;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015, 2018, 2019 Eric Bavier ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès ;;; Copyright © 2014 Ian Denhardt ;;; Copyright © 2016 Andreas Enge ;;; Copyright © 2017 Dave Love ;;; Copyright © 2017 Efraim Flashner ;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2018 Paul Garlick ;;; Copyright © 2019 Ricardo Wurmus ;;; ;;; 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 ;;; MERCHA
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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
;;; Copyright © 2016, 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; 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 iso-codes)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system python)
  #:use-module (gnu packages gettext)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages python))

(define-public iso-codes
  (package
    (name "iso-codes")
    (version "3.77")
    (source (origin
             (method url-fetch)
             (uri (string-append
                   "https://pkg-isocodes.alioth.debian.org/downloads/iso-codes-"
                   version ".tar.xz"))
             (sha256
              (base32
               "140dgygv22a49xb8x1941xr5ff12cphd9zzwxds98pgrqsj77k91"))))
    (build-system gnu-build-system)
    (inputs
     `(("gettext" ,gettext-minimal)
       ("perl" ,perl)
       ("python" ,python-wrapper)))
    (home-page "https://salsa.debian.org/iso-codes-team/iso-codes")
    (synopsis "Various ISO standards")
    (description
     "This package provides lists of various ISO standards (e.g. country,
language, language scripts, and currency names) in one place, rather
than repeated in many programs throughout the system.

Currently there are lists of languages and countries embedded in
several different programs, which leads to dozens of lists of
200 languages, translated into more than 30 languages... not
very efficient.

With this package, we create a single \"gettext domain\" for every
supported ISO standard which contains the translations of
that domain.  It is easy for a programmer to re-use those
translations instead of maintaining their own translation
infrastructure.  Moreover, the programmer does not need to follow
changes in the ISO standard and will not work with outdated
information.")
    (license license:gpl2+)))           ; some bits use the lgpl2

(define-public python-iso639
  (package
    (name "python-iso639")
    (version "0.4.5")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "iso-639" version))
       (sha256
        (base32
         "0jffmh4m20q8j27xb2fqbnlghjj0cx8pgsbzqisdg65qh2wd976w"))))
    (build-system python-build-system)
    (home-page "https://github.com/noumar/iso639")
    (synopsis "Python library for ISO 639 standard")
    (description "This package provides a Python library for ISO 639 standard
that is concerned with representation of names for languages and language
groups.")
    (license license:agpl3+)))

(define-public python2-iso639
  (package-with-python2 python-iso639))

(define-public python-iso3166
  (package
    (name "python-iso3166")
    (version "0.9")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "iso3166" version))
       (sha256
        (base32
         "0hm0xm30sprk1jssmn4cqks0x3nx5fp8r5ypvahcysmmayzrsnjl"))))
    (build-system python-build-system)
    (home-page "https://github.com/deactivated/python-iso3166")
    (synopsis "Self-contained ISO 3166-1 country definitions")
    (description "This package provides the ISO 3166-1 country definitions.")
    (license license:expat)))

(define-public python2-iso3166
  (package-with-python2 python-iso3166))
msg00388.html> ;; and ;; . (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 "https://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 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 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 license:bsd-3))) (define-public mpich (package (name "mpich") (version "3.3.2") (source (origin (method url-fetch) (uri (string-append "http://www.mpich.org/static/downloads/" version "/mpich-" version ".tar.gz")) (sha256 (base32 "1farz5zfx4cd0c3a0wb9pgfypzw0xxql1j1294z1sxslga1ziyjb")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib) ("hwloc" ,hwloc-2 "lib") ("slurm" ,slurm) ,@(if (and (not (%current-target-system)) (member (%current-system) (package-supported-systems ucx))) `(("ucx" ,ucx)) '()))) (native-inputs `(("perl" ,perl) ("which" ,which) ("gfortran" ,gfortran))) (outputs '("out" "debug")) (arguments `(#:configure-flags (list "--disable-silent-rules" ;let's see what's happening "--enable-debuginfo" ;; "--with-device=ch4:ucx" ; --with-device=ch4:ofi segfaults in tests (string-append "--with-hwloc-prefix=" (assoc-ref %build-inputs "hwloc")) ,@(if (assoc "ucx" (package-inputs this-package)) `((string-append "--with-ucx=" (assoc-ref %build-inputs "ucx"))) '())) #:phases (modify-phases %standard-phases (add-after 'unpack 'patch-sources (lambda _ (substitute* "./maint/gen_subcfg_m4" (("/usr/bin/env") (which "env"))) (substitute* "src/glue/romio/all_romio_symbols" (("/usr/bin/env") (which "env"))) (substitute* (find-files "." "buildiface") (("/usr/bin/env") (which "env"))) (substitute* "maint/extracterrmsgs" (("/usr/bin/env") (which "env"))) (substitute* (find-files "." "f77tof90") (("/usr/bin/env") (which "env"))) (substitute* (find-files "." "\\.sh$") (("/bin/sh") (which "sh"))) #t)) (add-before 'configure 'fix-makefile (lambda _ ;; Remove "@hwloclib@" from 'pmpi_convenience_libs'. ;; This fixes "No rule to make target '-lhwloc', needed ;; by 'lib/libmpi.la'". (substitute* "Makefile.in" (("^pmpi_convenience_libs = (.*) @hwloclib@ (.*)$" _ before after) (string-append "pmpi_convenience_libs = " before " " after))) #t))))) (home-page "https://www.mpich.org/") (synopsis "Implementation of the Message Passing Interface (MPI)") (description "MPICH is a high-performance and portable implementation of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3). MPICH provides an MPI implementation that efficiently supports different computation and communication platforms including commodity clusters, high-speed networks (10 Gigabit Ethernet, InfiniBand, Myrinet, Quadrics), and proprietary high-end computing systems (Blue Gene, Cray). It enables research in MPI through a modular framework for other derived implementations.") (license license:bsd-2)))