summaryrefslogtreecommitdiff
path: root/gnu/packages/mpi.scm
blob: 9f6597c6b356d47767e86f902d8aea1e4067d2c4 (plain)
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
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015, 2018, 2019 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2017 Dave Love <fx@gnu.org>
;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; 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 mpi)
  #:use-module (guix packages)
  #:use-module ((guix licenses)
                #:hide (expat))
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix utils)
  #:use-module (guix deprecation)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system python)
  #:use-module (gnu packages)
  #:use-module (gnu packages fabric-management)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages java)
  #:use-module (gnu packages libevent)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages pciutils)
  #:use-module (gnu packages xorg)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages parallel)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages valgrind)
  #:use-module (srfi srfi-1)
  #:use-module (ice-9 match))

(define-public hwloc-1
  ;; Note: For now we keep 1.x as the default because many packages have yet
  ;; to migrate to 2.0.
  (package
    (name "hwloc")
    (version "1.11.12")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://www.open-mpi.org/software/hwloc/v"
                                  (version-major+minor version)
                                  "/downloads/hwloc-" version ".tar.bz2"))
              (sha256
               (base32
                "0za1b9lvrm3rhn0lrxja5f64r0aq1qs4m0pxn1ji2mbi8ndppyyx"))))
    (build-system gnu-build-system)
    (outputs '("out"           ;'lstopo' & co., depends on Cairo, libx11, etc.
               "lib"           ;small closure
               "debug"))
    (inputs
     `(("libx11" ,libx11)
       ("cairo" ,cairo)
       ("ncurses" ,ncurses)
       ("expat" ,expat)
       ,@(if (not (string-prefix? "armhf"
                                  (or (%current-target-system)
                                      (%current-system))))
             `(("numactl" ,numactl))
             '())))
    (propagated-inputs
     ;; hwloc.pc lists it in 'Requires.private'.
     `(("libpciaccess" ,libpciaccess)))
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (arguments
     `(#:configure-flags '("--localstatedir=/var")
       #:phases
       (modify-phases %standard-phases
         (add-before 'check 'skip-linux-libnuma-test
           (lambda _
             ;; Arrange to skip 'tests/linux-libnuma', which fails on some
             ;; machines: <https://github.com/open-mpi/hwloc/issues/213>.
             (substitute* "tests/linux-libnuma.c"
               (("numa_available\\(\\)")
                "-1"))
             #t))
         (add-after 'install 'refine-libnuma
           ;; Give -L arguments for libraries to avoid propagation
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let ((out  (assoc-ref outputs "lib"))
                   (numa (assoc-ref inputs "numactl")))
               (substitute* (map (lambda (f) (string-append out "/" f))
                                 '("lib/pkgconfig/hwloc.pc" "lib/libhwloc.la"))
                 (("-lnuma" lib)
                  (string-append "-L" numa "/lib " lib))))))
         (add-after 'install 'avoid-circular-references
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((lib (assoc-ref outputs "lib")))
               ;; Suppress the 'prefix=' and 'exec_prefix=' lines so that the
               ;; "lib" output doesn't refer to "out".
               (substitute* (string-append lib "/lib/pkgconfig/hwloc.pc")
                 (("^.*prefix=.*$")
                  ""))
               #t))))))
    (home-page "https://www.open-mpi.org/projects/hwloc/")
    (synopsis "Abstraction of hardware architectures")
    (description
     "hwloc provides a portable abstraction (across OS,
versions, architectures, ...) of the hierarchical topology of modern
architectures, including NUMA memory nodes, sockets, shared caches, cores and
simultaneous multithreading.  It also gathers various attributes such as cache
and memory information.  It primarily aims at helping high-performance
computing applications with gathering information about the hardware so as to
exploit it accordingly and efficiently.

hwloc may display the topology in multiple convenient formats.  It also offers
a powerful programming interface to gather information about the hardware,
bind processes, and much more.")
    (license bsd-3)))

(define-public hwloc-2
  ;; Note: 2.0 isn't the default yet, see above.
  (package
    (inherit hwloc-1)
    (version "2.1.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://www.open-mpi.org/software/hwloc/v"
                                  (version-major+minor version)
                                  "/downloads/hwloc-" version ".tar.bz2"))
              (sha256
               (base32
                "0qh8s7pphz0m5cwb7liqmc17xzfs23xhz5wn24r6ikvjyx99fhhr"))))

    ;; libnuma is no longer needed.
    (inputs (alist-delete "numactl" (package-inputs hwloc-1)))
    (arguments
     (substitute-keyword-arguments (package-arguments hwloc-1)
       ((#:phases phases)
        `(modify-phases ,phases
           (replace 'skip-linux-libnuma-test
             (lambda _
               ;; Arrange to skip 'tests/hwloc/linux-libnuma', which fails on
               ;; some machines: <https://github.com/open-mpi/hwloc/issues/213>.
               (substitute* "tests/hwloc/linux-libnuma.c"
                 (("numa_available\\(\\)")
                  "-1"))
               #t))))))))

(define-deprecated hwloc-2.0 'hwloc-2
  hwloc-2)

(define-public hwloc
  ;; The latest stable series of hwloc.
  hwloc-2)

(define-public openmpi
  (package
    (name "openmpi")
    (version "4.0.2")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://www.open-mpi.org/software/ompi/v"
                          (version-major+minor version)
                          "/downloads/openmpi-" version ".tar.bz2"))
      (sha256
       (base32 "0ms0zvyxyy3pnx9qwib6zaljyp2b3ixny64xvq3czv3jpr8zf2wh"))
      (patches (search-patches "openmpi-psm2-priority.patch"))))
    (build-system gnu-build-system)
    (inputs
     `(("hwloc" ,hwloc-2 "lib")
       ("gfortran" ,gfortran)
       ("libfabric" ,libfabric)
       ("libevent" ,libevent)
       ("opensm" ,opensm)
       ,@(if (and (not (%current-target-system))
                  (member (%current-system) (package-supported-systems psm)))
             `(("psm" ,psm))
             '())
       ,@(if (and (not (%current-target-system))
                  (member (%current-system) (package-supported-systems psm2)))
             `(("psm2" ,psm2))
             '())
       ,@(if (and (not (%current-target-system))
                  (member (%current-system) (package-supported-systems ucx)))
             `(("ucx" ,ucx))
             '())
       ("rdma-core" ,rdma-core)
       ("valgrind" ,valgrind)
       ("slurm" ,slurm)))              ;for PMI support (launching via "srun")
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("perl" ,perl)))
    (outputs '("out" "debug"))
    (arguments
     `(#:configure-flags `("--enable-mpi-ext=affinity" ;cr doesn't work
                           "--enable-memchecker"
                           "--with-sge"
                           "--with-valgrind"
                           "--with-hwloc=external"
                           "--with-libevent"

                           ;; InfiniBand support
                           "--enable-openib-control-hdr-padding"
                           "--enable-openib-dynamic-sl"
                           "--enable-openib-udcm"
                           "--enable-openib-rdmacm"
                           "--enable-openib-rdmacm-ibaddr"

                           ;; Enable support for SLURM's Process Manager
                           ;; Interface (PMI).
                           ,(string-append "--with-pmi="
                                           (assoc-ref %build-inputs "slurm")))
       #:phases (modify-phases %standard-phases
                  ;; opensm is needed for InfiniBand support.
                  (add-after 'unpack 'find-opensm-headers
                    (lambda* (#:key inputs #:allow-other-keys)
                      (setenv "C_INCLUDE_PATH"
                              (string-append (assoc-ref inputs "opensm")
                                             "/include/infiniband"))
                      (setenv "CPLUS_INCLUDE_PATH"
                              (string-append (assoc-ref inputs "opensm")
                                             "/include/infiniband"))
                      #t))
                  (add-before 'build 'remove-absolute
                    (lambda _
                      ;; Remove compiler absolute file names (OPAL_FC_ABSOLUTE
                      ;; etc.) to reduce the closure size.  See
                      ;; <https://lists.gnu.org/archive/html/guix-devel/2017-07/msg00388.html>
                      ;; and
                      ;; <https://www.mail-archive.com/users@lists.open-mpi.org//msg31397.html>.
                      (substitute* '("orte/tools/orte-info/param.c"
                                     "oshmem/tools/oshmem_info/param.c"
                                     "ompi/tools/ompi_info/param.c")
                        (("_ABSOLUTE") ""))
                      ;; Avoid valgrind (which pulls in gdb etc.).
                      (substitute*
                          '("./ompi/mca/io/romio321/src/io_romio321_component.c")
                        (("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS")
                         "\"[elided to reduce closure]\""))
                      #t))
                  (add-before 'build 'scrub-timestamps ;reproducibility
                    (lambda _
                      (substitute* '("ompi/tools/ompi_info/param.c"
                                     "orte/tools/orte-info/param.c"
                                     "oshmem/tools/oshmem_info/param.c")
                        ((".*(Built|Configured) on.*") ""))
                      #t))
                  (add-after 'install 'remove-logs ;reproducibility
                    (lambda* (#:key outputs #:allow-other-keys)
                      (let ((out (assoc-ref outputs "out")))
                        (for-each delete-file (find-files out "config.log"))
                        #t))))))
    (home-page "http://www.open-mpi.org")
    (synopsis "MPI-3 implementation")
    (description
     "The Open MPI Project is an MPI-3 implementation that is developed and
maintained by a consortium of academic, research, and industry partners.  Open
MPI is therefore able to combine the expertise, technologies, and resources
from all across the High Performance Computing community in order to build the
best MPI library available.  Open MPI offers advantages for system and
software vendors, application developers and computer science researchers.")
    ;; See file://LICENSE
    (license bsd-2)))

;; TODO: javadoc files contain timestamps.
(define-public java-openmpi
  (package (inherit openmpi)
    (name "java-openmpi")
    (inputs
     `(("openmpi" ,openmpi)
       ,@(package-inputs openmpi)))
    (native-inputs
     `(("jdk" ,openjdk11 "jdk")
       ("zip" ,(@ (gnu packages compression) zip))
       ,@(package-native-inputs openmpi)))
    (outputs '("out"))
    (arguments
     `(#:modules ((guix build gnu-build-system)
                  ((guix build ant-build-system) #:prefix ant:)
                  (guix build utils))
       #:imported-modules ((guix build ant-build-system)
                           (guix build syscalls)
                           ,@%gnu-build-system-modules)
       ,@(substitute-keyword-arguments (package-arguments openmpi)
           ((#:configure-flags flags)
            `(cons "--enable-mpi-java" ,flags))
           ((#:make-flags flags ''())
            `(append '("-C" "ompi/mpi/java")
                     ,flags))
           ((#:phases phases)
            `(modify-phases ,phases
               ;; We could provide the location of the JDK in the configure
               ;; flags, but since the configure flags are embedded in the
               ;; info binaries that would leave a reference to the JDK in
               ;; the "out" output.  To avoid this we set JAVA_HOME.
               (add-after 'unpack 'set-JAVA_HOME
                 (lambda* (#:key inputs #:allow-other-keys)
                   (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
                   #t))
               (add-after 'unpack 'link-with-existing-mpi-libraries
                 (lambda* (#:key inputs #:allow-other-keys)
                   (substitute* "ompi/mpi/java/c/Makefile.in"
                     (("\\$\\(top_builddir\\)/ompi/lib@OMPI_LIBMPI_NAME@.la")
                      (string-append (assoc-ref inputs "openmpi") "/lib/libmpi.la")))
                   #t))
               (add-after 'install 'strip-jar-timestamps
                 (assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))))
    (synopsis "Java bindings for MPI")))

(define-public openmpi-thread-multiple
  (package
    (inherit openmpi)
    (name "openmpi-thread-multiple")
    (arguments
     (substitute-keyword-arguments (package-arguments openmpi)
       ((#:configure-flags flags)
        `(cons "--enable-mpi-thread-multiple" ,flags))))
    (description " This version of Open@tie{}MPI has an implementation of
@code{MPI_Init_thread} that provides @code{MPI_THREAD_MULTIPLE}.  This won't
work correctly with all transports (such as @code{openib}), and the
performance is generally worse than the vanilla @code{openmpi} package, which
only provides @code{MPI_THREAD_FUNNELED}.")))

;;; Build phase to be used for packages that execute MPI code.
(define-public %openmpi-setup
  '(lambda _
     ;; By default, running the test suite would fail because 'ssh' could not
     ;; be found in $PATH.  Define this variable to placate Open MPI without
     ;; adding a dependency on OpenSSH (the agent isn't used anyway.)
     (setenv "OMPI_MCA_plm_rsh_agent" (which "false"))
     ;; Allow oversubscription in case there are less physical cores available
     ;; in the build environment than the package wants while testing.
     (setenv "OMPI_MCA_rmaps_base_mapping_policy" "core:OVERSUBSCRIBE")

     ;; UCX sometimes outputs uninteresting warnings such as:
     ;;
     ;;   mpool.c:38   UCX  WARN  object 0x7ffff44fffc0 was not returned to mpool ucp_am_bufs
     ;;
     ;; These in turn leads to failures of test suites that capture and
     ;; compare stdout, such as that of 'hdf5-parallel-openmpi'.  Thus, tell
     ;; UCX to not emit those warnings.
     (setenv "UCX_LOG_LEVEL" "error")
     #t))

(define-public intel-mpi-benchmarks
  (package
    (name "intel-mpi-benchmarks")
    (version "2019.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/intel/mpi-benchmarks.git")
                    (commit (string-append "IMB-v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0si5xi6ilhd3w0gbsg124589pvp094hvf366rvjjb9pi7pdk5p4i"))))
    (build-system gnu-build-system)
    (arguments
     '(#:phases (modify-phases %standard-phases
                  (delete 'configure)
                  (delete 'check)
                  (replace 'install
                    (lambda* (#:key outputs #:allow-other-keys)
                      (define (benchmark? file stat)
                        (and (string-prefix? "IMB-" (basename file))
                             (executable-file? file)))

                      (let* ((out (assoc-ref outputs "out"))
                             (bin (string-append out "/bin")))
                        (for-each (lambda (file)
                                    (install-file file bin))
                                  (find-files "." benchmark?))
                        #t))))

       ;; The makefile doesn't express all the dependencies, it seems.
       #:parallel-build? #t

       #:make-flags (list (string-append "CC="
                                         (assoc-ref %build-inputs "openmpi")
                                         "/bin/mpicc")
                          (string-append "CXX="
                                         (assoc-ref %build-inputs "openmpi")
                                         "/bin/mpicxx"))))
    (inputs
     `(("openmpi" ,openmpi)))
    (home-page "https://github.com/intel/mpi-benchmarks")
    (synopsis "Benchmarks for the Message Passing Interface (MPI)")
    (description
     "Intel MPI Benchmarks (IMB) provides a set of elementary benchmarks that
conform with versions 1, 2, and 3 of the Message Passing Interface (MPI).")
    (license
     (fsf-free "https://directory.fsf.org/wiki/License:CPL-1.0"
               "https://www.gnu.org/licenses/license-list.html#CommonPublicLicense10"))))

(define-public python-mpi4py
  (package
    (name "python-mpi4py")
    (version "3.0.3")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "mpi4py" version))
       (sha256
        (base32 "07ssbhssv27rrjx1c5vd3vsr31vay5d8xcf4zh9yblcyidn72b81"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'build 'mpi-setup
           ,%openmpi-setup)
         (add-before 'check 'pre-check
           (lambda _
             ;; Skip BaseTestSpawn class (causes error 'ompi_dpm_dyn_init()
             ;; failed --> Returned "Unreachable"' in chroot environment).
             (substitute* "test/test_spawn.py"
               (("unittest.skipMPI\\('openmpi\\(<3.0.0\\)'\\)")
                "unittest.skipMPI('openmpi')"))
             #t)))))
    (inputs
     `(("openmpi" ,openmpi)))
    (home-page "https://bitbucket.org/mpi4py/mpi4py/")
    (synopsis "Python bindings for the Message Passing Interface standard")
    (description "MPI for Python (mpi4py) provides bindings of the Message
Passing Interface (MPI) standard for the Python programming language, allowing
any Python program to exploit multiple processors.

mpi4py is constructed on top of the MPI-1/MPI-2 specification and provides an
object oriented interface which closely follows MPI-2 C++ bindings.  It
supports point-to-point and collective communications of any picklable Python
object as well as optimized communications of Python objects (such as NumPy
arrays) that expose a buffer interface.")
    (license bsd-3)))