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 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 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)
  30                 #:hide (expat))
  31   #:use-module (guix download)
  32   #:use-module (guix git-download)
  33   #:use-module (guix utils)
  34   #:use-module (guix deprecation)
  35   #:use-module (guix build-system gnu)
  36   #:use-module (guix build-system python)
  37   #:use-module (gnu packages)
  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
  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 bsd-3)))
 133
 134 (define-public hwloc-2
 135   ;; Note: 2.0 isn't the default yet, see above.
 136   (package
 137     (inherit hwloc)
 138     (version "2.1.0")
 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                 "0qh8s7pphz0m5cwb7liqmc17xzfs23xhz5wn24r6ikvjyx99fhhr"))))
 147
 148     ;; libnuma is no longer needed.
 149     (inputs (alist-delete "numactl" (package-inputs hwloc)))
 150     (arguments
 151      (substitute-keyword-arguments (package-arguments hwloc)
 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
 163 (define-deprecated hwloc-2.0 'hwloc-2
 164   hwloc-2)
 165
 166 (define-public openmpi
 167   (package
 168     (name "openmpi")
 169     (version "4.0.2")
 170     (source
 171      (origin
 172       (method url-fetch)
 173       (uri (string-append "https://www.open-mpi.org/software/ompi/v"
 174                           (version-major+minor version)
 175                           "/downloads/openmpi-" version ".tar.bz2"))
 176       (sha256
 177        (base32 "0ms0zvyxyy3pnx9qwib6zaljyp2b3ixny64xvq3czv3jpr8zf2wh"))))
 178     (build-system gnu-build-system)
 179     (inputs
 180      `(("hwloc" ,hwloc "lib")
 181        ("gfortran" ,gfortran)
 182        ("libfabric" ,libfabric)
 183        ("libevent" ,libevent)
 184        ("opensm" ,opensm)
 185        ,@(if (and (not (%current-target-system))
 186                   (member (%current-system) (package-supported-systems psm)))
 187              `(("psm" ,psm))
 188              '())
 189        ,@(if (and (not (%current-target-system))
 190                   (member (%current-system) (package-supported-systems psm2)))
 191              `(("psm2" ,psm2))
 192              '())
 193        ,@(if (and (not (%current-target-system))
 194                   (member (%current-system) (package-supported-systems psm2)))
 195              `(("ucx" ,ucx))
 196              '())
 197        ("rdma-core" ,rdma-core)
 198        ("valgrind" ,valgrind)
 199        ("slurm" ,slurm)))              ;for PMI support (launching via "srun")
 200     (native-inputs
 201      `(("pkg-config" ,pkg-config)
 202        ("perl" ,perl)))
 203     (outputs '("out" "debug"))
 204     (arguments
 205      `(#:configure-flags `("--enable-mpi-ext=affinity" ;cr doesn't work
 206                            "--enable-memchecker"
 207                            "--with-sge"
 208                            "--with-valgrind"
 209                            "--with-hwloc=external"
 210                            "--with-libevent"
 211
 212                            ;; Make sure ./configure fails if one of these is
 213                            ;; missing.
 214                            "--with-ucx"
 215                            "--with-psm"
 216                            "--with-psm2"
 217
 218                            ;; InfiniBand support
 219                            "--enable-openib-control-hdr-padding"
 220                            "--enable-openib-dynamic-sl"
 221                            "--enable-openib-udcm"
 222                            "--enable-openib-rdmacm"
 223                            "--enable-openib-rdmacm-ibaddr"
 224
 225                            ;; Enable support for SLURM's Process Manager
 226                            ;; Interface (PMI).
 227                            ,(string-append "--with-pmi="
 228                                            (assoc-ref %build-inputs "slurm")))
 229        #:phases (modify-phases %standard-phases
 230                   ;; opensm is needed for InfiniBand support.
 231                   (add-after 'unpack 'find-opensm-headers
 232                     (lambda* (#:key inputs #:allow-other-keys)
 233                       (setenv "C_INCLUDE_PATH"
 234                               (string-append (assoc-ref inputs "opensm")
 235                                              "/include/infiniband"))
 236                       (setenv "CPLUS_INCLUDE_PATH"
 237                               (string-append (assoc-ref inputs "opensm")
 238                                              "/include/infiniband"))
 239                       #t))
 240                   (add-before 'build 'remove-absolute
 241                     (lambda _
 242                       ;; Remove compiler absolute file names (OPAL_FC_ABSOLUTE
 243                       ;; etc.) to reduce the closure size.  See
 244                       ;; <https://lists.gnu.org/archive/html/guix-devel/2017-07/msg00388.html>
 245                       ;; and
 246                       ;; <https://www.mail-archive.com/users@lists.open-mpi.org//msg31397.html>.
 247                       (substitute* '("orte/tools/orte-info/param.c"
 248                                      "oshmem/tools/oshmem_info/param.c"
 249                                      "ompi/tools/ompi_info/param.c")
 250                         (("_ABSOLUTE") ""))
 251                       ;; Avoid valgrind (which pulls in gdb etc.).
 252                       (substitute*
 253                           '("./ompi/mca/io/romio321/src/io_romio321_component.c")
 254                         (("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS")
 255                          "\"[elided to reduce closure]\""))
 256                       #t))
 257                   (add-before 'build 'scrub-timestamps ;reproducibility
 258                     (lambda _
 259                       (substitute* '("ompi/tools/ompi_info/param.c"
 260                                      "orte/tools/orte-info/param.c"
 261                                      "oshmem/tools/oshmem_info/param.c")
 262                         ((".*(Built|Configured) on.*") ""))
 263                       #t))
 264                   (add-after 'install 'remove-logs ;reproducibility
 265                     (lambda* (#:key outputs #:allow-other-keys)
 266                       (let ((out (assoc-ref outputs "out")))
 267                         (for-each delete-file (find-files out "config.log"))
 268                         #t))))))
 269     (home-page "http://www.open-mpi.org")
 270     (synopsis "MPI-3 implementation")
 271     (description
 272      "The Open MPI Project is an MPI-3 implementation that is developed and
 273 maintained by a consortium of academic, research, and industry partners.  Open
 274 MPI is therefore able to combine the expertise, technologies, and resources
 275 from all across the High Performance Computing community in order to build the
 276 best MPI library available.  Open MPI offers advantages for system and
 277 software vendors, application developers and computer science researchers.")
 278     ;; See file://LICENSE
 279     (license bsd-2)))
 280
 281 ;; TODO: javadoc files contain timestamps.
 282 (define-public java-openmpi
 283   (package (inherit openmpi)
 284     (name "java-openmpi")
 285     (inputs
 286      `(("openmpi" ,openmpi)
 287        ,@(package-inputs openmpi)))
 288     (native-inputs
 289      `(("jdk" ,openjdk11 "jdk")
 290        ("zip" ,(@ (gnu packages compression) zip))
 291        ,@(package-native-inputs openmpi)))
 292     (outputs '("out"))
 293     (arguments
 294      `(#:modules ((guix build gnu-build-system)
 295                   ((guix build ant-build-system) #:prefix ant:)
 296                   (guix build utils))
 297        #:imported-modules ((guix build ant-build-system)
 298                            (guix build syscalls)
 299                            ,@%gnu-build-system-modules)
 300        ,@(substitute-keyword-arguments (package-arguments openmpi)
 301            ((#:configure-flags flags)
 302             `(cons "--enable-mpi-java" ,flags))
 303            ((#:make-flags flags ''())
 304             `(append '("-C" "ompi/mpi/java")
 305                      ,flags))
 306            ((#:phases phases)
 307             `(modify-phases ,phases
 308                ;; We could provide the location of the JDK in the configure
 309                ;; flags, but since the configure flags are embedded in the
 310                ;; info binaries that would leave a reference to the JDK in
 311                ;; the "out" output.  To avoid this we set JAVA_HOME.
 312                (add-after 'unpack 'set-JAVA_HOME
 313                  (lambda* (#:key inputs #:allow-other-keys)
 314                    (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
 315                    #t))
 316                (add-after 'unpack 'link-with-existing-mpi-libraries
 317                  (lambda* (#:key inputs #:allow-other-keys)
 318                    (substitute* "ompi/mpi/java/c/Makefile.in"
 319                      (("\\$\\(top_builddir\\)/ompi/lib@OMPI_LIBMPI_NAME@.la")
 320                       (string-append (assoc-ref inputs "openmpi") "/lib/libmpi.la")))
 321                    #t))
 322                (add-after 'install 'strip-jar-timestamps
 323                  (assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))))
 324     (synopsis "Java bindings for MPI")))
 325
 326 (define-public openmpi-thread-multiple
 327   (package
 328     (inherit openmpi)
 329     (name "openmpi-thread-multiple")
 330     (arguments
 331      (substitute-keyword-arguments (package-arguments openmpi)
 332        ((#:configure-flags flags)
 333         `(cons "--enable-mpi-thread-multiple" ,flags))))
 334     (description " This version of Open@tie{}MPI has an implementation of
 335 @code{MPI_Init_thread} that provides @code{MPI_THREAD_MULTIPLE}.  This won't
 336 work correctly with all transports (such as @code{openib}), and the
 337 performance is generally worse than the vanilla @code{openmpi} package, which
 338 only provides @code{MPI_THREAD_FUNNELED}.")))
 339
 340 ;;; Build phase to be used for packages that execute MPI code.
 341 (define-public %openmpi-setup
 342   '(lambda _
 343      ;; By default, running the test suite would fail because 'ssh' could not
 344      ;; be found in $PATH.  Define this variable to placate Open MPI without
 345      ;; adding a dependency on OpenSSH (the agent isn't used anyway.)
 346      (setenv "OMPI_MCA_plm_rsh_agent" (which "false"))
 347      ;; Allow oversubscription in case there are less physical cores available
 348      ;; in the build environment than the package wants while testing.
 349      (setenv "OMPI_MCA_rmaps_base_mapping_policy" "core:OVERSUBSCRIBE")
 350      #t))
 351
 352 (define-public intel-mpi-benchmarks
 353   (package
 354     (name "intel-mpi-benchmarks")
 355     (version "2019.3")
 356     (source (origin
 357               (method git-fetch)
 358               (uri (git-reference
 359                     (url "https://github.com/intel/mpi-benchmarks.git")
 360                     (commit (string-append "IMB-v" version))))
 361               (file-name (git-file-name name version))
 362               (sha256
 363                (base32
 364                 "0si5xi6ilhd3w0gbsg124589pvp094hvf366rvjjb9pi7pdk5p4i"))))
 365     (build-system gnu-build-system)
 366     (arguments
 367      '(#:phases (modify-phases %standard-phases
 368                   (delete 'configure)
 369                   (delete 'check)
 370                   (replace 'install
 371                     (lambda* (#:key outputs #:allow-other-keys)
 372                       (define (benchmark? file stat)
 373                         (and (string-prefix? "IMB-" (basename file))
 374                              (executable-file? file)))
 375
 376                       (let* ((out (assoc-ref outputs "out"))
 377                              (bin (string-append out "/bin")))
 378                         (for-each (lambda (file)
 379                                     (install-file file bin))
 380                                   (find-files "." benchmark?))
 381                         #t))))
 382
 383        ;; The makefile doesn't express all the dependencies, it seems.
 384        #:parallel-build? #t
 385
 386        #:make-flags (list (string-append "CC="
 387                                          (assoc-ref %build-inputs "openmpi")
 388                                          "/bin/mpicc")
 389                           (string-append "CXX="
 390                                          (assoc-ref %build-inputs "openmpi")
 391                                          "/bin/mpicxx"))))
 392     (inputs
 393      `(("openmpi" ,openmpi)))
 394     (home-page "https://github.com/intel/mpi-benchmarks")
 395     (synopsis "Benchmarks for the Message Passing Interface (MPI)")
 396     (description
 397      "Intel MPI Benchmarks (IMB) provides a set of elementary benchmarks that
 398 conform with versions 1, 2, and 3 of the Message Passing Interface (MPI).")
 399     (license
 400      (fsf-free "https://directory.fsf.org/wiki/License:CPL-1.0"
 401                "https://www.gnu.org/licenses/license-list.html#CommonPublicLicense10"))))
 402
 403 (define-public python-mpi4py
 404   (package
 405     (name "python-mpi4py")
 406     (version "3.0.3")
 407     (source
 408      (origin
 409        (method url-fetch)
 410        (uri (pypi-uri "mpi4py" version))
 411        (sha256
 412         (base32 "07ssbhssv27rrjx1c5vd3vsr31vay5d8xcf4zh9yblcyidn72b81"))))
 413     (build-system python-build-system)
 414     (arguments
 415      `(#:phases
 416        (modify-phases %standard-phases
 417          (add-after 'build 'mpi-setup
 418            ,%openmpi-setup)
 419          (add-before 'check 'pre-check
 420            (lambda _
 421              ;; Skip BaseTestSpawn class (causes error 'ompi_dpm_dyn_init()
 422              ;; failed --> Returned "Unreachable"' in chroot environment).
 423              (substitute* "test/test_spawn.py"
 424                (("unittest.skipMPI\\('openmpi\\(<3.0.0\\)'\\)")
 425                 "unittest.skipMPI('openmpi')"))
 426              #t)))))
 427     (inputs
 428      `(("openmpi" ,openmpi)))
 429     (home-page "https://bitbucket.org/mpi4py/mpi4py/")
 430     (synopsis "Python bindings for the Message Passing Interface standard")
 431     (description "MPI for Python (mpi4py) provides bindings of the Message
 432 Passing Interface (MPI) standard for the Python programming language, allowing
 433 any Python program to exploit multiple processors.
 434
 435 mpi4py is constructed on top of the MPI-1/MPI-2 specification and provides an
 436 object oriented interface which closely follows MPI-2 C++ bindings.  It
 437 supports point-to-point and collective communications of any picklable Python
 438 object as well as optimized communications of Python objects (such as NumPy
 439 arrays) that expose a buffer interface.")
 440     (license bsd-3)))