From unknown Mon Jun 23 07:51:52 2025 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-Spam-Score: -1.3 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) --- 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 From unknown Mon Jun 23 07:51:52 2025 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 References: <20210228133314.22935-1-gheber@hdfgroup.org> In-Reply-To: <20210228133314.22935-1-gheber@hdfgroup.org> Resent-From: Gerd Heber via web Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Feb 2021 22:43:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46830 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 46830@debbugs.gnu.org Received: via spool by 46830-submit@debbugs.gnu.org id=B46830.16145521779570 (code B ref 46830); Sun, 28 Feb 2021 22:43:02 +0000 Received: (at 46830) by debbugs.gnu.org; 28 Feb 2021 22:42:57 +0000 Received: from localhost ([127.0.0.1]:47461 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lGUm9-0002UH-M3 for submit@debbugs.gnu.org; Sun, 28 Feb 2021 17:42:57 -0500 Received: from sender4-of-o56.zoho.com ([136.143.188.56]:21662) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lGUm7-0002U8-IK for 46830@debbugs.gnu.org; Sun, 28 Feb 2021 17:42:56 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1614552173; cv=none; d=zohomail.com; s=zohoarc; b=oJfLZoxAkX1ivvQVoVI6DUeoAWvpCWEQcLbJxtlh8QKH44nuOlDy/CpdOJ8bkJwCpzXKhAH5BAT1dFMi9vVGUkAsxWkHlXHcWziXxEcI6RnInuZe+QOkm1Xfeqg0XMYE2cWxIutluOl92b4KBbNycUJM8fIzBNoiHudR+eikiDw= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1614552173; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=9GmMsEaOWzX0hw+7mJJEhf3BERTor2xc3RilsEa2t6Q=; b=N8GUgzkzC6WIsMhwuQqhagbsxc2g1rRZNdxrgtI+iG0bVcq4ux7fgqpSHyTDH3FVm3vZMnYrCXoIZcZQFIX9AcHOSVvvTIC6Q0GmEakyGJtoO14/WTY/C3N/p/Lcyuzvby5sOuacGAVXSlLMClhYsfSR4P+wxB2eAgDoN0PPGfo= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=issues.guix.gnu.org@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1614552173; s=zoho; d=elephly.net; i=issues.guix.gnu.org@elephly.net; h=MIME-Version:Content-Type:From:To:Date:Message-ID:Subject; bh=9GmMsEaOWzX0hw+7mJJEhf3BERTor2xc3RilsEa2t6Q=; b=TLDlE0jP/pWhEwI/wZPUL4taTNJEReaT7txX1RgZPzkGSWydosHusK0tlU0B5PS8 A62922z+o6Se+KvQDxNlhjyCHxEzZfoSf7B32wLt72m3l1szDb2WTBfMbve3v9wAn86 5MCLeal4G4akSX6TbA7HW9ajuj/U+gY663hthrRo= Received: from localhost (185.220.101.22 [185.220.101.22]) by mx.zohomail.com with SMTPS id 161455217261494.64936889063176; Sun, 28 Feb 2021 14:42:52 -0800 (PST) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 From: Gerd Heber via web Date: Sun, 28 Feb 2021 23:42:43 +0100 Message-ID: <7f9bd991d490.1956b6a559d1e5c4@guile.gnu.org> X-ZohoMailClient: External X-Spam-Score: 4.2 (++++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: This needs to be a separate package since (as with all HDF5 major releases) it's not 100% API compatible with HDF5 1.10. It would break other packages, e.g., `petsc-lite` Content analysis details: (4.2 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 1.2 RCVD_IN_BL_SPAMCOP_NET RBL: Received via a relay in bl.spamcop.net [Blocked - see ] 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record -0.0 SPF_PASS SPF: sender matches SPF record -0.0 RCVD_IN_MSPIKE_H4 RBL: Very Good reputation (+4) [136.143.188.56 listed in wl.mailspike.net] -0.0 RCVD_IN_DNSWL_NONE RBL: Sender listed at https://www.dnswl.org/, no trust [136.143.188.56 listed in list.dnswl.org] -0.0 RCVD_IN_MSPIKE_WL Mailspike good senders 3.0 AC_FROM_MANY_DOTS Multiple periods in From user name X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 0.2 (/) This needs to be a separate package since (as with all HDF5 major releases) it's not 100% API compatible with HDF5 1.10. It would break other packages, e.g., `petsc-lite` From unknown Mon Jun 23 07:51:52 2025 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: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 01 Mar 2021 10:46:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46830 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Gerd Heber , 46830@debbugs.gnu.org Cc: Gerd Heber Received: via spool by 46830-submit@debbugs.gnu.org id=B46830.161459551929941 (code B ref 46830); Mon, 01 Mar 2021 10:46:02 +0000 Received: (at 46830) by debbugs.gnu.org; 1 Mar 2021 10:45:19 +0000 Received: from localhost ([127.0.0.1]:48232 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lGg3D-0007mr-0E for submit@debbugs.gnu.org; Mon, 01 Mar 2021 05:45:19 -0500 Received: from mail-wm1-f49.google.com ([209.85.128.49]:39779) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lGg3B-0007mc-7h for 46830@debbugs.gnu.org; Mon, 01 Mar 2021 05:45:17 -0500 Received: by mail-wm1-f49.google.com with SMTP id u125so13945224wmg.4 for <46830@debbugs.gnu.org>; Mon, 01 Mar 2021 02:45:17 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:in-reply-to:references:date:message-id :mime-version; bh=mK8XRlPRGbkt4W5WoJQne/t5vyVjcmfAjdA2SYMzxSc=; b=basHqjn5d0FjQy4gwUEhvmYXxdb5WWeTQbAWNtDMlpR/FcryA5d2vNVNAOz+cIw8o4 pOt6WfkjbYS/OJXnmlg2dvGr+A0oNRzJFBCDP163cQ7mN0AlQpvn+ZVVJ0j8LFyuVzjJ o7pqFL0xSUl8Sc9Qh8NtztXG4UdrLRZJdUL4oJ1wBZf3zQiUBbhCOPo5kWQrGd2InLwD 1cE6WnMSjxblyuJI2MrigJASps4AUjlgVROMqd+/ukamWegwvaOPGB+EJL/rNYUAEKOE iP++Ey8S186+7+4LiBsnlwsOlL86hQRx355VMbuo58qhDOxqHEInyL+9G39uaSpi6cHq eU1g== 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:in-reply-to:references:date :message-id:mime-version; bh=mK8XRlPRGbkt4W5WoJQne/t5vyVjcmfAjdA2SYMzxSc=; b=luAdTvq1KnFjpMAgo4xz8SZl9meadJytNK3GoW7HfIFHHVNldK+ebARCwGb+y0zWJR /tioEqXgqlUG1aV+hB/slPE9HlB6w+aesTPlEEjvGsyF0S1XsL1FWOi9hwpEtKakuZPW wMUyoqnrf11jkAuB+16TwonhqxsvODk6tYyd3/CYQ0QL5eitvzuj1WCysjsaegpHHQmu LUWwtf7RfDcIGMGbeOSju42gCs0iMdg00tuC1JBEkr7LszvkUruMTSP0xRsP8ZNgjywr dCTV0Fw3QZCTqhYGT+PDQcbLHiXKi1RNr6ZqKKU/Ksara7JoCyrgR+elx848OVgbrjce uz7g== X-Gm-Message-State: AOAM530NuaXqhi4Zl9lDhygxw66dSjDlfovL7FGzRviLSr2K4owYNqq2 PNIERPA/8iRFsfON2YJlYCw= X-Google-Smtp-Source: ABdhPJykoOU3RQreTJtwp989enkIJp6c+ibWkPFwOFsTxe7+nuw+qq7QC056QMe81zrrn/sBFgTIXw== X-Received: by 2002:a7b:c083:: with SMTP id r3mr15351801wmh.177.1614595511167; Mon, 01 Mar 2021 02:45:11 -0800 (PST) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id c26sm25123744wrb.87.2021.03.01.02.45.10 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 01 Mar 2021 02:45:10 -0800 (PST) From: zimoun In-Reply-To: <20210228133314.22935-1-gheber@hdfgroup.org> References: <20210228133314.22935-1-gheber@hdfgroup.org> Date: Mon, 01 Mar 2021 11:41:01 +0100 Message-ID: <86im6b9mwy.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi, On Sun, 28 Feb 2021 at 07:33, Gerd Heber wrote: > +(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"))) > + Why duplicates? Something like: --8<---------------cut here---------------start------------->8--- (define-public hdf5-1.12-parallel-openmpi (package/inherit hdf5-parallel-openmpi (version (package-version hdf5-1.12)) (source (package-source hdf5-1.12))) --8<---------------cut here---------------end--------------->8--- seems simpler. All the best, simon From unknown Mon Jun 23 07:51:52 2025 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: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 02 Mar 2021 09:42:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46830 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Gerd Heber , 46830@debbugs.gnu.org Received: via spool by 46830-submit@debbugs.gnu.org id=B46830.16146781072017 (code B ref 46830); Tue, 02 Mar 2021 09:42:02 +0000 Received: (at 46830) by debbugs.gnu.org; 2 Mar 2021 09:41:47 +0000 Received: from localhost ([127.0.0.1]:51849 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lH1XG-0000WR-TS for submit@debbugs.gnu.org; Tue, 02 Mar 2021 04:41:47 -0500 Received: from mail-qk1-f172.google.com ([209.85.222.172]:41601) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lH1XF-0000WE-4B for 46830@debbugs.gnu.org; Tue, 02 Mar 2021 04:41:45 -0500 Received: by mail-qk1-f172.google.com with SMTP id q85so19563436qke.8 for <46830@debbugs.gnu.org>; Tue, 02 Mar 2021 01:41:45 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to; bh=FToqDEnehPEX54bb4DUoutN6Q5HJckZCD12DPcdMC3Q=; b=Fo3CcbUFdSI36cXOU+ifBnVlv22HNQLihc0IvFk7q7CZmCCkgxbb4XGmluyrI8cN8S o+ZmsIvrShNdteO4grsvGvBAVOe1NKXA0cf+v2VfQFLNvbnyHy3n/TXRH5dzm+J/Q23d cXyb99DUcs/jaiC19xZXbjMThbQeMKC0dXrUU9iWm5WZaFljzWoGPN+KvLr28+Vlol3p Px6xkZIWwhtpMn0GoHZXDBqRK6dMu5agj7XjbSKtkCmqJi7doLqV6TmuBoZ7MoejoFuP pzWPWeolVxaxlAvQXd6xoo9GccaOtBUkqw1WafY6/4USzSXb+GWF+vfrB2ZMqMHksypP SZhQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=FToqDEnehPEX54bb4DUoutN6Q5HJckZCD12DPcdMC3Q=; b=GC50uZAiYtiLjEtrkdUImnm0OgQkYmSqe2CIy+d6dGyRYVyShmaxqW6tyTwd+S0dAV MjFTSIAKdh1qZ1ly4YRhXgA7BdJpC0FkG3O/UeaGwR6xYUI4XWhq1Un8UlJl1ZtBV49l R4AS3xuspT4zm/CQ/sRp7ctAq0f9tXLSK/Y1LtW+sSHBH05+/E0M4yCFzcnC3wot3urK edTz3FCI0vQxd2qHi20gxJyP1bor5szAh+0simKADHRrogzBc15dl7Vy4tZ548wzL/EJ dSbnmXibtbYZrqppmODf8Khlpjq4t9hcMYMmmNqRG4P+GtFG1v5Eq7sHpAm67Srq2FHc aRqg== X-Gm-Message-State: AOAM532shymmgrMv6fkK59we5ySig9Qzuw1AhMDpdy2WvqrUmut3eWL8 jfeH0II9bL6xxZHHhgloVWN+1fnpKyZ1EHS7Ixk= X-Google-Smtp-Source: ABdhPJzyRJxWOg4Lcb02dgMsx5L7LxzGNvEVhZSG4K9jxSXxvJVcFLFz0yvPiYupGrkyPLmyqA54TzXTgj6RHYJSwC8= X-Received: by 2002:a05:620a:91b:: with SMTP id v27mr4885276qkv.201.1614678099396; Tue, 02 Mar 2021 01:41:39 -0800 (PST) MIME-Version: 1.0 References: <20210228133314.22935-1-gheber@hdfgroup.org> <86im6b9mwy.fsf@gmail.com> In-Reply-To: From: zimoun Date: Tue, 2 Mar 2021 10:41:28 +0100 Message-ID: Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi, (Please CC the bug number.) On Tue, 2 Mar 2021 at 01:32, Gerd Heber wrote: > On Mon, Mar 1, 2021 at 4:45 AM zimoun wrote: > > --8<---------------cut here---------------start------------->8--- > > (define-public hdf5-1.12-parallel-openmpi > > (package/inherit hdf5-parallel-openmpi > > (version (package-version hdf5-1.12)) > > (source (package-source hdf5-1.12))) > > --8<---------------cut here---------------end--------------->8--- > Hey, thanks, very clever! Should I submit a new patch or is there a > way to patch the patch? The usual way is to send a v2 which is the patch to apply to the Git tree (and *not* a patch to apply to a patch to apply to the tree). However, personally I am not in favor to add to Guix proper too much versions of variant packages; but that's just my humble opinion. Instead, it could be submitted to specific channels, for instance or any other listed in Guix-HPC. Cheers, simon From unknown Mon Jun 23 07:51:52 2025 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: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 02 Mar 2021 19:40:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46830 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: zimoun Cc: 46830@debbugs.gnu.org, Gerd Heber Received: via spool by 46830-submit@debbugs.gnu.org id=B46830.161471398812156 (code B ref 46830); Tue, 02 Mar 2021 19:40:01 +0000 Received: (at 46830) by debbugs.gnu.org; 2 Mar 2021 19:39:48 +0000 Received: from localhost ([127.0.0.1]:54248 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHAs0-0003A0-4d for submit@debbugs.gnu.org; Tue, 02 Mar 2021 14:39:48 -0500 Received: from eggs.gnu.org ([209.51.188.92]:40450) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHArz-00039n-Go for 46830@debbugs.gnu.org; Tue, 02 Mar 2021 14:39:47 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:46610) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lHAru-000613-2I; Tue, 02 Mar 2021 14:39:42 -0500 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=59548 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1lHArt-0004Hb-0u; Tue, 02 Mar 2021 14:39:41 -0500 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= References: <20210228133314.22935-1-gheber@hdfgroup.org> <86im6b9mwy.fsf@gmail.com> Date: Tue, 02 Mar 2021 20:39:38 +0100 In-Reply-To: (zimoun's message of "Tue, 2 Mar 2021 10:41:28 +0100") Message-ID: <874khtuyyt.fsf_-_@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -0.7 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) zimoun skribis: > On Tue, 2 Mar 2021 at 01:32, Gerd Heber wrote: >> On Mon, Mar 1, 2021 at 4:45 AM zimoun wrote: > >> > --8<---------------cut here---------------start------------->8--- >> > (define-public hdf5-1.12-parallel-openmpi >> > (package/inherit hdf5-parallel-openmpi >> > (version (package-version hdf5-1.12)) >> > (source (package-source hdf5-1.12))) >> > --8<---------------cut here---------------end--------------->8--- > >> Hey, thanks, very clever! Should I submit a new patch or is there a >> way to patch the patch? > > The usual way is to send a v2 which is the patch to apply to the Git > tree (and *not* a patch to apply to a patch to apply to the tree). > > However, personally I am not in favor to add to Guix proper too much > versions of variant packages; but that's just my humble opinion. > Instead, it could be submitted to specific channels, for instance > or any other listed in > Guix-HPC. In this particular case, I think the proposed variant is fine; it=E2=80=99s consistent with what we=E2=80=99re already doing with hdf5. Ludo=E2=80=99. From unknown Mon Jun 23 07:51:52 2025 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: Wed, 03 Mar 2021 14:11:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46830 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ludovic =?UTF-8?Q?Court=C3=A8s?= Cc: 46830@debbugs.gnu.org, zimoun Received: via spool by 46830-submit@debbugs.gnu.org id=B46830.161478062819585 (code B ref 46830); Wed, 03 Mar 2021 14:11:01 +0000 Received: (at 46830) by debbugs.gnu.org; 3 Mar 2021 14:10:28 +0000 Received: from localhost ([127.0.0.1]:55448 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHSCn-00055k-4P for submit@debbugs.gnu.org; Wed, 03 Mar 2021 09:10:28 -0500 Received: from mail-ej1-f44.google.com ([209.85.218.44]:38724) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHSCl-00055X-2X for 46830@debbugs.gnu.org; Wed, 03 Mar 2021 09:10:23 -0500 Received: by mail-ej1-f44.google.com with SMTP id mj10so22363798ejb.5 for <46830@debbugs.gnu.org>; Wed, 03 Mar 2021 06:10:23 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc:content-transfer-encoding; bh=WZCvwZAdCkpkiScp7ApXiSjQAPUtDooY1ZMY21aMEIc=; b=W5jHOWYwelxur7mh5iNZqZG8Z+rgIiYG1YwQxjzbo7cTYEic+3p37P9GiII02r9oPq uaY0HTZyDN0+OFKy6bwbQIya256PEyPUDOAIJLxUIcuEO+yzaEmt5bb4zTbRscf55JnG gdD1VHA+mHw6BsAhj6y7Nbuk7yGgC9DK5Lb+Eq8mSwtqxNeLpO35r7FfIrOlckceaz8S aRUtQAlY3oomj975zAt7lONGS26eeqByLpHylImriyWiaoxJ33rbi6bxkvj4JOVN7pIz nCb6xugKrkZfZoMEc74m6QVybYerJ7YsBrDVUz4zfSzy5fvVwg3TNKAfWog6ifeM0K55 Eqlw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc:content-transfer-encoding; bh=WZCvwZAdCkpkiScp7ApXiSjQAPUtDooY1ZMY21aMEIc=; b=EvTAFUsNxl1kLVmB/wb4q5Zh3s5cDjcWQ17WZwiqrKTdzYpsubIwEIWh1OFkMJxbRx hz4bhhFTka0+vm/iGUk/5sasq/5EQzHxOJVDbjbrdNhlK+GJqqcefPneYUPTXV2FdQSj +7U/oB4KNT83Oo/p9LX1WlqC7KzyZH+NHs+mB07t8AtoO5dxiq5pdYvaXGNB6oMeg4HP VhJ+LMnH3LmA5/RJf1eON5mWvFap1uCb6THQkH15HEXMGnJJu8Ge4xg6IR/d88DfasfC eGtA6xYs3P5SGstW6VifbbLTlOQr3LngsiOa6NDByZSHBBV2bZ+j20Zj+h3Bfa1/dBaZ 2YLw== X-Gm-Message-State: AOAM531Ddp7rNogkrAetmHMVEoedM1ao8TGvZfndeaZp0uP7WCm+WTKp 6QXNcLd3XUmBBqJ6NPCHXFrB3psnMpjocl9uvJ8= X-Google-Smtp-Source: ABdhPJxfCZDvgSpLLG4Yhk0/Hu3X68vHZ23j5uCl5IMHclaWejYN4jemyCByQIONigmucYJ9Ms+HxDxn8Qiy5lM0Bj0= X-Received: by 2002:a17:906:684b:: with SMTP id a11mr16966521ejs.329.1614780617292; Wed, 03 Mar 2021 06:10:17 -0800 (PST) MIME-Version: 1.0 References: <20210228133314.22935-1-gheber@hdfgroup.org> <86im6b9mwy.fsf@gmail.com> <874khtuyyt.fsf_-_@gnu.org> In-Reply-To: <874khtuyyt.fsf_-_@gnu.org> From: Gerd Heber Date: Wed, 3 Mar 2021 08:10:05 -0600 Message-ID: Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Ludovic, how are you? Thanks for taking the time to reply. This conversation makes me wonder what the Guix model for packages such as HDF5 might be. On the one hand, there should be defaults for typical, i.e., non-HPC users,= and they probably belong into gnu/packages/maths.scm. Once you add MPI to the mix, things get a little more complicated, and channels, such as Guix-HPC might be the better place. (?) Should we run our own channel? In HDF5's case, we also use versions in a peculiar way, where the expectati= on is that 1.8.x, 1.10.x, and 1.12.x, etc. version are not compatible for end-user applications, mostly because of API changes. What's your recommendation? Maybe (hdf5-1.6?), hdf5-1.8, hdf-1.10, and hdf5= -1.12 belong into maths.scm, plus the thread-safe builds, but not hdf5-parallel-openmpi? I tried to build hdf5-1.8.22-parallel-openmpi, but some of the (MPI) atomicity tests fail with the OpenMPI version used in the current hdf5-parallel-openmpi. And then there is MPICH... I would also like to see HDFView as a Guix package. We have a Spack package= , but the Java story on Guix (I don't blame you ;-) is a little confusing. I'm sold on the merits of Guix and you are doing fantastic work. What's your recommendation, and what can we (The HDF Group) do to help? Best, G. On Tue, Mar 2, 2021 at 1:39 PM Ludovic Court=C3=A8s wrote: > > zimoun skribis: > > > On Tue, 2 Mar 2021 at 01:32, Gerd Heber wrote: > >> On Mon, Mar 1, 2021 at 4:45 AM zimoun wrote= : > > > >> > --8<---------------cut here---------------start------------->8--- > >> > (define-public hdf5-1.12-parallel-openmpi > >> > (package/inherit hdf5-parallel-openmpi > >> > (version (package-version hdf5-1.12)) > >> > (source (package-source hdf5-1.12))) > >> > --8<---------------cut here---------------end--------------->8--- > > > >> Hey, thanks, very clever! Should I submit a new patch or is there a > >> way to patch the patch? > > > > The usual way is to send a v2 which is the patch to apply to the Git > > tree (and *not* a patch to apply to a patch to apply to the tree). > > > > However, personally I am not in favor to add to Guix proper too much > > versions of variant packages; but that's just my humble opinion. > > Instead, it could be submitted to specific channels, for instance > > or any other listed in > > Guix-HPC. > > In this particular case, I think the proposed variant is fine; it=E2=80= =99s > consistent with what we=E2=80=99re already doing with hdf5. > > Ludo=E2=80=99. From unknown Mon Jun 23 07:51:52 2025 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: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 05 Mar 2021 01:11:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46830 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Gerd Heber , Ludovic =?UTF-8?Q?Court=C3=A8s?= Cc: 46830@debbugs.gnu.org Received: via spool by 46830-submit@debbugs.gnu.org id=B46830.161490663520575 (code B ref 46830); Fri, 05 Mar 2021 01:11:02 +0000 Received: (at 46830) by debbugs.gnu.org; 5 Mar 2021 01:10:35 +0000 Received: from localhost ([127.0.0.1]:60634 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHyzC-0005Ln-W6 for submit@debbugs.gnu.org; Thu, 04 Mar 2021 20:10:35 -0500 Received: from mail-wr1-f51.google.com ([209.85.221.51]:39608) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHyzB-0005La-EI for 46830@debbugs.gnu.org; Thu, 04 Mar 2021 20:10:34 -0500 Received: by mail-wr1-f51.google.com with SMTP id b18so268677wrn.6 for <46830@debbugs.gnu.org>; Thu, 04 Mar 2021 17:10:33 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:in-reply-to:references:date:message-id :mime-version:content-transfer-encoding; bh=uha63o3OnyOjolqtdQnEhl41gvA1clNylKUSWyXLgow=; b=sjx5rnFkuTPinorDR8qsZ8sm+TfCnqKB+tgZI4XgGocj6/QN8VE55Wl+iT6I+iTAkp D6Buftklz+WzMnXAA2pF5Daj29K2OVEFKnAFPEm81STPqV18vcNxZW1Syhzb7mTd5FgH L1oG1Kwmn0nu1Q/M6oagCJAVC74M/PV6X0ey/ZOa8snWcLHM3YSUuNfNOG4hCLUPYxsW NIr6n18XgVEm7FKrnSVf38RE/UegjPoJ+liZrK5y9O/9Vea4p2UnQheQ/P6sbxc+Kidq OYHyDKtK4+NnOywF8cIlNwMJWoHyW8dMeqKOXFobPkQnz++YrtW8wubAQB2XRD7rOy6R WrhA== 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:in-reply-to:references:date :message-id:mime-version:content-transfer-encoding; bh=uha63o3OnyOjolqtdQnEhl41gvA1clNylKUSWyXLgow=; b=Of+2yEK+ELuepwdhShXhUj6ibrG3kAwtpz28J8fwJWSyip4K1x+u0G1oDzIe0lsTsu ztJPoDtQXzkodEsTgR4gyEe9mWWskrkkNkUldXYicttV69CY4rQx8TXvN9F7iIgnwKCC aSvdKCrUQtxZf8L1QhYnS/agP3U2kvJY7zgKSM1ugoBNFWtS1f9xP+zVHPLnZVAdZuCj RpYLpd3qYdf+QDJPK86UISF7Pq21YulKzKGlOEXGndoIxUNavBpMeetH4Kjgh+Wb4+8L aUwc4ft4nfRyxZ40gYNDCPf1YMzQ6C4HqGQGG5MBvm5lr63yGZDusEvhGYJRBys0DJdi BxiA== X-Gm-Message-State: AOAM532kmFYwmMmRhFMMyOotbaZlIGp28jNwA9++OslGzgE+VgWd44nu IQ5JxzxEZykAEczBvop7+Tx3SvQ5XH4= X-Google-Smtp-Source: ABdhPJwtDvFF3UKHE+uBPbE8Qomvfq1EJmHuU4ahvQNnmpcFGm3Zbcq7P/v3uOmv4+zuT73cvbOcRg== X-Received: by 2002:a5d:404f:: with SMTP id w15mr7041199wrp.106.1614906627631; Thu, 04 Mar 2021 17:10:27 -0800 (PST) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id g9sm1604817wrp.14.2021.03.04.17.10.26 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Thu, 04 Mar 2021 17:10:27 -0800 (PST) From: zimoun In-Reply-To: References: <20210228133314.22935-1-gheber@hdfgroup.org> <86im6b9mwy.fsf@gmail.com> <874khtuyyt.fsf_-_@gnu.org> Date: Fri, 05 Mar 2021 02:08:57 +0100 Message-ID: <86r1ku76fq.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi Gerd, On Wed, 03 Mar 2021 at 08:10, Gerd Heber wrote: > What's your recommendation? Maybe (hdf5-1.6?), hdf5-1.8, hdf-1.10, and hd= f5-1.12 > belong into maths.scm, plus the thread-safe builds, but not > hdf5-parallel-openmpi? >From my understanding, hdf5 at versions 1.8 and 1.10 are used by other packages. When those very packages will not use at one of these versions, I guess the very version will be removed. hdf5-parallel-openmpi is used by petsc-openmpi for instance. And this hdf5 variant is built with version 1.10. Since there is no package that requires hdf5-parallel-openmpi at another version than 1.10, I do not see the point to include it in Guix proper. Especially when the custom variant is straightforward to locally create and buildable on a reasonable amount of time. However, these words are not totally acceptable. :-) If I take the shoes of a regular scientist, then they only wants the package at hand and not necessary RTFM how to do package transformations. > I tried to build hdf5-1.8.22-parallel-openmpi, but some of the (MPI) > atomicity tests fail > with the OpenMPI version used in the current hdf5-parallel-openmpi. Yes, and we could imagine different versions of openmpi. And then compiled with different compiler versions, etc=E2=80=A6 > And then there is MPICH... =E2=80=A6and the matrix of combinations is exploding. ;-) One issue with the channel is to provide substitutes for that channel. For example, the channel guix-science uses TravisCI to build the package from GitHub. That=E2=80=99s said, the cons about channels=E2=80=93and so the pros about = include the hdf5 variant in Guix proper=E2=80=93is to keep consistency and detect break= age: Guix proper updates a package that becomes incompatible with one the variant living a channel. All in Guix proper, then Guix CI will detect it. Some dependencies in Guix proper and hdf variant in a channel, then the channel CI probably not since nothing changed (from the channel side) and so nothing triggered a build. I do not know. Well, let stay pragmatic. :-) > I would also like to see HDFView as a Guix package. We have a Spack > package, but It would be really cool! > I'm sold on the merits of Guix and you are doing fantastic work. > What's your recommendation, and what can we (The HDF Group) do to help? Thanks the HDF Group for their interest on Guix. Where the package definition ends (channel vs Guix proper) is one thing, maybe a start should to have these hdf5 variant definitions. Then from a pragmatic point of view, depending on these definitions (number, length, etc.), they could ends in (gnu packages maths) or maybe its own module (gnu packages hdf) or maybe in a channel. WDYT? All the best, simon From unknown Mon Jun 23 07:51:52 2025 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: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 14:03:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46830 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Gerd Heber Cc: 46830@debbugs.gnu.org, zimoun Received: via spool by 46830-submit@debbugs.gnu.org id=B46830.16152121329553 (code B ref 46830); Mon, 08 Mar 2021 14:03:02 +0000 Received: (at 46830) by debbugs.gnu.org; 8 Mar 2021 14:02:12 +0000 Received: from localhost ([127.0.0.1]:42420 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJGSZ-0002U1-RZ for submit@debbugs.gnu.org; Mon, 08 Mar 2021 09:02:12 -0500 Received: from mail3-relais-sop.national.inria.fr ([192.134.164.104]:52402) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJGSY-0002To-7A for 46830@debbugs.gnu.org; Mon, 08 Mar 2021 09:02:10 -0500 X-IronPort-AV: E=Sophos;i="5.81,232,1610406000"; d="scan'208";a="375101630" Received: from 91-160-117-201.subs.proxad.net (HELO ribbon) ([91.160.117.201]) by mail3-relais-sop.national.inria.fr with ESMTP/TLS/DHE-RSA-AES256-GCM-SHA384; 08 Mar 2021 15:01:42 +0100 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= References: <20210228133314.22935-1-gheber@hdfgroup.org> <86im6b9mwy.fsf@gmail.com> <874khtuyyt.fsf_-_@gnu.org> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 18 =?UTF-8?Q?Vent=C3=B4se?= an 229 de la =?UTF-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Mon, 08 Mar 2021 15:01:42 +0100 In-Reply-To: (Gerd Heber's message of "Wed, 3 Mar 2021 08:10:05 -0600") Message-ID: <87r1kpd9rt.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) Hi Gerd, Gerd Heber skribis: > Ludovic, how are you? Thanks for taking the time to reply. This > conversation makes > me wonder what the Guix model for packages such as HDF5 might be. > On the one hand, there should be defaults for typical, i.e., non-HPC user= s, and > they probably belong into gnu/packages/maths.scm. Once you add MPI to the > mix, things get a little more complicated, and channels, such as > Guix-HPC might be > the better place. (?) Should we run our own channel? As you write, the goal for packages in Guix proper should be to have =E2=80=9Cgood defaults=E2=80=9D, and possibly useful variants, as is curren= tly the case with HDF5. We won=E2=80=99t keep all versions and variants in Guix proper because that= =E2=80=99d be too much of a maintenance burden. For =E2=80=9Cunusual=E2=80=9D variants, = I recommend maintaining your own channel. (This is something we did at Inria for example with an Open=C2=A0MPI variant that includes the MPI1 compatibility layer.) Additionally, you can use things like =E2=80=98--with-input=3Dopenmpi=3Dmpi= ch=E2=80=99. We may eventually get support for =E2=80=9Cparameterized packages=E2=80=9D, wh= ich will allow users to choose between HDF5 variants from the command line: https://lists.gnu.org/archive/html/guix-devel/2020-11/msg00312.html > What's your recommendation? Maybe (hdf5-1.6?), hdf5-1.8, hdf-1.10, and hd= f5-1.12 > belong into maths.scm, plus the thread-safe builds, but not > hdf5-parallel-openmpi? For Guix proper, I think we should keep the number of HDF5 variants stable. We should remove old versions once they=E2=80=99re no longer neede= d by any in-tree package. > I tried to build hdf5-1.8.22-parallel-openmpi, but some of the (MPI) > atomicity tests fail > with the OpenMPI version used in the current hdf5-parallel-openmpi. > And then there is MPICH... > > I would also like to see HDFView as a Guix package. We have a Spack packa= ge, but > the Java story on Guix (I don't blame you ;-) is a little confusing. That=E2=80=99s a different story :-) but please don=E2=80=99t hesitate to s= hare your experience, frustration, and questions regarding Java on the mailing lists, I=E2=80=99m sure you=E2=80=99ll get some guidance. > I'm sold on the merits of Guix and you are doing fantastic work. > What's your recommendation, and what can we (The HDF Group) do to help? It=E2=80=99s great to get feedback from upstream; you can certainly help us= make wise(r) decisions regarding HDF5 packaging, in particular in deciding which variants and versions make sense, what defaults are reasonable, and how well they work in an HPC and non-HPC setting. WDYT? What changes would you like to see? Thanks for your interest! Ludo=E2=80=99. From unknown Mon Jun 23 07:51:52 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Gerd Heber Subject: bug#46830: closed (Closing) Message-ID: References: <20210228133314.22935-1-gheber@hdfgroup.org> X-Gnu-PR-Message: they-closed 46830 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 46830@debbugs.gnu.org Date: Wed, 13 Sep 2023 09:30:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1694597402-19033-1" This is a multi-part message in MIME format... ------------=_1694597402-19033-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #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 which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 46830@debbugs.gnu.org. --=20 46830: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D46830 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1694597402-19033-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 46830-done) by debbugs.gnu.org; 13 Sep 2023 09:29:41 +0000 Received: from localhost ([127.0.0.1]:60806 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qgMBp-0004wG-CV for submit@debbugs.gnu.org; Wed, 13 Sep 2023 05:29:41 -0400 Received: from hera.aquilenet.fr ([2a0c:e300::1]:41868) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qgMBl-0004vv-C2 for 46830-done@debbugs.gnu.org; Wed, 13 Sep 2023 05:29:39 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 7240114A4; Wed, 13 Sep 2023 11:29:24 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id VXpn7gPW1dSG; Wed, 13 Sep 2023 11:29:24 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0::c64]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 059DF3D0; Wed, 13 Sep 2023 11:29:23 +0200 (CEST) Date: Wed, 13 Sep 2023 11:29:22 +0200 From: Andreas Enge To: 46830-done@debbugs.gnu.org Subject: Closing Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 46830-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hello, thanks for your patch, that I only see just now (teams were not yet a thing in 2021...). This version of hdf5 has been retired, so I am closing this issue. It might be useful to add a parallel package to hdf5@1.14 instead. Andreas ------------=_1694597402-19033-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit 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 To: guix-patches@gnu.org Subject: [PATCH Added hdf5-1.12-parallel-openmpi] * gnu/packages/maths.scm (hdf5-1.12-parallel-openmpi): New package based on HDF5 1.12.0 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-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: Gerd Heber X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) --- 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 ------------=_1694597402-19033-1--