From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id 8P/vC+LQO2DWJwAA0tVLHw (envelope-from ) for ; Sun, 28 Feb 2021 17:20:34 +0000 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id MLmbB+LQO2B2SAAAbx9fmQ (envelope-from ) for ; Sun, 28 Feb 2021 17:20:34 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id B5C3E18C19 for ; Sun, 28 Feb 2021 18:20:33 +0100 (CET) Received: from localhost ([::1]:46424 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lGPk8-0005zg-OR for larch@yhetil.org; Sun, 28 Feb 2021 12:20:32 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:52514) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lGPct-0008VJ-E0 for guix-patches@gnu.org; Sun, 28 Feb 2021 12:13:04 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:35555) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lGPcs-0005VV-8b for guix-patches@gnu.org; Sun, 28 Feb 2021 12:13:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lGPcs-0006z2-K7 for guix-patches@gnu.org; Sun, 28 Feb 2021 12:13:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#46830] [PATCH Added hdf5-1.12-parallel-openmpi] * gnu/packages/maths.scm (hdf5-1.12-parallel-openmpi): New package based on HDF5 1.12.0 Resent-From: Gerd Heber Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Feb 2021 17:13:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 46830 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 46830@debbugs.gnu.org Cc: Gerd Heber X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.161453235726809 (code B ref -1); Sun, 28 Feb 2021 17:13:02 +0000 Received: (at submit) by debbugs.gnu.org; 28 Feb 2021 17:12:37 +0000 Received: from localhost ([127.0.0.1]:47101 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lGPcS-0006yK-MD for submit@debbugs.gnu.org; Sun, 28 Feb 2021 12:12:36 -0500 Received: from lists.gnu.org ([209.51.188.17]:36256) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lGPcQ-0006yD-Mz for submit@debbugs.gnu.org; Sun, 28 Feb 2021 12:12:35 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:52010) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lGPcP-000858-NK for guix-patches@gnu.org; Sun, 28 Feb 2021 12:12:33 -0500 Received: from mail-pg1-x536.google.com ([2607:f8b0:4864:20::536]:40929) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lGPcI-0005Hr-US for guix-patches@gnu.org; Sun, 28 Feb 2021 12:12:33 -0500 Received: by mail-pg1-x536.google.com with SMTP id b21so9970031pgk.7 for ; Sun, 28 Feb 2021 09:12:26 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=o8T/XcOoDUTqvW50Up6lxktWCLDIkDSbLtvbZn+MMF8=; b=O03e1yU9utteiDKbpJ+VAcRFiXRaa0u1/rln4LYmthnUyGYkUeNXgFYQM7D3bH5mK2 HL/O9MqDA2VtoU90hjGhCXCY+GJzh5E+iYTBnKtY0ik90BFpmaI4WlKy0ASLMDO9weqt TbuR9gc/Gjd0doQpXuysWNDZmZ6BR7CLsIIJ3wWymHJhDD0Wq3gTGQe7OPM1QimI3iwc lK7Wd8AidOXuebeEBC6LXeFqyJWc8xUpxYYecotGCeOMD39ZvhqbtwdV2DlYFi3yIobf meZ6F8rAmJZDf5mbKrXdV3wHGfEoPsNHjTZF9vPZUWOSTXVw6vMv+6s6RiNIcuBejoip z17w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=o8T/XcOoDUTqvW50Up6lxktWCLDIkDSbLtvbZn+MMF8=; b=bEJwLpfaAVsQGBQ8AtC58t2U5EO86LQ28loM2qeZfgw9Vf0yp5bYSnKYmecOK3Aufb x2vdDjbCUGoeW/VgE9/feu6SZ9nwznK00ifO+ayts1fagSTK4iNCJwNOravODo4BfigU atq3NMxhuXr0t3wN1U6L2zuihD8Wj3/3rE9Y7WMMOzdkRhs2AIcWUUtvVFL740ztiA9D x+4ycUhQhqs6fz6Ksv71YWXeOPr4JiLVWqTbjh6D6DzpZynNbDYAjS6fDFdW/Qs5/r1m TS96SyjqM1r3nVParmEF7Wbi/oD5XijOiUTNf2pG5/jsWPVeTOsugTxFwIy7po8o/1Aj ONqg== X-Gm-Message-State: AOAM531MZq2jSQaKo/naYFmFQhtewYpWDGjjghDqD4MrV7TE+dZyUeWP xXD2VCdSby3J5JgeeDERuo+1f1noKukOMQ== X-Google-Smtp-Source: ABdhPJz0GMQbHwFZf5pLqew1O/iJegj4lRQEa2Iai1yDMI8go6f4uXSiatejs5tk6IySV7dlAWOFTQ== X-Received: by 2002:a5d:9717:: with SMTP id h23mr10041319iol.4.1614519198948; Sun, 28 Feb 2021 05:33:18 -0800 (PST) Received: from guix.attlocal.net ([2600:1702:30b0:1f50:c567:9d5f:23a4:7f67]) by smtp.gmail.com with ESMTPSA id m15sm7290904ilh.6.2021.02.28.05.33.18 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 28 Feb 2021 05:33:18 -0800 (PST) From: Gerd Heber X-Google-Original-From: Gerd Heber Date: Sun, 28 Feb 2021 07:33:14 -0600 Message-Id: <20210228133314.22935-1-gheber@hdfgroup.org> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2607:f8b0:4864:20::536; envelope-from=gerd.heber@gmail.com; helo=mail-pg1-x536.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1614532833; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:list-id:list-help: list-unsubscribe:list-subscribe:list-post:dkim-signature; bh=o8T/XcOoDUTqvW50Up6lxktWCLDIkDSbLtvbZn+MMF8=; b=f7yzsNGeYDCza4zhPFcuOI2tlZDmvid7AUiQjAl+1RsGih2Q5J+x45vHjpLqNh2F5W9dEo FCvIhr4nKTepb/2FkcsMzeKC5bV3p6iqNuExygBNDUIsrs/ntIuTH9Yv2NhulWSdctkJXp OFk0+WuzAjxmFxx9RCmxj/LQ16Brej7c9kS/0Cj1dQwE5NzBNozO4o+qrVzXEckGwdBHW5 qZTUvid8VhbL+m/CtwRBG5GxhGqp4rqWDcvTCilxD9eeQXoY/dP/yKoOXmwy/pTqJluD9P qdmU2dbiPOmNsPcg2+Gv7lNRSGlzh5EJIRKsL5gV/mgKDph+q4V3C16IOQJOZg== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1614532833; a=rsa-sha256; cv=none; b=Jg6ZBI6HVNsDkwqMLC6tKIdyyQu2MkJobjjQ7TAX5uN1iR9B2j6I+KJAeTw3XPG69tnU7M MGE3+bvsrY2yEB+ZYB2ZDXAqNov83XGzCZaebypgRyJwQGNbNWdAlWRd09QEyn1tc/lDQV uix3bvtjQ7w2piRzlkaPc809Ae1hcuMsT05RtRuJ45le2IXLug331bUpwtiCw/ReyOzCP2 e8XhsPMXfy6Wie1SIpB0rPfolVM5hr7KzxQA9dOYCANITxoO+BSxw7f+WWRnSONeipVjjM SxudNqMsgWxjDm6MtXcVFhbgTigv/cISILZcIGSDHaD19kzRFF8EDu92HOJORg== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=O03e1yU9; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: 2.73 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=O03e1yU9; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: B5C3E18C19 X-Spam-Score: 2.73 X-Migadu-Scanner: scn1.migadu.com X-TUID: qCl3IeIcsfMO --- gnu/packages/maths.scm | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 58433d4b0c..df101635ab 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1451,7 +1451,7 @@ Swath).") (license (license:non-copyleft home-page)))) (define-public hdf5-parallel-openmpi - (package/inherit hdf5-1.10 ;use the latest + (package/inherit hdf5-1.10 (name "hdf5-parallel-openmpi") (inputs `(("mpi" ,openmpi) @@ -1482,6 +1482,38 @@ Swath).") #t)))))) (synopsis "Management suite for data with parallel IO support"))) +(define-public hdf5-1.12-parallel-openmpi + (package/inherit hdf5-1.12 + (name "hdf5-1.12-parallel-openmpi") + (inputs + `(("mpi" ,openmpi) + ,@(package-inputs hdf5))) + (arguments + (substitute-keyword-arguments (package-arguments hdf5) + ((#:configure-flags flags) + ``("--enable-parallel" + ,@(delete "--enable-cxx" + (delete "--enable-threadsafe" ,flags)))) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'build 'mpi-setup + ,%openmpi-setup) + (add-before 'check 'patch-tests + (lambda _ + ;; OpenMPI's mpirun will exit with non-zero status if it + ;; detects an "abnormal termination", i.e. any process not + ;; calling MPI_Finalize(). Since the test is explicitly + ;; avoiding MPI_Finalize so as not to have at_exit and thus + ;; H5C_flush_cache from being called, mpirun will always + ;; complain, so turn this test off. + (substitute* "testpar/Makefile" + (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back) + (string-append front back "\n"))) + (substitute* "tools/test/h5diff/testph5diff.sh" + (("/bin/sh") (which "sh"))) + #t)))))) + (synopsis "Management suite for data with parallel IO support"))) + (define-public hdf5-blosc (package (name "hdf5-blosc") -- 2.30.1