gnu/packages/mpi.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2014, 2015, 2018, 2019 Eric Bavier <bavier@member.fsf.org>
   3 ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
   4 ;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
   5 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
   6 ;;; Copyright © 2017 Dave Love <fx@gnu.org>
   7 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
   8 ;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
   9 ;;; Copyright © 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
  10 ;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
  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)
  29   #:use-module ((guix licenses) #:prefix license:)
  30   #:use-module (guix download)
  31   #:use-module (guix utils)
  32   #:use-module (guix deprecation)
  33   #:use-module (guix build-system gnu)
  34   #:use-module (guix build-system python)
  35   #:use-module (gnu packages)
  36   #:use-module (gnu packages base)
  37   #:use-module (gnu packages compression)
  38   #:use-module (gnu packages fabric-management)
  39   #:use-module (gnu packages gcc)
  40   #:use-module (gnu packages java)
  41   #:use-module (gnu packages libevent)
  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)
  47   #:use-module (gnu packages perl)
  48   #:use-module (gnu packages ncurses)
  49   #:use-module (gnu packages parallel)
  50   #:use-module (gnu packages pkg-config)
  51   #:use-module (gnu packages valgrind)
  52   #:use-module (srfi srfi-1)
  53   #:use-module (ice-9 match))
  54
  55 (define-public hwloc-1
  56   ;; Note: For now we keep 1.x as the default because many packages have yet
  57   ;; to migrate to 2.0.
  58   (package
  59     (name "hwloc")
  60     (version "1.11.12")
  61     (source (origin
  62               (method url-fetch)
  63               (uri (string-append "https://www.open-mpi.org/software/hwloc/v"
  64                                   (version-major+minor version)
  65                                   "/downloads/hwloc-" version ".tar.bz2"))
  66               (sha256
  67                (base32
  68                 "0za1b9lvrm3rhn0lrxja5f64r0aq1qs4m0pxn1ji2mbi8ndppyyx"))))
  69     (build-system gnu-build-system)
  70     (outputs '("out"           ;'lstopo' & co., depends on Cairo, libx11, etc.
  71                "lib"           ;small closure
  72                "debug"))
  73     (inputs
  74      `(("libx11" ,libx11)
  75        ("cairo" ,cairo)
  76        ("ncurses" ,ncurses)
  77        ("expat" ,expat)
  78        ,@(if (not (string-prefix? "armhf"
  79                                   (or (%current-target-system)
  80                                       (%current-system))))
  81              `(("numactl" ,numactl))
  82              '())))
  83     (propagated-inputs
  84      ;; hwloc.pc lists it in 'Requires.private'.
  85      `(("libpciaccess" ,libpciaccess)))
  86     (native-inputs
  87      `(("pkg-config" ,pkg-config)))
  88     (arguments
  89      `(#:configure-flags '("--localstatedir=/var")
  90        #:phases
  91        (modify-phases %standard-phases
  92          (add-before 'check 'skip-linux-libnuma-test
  93            (lambda _
  94              ;; Arrange to skip 'tests/linux-libnuma', which fails on some
  95              ;; machines: <https://github.com/open-mpi/hwloc/issues/213>.
  96              (substitute* "tests/linux-libnuma.c"
  97                (("numa_available\\(\\)")
  98                 "-1"))
  99              #t))
 100          (add-after 'install 'refine-libnuma
 101            ;; Give -L arguments for libraries to avoid propagation
 102            (lambda* (#:key inputs outputs #:allow-other-keys)
 103              (let ((out  (assoc-ref outputs "lib"))
 104                    (numa (assoc-ref inputs "numactl")))
 105                (substitute* (map (lambda (f) (string-append out "/" f))
 106                                  '("lib/pkgconfig/hwloc.pc" "lib/libhwloc.la"))
 107                  (("-lnuma" lib)
 108                   (string-append "-L" numa "/lib " lib))))))
 109          (add-after 'install 'avoid-circular-references
 110            (lambda* (#:key outputs #:allow-other-keys)
 111              (let ((lib (assoc-ref outputs "lib")))
 112                ;; Suppress the 'prefix=' and 'exec_prefix=' lines so that the
 113                ;; "lib" output doesn't refer to "out".
 114                (substitute* (string-append lib "/lib/pkgconfig/hwloc.pc")
 115                  (("^.*prefix=.*$")
 116                   ""))
 117                #t))))))
 118     (home-page "https://www.open-mpi.org/projects/hwloc/")
 119     (synopsis "Abstraction of hardware architectures")
 120     (description
 121      "hwloc provides a portable abstraction (across OS,
 122 versions, architectures, ...) of the hierarchical topology of modern
 123 architectures, including NUMA memory nodes, sockets, shared caches, cores and
 124 simultaneous multithreading.  It also gathers various attributes such as cache
 125 and memory information.  It primarily aims at helping high-performance
 126 computing applications with gathering information about the hardware so as to
 127 exploit it accordingly and efficiently.
 128
 129 hwloc may display the topology in multiple convenient formats.  It also offers
 130 a powerful programming interface to gather information about the hardware,
 131 bind processes, and much more.")
 132     (license license:bsd-3)))
 133
 134 (define-public hwloc-2
 135   ;; Note: 2.0 isn't the default yet, see above.
 136   (package
 137     (inherit hwloc-1)
 138     (version "2.2.0")
 139     (source (origin
 140               (method url-fetch)
 141               (uri (string-append "https://www.open-mpi.org/software/hwloc/v"
 142                                   (version-major+minor version)
 143                                   "/downloads/hwloc-" version ".tar.bz2"))
 144               (sha256
 145                (base32
 146                 "0li27a3lnmb77qxpijj0kpblz32wmqd3b386sypq8ar7vy9vhw5f"))))
 147
 148     ;; libnuma is no longer needed.
 149     (inputs (alist-delete "numactl" (package-inputs hwloc-1)))
 150     (arguments
 151      (substitute-keyword-arguments (package-arguments hwloc-1)
 152        ((#:phases phases)
 153         `(modify-phases ,phases
 154            (replace 'skip-linux-libnuma-test
 155              (lambda _
 156                ;; Arrange to skip 'tests/hwloc/linux-libnuma', which fails on
 157                ;; some machines: <https://github.com/open-mpi/hwloc/issues/213>.
 158                (substitute* "tests/hwloc/linux-libnuma.c"
 159                  (("numa_available\\(\\)")
 160                   "-1"))
 161                #t))
 162            (add-before 'check 'skip-test-that-fails-on-qemu
 163              (lambda _
 164                ;; Skip test that fails on emulated hardware due to QEMU bug:
 165                ;; <https://bugs.gnu.org/40342>.
 166                (substitute* "tests/hwloc/hwloc_get_last_cpu_location.c"
 167                  (("hwloc_topology_init" all)
 168                   (string-append "exit (77);\n" all)))
 169                #t))))))))
 170
 171 (define-deprecated hwloc-2.0 hwloc-2)
 172
 173 (define-public hwloc
 174   ;; The latest stable series of hwloc.
 175   hwloc-2)
 176
 177 (define-public openmpi
 178   (package
 179     (name "openmpi")
 180     (version "4.0.5")
 181     (source
 182      (origin
 183       (method url-fetch)
 184       (uri (string-append "https://www.open-mpi.org/software/ompi/v"
 185                           (version-major+minor version)
 186                           "/downloads/openmpi-" version ".tar.bz2"))
 187       (sha256
 188        (base32 "02f0r9d3xgs08svkmj8v7lzviyxqnkk4yd3z0wql550xnriki3y5"))
 189       (patches (search-patches "openmpi-mtl-priorities.patch"))))
 190     (build-system gnu-build-system)
 191     (inputs
 192      `(("hwloc" ,hwloc-2 "lib")
 193        ("gfortran" ,gfortran)
 194        ("libfabric" ,libfabric)
 195        ("libevent" ,libevent)
 196        ("opensm" ,opensm)
 197        ,@(if (and (not (%current-target-system))
 198                   (member (%current-system) (package-supported-systems psm)))
 199              `(("psm" ,psm))
 200              '())
 201        ,@(if (and (not (%current-target-system))
 202                   (member (%current-system) (package-supported-systems psm2)))
 203              `(("psm2" ,psm2))
 204              '())
 205        ,@(if (and (not (%current-target-system))
 206                   (member (%current-system) (package-supported-systems ucx)))
 207              `(("ucx" ,ucx))
 208              '())
 209        ("rdma-core" ,rdma-core)
 210        ("valgrind" ,valgrind)
 211        ("slurm" ,slurm)))              ;for PMI support (launching via "srun")
 212     (native-inputs
 213      `(("pkg-config" ,pkg-config)
 214        ("perl" ,perl)))
 215     (outputs '("out" "debug"))
 216     (arguments
 217      `(#:configure-flags `("--enable-mpi-ext=affinity" ;cr doesn't work
 218                            "--enable-memchecker"
 219                            "--with-sge"
 220                            "--with-valgrind"
 221                            "--with-hwloc=external"
 222                            "--with-libevent"
 223
 224                            ;; Help 'orterun' and 'mpirun' find their tools
 225                            ;; under $prefix by default.
 226                            "--enable-mpirun-prefix-by-default"
 227
 228                            ;; InfiniBand support
 229                            "--enable-openib-control-hdr-padding"
 230                            "--enable-openib-dynamic-sl"
 231                            "--enable-openib-udcm"
 232                            "--enable-openib-rdmacm"
 233                            "--enable-openib-rdmacm-ibaddr"
 234
 235                            ;; Enable support for SLURM's Process Manager
 236                            ;; Interface (PMI).
 237                            ,(string-append "--with-pmi="
 238                                            (assoc-ref %build-inputs "slurm")))
 239        #:phases (modify-phases %standard-phases
 240                   ;; opensm is needed for InfiniBand support.
 241                   (add-after 'unpack 'find-opensm-headers
 242                     (lambda* (#:key inputs #:allow-other-keys)
 243                       (setenv "C_INCLUDE_PATH"
 244                               (string-append (assoc-ref inputs "opensm")
 245                                              "/include/infiniband"))
 246                       (setenv "CPLUS_INCLUDE_PATH"
 247                               (string-append (assoc-ref inputs "opensm")
 248                                              "/include/infiniband"))
 249                       #t))
 250                   (add-before 'build 'remove-absolute
 251                     (lambda _
 252                       ;; Remove compiler absolute file names (OPAL_FC_ABSOLUTE
 253                       ;; etc.) to reduce the closure size.  See
 254                       ;; <https://lists.gnu.org/archive/html/guix-devel/2017-07/msg00388.html>
 255                       ;; and
 256                       ;; <https://www.mail-archive.com/users@lists.open-mpi.org//msg31397.html>.
 257                       (substitute* '("orte/tools/orte-info/param.c"
 258                                      "oshmem/tools/oshmem_info/param.c"
 259                                      "ompi/tools/ompi_info/param.c")
 260                         (("_ABSOLUTE") ""))
 261                       ;; Avoid valgrind (which pulls in gdb etc.).
 262                       (substitute*
 263                           '("./ompi/mca/io/romio321/src/io_romio321_component.c")
 264                         (("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS")
 265                          "\"[elided to reduce closure]\""))
 266                       #t))
 267                   (add-before 'build 'scrub-timestamps ;reproducibility
 268                     (lambda _
 269                       (substitute* '("ompi/tools/ompi_info/param.c"
 270                                      "orte/tools/orte-info/param.c"
 271                                      "oshmem/tools/oshmem_info/param.c")
 272                         ((".*(Built|Configured) on.*") ""))
 273                       #t))
 274                   (add-after 'install 'remove-logs ;reproducibility
 275                     (lambda* (#:key outputs #:allow-other-keys)
 276                       (let ((out (assoc-ref outputs "out")))
 277                         (for-each delete-file (find-files out "config.log"))
 278                         #t))))))
 279     (home-page "https://www.open-mpi.org")
 280     (synopsis "MPI-3 implementation")
 281     (description
 282      "The Open MPI Project is an MPI-3 implementation that is developed and
 283 maintained by a consortium of academic, research, and industry partners.  Open
 284 MPI is therefore able to combine the expertise, technologies, and resources
 285 from all across the High Performance Computing community in order to build the
 286 best MPI library available.  Open MPI offers advantages for system and
 287 software vendors, application developers and computer science researchers.")
 288     ;; See file://LICENSE
 289     (license license:bsd-2)))
 290
 291 ;; TODO: javadoc files contain timestamps.
 292 (define-public java-openmpi
 293   (package (inherit openmpi)
 294     (name "java-openmpi")
 295     (inputs
 296      `(("openmpi" ,openmpi)
 297        ,@(package-inputs openmpi)))
 298     (native-inputs
 299      `(("jdk" ,openjdk11 "jdk")
 300        ("zip" ,(@ (gnu packages compression) zip))
 301        ,@(package-native-inputs openmpi)))
 302     (outputs '("out"))
 303     (arguments
 304      `(#:modules ((guix build gnu-build-system)
 305                   ((guix build ant-build-system) #:prefix ant:)
 306                   (guix build utils))
 307        #:imported-modules ((guix build ant-build-system)
 308                            (guix build syscalls)
 309                            ,@%gnu-build-system-modules)
 310        ,@(substitute-keyword-arguments (package-arguments openmpi)
 311            ((#:configure-flags flags)
 312             `(cons "--enable-mpi-java" ,flags))
 313            ((#:make-flags flags ''())
 314             `(append '("-C" "ompi/mpi/java")
 315                      ,flags))
 316            ((#:phases phases)
 317             `(modify-phases ,phases
 318                ;; We could provide the location of the JDK in the configure
 319                ;; flags, but since the configure flags are embedded in the
 320                ;; info binaries that would leave a reference to the JDK in
 321                ;; the "out" output.  To avoid this we set JAVA_HOME.
 322                (add-after 'unpack 'set-JAVA_HOME
 323                  (lambda* (#:key inputs #:allow-other-keys)
 324                    (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
 325                    #t))
 326                (add-after 'unpack 'link-with-existing-mpi-libraries
 327                  (lambda* (#:key inputs #:allow-other-keys)
 328                    (substitute* "ompi/mpi/java/c/Makefile.in"
 329                      (("\\$\\(top_builddir\\)/ompi/lib@OMPI_LIBMPI_NAME@.la")
 330                       (string-append (assoc-ref inputs "openmpi") "/lib/libmpi.la")))
 331                    #t))
 332                (add-after 'install 'strip-jar-timestamps
 333                  (assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))))
 334     (synopsis "Java bindings for MPI")))
 335
 336 (define-public openmpi-thread-multiple
 337   (package
 338     (inherit openmpi)
 339     (name "openmpi-thread-multiple")
 340     (arguments
 341      (substitute-keyword-arguments (package-arguments openmpi)
 342        ((#:configure-flags flags)
 343         `(cons "--enable-mpi-thread-multiple" ,flags))))
 344     (description " This version of Open@tie{}MPI has an implementation of
 345 @code{MPI_Init_thread} that provides @code{MPI_THREAD_MULTIPLE}.  This won't
 346 work correctly with all transports (such as @code{openib}), and the
 347 performance is generally worse than the vanilla @code{openmpi} package, which
 348 only provides @code{MPI_THREAD_FUNNELED}.")))
 349
 350 ;;; Build phase to be used for packages that execute MPI code.
 351 (define-public %openmpi-setup
 352   '(lambda _
 353      ;; By default, running the test suite would fail because 'ssh' could not
 354      ;; be found in $PATH.  Define this variable to placate Open MPI without
 355      ;; adding a dependency on OpenSSH (the agent isn't used anyway.)
 356      (setenv "OMPI_MCA_plm_rsh_agent" (which "false"))
 357      ;; Allow oversubscription in case there are less physical cores available
 358      ;; in the build environment than the package wants while testing.
 359      (setenv "OMPI_MCA_rmaps_base_mapping_policy" "core:OVERSUBSCRIBE")
 360
 361      ;; UCX sometimes outputs uninteresting warnings such as:
 362      ;;
 363      ;;   mpool.c:38   UCX  WARN  object 0x7ffff44fffc0 was not returned to mpool ucp_am_bufs
 364      ;;
 365      ;; These in turn leads to failures of test suites that capture and
 366      ;; compare stdout, such as that of 'hdf5-parallel-openmpi'.  Thus, tell
 367      ;; UCX to not emit those warnings.
 368      (setenv "UCX_LOG_LEVEL" "error")
 369      #t))
 370
 371 (define-public python-mpi4py
 372   (package
 373     (name "python-mpi4py")
 374     (version "3.0.3")
 375     (source
 376      (origin
 377        (method url-fetch)
 378        (uri (pypi-uri "mpi4py" version))
 379        (sha256
 380         (base32 "07ssbhssv27rrjx1c5vd3vsr31vay5d8xcf4zh9yblcyidn72b81"))))
 381     (build-system python-build-system)
 382     (arguments
 383      `(#:phases
 384        (modify-phases %standard-phases
 385          (add-after 'build 'mpi-setup
 386            ,%openmpi-setup)
 387          (add-before 'check 'pre-check
 388            (lambda _
 389              ;; Skip BaseTestSpawn class (causes error 'ompi_dpm_dyn_init()
 390              ;; failed --> Returned "Unreachable"' in chroot environment).
 391              (substitute* "test/test_spawn.py"
 392                (("unittest.skipMPI\\('openmpi\\(<3.0.0\\)'\\)")
 393                 "unittest.skipMPI('openmpi')"))
 394              #t)))))
 395     (inputs
 396      `(("openmpi" ,openmpi)))
 397     (home-page "https://bitbucket.org/mpi4py/mpi4py/")
 398     (synopsis "Python bindings for the Message Passing Interface standard")
 399     (description "MPI for Python (mpi4py) provides bindings of the Message
 400 Passing Interface (MPI) standard for the Python programming language, allowing
 401 any Python program to exploit multiple processors.
 402
 403 mpi4py is constructed on top of the MPI-1/MPI-2 specification and provides an
 404 object oriented interface which closely follows MPI-2 C++ bindings.  It
 405 supports point-to-point and collective communications of any picklable Python
 406 object as well as optimized communications of Python objects (such as NumPy
 407 arrays) that expose a buffer interface.")
 408     (license license:bsd-3)))
 409
 410 (define-public mpich
 411   (package
 412     (name "mpich")
 413     (version "3.3.2")
 414     (source (origin
 415               (method url-fetch)
 416               (uri (string-append "http://www.mpich.org/static/downloads/"
 417                                   version "/mpich-" version ".tar.gz"))
 418               (sha256
 419                (base32
 420                 "1farz5zfx4cd0c3a0wb9pgfypzw0xxql1j1294z1sxslga1ziyjb"))))
 421     (build-system gnu-build-system)
 422     (inputs
 423      `(("zlib" ,zlib)
 424        ("hwloc" ,hwloc-2 "lib")
 425        ("slurm" ,slurm)
 426        ,@(if (and (not (%current-target-system))
 427                   (member (%current-system) (package-supported-systems ucx)))
 428              `(("ucx" ,ucx))
 429              '())))
 430     (native-inputs
 431      `(("perl" ,perl)
 432        ("which" ,which)
 433        ("gfortran" ,gfortran)))
 434     (outputs '("out" "debug"))
 435     (arguments
 436      `(#:configure-flags
 437        (list "--disable-silent-rules"             ;let's see what's happening
 438              "--enable-debuginfo"
 439
 440              ;; Default to "ch4", as will be the case in 3.4.  It also works
 441              ;; around issues when running test suites of packages that use
 442              ;; MPICH: <https://issues.guix.gnu.org/39588#15>.
 443              "--with-device=ch4:ucx" ; --with-device=ch4:ofi segfaults in tests
 444
 445              (string-append "--with-hwloc-prefix="
 446                             (assoc-ref %build-inputs "hwloc"))
 447
 448              ,@(if (assoc "ucx" (package-inputs this-package))
 449                    `((string-append "--with-ucx="
 450                                     (assoc-ref %build-inputs "ucx")))
 451                    '()))
 452
 453        #:phases (modify-phases %standard-phases
 454                   (add-after 'unpack 'patch-sources
 455                     (lambda _
 456                       (substitute* "./maint/gen_subcfg_m4"
 457                         (("/usr/bin/env") (which "env")))
 458                       (substitute* "src/glue/romio/all_romio_symbols"
 459                         (("/usr/bin/env") (which "env")))
 460                       (substitute* (find-files "." "buildiface")
 461                         (("/usr/bin/env") (which "env")))
 462                       (substitute* "maint/extracterrmsgs"
 463                         (("/usr/bin/env") (which "env")))
 464                       (substitute* (find-files "." "f77tof90")
 465                         (("/usr/bin/env") (which "env")))
 466                       (substitute* (find-files "." "\\.sh$")
 467                         (("/bin/sh") (which "sh")))
 468                       #t))
 469                   (add-before 'configure 'fix-makefile
 470                     (lambda _
 471                       ;; Remove "@hwloclib@" from 'pmpi_convenience_libs'.
 472                       ;; This fixes "No rule to make target '-lhwloc', needed
 473                       ;; by 'lib/libmpi.la'".
 474                       (substitute* "Makefile.in"
 475                         (("^pmpi_convenience_libs = (.*) @hwloclib@ (.*)$" _
 476                           before after)
 477                          (string-append "pmpi_convenience_libs = "
 478                                         before " " after)))
 479                       #t)))))
 480     (home-page "https://www.mpich.org/")
 481     (synopsis "Implementation of the Message Passing Interface (MPI)")
 482     (description
 483      "MPICH is a high-performance and portable implementation of the Message
 484 Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).  MPICH provides an
 485 MPI implementation that efficiently supports different computation and
 486 communication platforms including commodity clusters, high-speed networks (10
 487 Gigabit Ethernet, InfiniBand, Myrinet, Quadrics), and proprietary high-end
 488 computing systems (Blue Gene, Cray).  It enables research in MPI through a
 489 modular framework for other derived implementations.")
 490     (license license:bsd-2)))