From patchwork Thu Feb 13 10:44:07 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?q?Maurice_Br=C3=A9mond?= X-Patchwork-Id: 20239 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id B563127BBEA; Thu, 13 Feb 2020 14:36:19 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.9 required=5.0 tests=BAYES_00,MAILING_LIST_MULTI, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 1E8ED27BBE4 for ; Thu, 13 Feb 2020 14:36:19 +0000 (GMT) Received: from localhost ([::1]:53312 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1j2FbF-0000gl-LJ for patchwork@mira.cbaines.net; Thu, 13 Feb 2020 09:36:17 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:58905) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1j2Fb4-0000d8-EY for guix-patches@gnu.org; Thu, 13 Feb 2020 09:36:09 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1j2Fb1-0004H8-MD for guix-patches@gnu.org; Thu, 13 Feb 2020 09:36:06 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:53504) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1j2Fb1-0004Fk-Ia for guix-patches@gnu.org; Thu, 13 Feb 2020 09:36:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1j2Fb0-0006h5-Fv for guix-patches@gnu.org; Thu, 13 Feb 2020 09:36:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#39588] gnu: Add mpich, scalapack-mpich, mumps-mpich, pt-scotch-mpich, python-mpi4py-mpich Resent-From: Maurice =?utf-8?q?Br=C3=A9mond?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 13 Feb 2020 14:36:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 39588 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 39588@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.158160450325638 (code B ref -1); Thu, 13 Feb 2020 14:36:02 +0000 Received: (at submit) by debbugs.gnu.org; 13 Feb 2020 14:35:03 +0000 Received: from localhost ([127.0.0.1]:59472 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j2Fa2-0006fQ-Iu for submit@debbugs.gnu.org; Thu, 13 Feb 2020 09:35:03 -0500 Received: from lists.gnu.org ([209.51.188.17]:58483) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j2BzF-0007iU-VK for submit@debbugs.gnu.org; Thu, 13 Feb 2020 05:44:50 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:55346) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1j2BzE-0001Nw-6A for guix-patches@gnu.org; Thu, 13 Feb 2020 05:44:49 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1j2BzC-0008Ko-4E for guix-patches@gnu.org; Thu, 13 Feb 2020 05:44:47 -0500 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:48768) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1j2BzB-0008Il-Mh for guix-patches@gnu.org; Thu, 13 Feb 2020 05:44:46 -0500 X-IronPort-AV: E=Sophos;i="5.70,436,1574118000"; d="scan'208,223";a="435785723" Received: from bremondm.imag.fr (HELO maurice-HP-ZBook-15-G3.inria.fr) ([129.88.37.91]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/AES256-GCM-SHA384; 13 Feb 2020 11:44:07 +0100 From: Maurice =?utf-8?q?Br=C3=A9mond?= Date: Thu, 13 Feb 2020 11:44:07 +0100 Message-ID: <87blq2rclk.fsf@inria.fr> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1.50 (gnu/linux) MIME-Version: 1.0 Content-Disposition: inline; filename=0001-gnu-Add-mpich-scalapack-mpich-mumps-mpich-pt-scotch-.patch Content-Description: gnu: Add mpich, scalapack-mpich, mumps-mpich, pt-scotch-mpich, python-mpi4py-mpich X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Mailman-Approved-At: Thu, 13 Feb 2020 09:35:00 -0500 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-To: Maurice =?utf-8?q?Br=C3=A9mond?= Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches From 4ba3d43d97389c76a06c342d4c4ee91f02d8aaf1 Mon Sep 17 00:00:00 2001 From: Maurice Bremond Date: Thu, 23 Jan 2020 15:48:41 +0100 Subject: [PATCH] gnu: Add mpich, scalapack-mpich, mumps-mpich, pt-scotch-mpich, python-mpi4py-mpich. --- gnu/packages/maths.scm | 34 +++++++++++++ gnu/packages/mpi.scm | 108 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 142 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 8f4478b6bb..feba11663f 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -643,6 +643,14 @@ singular value problems.") (license (license:non-copyleft "file://LICENSE" "See LICENSE in the distribution.")))) +(define-public scalapack-mpich + (package + (inherit scalapack) + (name "scalapack-mpich") + (inputs + `(("mpi" ,mpich) + ,@(alist-delete "mpi" (package-inputs scalapack)))))) + (define-public gnuplot (package (name "gnuplot") @@ -2371,6 +2379,24 @@ sparse system of linear equations A x = b using Gaussian elimination.") (inputs (alist-delete "pt-scotch" (package-inputs mumps-openmpi))))) +(define-public mumps-mpich + (package (inherit mumps) + (name "mumps-mpich") + (inputs + `(("mpi" ,mpich) + ("scalapack" ,scalapack-mpich) + ("pt-scotch" ,pt-scotch-mpich) + ,@(alist-delete "scotch" (package-inputs mumps)))) + (arguments + (substitute-keyword-arguments (package-arguments mumps) + ((#:phases phases) + `(modify-phases ,phases + (replace 'check + (lambda _ + ((assoc-ref ,phases 'check) + #:exec-prefix '("mpirun" "-genv" "LD_LIBRARY_PATH" "../lib" "-n" "2" )))))))) + (synopsis "Multifrontal sparse direct solver (with MPI)"))) + (define-public ruby-asciimath (package (name "ruby-asciimath") @@ -2729,6 +2755,14 @@ YACC = bison -pscotchyy -y -b y (invoke "make" "ptcheck"))))))) (synopsis "Programs and libraries for graph algorithms (with MPI)"))) +(define-public pt-scotch-mpich + (package + (inherit pt-scotch) + (name "pt-scotch-mpich") + (inputs + `(("mpi" ,mpich) + ,@(alist-delete "mpi" (package-inputs pt-scotch)))))) + (define-public pt-scotch32 (package (inherit scotch32) (name "pt-scotch32") diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm index 00e0d12eab..3f644e7dbb 100644 --- a/gnu/packages/mpi.scm +++ b/gnu/packages/mpi.scm @@ -29,16 +29,23 @@ #: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 autogen) + #:use-module (gnu packages autotools) + #:use-module (gnu packages base) + #:use-module (gnu packages bash) #:use-module (gnu packages fabric-management) + #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) #:use-module (gnu packages java) #:use-module (gnu packages libevent) #:use-module (gnu packages linux) + #:use-module (gnu packages m4) #:use-module (gnu packages pciutils) #:use-module (gnu packages xorg) #:use-module (gnu packages gtk) @@ -47,6 +54,7 @@ #:use-module (gnu packages ncurses) #:use-module (gnu packages parallel) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages version-control) #:use-module (gnu packages valgrind) #:use-module (srfi srfi-1) #:use-module (ice-9 match)) @@ -393,3 +401,103 @@ 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))) + +(define-public mpich + (package + (name "mpich") + (version "3.4a2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pmodels/mpich") + (commit "644051d13dc20aecd460ba3db088756659c3dad3") ; tag v3.4a2 + (recursive? #t))) + (sha256 + (base32 + "02ildr7wh40q1qaq5k8npb6vw6kv9szmrm3lspr6skqa5csmrrxw")))) + (build-system gnu-build-system) + (inputs + `(("libnuma" ,numactl))) ; for ch4:ucx + (native-inputs + `(("gawk" ,gawk) + ("bash" ,bash) + ("diffutils" ,diffutils) + ("git" ,git) + ("sed" ,sed) + ("perl" ,perl) + ("patch" ,patch) + ("findutils" ,findutils) + ("m4" ,m4) + ("grep" ,grep) + ("which" ,which) + ("gfortran" ,gfortran) + ("gcc" ,gcc) + ("gnu-make" ,gnu-make) + ("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("autogen" ,autogen) + ("zlib" ,(@ (gnu packages compression) zlib)))) + (outputs '("out" "debug")) + (arguments + `(#:modules ((ice-9 match) + (ice-9 popen) + (srfi srfi-1) + ,@%gnu-build-system-modules) + #:configure-flags + '("--disable-dependency-tracking" + "--enable-debuginfo" + "--with-device=ch4:ucx") ; --with-device=ch4:ofi segfault in tests + #: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"))))) + (add-after 'bootstrap 'patch-after-bootstrap + (lambda _ + (use-modules (ice-9 popen) + (ice-9 rdelim)) + (substitute* "maint/configure" + (("/bin/sh") (which "sh"))) + (with-directory-excursion + "maint" + (invoke "sh" "./configure") + (let ((cvardirs + (let* ((p (open-pipe* OPEN_READ + "cat" "cvardirs")) + (l (read-line p))) + (and (zero? (close-pipe p)) l)))) + (invoke "perl" "extractcvars" "--dirs" cvardirs)))))))) + (home-page "https://www.mpich.org/") + (synopsis "MPICH is a high performance and widely portable +implementation of the Message Passing Interface (MPI) standard.") + (description "MPICH is a high-performance and widely portable +implementation of the Message Passing Interface (MPI) standard (MPI-1, +MPI-2 and MPI-3). The goals of MPICH are: (1) to provide an MPI +implementation that efficiently supports different computation and +communication platforms including commodity clusters (desktop systems, +shared-memory systems, multicore architectures), high-speed +networks (10 Gigabit Ethernet, InfiniBand, Myrinet, Quadrics) and +proprietary high-end computing systems (Blue Gene, Cray) and (2) to +enable cutting-edge research in MPI through an easy-to-extend modular +framework for other derived implementations.") + (license bsd-2))) + +(define-public python-mpi4py-mpich + (package + (inherit python-mpi4py) + (name "python-mpi4py-mpich") + (inputs + `(("mpi" ,mpich) + ,@(alist-delete "mpi" (package-inputs python-mpi4py)))))) -- 2.17.1