) |
fb0e3709 | 36 | #:use-module (gnu packages) |
e9823f9c | 37 | #:use-module (gnu packages fabric-management) |
fb0e3709 | 38 | #:use-module (gnu packages gcc) |
fa5a2538 | 39 | #:use-module (gnu packages java) |
41313ace | 40 | #:use-module (gnu packages libevent) |
2b0d560a LC |
41 | #:use-module (gnu packages linux) |
42 | #:use-module (gnu packages pciutils) | |
43 | #:use-module (gnu packages xorg) | |
44 | #:use-module (gnu packages gtk) | |
45 | #:use-module (gnu packages xml) | |
38f0a2ba | 46 | #:use-module (gnu packages perl) |
2b0d560a | 47 | #:use-module (gnu packages ncurses) |
b07712bf | 48 | #:use-module (gnu packages parallel) |
2b0d560a | 49 | #:use-module (gnu packages pkg-config) |
91298042 | 50 | #:use-module (gnu packages valgrind) |
71e78931 | 51 | #:use-module (srfi srfi-1) |
91298042 | 52 | #:use-module (ice-9 match)) |
fb0e3709 | 53 | |
8ec7ca22 | 54 | (define-public hwloc-1 |
71e78931 LC |
55 | ;; Note: For now we keep 1.x as the default because many packages have yet |
56 | ;; to migrate to 2.0. | |
2b0d560a LC |
57 | (package |
58 | (name "hwloc") | |
9dd50845 | 59 | (version "1.11.12") |
2b0d560a LC |
60 | (source (origin |
61 | (method url-fetch) | |
a2d0e200 | 62 | (uri (string-append "https://www.open-mpi.org/software/hwloc/v" |
ce7d9c98 EB |
63 | (version-major+minor version) |
64 | "/downloads/hwloc-" version ".tar.bz2")) | |
2b0d560a LC |
65 | (sha256 |
66 | (base32 | |
9dd50845 | 67 | "0za1b9lvrm3rhn0lrxja5f64r0aq1qs4m0pxn1ji2mbi8ndppyyx")))) |
2b0d560a | 68 | (build-system gnu-build-system) |
798b7678 LC |
69 | (outputs '("out" ;'lstopo' & co., depends on Cairo, libx11, etc. |
70 | "lib" ;small closure | |
71 | "debug")) | |
2b0d560a | 72 | (inputs |
5b527256 | 73 | `(("libx11" ,libx11) |
2b0d560a LC |
74 | ("cairo" ,cairo) |
75 | ("ncurses" ,ncurses) | |
37d6b097 AE |
76 | ("expat" ,expat) |
77 | ,@(if (not (string-prefix? "armhf" | |
78 | (or (%current-target-system) | |
79 | (%current-system)))) | |
80 | `(("numactl" ,numactl)) | |
81 | '()))) | |
c6e59259 LC |
82 | (propagated-inputs |
83 | ;; hwloc.pc lists it in 'Requires.private'. | |
84 | `(("libpciaccess" ,libpciaccess))) | |
2b0d560a LC |
85 | (native-inputs |
86 | `(("pkg-config" ,pkg-config))) | |
579f5c8a | 87 | (arguments |
7eb9f31c LC |
88 | `(#:configure-flags '("--localstatedir=/var") |
89 | #:phases | |
579f5c8a | 90 | (modify-phases %standard-phases |
10de06bd LC |
91 | (add-before 'check 'skip-linux-libnuma-test |
92 | (lambda _ | |
93 | ;; Arrange to skip 'tests/linux-libnuma', which fails on some | |
94 | ;; machines: <https://github.com/open-mpi/hwloc/issues/213>. | |
95 | (substitute* "tests/linux-libnuma.c" | |
96 | (("numa_available\\(\\)") | |
97 | "-1")) | |
98 | #t)) | |
798b7678 LC |
99 | (add-after 'install 'refine-libnuma |
100 | ;; Give -L arguments for libraries to avoid propagation | |
101 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
102 | (let ((out (assoc-ref outputs "lib")) | |
103 | (numa (assoc-ref inputs "numactl"))) | |
104 | (substitute* (map (lambda (f) (string-append out "/" f)) | |
105 | '("lib/pkgconfig/hwloc.pc" "lib/libhwloc.la")) | |
106 | (("-lnuma" lib) | |
107 | (string-append "-L" numa "/lib " lib)))))) | |
108 | (add-after 'install 'avoid-circular-references | |
109 | (lambda* (#:key outputs #:allow-other-keys) | |
110 | (let ((lib (assoc-ref outputs "lib"))) | |
111 | ;; Suppress the 'prefix=' and 'exec_prefix=' lines so that the | |
112 | ;; "lib" output doesn't refer to "out". | |
113 | (substitute* (string-append lib "/lib/pkgconfig/hwloc.pc") | |
114 | (("^.*prefix=.*$") | |
115 | "")) | |
116 | #t)))))) | |
a2d0e200 | 117 | (home-page "https://www.open-mpi.org/projects/hwloc/") |
2b0d560a LC |
118 | (synopsis "Abstraction of hardware architectures") |
119 | (description | |
120 | "hwloc provides a portable abstraction (across OS, | |
121 | versions, architectures, ...) of the hierarchical topology of modern | |
122 | architectures, including NUMA memory nodes, sockets, shared caches, cores and | |
123 | simultaneous multithreading. It also gathers various attributes such as cache | |
124 | and memory information. It primarily aims at helping high-performance | |
125 | computing applications with gathering information about the hardware so as to | |
126 | exploit it accordingly and efficiently. | |
127 | ||
128 | hwloc may display the topology in multiple convenient formats. It also offers | |
129 | a powerful programming interface to gather information about the hardware, | |
130 | bind processes, and much more.") | |
2b0d560a LC |
131 | (license bsd-3))) |
132 | ||
8c8e1089 | 133 | (define-public hwloc-2 |
71e78931 LC |
134 | ;; Note: 2.0 isn't the default yet, see above. |
135 | (package | |
8ec7ca22 | 136 | (inherit hwloc-1) |
8c8e1089 | 137 | (version "2.1.0") |
71e78931 LC |
138 | (source (origin |
139 | (method url-fetch) | |
140 | (uri (string-append "https://www.open-mpi.org/software/hwloc/v" | |
141 | (version-major+minor version) | |
142 | "/downloads/hwloc-" version ".tar.bz2")) | |
143 | (sha256 | |
144 | (base32 | |
8c8e1089 | 145 | "0qh8s7pphz0m5cwb7liqmc17xzfs23xhz5wn24r6ikvjyx99fhhr")))) |
71e78931 LC |
146 | |
147 | ;; libnuma is no longer needed. | |
0d8a8234 | 148 | (inputs (alist-delete "numactl" (package-inputs hwloc-1))) |
10de06bd | 149 | (arguments |
0d8a8234 | 150 | (substitute-keyword-arguments (package-arguments hwloc-1) |
10de06bd LC |
151 | ((#:phases phases) |
152 | `(modify-phases ,phases | |
153 | (replace 'skip-linux-libnuma-test | |
154 | (lambda _ | |
155 | ;; Arrange to skip 'tests/hwloc/linux-libnuma', which fails on | |
156 | ;; some machines: <https://github.com/open-mpi/hwloc/issues/213>. | |
157 | (substitute* "tests/hwloc/linux-libnuma.c" | |
158 | (("numa_available\\(\\)") | |
159 | "-1")) | |
160 | #t)))))))) | |
71e78931 | 161 | |
8c8e1089 LC |
162 | (define-deprecated hwloc-2.0 'hwloc-2 |
163 | hwloc-2) | |
164 | ||
8ec7ca22 LC |
165 | (define-public hwloc |
166 | ;; The latest stable series of hwloc. | |
167 | hwloc-2) | |
168 | ||
fb0e3709 EB |
169 | (define-public openmpi |
170 | (package | |
171 | (name "openmpi") | |
8f02e5ac | 172 | (version "4.0.2") |
fb0e3709 EB |
173 | (source |
174 | (origin | |
175 | (method url-fetch) | |
6876590f | 176 | (uri (string-append "https://www.open-mpi.org/software/ompi/v" |
29a7c98a | 177 | (version-major+minor version) |
fb0e3709 EB |
178 | "/downloads/openmpi-" version ".tar.bz2")) |
179 | (sha256 | |
faab7082 | 180 | (base32 "0ms0zvyxyy3pnx9qwib6zaljyp2b3ixny64xvq3czv3jpr8zf2wh")) |
68ac34e1 | 181 | (patches (search-patches "openmpi-mtl-priorities.patch")))) |
fb0e3709 | 182 | (build-system gnu-build-system) |
5b527256 | 183 | (inputs |
58a536bb | 184 | `(("hwloc" ,hwloc-2 "lib") |
19afbea1 | 185 | ("gfortran" ,gfortran) |
a0995702 | 186 | ("libfabric" ,libfabric) |
41313ace | 187 | ("libevent" ,libevent) |
e9823f9c | 188 | ("opensm" ,opensm) |
a560641a LC |
189 | ,@(if (and (not (%current-target-system)) |
190 | (member (%current-system) (package-supported-systems psm))) | |
191 | `(("psm" ,psm)) | |
192 | '()) | |
fbe1b85b LC |
193 | ,@(if (and (not (%current-target-system)) |
194 | (member (%current-system) (package-supported-systems psm2))) | |
195 | `(("psm2" ,psm2)) | |
196 | '()) | |
8ba94edd | 197 | ,@(if (and (not (%current-target-system)) |
96a469f1 | 198 | (member (%current-system) (package-supported-systems ucx))) |
8ba94edd LC |
199 | `(("ucx" ,ucx)) |
200 | '()) | |
a0995702 | 201 | ("rdma-core" ,rdma-core) |
b07712bf LC |
202 | ("valgrind" ,valgrind) |
203 | ("slurm" ,slurm))) ;for PMI support (launching via "srun") | |
5b527256 | 204 | (native-inputs |
38f0a2ba EB |
205 | `(("pkg-config" ,pkg-config) |
206 | ("perl" ,perl))) | |
c971d9ef | 207 | (outputs '("out" "debug")) |
fb0e3709 | 208 | (arguments |
b08952f1 | 209 | `(#:configure-flags `("--enable-mpi-ext=affinity" ;cr doesn't work |
1691b4cd | 210 | "--enable-memchecker" |
efcacc17 | 211 | "--with-sge" |
41313ace EB |
212 | "--with-valgrind" |
213 | "--with-hwloc=external" | |
214 | "--with-libevent" | |
e9823f9c RW |
215 | |
216 | ;; InfiniBand support | |
217 | "--enable-openib-control-hdr-padding" | |
218 | "--enable-openib-dynamic-sl" | |
219 | "--enable-openib-udcm" | |
220 | "--enable-openib-rdmacm" | |
221 | "--enable-openib-rdmacm-ibaddr" | |
222 | ||
b07712bf LC |
223 | ;; Enable support for SLURM's Process Manager |
224 | ;; Interface (PMI). | |
225 | ,(string-append "--with-pmi=" | |
226 | (assoc-ref %build-inputs "slurm"))) | |
9474a4b3 | 227 | #:phases (modify-phases %standard-phases |
e9823f9c RW |
228 | ;; opensm is needed for InfiniBand support. |
229 | (add-after 'unpack 'find-opensm-headers | |
230 | (lambda* (#:key inputs #:allow-other-keys) | |
231 | (setenv "C_INCLUDE_PATH" | |
232 | (string-append (assoc-ref inputs "opensm") | |
97149c57 | 233 | "/include/infiniband")) |
e9823f9c RW |
234 | (setenv "CPLUS_INCLUDE_PATH" |
235 | (string-append (assoc-ref inputs "opensm") | |
97149c57 | 236 | "/include/infiniband")) |
e9823f9c | 237 | #t)) |
0d97d3cb | 238 | (add-before 'build 'remove-absolute |
0d97d3cb | 239 | (lambda _ |
a247fe7b DL |
240 | ;; Remove compiler absolute file names (OPAL_FC_ABSOLUTE |
241 | ;; etc.) to reduce the closure size. See | |
242 | ;; <https://lists.gnu.org/archive/html/guix-devel/2017-07/msg00388.html> | |
243 | ;; and | |
244 | ;; <https://www.mail-archive.com/users@lists.open-mpi.org//msg31397.html>. | |
0d97d3cb DL |
245 | (substitute* '("orte/tools/orte-info/param.c" |
246 | "oshmem/tools/oshmem_info/param.c" | |
247 | "ompi/tools/ompi_info/param.c") | |
248 | (("_ABSOLUTE") "")) | |
a247fe7b DL |
249 | ;; Avoid valgrind (which pulls in gdb etc.). |
250 | (substitute* | |
41313ace EB |
251 | '("./ompi/mca/io/romio321/src/io_romio321_component.c") |
252 | (("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS") | |
a247fe7b | 253 | "\"[elided to reduce closure]\"")) |
0d97d3cb | 254 | #t)) |
9474a4b3 EB |
255 | (add-before 'build 'scrub-timestamps ;reproducibility |
256 | (lambda _ | |
257 | (substitute* '("ompi/tools/ompi_info/param.c" | |
258 | "orte/tools/orte-info/param.c" | |
259 | "oshmem/tools/oshmem_info/param.c") | |
260 | ((".*(Built|Configured) on.*") "")) | |
261 | #t)) | |
262 | (add-after 'install 'remove-logs ;reproducibility | |
263 | (lambda* (#:key outputs #:allow-other-keys) | |
264 | (let ((out (assoc-ref outputs "out"))) | |
265 | (for-each delete-file (find-files out "config.log")) | |
266 | #t)))))) | |
fb0e3709 | 267 | (home-page "http://www.open-mpi.org") |
bb0f6d75 | 268 | (synopsis "MPI-3 implementation") |
fb0e3709 | 269 | (description |
bb0f6d75 | 270 | "The Open MPI Project is an MPI-3 implementation that is developed and |
8ede638c EB |
271 | maintained by a consortium of academic, research, and industry partners. Open |
272 | MPI is therefore able to combine the expertise, technologies, and resources | |
273 | from all across the High Performance Computing community in order to build the | |
274 | best MPI library available. Open MPI offers advantages for system and | |
275 | software vendors, application developers and computer science researchers.") | |
fb0e3709 EB |
276 | ;; See file://LICENSE |
277 | (license bsd-2))) | |
685bef2b | 278 | |
fa5a2538 RW |
279 | ;; TODO: javadoc files contain timestamps. |
280 | (define-public java-openmpi | |
281 | (package (inherit openmpi) | |
282 | (name "java-openmpi") | |
283 | (inputs | |
284 | `(("openmpi" ,openmpi) | |
285 | ,@(package-inputs openmpi))) | |
286 | (native-inputs | |
287 | `(("jdk" ,openjdk11 "jdk") | |
288 | ("zip" ,(@ (gnu packages compression) zip)) | |
289 | ,@(package-native-inputs openmpi))) | |
290 | (outputs '("out")) | |
291 | (arguments | |
292 | `(#:modules ((guix build gnu-build-system) | |
293 | ((guix build ant-build-system) #:prefix ant:) | |
294 | (guix build utils)) | |
295 | #:imported-modules ((guix build ant-build-system) | |
296 | (guix build syscalls) | |
297 | ,@%gnu-build-system-modules) | |
298 | ,@(substitute-keyword-arguments (package-arguments openmpi) | |
299 | ((#:configure-flags flags) | |
300 | `(cons "--enable-mpi-java" ,flags)) | |
301 | ((#:make-flags flags ''()) | |
302 | `(append '("-C" "ompi/mpi/java") | |
303 | ,flags)) | |
304 | ((#:phases phases) | |
305 | `(modify-phases ,phases | |
306 | ;; We could provide the location of the JDK in the configure | |
307 | ;; flags, but since the configure flags are embedded in the | |
308 | ;; info binaries that would leave a reference to the JDK in | |
309 | ;; the "out" output. To avoid this we set JAVA_HOME. | |
310 | (add-after 'unpack 'set-JAVA_HOME | |
311 | (lambda* (#:key inputs #:allow-other-keys) | |
312 | (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) | |
313 | #t)) | |
314 | (add-after 'unpack 'link-with-existing-mpi-libraries | |
315 | (lambda* (#:key inputs #:allow-other-keys) | |
316 | (substitute* "ompi/mpi/java/c/Makefile.in" | |
317 | (("\\$\\(top_builddir\\)/ompi/lib@OMPI_LIBMPI_NAME@.la") | |
318 | (string-append (assoc-ref inputs "openmpi") "/lib/libmpi.la"))) | |
319 | #t)) | |
320 | (add-after 'install 'strip-jar-timestamps | |
321 | (assoc-ref ant:%standard-phases 'strip-jar-timestamps))))))) | |
322 | (synopsis "Java bindings for MPI"))) | |
323 | ||
685bef2b DL |
324 | (define-public openmpi-thread-multiple |
325 | (package | |
326 | (inherit openmpi) | |
327 | (name "openmpi-thread-multiple") | |
328 | (arguments | |
329 | (substitute-keyword-arguments (package-arguments openmpi) | |
330 | ((#:configure-flags flags) | |
331 | `(cons "--enable-mpi-thread-multiple" ,flags)))) | |
332 | (description " This version of Open@tie{}MPI has an implementation of | |
333 | @code{MPI_Init_thread} that provides @code{MPI_THREAD_MULTIPLE}. This won't | |
334 | work correctly with all transports (such as @code{openib}), and the | |
335 | performance is generally worse than the vanilla @code{openmpi} package, which | |
336 | only provides @code{MPI_THREAD_FUNNELED}."))) | |
bbe46a4a EB |
337 | |
338 | ;;; Build phase to be used for packages that execute MPI code. | |
339 | (define-public %openmpi-setup | |
340 | '(lambda _ | |
341 | ;; By default, running the test suite would fail because 'ssh' could not | |
342 | ;; be found in $PATH. Define this variable to placate Open MPI without | |
343 | ;; adding a dependency on OpenSSH (the agent isn't used anyway.) | |
344 | (setenv "OMPI_MCA_plm_rsh_agent" (which "false")) | |
345 | ;; Allow oversubscription in case there are less physical cores available | |
346 | ;; in the build environment than the package wants while testing. | |
41313ace | 347 | (setenv "OMPI_MCA_rmaps_base_mapping_policy" "core:OVERSUBSCRIBE") |
b1077c22 LC |
348 | |
349 | ;; UCX sometimes outputs uninteresting warnings such as: | |
350 | ;; | |
351 | ;; mpool.c:38 UCX WARN object 0x7ffff44fffc0 was not returned to mpool ucp_am_bufs | |
352 | ;; | |
353 | ;; These in turn leads to failures of test suites that capture and | |
354 | ;; compare stdout, such as that of 'hdf5-parallel-openmpi'. Thus, tell | |
355 | ;; UCX to not emit those warnings. | |
356 | (setenv "UCX_LOG_LEVEL" "error") | |
bbe46a4a | 357 | #t)) |
54fcd547 PG |
358 | |
359 | (define-public python-mpi4py | |
360 | (package | |
361 | (name "python-mpi4py") | |
fe390200 | 362 | (version "3.0.3") |
54fcd547 | 363 | (source |
fe390200 TGR |
364 | (origin |
365 | (method url-fetch) | |
366 | (uri (pypi-uri "mpi4py" version)) | |
367 | (sha256 | |
368 | (base32 "07ssbhssv27rrjx1c5vd3vsr31vay5d8xcf4zh9yblcyidn72b81")))) | |
54fcd547 PG |
369 | (build-system python-build-system) |
370 | (arguments | |
371 | `(#:phases | |
372 | (modify-phases %standard-phases | |
373 | (add-after 'build 'mpi-setup | |
374 | ,%openmpi-setup) | |
375 | (add-before 'check 'pre-check | |
376 | (lambda _ | |
377 | ;; Skip BaseTestSpawn class (causes error 'ompi_dpm_dyn_init() | |
378 | ;; failed --> Returned "Unreachable"' in chroot environment). | |
379 | (substitute* "test/test_spawn.py" | |
380 | (("unittest.skipMPI\\('openmpi\\(<3.0.0\\)'\\)") | |
381 | "unittest.skipMPI('openmpi')")) | |
382 | #t))))) | |
383 | (inputs | |
384 | `(("openmpi" ,openmpi))) | |
385 | (home-page "https://bitbucket.org/mpi4py/mpi4py/") | |
386 | (synopsis "Python bindings for the Message Passing Interface standard") | |
387 | (description "MPI for Python (mpi4py) provides bindings of the Message | |
388 | Passing Interface (MPI) standard for the Python programming language, allowing | |
389 | any Python program to exploit multiple processors. | |
390 | ||
391 | mpi4py is constructed on top of the MPI-1/MPI-2 specification and provides an | |
392 | object oriented interface which closely follows MPI-2 C++ bindings. It | |
393 | supports point-to-point and collective communications of any picklable Python | |
394 | object as well as optimized communications of Python objects (such as NumPy | |
395 | arrays) that expose a buffer interface.") | |
396 | (license bsd-3))) |