From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 02 11:38:15 2024 Received: (at submit) by debbugs.gnu.org; 2 Oct 2024 15:38:16 +0000 Received: from localhost ([127.0.0.1]:59034 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sw1Qd-00080k-H8 for submit@debbugs.gnu.org; Wed, 02 Oct 2024 11:38:15 -0400 Received: from lists.gnu.org ([209.51.188.17]:44798) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sw1Qb-00080Y-Rh for submit@debbugs.gnu.org; Wed, 02 Oct 2024 11:38:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sw1OS-0003im-G5 for guix-patches@gnu.org; Wed, 02 Oct 2024 11:36:00 -0400 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sw1OP-0006w5-VG for guix-patches@gnu.org; Wed, 02 Oct 2024 11:36:00 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=from:to:cc:subject:date:message-id:mime-version: content-transfer-encoding; bh=yByJyu/5pADJNTBtcTTUy/h9eAV/6CcYEUXZWk3ciTw=; b=T+YZJQAiM9i4W+yk2OSj39x9nVjy+bzpD6nuexNVKBup/J4gzdJVaQc9 aKrgdO2f+dDEwol4mqcPvF30kDCGAGCTittXl01ttz92gRolporEXmQ1W LvT5OiYbb6MGdGd5Km9XTnnq2V8r+6F9rPmEyI+8kQ94fw2kwdMPnTuq0 E=; Authentication-Results: mail2-relais-roc.national.inria.fr; dkim=none (message not signed) header.i=none; spf=SoftFail smtp.mailfrom=romain.garbage@inria.fr; dmarc=fail (p=none dis=none) d=inria.fr X-IronPort-AV: E=Sophos;i="6.11,172,1725314400"; d="scan'208";a="186568719" Received: from 91-160-179-8.subs.proxad.net (HELO localhost.localdomain) ([91.160.179.8]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 02 Oct 2024 17:35:52 +0200 From: Romain GARBAGE To: guix-patches@gnu.org Subject: [PATCH 0/2] Add support for parallel I/O in netcdf Date: Wed, 2 Oct 2024 17:32:24 +0200 Message-ID: <20241002153544.7444-1-romain.garbage@inria.fr> X-Mailer: git-send-email 2.46.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=192.134.164.83; envelope-from=romain.garbage@inria.fr; helo=mail2-relais-roc.national.inria.fr X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_VALIDITY_CERTIFIED_BLOCKED=0.001, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, 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: ludovic.courtes@inria.fr, Romain GARBAGE 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 (--) According to the documentation at [1], parallel I/O support for classic netCDF files, i.e. CDF-1, 2 and 5 formats, requires the PnetCDF library. This patch series adds the pnetcdf package (first commit) and activates the pnetcdf support in the parallel variant of the netcdf package. [1]: https://docs.unidata.ucar.edu/nug/current/getting_and_building_netcdf.html#build_parallel Romain GARBAGE (2): gnu: Add pnetcdf. gnu: netcdf-parallel-openmpi: Enable pnetcdf support. gnu/packages/maths.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) base-commit: 71fef00c95b22a1d917abdb28de5aa217b023e31 -- 2.46.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 02 11:40:24 2024 Received: (at 73603) by debbugs.gnu.org; 2 Oct 2024 15:40:24 +0000 Received: from localhost ([127.0.0.1]:59040 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sw1Si-0008Cv-1G for submit@debbugs.gnu.org; Wed, 02 Oct 2024 11:40:24 -0400 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:24900) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sw1Sf-0008Cd-Qs for 73603@debbugs.gnu.org; Wed, 02 Oct 2024 11:40:22 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=from:to:cc:subject:date:message-id:mime-version: content-transfer-encoding; bh=RUyruwCctMwa5zoTOZGUXv2NeIwN+IBm11TOc+0rtos=; b=G+MljhjobIt9UFVdxb/rx/YHGfqlOy6UlaN5w95CpLfm5u2AlRH9V/RA BN1eA4Hdp+wzRuH2tuG9aYmsMcM9u8z7cgfHgkqlXICevhPoR49ApqWup JkfhmoFXQ8LCNNrmxeUScy2q9JwPl9E50lT2jMOQBJvmY6f5dnBnr2axJ A=; Authentication-Results: mail2-relais-roc.national.inria.fr; dkim=none (message not signed) header.i=none; spf=SoftFail smtp.mailfrom=romain.garbage@inria.fr; dmarc=fail (p=none dis=none) d=inria.fr X-IronPort-AV: E=Sophos;i="6.11,172,1725314400"; d="scan'208";a="186569687" Received: from 91-160-179-8.subs.proxad.net (HELO localhost.localdomain) ([91.160.179.8]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 02 Oct 2024 17:40:14 +0200 From: Romain GARBAGE To: 73603@debbugs.gnu.org Subject: [PATCH 1/2] gnu: Add pnetcdf. Date: Wed, 2 Oct 2024 17:40:00 +0200 Message-ID: <20241002154001.8275-1-romain.garbage@inria.fr> X-Mailer: git-send-email 2.46.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 73603 Cc: ludovic.courtes@inria.fr, Romain GARBAGE 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 (---) * gnu/packages/maths.scm (pnetcdf): New variable. Change-Id: I419161be82cd45585187abfd1e63a23feac73d59 --- gnu/packages/maths.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 03fa4d2fae..51812c5a0d 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2350,6 +2350,37 @@ (define-public netcdf sharing of scientific data.") (license (license:x11-style "file://COPYRIGHT")))) +(define-public pnetcdf + (package + (name "pnetcdf") + (version "1.13.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://parallel-netcdf.github.io/Release/pnetcdf-" + version ".tar.gz")) + (sha256 + (base32 + "14f4nbcnw80y59cl0kjpxqqfaxzzd62kixnhb6ihp6aigb3z385b")))) + (build-system gnu-build-system) + (arguments + (list #:configure-flags + #~(list "--enable-shared" + (string-append "--with-mpi=" #$(this-package-input "openmpi"))) + #:phases + #~(modify-phases %standard-phases + (add-after 'build 'mpi-setup + #$%openmpi-setup)))) + (inputs (list openmpi)) + (native-inputs (list m4)) + (home-page "https://parallel-netcdf.github.io/") + (synopsis "Parallel I/O Library for NetCDF File Access") + (description "PnetCDF is a high-performance parallel I/O library for accessing +Unidata's NetCDF, files in classic formats, specifically the formats of CDF-1, 2, and +5.") + (license (license:x11-style "file://COPYRIGHT")))) + (define-public netcdf-parallel-openmpi (package (inherit netcdf) (name "netcdf-parallel-openmpi") base-commit: 71fef00c95b22a1d917abdb28de5aa217b023e31 -- 2.46.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 02 11:40:25 2024 Received: (at 73603) by debbugs.gnu.org; 2 Oct 2024 15:40:25 +0000 Received: from localhost ([127.0.0.1]:59042 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sw1Sj-0008D5-DQ for submit@debbugs.gnu.org; Wed, 02 Oct 2024 11:40:25 -0400 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:24900) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sw1Sh-0008Cd-05 for 73603@debbugs.gnu.org; Wed, 02 Oct 2024 11:40:23 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=from:to:cc:subject:date:message-id:in-reply-to: references:mime-version:content-transfer-encoding; bh=f6aNNEHe3V0wURdKXso5ouQ+2USW61twZJm5cQacdlk=; b=TwyuRRuHHsvRqYUgVYquo9zCGFU1FxoQOwFf7BPHpA6GxVA7jhoXaDHF pqPu5hB1MRBWhET6ZRQZln6q2yqOsRTrtwmzTdxQf6Hex8k2ChZ/6WiSX 9Ibb0o+sOXfy4SkVpSiokjDrsLRKnWrm9S5O6SMnwPbJAGm9yzAbCw3Q4 4=; Authentication-Results: mail2-relais-roc.national.inria.fr; dkim=none (message not signed) header.i=none; spf=SoftFail smtp.mailfrom=romain.garbage@inria.fr; dmarc=fail (p=none dis=none) d=inria.fr X-IronPort-AV: E=Sophos;i="6.11,172,1725314400"; d="scan'208";a="186569699" Received: from 91-160-179-8.subs.proxad.net (HELO localhost.localdomain) ([91.160.179.8]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 02 Oct 2024 17:40:15 +0200 From: Romain GARBAGE To: 73603@debbugs.gnu.org Subject: [PATCH 2/2] gnu: netcdf-parallel-openmpi: Enable pnetcdf support. Date: Wed, 2 Oct 2024 17:40:01 +0200 Message-ID: <20241002154001.8275-2-romain.garbage@inria.fr> X-Mailer: git-send-email 2.46.0 In-Reply-To: <20241002154001.8275-1-romain.garbage@inria.fr> References: <20241002154001.8275-1-romain.garbage@inria.fr> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 73603 Cc: ludovic.courtes@inria.fr, Romain GARBAGE 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 (---) * gnu/packages/maths.scm (netcdf-parallel-openmpi) [arguments]: Enable pnetcdf support. Change-Id: I7f3fc6abdb262be86840ea3f68bb6416a0ab1fad --- gnu/packages/maths.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 51812c5a0d..f4edd546e2 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2386,6 +2386,7 @@ (define-public netcdf-parallel-openmpi (name "netcdf-parallel-openmpi") (inputs `(("mpi" ,openmpi) + ("pnetcdf" ,pnetcdf) ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi) (package-inputs netcdf)))) ;; TODO: Replace pkg-config references in nc-config with absolute references @@ -2394,6 +2395,8 @@ (define-public netcdf-parallel-openmpi ((#:configure-flags flags) `(cons* "CC=mpicc" "CXX=mpicxx" "--enable-parallel-tests" + ;; Enable support of CDF-1, 2 and 5 formats. + "--enable-pnetcdf" ;; NetCDF supports both parallel and shared library building ;; See https://docs.unidata.ucar.edu/nug/current/getting_and_building_netcdf.html#build_parallel "--enable-shared" "--with-pic" -- 2.46.0 From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 04 07:53:22 2024 Received: (at 73603-done) by debbugs.gnu.org; 4 Oct 2024 11:53:22 +0000 Received: from localhost ([127.0.0.1]:34553 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1swgs5-0000Ob-Mo for submit@debbugs.gnu.org; Fri, 04 Oct 2024 07:53:21 -0400 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:37942) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1swgs2-0000OE-IZ for 73603-done@debbugs.gnu.org; Fri, 04 Oct 2024 07:53:20 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=from:to:cc:subject:in-reply-to:references:date: message-id:mime-version; bh=Z/BpYRfvVe9GVK8J4fX/enxMpVGBIcASnd6Pc11qR98=; b=UMQGCgQOVLKQjqhSJxdMnGERQ/4bNd3XIuQJxv7swRcmIcBbwWrzQVJq 4u3ST3Z3+Tap/SktWQyWpSWMcxX1njxhvkmzx54Pcc68d7Gmflud2iVwK yyCdWR6+MCrhN5eWHrG0JfCOQ5Ohaq712RghP8DHMN++8OdBKg68Qjwro U=; Authentication-Results: mail2-relais-roc.national.inria.fr; dkim=none (message not signed) header.i=none; spf=SoftFail smtp.mailfrom=ludovic.courtes@inria.fr; dmarc=fail (p=none dis=none) d=inria.fr X-IronPort-AV: E=Sophos;i="6.11,177,1725314400"; d="scan'208";a="186992534" Received: from unknown (HELO ribbon) ([193.50.110.50]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 04 Oct 2024 13:53:09 +0200 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Romain GARBAGE Subject: Re: [bug#73603] [PATCH 0/2] Add support for parallel I/O in netcdf In-Reply-To: <20241002153544.7444-1-romain.garbage@inria.fr> (Romain GARBAGE's message of "Wed, 2 Oct 2024 17:32:24 +0200") References: <20241002153544.7444-1-romain.garbage@inria.fr> Date: Fri, 04 Oct 2024 13:53:09 +0200 Message-ID: <87cykgrsnu.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 73603-done Cc: 73603-done@debbugs.gnu.org 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 (---) Romain GARBAGE skribis: > According to the documentation at [1], parallel I/O support for classic > netCDF files, i.e. CDF-1, 2 and 5 formats, requires the PnetCDF library. > This patch series adds the pnetcdf package (first commit) and activates > the pnetcdf support in the parallel variant of the netcdf package. > > [1]: https://docs.unidata.ucar.edu/nug/current/getting_and_building_netcdf.html#build_parallel > > Romain GARBAGE (2): > gnu: Add pnetcdf. > gnu: netcdf-parallel-openmpi: Enable pnetcdf support. Applied, thanks! From unknown Sun Jun 22 03:51:24 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Sat, 02 Nov 2024 11:24:05 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator