From unknown Sat Jun 21 10:43:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#72877] [PATCH 0/8] Upgrade PETSc, SLEPc, SUNDIALS, and DealII Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Thu, 29 Aug 2024 15:40:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 72877 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 72877@debbugs.gnu.org Cc: Ludovic =?UTF-8?Q?Court=C3=A8s?= , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-To: guix-patches@gnu.org X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by submit@debbugs.gnu.org id=B.172494599113673 (code B ref -1); Thu, 29 Aug 2024 15:40:02 +0000 Received: (at submit) by debbugs.gnu.org; 29 Aug 2024 15:39:51 +0000 Received: from localhost ([127.0.0.1]:51936 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhFW-0003YT-MS for submit@debbugs.gnu.org; Thu, 29 Aug 2024 11:39:51 -0400 Received: from lists.gnu.org ([209.51.188.17]:44924) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhFU-0003YK-D7 for submit@debbugs.gnu.org; Thu, 29 Aug 2024 11:39:49 -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 1sjhEa-0004uq-Fc for guix-patches@gnu.org; Thu, 29 Aug 2024 11:38:52 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sjhEZ-0000ud-Hr; Thu, 29 Aug 2024 11:38:51 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:Date:Subject:To:From:in-reply-to: references; bh=8s28w3slW+ZNHMgxJ3IpXDSlDAtYAmvIP1oHotcppVQ=; b=g2tjpr1os3rBRs rZegA7urIJ7AahVXPmQ6xtM8Ah/we2VP5rOh1s7WCtfE9BG31/SEHoMEzuc5ae3gdewLkriUHKvo/ Y5bIvKDRdVXFUEJ0Ns+3AHW/SH6+JahAGsmZPWyrXlOvaeFNFFQ06zUOPZhJAGSq5ZhHUGDgtT9p1 5QjxuljEwUdQSuptJOd+RlHZG7Q86IC/6V5AfDd0BsyrYAR+k1ataMZVgYQ3+3Q+j5a9E84MFRp6E srf4jTxDv4ZIeSiMBcOgsQNv9y+to+sd/wCKjHzHNfc2S1mkcj+LC1NKYeXsSuECil8CbHGBFWRxP xm1tv12fZZQh60d8QKwQ==; From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Date: Thu, 29 Aug 2024 17:38:43 +0200 Message-ID: X-Mailer: git-send-email 2.45.2 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 (---) Hello Guix! The impetus for this patch series is that PETSc fails to build on ‘core-updates’ (soon to be merged) and it’s pretty critical in applied maths and HPC: --8<---------------cut here---------------start------------->8--- Using MAKE: /gnu/store/lc6r1mh0jlcwixjziiw1zsx1my478rv1-make-4.4.1/bin/make Using MAKEFLAGS: -j16 -l96.0 w -- PETSC_DIR=/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1 PETSC_ARCH=arch-linux-c-opt MAKE_NP=16 ========================================== make[3]: Entering directory '/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1' /gnu/store/nvpcidxh4wqp5prdlyfsbcymg67xqqn9-python-3.10.7/bin/python3 ./config/gmakegen.py --petsc-arch=arch-linux-c-opt /gnu/store/nvpcidxh4wqp5prdlyfsbcymg67xqqn9-python-3.10.7/bin/python3 /tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1/config/gmakegentest.py --petsc-dir=/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1 --petsc-arch=arch-linux-c-opt --testdir=./arch-linux-c-opt/tests make[3]: *** No rule to make target 'w'. Stop. make[3]: Leaving directory '/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1' make[2]: *** [/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1/lib/petsc/conf/rules:50: libs] Error 2 make[2]: Leaving directory '/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1' egrep: warning: egrep is obsolescent; using grep -E egrep: warning: egrep is obsolescent; using grep -E **************************ERROR************************************* Error during compile, check arch-linux-c-opt/lib/petsc/conf/make.log Send it and arch-linux-c-opt/lib/petsc/conf/configure.log to petsc-maint@mcs.anl.gov ******************************************************************** make[1]: *** [makefile:40: all] Error 1 make: *** [GNUmakefile:9: all] Error 2 error: in phase 'build': uncaught exception: %exception #<&invoke-error program: "make" arguments: ("MAKE_NP=16") exit-status: 2 term-signal: #f stop-signal: #f> phase `build' failed after 9.7 seconds command "make" "MAKE_NP=16" failed with status 2 build process 18 exited with status 256 builder for `/gnu/store/wxzwzjlcq10grqrjl9w144fv3myr0kf9-petsc-3.16.1.drv' failed with exit code 1 --8<---------------cut here---------------end--------------->8--- (From .) Ironically I tested this on top of today’s ‘master’ but I’m hopeful that it’ll work on ‘core-updates’ (because of this, I think we should get this series merged shortly once ‘core-updates’ is merged). I rebuilt all dependents, but ‘fenics’ and its dependents remain broken: fenics, python-vedo, and python-dolfin-adjoint. Thanks, Ludo’. Ludovic Courtès (8): gnu: petsc: Update to 3.21.4. gnu: python-petsc4py: Update to 3.21.4. gnu: slepc: Update to 3.21.1. gnu: python-slepc4py: Update to 3.21.1. gnu: petsc: Make ‘petscvariables’ reproducible. gnu: sundials: Upgrade to 7.1.1. gnu: sundials, sundials-openmpi: Use gexps. gnu: dealii: Update to 9.6.0. gnu/packages/maths.scm | 190 ++++++++++++++++++++++------------------- 1 file changed, 100 insertions(+), 90 deletions(-) base-commit: d5312370b46ace47e138d84e1bb28e5651cee94b -- 2.45.2 From unknown Sat Jun 21 10:43:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#72877] [PATCH 1/8] gnu: petsc: Update to 3.21.4. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Thu, 29 Aug 2024 15:41:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 72877 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 72877@debbugs.gnu.org Cc: Ludovic =?UTF-8?Q?Court=C3=A8s?= , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 72877-submit@debbugs.gnu.org id=B72877.172494605713888 (code B ref 72877); Thu, 29 Aug 2024 15:41:02 +0000 Received: (at 72877) by debbugs.gnu.org; 29 Aug 2024 15:40:57 +0000 Received: from localhost ([127.0.0.1]:51954 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGa-0003bq-7D for submit@debbugs.gnu.org; Thu, 29 Aug 2024 11:40:56 -0400 Received: from eggs.gnu.org ([209.51.188.92]:46908) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGX-0003b9-Ba for 72877@debbugs.gnu.org; Thu, 29 Aug 2024 11:40:54 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sjhFX-0000zL-Fc; Thu, 29 Aug 2024 11:39:51 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:References:In-Reply-To:Date:Subject:To: From; bh=gQGywjx7WKxqmesDS1dQpuDZ2awkwq+ODBiIHFwhjeA=; b=bjABDa92xrtg4sRoOi4Q 3kzCMlKMbWDouSpl0a2wfGnTSjLkznaUX11QebZftCqVpNdOFWTqFFm8xj+hKFqR5xYWLFXHeQ3nr 9/gfMRww8QyTPJJTEJDtKYz9aQV/UmltKvnaNCQZ1S1+rPAdBd8+MNvmFYzu7DOinjLM1fvKaEmu7 kg5eXlWPi0VRhK6bZh2pi6cZun0sZ3MfTc5z6dU/tLv1kCHaK7kgFLoasPSpUi0tCHhVe8gRCquHf MsexgNSMPl9NEex80kNol2scYIJ9DLdWKUHTQGqOYOiPZrRhpxLwvgkaBo6yRRmc/DJEFc67TMWdq 3ZGdnj84XljTsw==; From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Date: Thu, 29 Aug 2024 17:39:34 +0200 Message-ID: <7c1e3b92955a4133ffae9bc277f0b8a2d89df6d4.1724945557.git.ludo@gnu.org> X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 (---) From: Ludovic Courtès * gnu/packages/maths.scm (petsc): Update to 3.21.4. Update source URL. [arguments]: Move ‘check’ phase after ‘install’. [home-page]: Update. Change-Id: I8e7244ad4f8566119bc259f1dccec9589760a491 --- gnu/packages/maths.scm | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 557d9acc48..4be9ad9d7e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3510,15 +3510,15 @@ (define-public maxflow (define-public petsc (package (name "petsc") - (version "3.16.1") + (version "3.21.4") (source (origin (method url-fetch) ;; The *-lite-* tarball does not contain the *large* documentation - (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" + (uri (string-append "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/" "petsc-lite-" version ".tar.gz")) (sha256 - (base32 "0sm03vpg010q9icidiq587n325m0598cj6hab2rdv85nwyygg74h")))) + (base32 "1394ybnchawb2kghx4xk36gw26930aa73lxyw96diiqp8rnhgbm9")))) (outputs '("out" ; libraries and headers "examples")) ; ~30MiB of examples (build-system gnu-build-system) @@ -3614,6 +3614,16 @@ (define-public petsc (("([[:graph:]]+)/bin/diff") "diff") (("([[:graph:]]+)/bin/sed") "sed") (("([[:graph:]]+)/bin/gfortran") "gfortran"))))) + + ;; Some of the tests get linked with '-L$prefix/lib -lpetsc' (even + ;; though that's unnecessary because they also explicitly link + ;; against 'libpetsc.so' from the build directory). To work around + ;; it, run tests after installation. See + ;; . + (delete 'check) + (add-after 'install 'check + (assoc-ref %standard-phases 'check)) + (add-after 'install 'move-examples (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -3622,7 +3632,7 @@ (define-public petsc (exdir' (string-append examples "/share/petsc/examples"))) (copy-recursively exdir exdir') (delete-file-recursively exdir))))))) - (home-page "https://www.mcs.anl.gov/petsc") + (home-page "https://petsc.org") (synopsis "Library to solve PDEs") (description "PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of -- 2.45.2 From unknown Sat Jun 21 10:43:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#72877] [PATCH 2/8] gnu: python-petsc4py: Update to 3.21.4. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Thu, 29 Aug 2024 15:41:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 72877 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 72877@debbugs.gnu.org Cc: Ludovic =?UTF-8?Q?Court=C3=A8s?= , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 72877-submit@debbugs.gnu.org id=B72877.172494605713896 (code B ref 72877); Thu, 29 Aug 2024 15:41:02 +0000 Received: (at 72877) by debbugs.gnu.org; 29 Aug 2024 15:40:57 +0000 Received: from localhost ([127.0.0.1]:51956 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGa-0003bx-To for submit@debbugs.gnu.org; Thu, 29 Aug 2024 11:40:57 -0400 Received: from eggs.gnu.org ([209.51.188.92]:46906) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGX-0003b8-L9 for 72877@debbugs.gnu.org; Thu, 29 Aug 2024 11:40:54 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sjhFY-0000zQ-Cz; Thu, 29 Aug 2024 11:39:52 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:References:In-Reply-To:Date:Subject:To: From; bh=EyMhyTK63xqlEYrKPlL3q6I7IBJpaBM/ZVeXx3L13S0=; b=TiYheFQ/s6AW9zctIjTR Ja0cHLs3Ut/GMJTv9cjNscJdOcu9H6Cr67pyUxSctn/KxkZWOSxdaZlAO/XsZ3iYC91AIa65emMKA g7+V6b5/Vimb3Iq6rnXz9Xs1TS1qIK/LWyL1Et1cGC8ywJybO20nB4ZUCwm9LLdztun7/F/Tl4QsX VOdRjcc/NGGaqyhuAoWnUqOetIln6xsmwnagkUBowQPBczVR9JELOPNoe70cR4UpMAjq9f/TMjsf/ VyFou5KFXHIiBH9aoqnpGOuAoYplhFtGOWIsMiqG/1njjoGiDDPbtiTBuP3OaZAP4E81EGIdkk0Ly OMosvGnqzoMOLQ==; From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Date: Thu, 29 Aug 2024 17:39:35 +0200 Message-ID: <77468fe53b0ea23abc1e544d71c0c31dcf49a078.1724945557.git.ludo@gnu.org> X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 (---) From: Ludovic Courtès * gnu/packages/maths.scm (python-petsc4py): Update to 3.21.4. [source](modules, snippet): Remove. [arguments]: Switch to gexps. Rename ‘pre-build’ phase to ‘set-PETSC_DIR’. Replace ‘check’ phase. [native-inputs]: Switch to ‘python-cython-3’. [inputs]: Remove labels. Change-Id: I2d8ef3519f6ffe93ff761ef99c4b8951b6107e1c --- gnu/packages/maths.scm | 44 ++++++++++++++++-------------------------- 1 file changed, 17 insertions(+), 27 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 4be9ad9d7e..c6a40a2652 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3727,41 +3727,31 @@ (define-public petsc-complex-openmpi (define-public python-petsc4py (package (name "python-petsc4py") - (version "3.16.1") + (version "3.21.4") (source (origin (method url-fetch) (uri (pypi-uri "petsc4py" version)) (sha256 (base32 - "0pxr6qa7p0pmpq0av29lx8lzlrdcfdzj87ynixzr8dn42y13a662")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Ensure source file is regenerated in the build phase. - (delete-file "src/petsc4py.PETSc.c") - ;; Remove legacy GC code. See - ;; https://bitbucket.org/petsc/petsc4py/issues/125. - (substitute* "src/PETSc/cyclicgc.pxi" - ((".*gc_refs.*") "" ) - ((".*PyGC_Head.*") "")) - #t)))) + "1kffxhcwkx6283n2p83ymanz6m8j2xmz5kpa5s8qc4f9iiah59sb")))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'build 'pre-build - (lambda _ - ;; Define path to PETSc installation. - (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) - #t)) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) - (native-inputs - (list python-cython)) - (inputs - `(("petsc" ,petsc-openmpi) - ("python-numpy" ,python-numpy))) + (list #:phases + #~(modify-phases %standard-phases + (add-before 'build 'set-PETSC_DIR + (lambda* (#:key inputs #:allow-other-keys) + ;; Define path to PETSc installation. + (setenv "PETSC_DIR" + (assoc-ref inputs "petsc-openmpi")))) + (add-before 'check 'mpi-setup + #$%openmpi-setup) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "test/runtests.py"))))))) + (native-inputs (list python-cython-3)) + (inputs (list petsc-openmpi python-numpy)) (home-page "https://bitbucket.org/petsc/petsc4py/") (synopsis "Python bindings for PETSc") (description "PETSc, the Portable, Extensible Toolkit for -- 2.45.2 From unknown Sat Jun 21 10:43:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#72877] [PATCH 3/8] gnu: slepc: Update to 3.21.1. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Thu, 29 Aug 2024 15:41:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 72877 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 72877@debbugs.gnu.org Cc: Ludovic =?UTF-8?Q?Court=C3=A8s?= , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 72877-submit@debbugs.gnu.org id=B72877.172494605713902 (code B ref 72877); Thu, 29 Aug 2024 15:41:03 +0000 Received: (at 72877) by debbugs.gnu.org; 29 Aug 2024 15:40:57 +0000 Received: from localhost ([127.0.0.1]:51958 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGb-0003c5-Bw for submit@debbugs.gnu.org; Thu, 29 Aug 2024 11:40:57 -0400 Received: from eggs.gnu.org ([209.51.188.92]:46924) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGY-0003bB-Dr for 72877@debbugs.gnu.org; Thu, 29 Aug 2024 11:40:54 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sjhFZ-0000zb-EP; Thu, 29 Aug 2024 11:39:53 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:References:In-Reply-To:Date:Subject:To: From; bh=H20RXi/7mqNL+IqlkFRxVtF09eF36Gbxn/z9DgBK71s=; b=VmH6V2M5/PrVgnQx/kZU WC7yPlDTYLCLHTf0DVMYltp1frReCsqGQjULoHIoGWHLi23Q1pE3W/L+hHpTz4OVZ6CPB0GWnLusA q3U++DlxlHDEAM1+uHewqIJMqcC+Y8oUmuYdGGnWtBHvV2oAP6V53jEINEmWaAbK25dJdLA0PvZCE 1k0P24fVc7M2cNFviOq1tQGiMVJy1PYZSIW+oTcLdoEtY7KjdSKuNdfxwEq9od2uywU661AnLdBQ1 vhmR1sW7pHpsEVYukoT7ZM07nlQnb0jyEasYYofckf4TK0nFhOhs860lrdi/YcAcJsdzyWglzNSCM WhK4I0QLvE0FAQ==; From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Date: Thu, 29 Aug 2024 17:39:36 +0200 Message-ID: <32d909e4f934e6bf116cbe62e90ffa355bed1caa.1724945557.git.ludo@gnu.org> X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 (---) From: Ludovic Courtès * gnu/packages/maths.scm (slepc): Update to 3.21.1. Change-Id: Ib82754c351100de94b57c650a3688747bf706713 --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index c6a40a2652..22e7fc5804 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3928,7 +3928,7 @@ (define-public python-quadpy (define-public slepc (package (name "slepc") - (version "3.16.1") + (version "3.21.1") (source (origin (method url-fetch) @@ -3936,7 +3936,7 @@ (define-public slepc version ".tar.gz")) (sha256 (base32 - "1ysfm77s5fcissv3q0k5d65mlp93zi4anqg62q3cd25dn66sva5i")))) + "12kdgnw9lm5q6bq5wp27ygdp1bjdz3fhkb8m9ds83kn32l53zcxy")))) (build-system gnu-build-system) (native-inputs `(("python" ,python) -- 2.45.2 From unknown Sat Jun 21 10:43:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#72877] [PATCH 4/8] gnu: python-slepc4py: Update to 3.21.1. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Thu, 29 Aug 2024 15:42:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 72877 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 72877@debbugs.gnu.org Cc: Ludovic =?UTF-8?Q?Court=C3=A8s?= , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 72877-submit@debbugs.gnu.org id=B72877.172494606513981 (code B ref 72877); Thu, 29 Aug 2024 15:42:01 +0000 Received: (at 72877) by debbugs.gnu.org; 29 Aug 2024 15:41:05 +0000 Received: from localhost ([127.0.0.1]:51972 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGi-0003dP-OM for submit@debbugs.gnu.org; Thu, 29 Aug 2024 11:41:05 -0400 Received: from eggs.gnu.org ([209.51.188.92]:46930) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGZ-0003bF-6R for 72877@debbugs.gnu.org; Thu, 29 Aug 2024 11:40:55 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sjhFa-0000zl-D0; Thu, 29 Aug 2024 11:39:54 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:References:In-Reply-To:Date:Subject:To: From; bh=/eHFcDckU2EBycShZAbzte5+goaGJhTBT72L6A9Ghns=; b=pxnzwZtpJqAxiKzKiTmb tJvOC6rxtqzJMzx95xriAOiSPLNntXt1x4Y5IKboxc3u0m+38uJPTQKYjoJMsIGznVmpa7aD6e0nw MN4TwfbWiMagglVPXfKAqSQ2pzTmpoiLFvxEQF0+LHYhYVEM6g5o9KjCjzkdNTQkTKMHoKFSFNwEa qMXoTagqO6O4qkvnOL4ipKmngQcky2ctKz33bhP2cYNsPl/33tf2tAyMow7frDLbN4KcTY8AqNz7a nUEd25clseCkZOQP+i23fMpM0BeNvZDSGVrweXXBf5sG3zzJryNyvwNMd4cIYs9BbsD1RZF38NeVf g0lTrum5U/XXLA==; From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Date: Thu, 29 Aug 2024 17:39:37 +0200 Message-ID: <52bd9a22889bd47f077bc6b8240a748ce2cb30e7.1724945557.git.ludo@gnu.org> X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 (---) From: Ludovic Courtès * gnu/packages/maths.scm (python-slepc4py): Update to 3.21.1. [arguments]: Switch to gexps. Replace ‘check’ phase. [native-inputs]: New field. [inputs]: Remove labels. Add ‘petsc-openmpi’. Change-Id: Ib6f1480415ac5128399c32c1974779b67edb5550 --- gnu/packages/maths.scm | 35 ++++++++++++++++++----------------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 22e7fc5804..7249eb68da 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4042,31 +4042,32 @@ (define-public slepc-complex-openmpi (define-public python-slepc4py (package (name "python-slepc4py") - (version "3.16.1") + (version "3.21.1") (source (origin (method url-fetch) (uri (pypi-uri "slepc4py" version)) (sha256 (base32 - "0fq997y73ymvcvdrxycp450pxwdgnqaw62gv9rwncfgsfplkvs9w")))) + "01vvpl8g73knkwnh6mbxd45vwcs4zsw814147fvgkvj30qkhx3mw")))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'build 'pre-build - (lambda _ - ;; Define path to PETSc installation. - (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) - ;; Define path to SLEPc installation. - (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc")) - #t)) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) - (inputs - `(("python-numpy" ,python-numpy) - ("python-petsc4py" ,python-petsc4py) - ("slepc" ,slepc-openmpi))) + (list #:phases + #~(modify-phases %standard-phases + (add-before 'build 'pre-build + (lambda* (#:key inputs #:allow-other-keys) + ;; Define path to PETSc installation. + (setenv "PETSC_DIR" (assoc-ref inputs "petsc-openmpi")) + ;; Define path to SLEPc installation. + (setenv "SLEPC_DIR" (assoc-ref inputs "slepc-openmpi")))) + (add-before 'check 'mpi-setup + #$%openmpi-setup) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "test/runtests.py"))))))) + (native-inputs (list python-cython-3)) + (inputs (list python-numpy python-petsc4py petsc-openmpi slepc-openmpi)) (home-page "https://bitbucket.org/slepc/slepc4py/") (synopsis "Python bindings for SLEPc") (description "SLEPc, the Scalable Library for Eigenvalue Problem -- 2.45.2 From unknown Sat Jun 21 10:43:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#72877] [PATCH 5/8] gnu: petsc: Make =?UTF-8?Q?=E2=80=98petscvariables=E2=80=99?= reproducible. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Thu, 29 Aug 2024 15:42:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 72877 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 72877@debbugs.gnu.org Cc: Ludovic =?UTF-8?Q?Court=C3=A8s?= , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 72877-submit@debbugs.gnu.org id=B72877.172494606513987 (code B ref 72877); Thu, 29 Aug 2024 15:42:02 +0000 Received: (at 72877) by debbugs.gnu.org; 29 Aug 2024 15:41:05 +0000 Received: from localhost ([127.0.0.1]:51974 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGj-0003dS-Gi for submit@debbugs.gnu.org; Thu, 29 Aug 2024 11:41:05 -0400 Received: from eggs.gnu.org ([209.51.188.92]:46932) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGa-0003bH-48 for 72877@debbugs.gnu.org; Thu, 29 Aug 2024 11:40:56 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sjhFb-0000zu-Au; Thu, 29 Aug 2024 11:39:55 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:References:In-Reply-To:Date:Subject:To: From; bh=6m8Crqi7wonWIBZV1H4vV3P8vg4OwraClOOAo3pw2DM=; b=QbedxI51ht6kCRXJNcsz 0jrqlTOmxwiDymdZ313Co8Fl73S1MttjlxgRT2Dg30+iS+dqQkJ2uwxY6RxCxlED/Ccou1Lm+xYWS 5HhoUYcvLIDN0u/fHsZX+l0Dxsx9PEMWiPj1vSvi1Qy0cXOlJ1t2iBdV1uuVXQYpCDWnzqzDFLqTs eb+h4VbpzQbyJQ7EZsIaNPH2Q6IwRF5EWHS/gi96OcjxqZdaOEq1ESWSU5EPf5H5f+nEjTWy82K1p Lmb2zc09WAdedp4df7iUb+fRhGDPd0HzTiX++RDLsWRgLJ/DRN108YeksOBTqhCmZS4R3F2wopAhA BnlUsqLCZxrt2g==; From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Date: Thu, 29 Aug 2024 17:39:38 +0200 Message-ID: <4785fd2599682973b16ea0bdab44c909568b0292.1724945557.git.ludo@gnu.org> X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 (---) This is a followup to 31fe177a97bacec643180cc5bcf8805a6cb07481. * gnu/packages/maths.scm (petsc)[arguments]: In ‘clean-local-references’, fix typo in ‘MAKE_NP’ and ‘NPMAX’ regexps. Substitute ‘MAKE_TEST_NP’ and ‘MAKE_LOAD’ as well. Change-Id: I41b4279a3cdc4b077fab21f0f99273d0d50ed8e1 --- gnu/packages/maths.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 7249eb68da..ff1be6d35a 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3578,8 +3578,10 @@ (define-public petsc "Machine characteristics: Linux-x.x.x")) (substitute* (find-files "." "petscvariables") ;; Do not expose build machine characteristics, set to defaults. - (("MAKE_NP = [:digit:]+") "MAKE_NP = 2") - (("NPMAX = [:digit:]+") "NPMAX = 2"))))) + (("MAKE_NP = [[:digit:]]+") "MAKE_NP = 2") + (("MAKE_TEST_NP = [[:digit:]]+") "MAKE_TEST_NP = 2") + (("MAKE_LOAD = .*") "MAKE_LOAD = 256.0\n") + (("NPMAX = [[:digit:]]+") "NPMAX = 2"))))) (add-after 'install 'clean-install ;; Try to keep installed files from leaking build directory names. (lambda* (#:key inputs outputs #:allow-other-keys) -- 2.45.2 From unknown Sat Jun 21 10:43:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#72877] [PATCH 6/8] gnu: sundials: Upgrade to 7.1.1. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Thu, 29 Aug 2024 15:42:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 72877 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 72877@debbugs.gnu.org Cc: Ludovic =?UTF-8?Q?Court=C3=A8s?= , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 72877-submit@debbugs.gnu.org id=B72877.172494607014014 (code B ref 72877); Thu, 29 Aug 2024 15:42:02 +0000 Received: (at 72877) by debbugs.gnu.org; 29 Aug 2024 15:41:10 +0000 Received: from localhost ([127.0.0.1]:51982 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGn-0003dx-Sv for submit@debbugs.gnu.org; Thu, 29 Aug 2024 11:41:10 -0400 Received: from eggs.gnu.org ([209.51.188.92]:47084) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGl-0003cn-OG for 72877@debbugs.gnu.org; Thu, 29 Aug 2024 11:41:08 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sjhFl-0001AV-Or; Thu, 29 Aug 2024 11:40:06 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:References:In-Reply-To:Date:Subject:To: From; bh=/h5FXxA/Fn4t6WBjzvyT+uNDQ9DRgc9vj2lfmYO3aWk=; b=I28QqxnLo3DlztfccAKi 9GDWJnE3dMjIB1zSNMh3FXf8bMzHsIbsMNuogOO6Wm/uH9TOYXLVE8HHKOGO1pllkFpCaZazV8V3i WryoMOpLs5YTgOPfKL+sV6hOcALPUypDxXRxw74c9E1nsCaDnyk1eaW2c3G1lY/8pjwQITXciSO1P FMoHJ04nZmmah2osQA5L01qWzd9mILtft9Bi9c4AUuDSEvvpCag0e85WTGxUW0lrbE1FmWdumsXKq YfjXlaGNnNz3znhL9cgB7hx0f3u5fC77K9G5vPo3bPx/IY5GI0B5e5NNbrOTrmvU+YMw/7TtQPA/y WkaVT3IIDzQ3KA==; From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Date: Thu, 29 Aug 2024 17:39:39 +0200 Message-ID: X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 (---) From: Ludovic Courtès * gnu/packages/maths.scm (sundials): Update to 7.1.1. [native-inputs]: Add PKG-CONFIG. (sundials-openmpi)[arguments]: Pass ‘-DPETSC_INCLUDE_DIRS’ instead of ‘-DPETSC_DIR’. Change-Id: I750415109d69b53afbcf461dc98b2028af03c35a --- gnu/packages/maths.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ff1be6d35a..4dc67ea313 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -8036,7 +8036,7 @@ (define-public tiny-bignum (define-public sundials (package (name "sundials") - (version "6.2.0") + (version "7.1.1") (source (origin (method url-fetch) @@ -8044,10 +8044,10 @@ (define-public sundials version "/sundials-" version ".tar.gz")) (sha256 (base32 - "07gk9060xk3bzfqf8v4fqlp0rcxswiwlsy887zv87i1gfy9map8r")))) + "1fwlgbcdxz30dzsqw3y1b6ic1rhzfadghj7cq7yxsj14npgnwzga")))) (build-system cmake-build-system) (native-inputs - (list python-2)) ; For tests; syntax incompatible with Python 3. + (list pkg-config python-2)) ;for tests; syntax incompatible with Python 3 (inputs (list openblas suitesparse)) (arguments @@ -8100,8 +8100,9 @@ (define-public sundials-openmpi (assoc-ref %build-inputs "hypre-openmpi") "/lib") "-DENABLE_PETSC:BOOL=ON" - (string-append "-DPETSC_DIR=" - (assoc-ref %build-inputs "petsc-openmpi")) + (string-append "-DPETSC_INCLUDE_DIRS=" + (assoc-ref %build-inputs "petsc-openmpi") + "/include") ,flags)) ((#:phases phases '%standard-phases) `(modify-phases ,phases -- 2.45.2 From unknown Sat Jun 21 10:43:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#72877] [PATCH 7/8] gnu: sundials, sundials-openmpi: Use gexps. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Thu, 29 Aug 2024 15:42:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 72877 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 72877@debbugs.gnu.org Cc: Ludovic =?UTF-8?Q?Court=C3=A8s?= , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 72877-submit@debbugs.gnu.org id=B72877.172494607114024 (code B ref 72877); Thu, 29 Aug 2024 15:42:02 +0000 Received: (at 72877) by debbugs.gnu.org; 29 Aug 2024 15:41:11 +0000 Received: from localhost ([127.0.0.1]:51984 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGp-0003dz-9m for submit@debbugs.gnu.org; Thu, 29 Aug 2024 11:41:11 -0400 Received: from eggs.gnu.org ([209.51.188.92]:47090) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGl-0003co-OH for 72877@debbugs.gnu.org; Thu, 29 Aug 2024 11:41:08 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sjhFm-0001CH-P5; Thu, 29 Aug 2024 11:40:06 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:References:In-Reply-To:Date:Subject:To: From; bh=BohfSXq2ZZstN8RLNEYGJOeWZzdqo+tBhzKn5tnkIQQ=; b=jZH26Hba5tmO8eAsufVu U5uvJPUYDFsg6GgtYs+1emnDC0pG9eg9XoM1505UCto1SjoN725qydTMXejrxuub8bheN5aMHtiGg b8e++y4cyH1Ra6M/YZzdFTDSaXmjK9Sav7mo8t6vv2YP0dWdkLBhkMGeyTLyq5wBO4CiBBhtkdtQr 9uwG/gUifQsr+Cq2aVaBh5Y91TY4bc/Wte1qN5eLRyuPIvuCT/UM+Yz3CgghQBKTtok5gi0faDEpr j4Fy75QhNck9YwAKBIr2Z6LeLZjD2LqExeWZyYqQwPpoZPLuXOELEzvVGQHeS3eRVOLQ6HEigvRkP tW1rE2D14hYxkg==; From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Date: Thu, 29 Aug 2024 17:39:40 +0200 Message-ID: X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 (---) * gnu/packages/maths.scm (sundials)[arguments]: Use gexps and use ‘search-input-file’ rather than ‘assoc-ref’. (sundials-openmpi)[arguments]: Likewise. Change-Id: Ife0c2ae3604cf66c90ec4a13fe9242f7fe7d550f --- gnu/packages/maths.scm | 74 +++++++++++++++++++++++------------------- 1 file changed, 40 insertions(+), 34 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 4dc67ea313..194e4ea399 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -8051,25 +8051,28 @@ (define-public sundials (inputs (list openblas suitesparse)) (arguments - '(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon" + (list #:configure-flags + #~(list "-DCMAKE_C_FLAGS=-O2 -g -fcommon" - "-DSUNDIALS_INDEX_SIZE=32" - ;; Incompatible with 32-bit indices. - ;;"-DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON" + "-DSUNDIALS_INDEX_SIZE=32" + ;; Incompatible with 32-bit indices. + ;;"-DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON" - "-DEXAMPLES_ENABLE_C:BOOL=ON" - "-DEXAMPLES_ENABLE_CXX:BOOL=ON" - ;; Requires -DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON. - ;;"-DEXAMPLES_ENABLE_F2003:BOOL=ON" - "-DEXAMPLES_INSTALL:BOOL=OFF" + "-DEXAMPLES_ENABLE_C:BOOL=ON" + "-DEXAMPLES_ENABLE_CXX:BOOL=ON" + ;; Requires -DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON. + ;;"-DEXAMPLES_ENABLE_F2003:BOOL=ON" + "-DEXAMPLES_INSTALL:BOOL=OFF" - "-DENABLE_KLU:BOOL=ON" - ,(string-append "-DKLU_INCLUDE_DIR=" - (assoc-ref %build-inputs "suitesparse") - "/include") - ,(string-append "-DKLU_LIBRARY_DIR=" - (assoc-ref %build-inputs "suitesparse") - "/lib")))) + "-DENABLE_KLU:BOOL=ON" + (string-append "-DKLU_INCLUDE_DIR=" + (dirname + (search-input-file %build-inputs + "include/klu.h"))) + (string-append "-DKLU_LIBRARY_DIR=" + (dirname + (search-input-file %build-inputs + "lib/libklu.so")))))) (home-page "https://computation.llnl.gov/projects/sundials") (synopsis "Suite of nonlinear and differential/algebraic equation solvers") (description "SUNDIALS is a family of software packages implemented with @@ -8090,24 +8093,27 @@ (define-public sundials-openmpi petsc-openmpi)) (arguments (substitute-keyword-arguments (package-arguments sundials) - ((#:configure-flags flags '()) - `(cons* "-DENABLE_MPI:BOOL=ON" - "-DENABLE_HYPRE:BOOL=ON" - (string-append "-DHYPRE_INCLUDE_DIR=" - (assoc-ref %build-inputs "hypre-openmpi") - "/include") - (string-append "-DHYPRE_LIBRARY_DIR=" - (assoc-ref %build-inputs "hypre-openmpi") - "/lib") - "-DENABLE_PETSC:BOOL=ON" - (string-append "-DPETSC_INCLUDE_DIRS=" - (assoc-ref %build-inputs "petsc-openmpi") - "/include") - ,flags)) - ((#:phases phases '%standard-phases) - `(modify-phases ,phases - (add-before 'check 'mpi-setup - ,%openmpi-setup))))) + ((#:configure-flags flags #~()) + #~(cons* "-DENABLE_MPI:BOOL=ON" + "-DENABLE_HYPRE:BOOL=ON" + (string-append "-DHYPRE_INCLUDE_DIR=" + (dirname + (search-input-file %build-inputs + "include/HYPRE.h"))) + (string-append "-DHYPRE_LIBRARY_DIR=" + (dirname + (search-input-file %build-inputs + "lib/libHYPRE.so"))) + "-DENABLE_PETSC:BOOL=ON" + (string-append "-DPETSC_INCLUDE_DIRS=" + (dirname + (search-input-file %build-inputs + "include/petsc.h"))) + #$flags)) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-before 'check 'mpi-setup + #$%openmpi-setup))))) (synopsis "SUNDIALS with MPI support"))) (define-public sundials-5 -- 2.45.2 From unknown Sat Jun 21 10:43:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#72877] [PATCH 8/8] gnu: dealii: Update to 9.6.0. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Thu, 29 Aug 2024 15:42:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 72877 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 72877@debbugs.gnu.org Cc: Ludovic =?UTF-8?Q?Court=C3=A8s?= , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 72877-submit@debbugs.gnu.org id=B72877.172494607214031 (code B ref 72877); Thu, 29 Aug 2024 15:42:03 +0000 Received: (at 72877) by debbugs.gnu.org; 29 Aug 2024 15:41:12 +0000 Received: from localhost ([127.0.0.1]:51986 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGp-0003e9-Pg for submit@debbugs.gnu.org; Thu, 29 Aug 2024 11:41:12 -0400 Received: from eggs.gnu.org ([209.51.188.92]:47098) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhGn-0003dL-0Q for 72877@debbugs.gnu.org; Thu, 29 Aug 2024 11:41:09 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sjhFo-0001Cc-31; Thu, 29 Aug 2024 11:40:08 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:References:In-Reply-To:Date:Subject:To: From; bh=cGIEKGLjwrOFIsADFDNJsJdNzKuCfd7BmwBLbxsYeYo=; b=hFd9l51MS+KuF5n1v5KN y3zPDBO5Fbb8ZMomcJ1WsxwU0CU73e6IJ9wlid7pfZe4KVU7yo2msFCLeOOl0M/i8qrl/T2AvxAkI ihiuIMk3xQutdqZUnMcp52+86bWrPyaLNOKmA97vbH4AspXK4E2tApL2acei+BqxxBFqPCynn8DMc XsMHli4JVt5joaqOIxmVBkwY5YIlCzSG2gVDsogoImqLuwFJ1muCXZA1qkDJfOKkt2EVC1XQSMS47 /4VS6SfT2zvNVUgIPKy7u8U8kVuNJ5NA58XrUmRyWG5f71SOTZ7j+ewhYE45OJ/lldbRCW6yldmJm eYzWL7ro5ErJgg==; From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Date: Thu, 29 Aug 2024 17:39:41 +0200 Message-ID: <66aa3e6c1221344b4129d2c4f82ced06a082a94a.1724945557.git.ludo@gnu.org> X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 (---) From: Ludovic Courtès * gnu/packages/maths.scm (dealii): Update to 9.6.0. Change-Id: I197511908d9ac27dd4ba1356515f1fbf7bafd218 --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 194e4ea399..7d0d4127cf 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -6874,14 +6874,14 @@ (define trilinos-for-dealii-openmpi (define-public dealii (package (name "dealii") - (version "9.5.1") + (version "9.6.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/dealii/dealii/releases/" "download/v" version "/dealii-" version ".tar.gz")) (sha256 - (base32 "0phgcfnil4rb41xipsdbm4lxrymlqxbiccakg3pkm3a8wqsva658")) + (base32 "1vbvw76xv8h1diwfgybgarm7qwn51rxd1kp2jgy2rvcfxgq26lv7")) (modules '((guix build utils))) (snippet ;; Remove bundled boost, Kokkos, muparser, TBB and UMFPACK. -- 2.45.2 From unknown Sat Jun 21 10:43:28 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: Ludovic =?UTF-8?Q?Court=C3=A8s?= Subject: bug#72877: closed (Re: [bug#72877] [PATCH 0/8] Upgrade PETSc, SLEPc, SUNDIALS, and DealII) Message-ID: References: <87seue8qg8.fsf@gnu.org> X-Gnu-PR-Message: they-closed 72877 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 72877@debbugs.gnu.org Date: Thu, 05 Sep 2024 08:20:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1725524402-9844-1" This is a multi-part message in MIME format... ------------=_1725524402-9844-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #72877: [PATCH 0/8] Upgrade PETSc, SLEPc, SUNDIALS, and DealII 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 72877@debbugs.gnu.org. --=20 72877: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D72877 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1725524402-9844-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 72877-done) by debbugs.gnu.org; 5 Sep 2024 08:19:42 +0000 Received: from localhost ([127.0.0.1]:36076 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sm7iQ-0002X0-2e for submit@debbugs.gnu.org; Thu, 05 Sep 2024 04:19:42 -0400 Received: from mail3-relais-sop.national.inria.fr ([192.134.164.104]:64121) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sm7iN-0002Wg-Tu for 72877-done@debbugs.gnu.org; Thu, 05 Sep 2024 04:19:41 -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:content-transfer-encoding; bh=2WXsAo0E0AcAFg5fJSenrLWwrHkqhAqCWq7El/YsXqc=; b=MhTCVCzbD82oFcfPadq3ua34wc+uawEpPNu3TX3zcnoXPBVgwvfNZ6on XitMueDIonWlidBTlkCmNFWbAl9GO+YIwqOrzTM0n9hOlKGqVys4qEkBG t7MDY0meR2XcmV3KisFQw33/6O+aVG8KfrIOYPkAmlS9OsHCwdebnC0a/ E=; Authentication-Results: mail3-relais-sop.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="6.10,204,1719871200"; d="scan'208";a="95503671" 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/ECDHE-RSA-AES256-GCM-SHA384; 05 Sep 2024 10:17:29 +0200 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: 72877-done@debbugs.gnu.org Subject: Re: [bug#72877] [PATCH 0/8] Upgrade PETSc, SLEPc, SUNDIALS, and DealII In-Reply-To: ("Ludovic =?utf-8?Q?Court?= =?utf-8?Q?=C3=A8s=22's?= message of "Thu, 29 Aug 2024 17:38:43 +0200") References: Date: Thu, 05 Sep 2024 10:17:27 +0200 Message-ID: <87seue8qg8.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 72877-done Cc: Andreas Enge , Sharlatan Hellseher , Eric Bavier 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, Ludovic Court=C3=A8s skribis: > gnu: petsc: Update to 3.21.4. > gnu: python-petsc4py: Update to 3.21.4. > gnu: slepc: Update to 3.21.1. > gnu: python-slepc4py: Update to 3.21.1. > gnu: petsc: Make =E2=80=98petscvariables=E2=80=99 reproducible. > gnu: sundials: Upgrade to 7.1.1. > gnu: sundials, sundials-openmpi: Use gexps. > gnu: dealii: Update to 9.6.0. Pushed as 993d6d2e7be4dac738629c76a51058f4dc5bc449 after re-testing locally. I had to fix =E2=80=98hypre=E2=80=99 as well in 6bf70cf9a60464701ca0741d9f6= 3f5ace9810fc9 since it broke on =E2=80=98core-updates=E2=80=99 due to a missing TeX Live = dependency. Ludo=E2=80=99. ------------=_1725524402-9844-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 29 Aug 2024 15:39:51 +0000 Received: from localhost ([127.0.0.1]:51936 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhFW-0003YT-MS for submit@debbugs.gnu.org; Thu, 29 Aug 2024 11:39:51 -0400 Received: from lists.gnu.org ([209.51.188.17]:44924) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sjhFU-0003YK-D7 for submit@debbugs.gnu.org; Thu, 29 Aug 2024 11:39:49 -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 1sjhEa-0004uq-Fc for guix-patches@gnu.org; Thu, 29 Aug 2024 11:38:52 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sjhEZ-0000ud-Hr; Thu, 29 Aug 2024 11:38:51 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:Date:Subject:To:From:in-reply-to: references; bh=8s28w3slW+ZNHMgxJ3IpXDSlDAtYAmvIP1oHotcppVQ=; b=g2tjpr1os3rBRs rZegA7urIJ7AahVXPmQ6xtM8Ah/we2VP5rOh1s7WCtfE9BG31/SEHoMEzuc5ae3gdewLkriUHKvo/ Y5bIvKDRdVXFUEJ0Ns+3AHW/SH6+JahAGsmZPWyrXlOvaeFNFFQ06zUOPZhJAGSq5ZhHUGDgtT9p1 5QjxuljEwUdQSuptJOd+RlHZG7Q86IC/6V5AfDd0BsyrYAR+k1ataMZVgYQ3+3Q+j5a9E84MFRp6E srf4jTxDv4ZIeSiMBcOgsQNv9y+to+sd/wCKjHzHNfc2S1mkcj+LC1NKYeXsSuECil8CbHGBFWRxP xm1tv12fZZQh60d8QKwQ==; From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= To: guix-patches@gnu.org Subject: [PATCH 0/8] Upgrade PETSc, SLEPc, SUNDIALS, and DealII Date: Thu, 29 Aug 2024 17:38:43 +0200 Message-ID: X-Mailer: git-send-email 2.45.2 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 X-Debbugs-Cc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: submit Cc: =?UTF-8?q?Ludovic=20Court=C3=A8s?= 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 (---) Hello Guix! The impetus for this patch series is that PETSc fails to build on ‘core-updates’ (soon to be merged) and it’s pretty critical in applied maths and HPC: --8<---------------cut here---------------start------------->8--- Using MAKE: /gnu/store/lc6r1mh0jlcwixjziiw1zsx1my478rv1-make-4.4.1/bin/make Using MAKEFLAGS: -j16 -l96.0 w -- PETSC_DIR=/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1 PETSC_ARCH=arch-linux-c-opt MAKE_NP=16 ========================================== make[3]: Entering directory '/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1' /gnu/store/nvpcidxh4wqp5prdlyfsbcymg67xqqn9-python-3.10.7/bin/python3 ./config/gmakegen.py --petsc-arch=arch-linux-c-opt /gnu/store/nvpcidxh4wqp5prdlyfsbcymg67xqqn9-python-3.10.7/bin/python3 /tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1/config/gmakegentest.py --petsc-dir=/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1 --petsc-arch=arch-linux-c-opt --testdir=./arch-linux-c-opt/tests make[3]: *** No rule to make target 'w'. Stop. make[3]: Leaving directory '/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1' make[2]: *** [/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1/lib/petsc/conf/rules:50: libs] Error 2 make[2]: Leaving directory '/tmp/guix-build-petsc-3.16.1.drv-0/petsc-3.16.1' egrep: warning: egrep is obsolescent; using grep -E egrep: warning: egrep is obsolescent; using grep -E **************************ERROR************************************* Error during compile, check arch-linux-c-opt/lib/petsc/conf/make.log Send it and arch-linux-c-opt/lib/petsc/conf/configure.log to petsc-maint@mcs.anl.gov ******************************************************************** make[1]: *** [makefile:40: all] Error 1 make: *** [GNUmakefile:9: all] Error 2 error: in phase 'build': uncaught exception: %exception #<&invoke-error program: "make" arguments: ("MAKE_NP=16") exit-status: 2 term-signal: #f stop-signal: #f> phase `build' failed after 9.7 seconds command "make" "MAKE_NP=16" failed with status 2 build process 18 exited with status 256 builder for `/gnu/store/wxzwzjlcq10grqrjl9w144fv3myr0kf9-petsc-3.16.1.drv' failed with exit code 1 --8<---------------cut here---------------end--------------->8--- (From .) Ironically I tested this on top of today’s ‘master’ but I’m hopeful that it’ll work on ‘core-updates’ (because of this, I think we should get this series merged shortly once ‘core-updates’ is merged). I rebuilt all dependents, but ‘fenics’ and its dependents remain broken: fenics, python-vedo, and python-dolfin-adjoint. Thanks, Ludo’. Ludovic Courtès (8): gnu: petsc: Update to 3.21.4. gnu: python-petsc4py: Update to 3.21.4. gnu: slepc: Update to 3.21.1. gnu: python-slepc4py: Update to 3.21.1. gnu: petsc: Make ‘petscvariables’ reproducible. gnu: sundials: Upgrade to 7.1.1. gnu: sundials, sundials-openmpi: Use gexps. gnu: dealii: Update to 9.6.0. gnu/packages/maths.scm | 190 ++++++++++++++++++++++------------------- 1 file changed, 100 insertions(+), 90 deletions(-) base-commit: d5312370b46ace47e138d84e1bb28e5651cee94b -- 2.45.2 ------------=_1725524402-9844-1-- From unknown Sat Jun 21 10:43:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#72877] [PATCH 0/8] Upgrade PETSc, SLEPc, SUNDIALS, and DealII Resent-From: Eric Bavier Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 05 Sep 2024 13:09:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 72877 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ludovic =?UTF-8?Q?Court=C3=A8s?= Cc: 72877-done@debbugs.gnu.org, Andreas Enge , Sharlatan Hellseher Received: via spool by 72877-done@debbugs.gnu.org id=D72877.172554172230086 (code D ref 72877); Thu, 05 Sep 2024 13:09:02 +0000 Received: (at 72877-done) by debbugs.gnu.org; 5 Sep 2024 13:08:42 +0000 Received: from localhost ([127.0.0.1]:36409 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1smCE5-0007pA-VM for submit@debbugs.gnu.org; Thu, 05 Sep 2024 09:08:42 -0400 Received: from mout02.posteo.de ([185.67.36.66]:59227) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1smCE3-0007or-EY for 72877-done@debbugs.gnu.org; Thu, 05 Sep 2024 09:08:40 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 205FD240103 for <72877-done@debbugs.gnu.org>; Thu, 5 Sep 2024 15:07:26 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1725541647; bh=XB1W4g+Q2L+xF1sBJiZmGjO6CkRD1O0l+s0xXSOvqZw=; h=MIME-Version:Date:From:To:Cc:Subject:Message-ID:Content-Type: Content-Transfer-Encoding:From; b=qccKh61r0XaANTkMmy/92tUhECqARPl/sewxr9rmTW+qSdaBm89SZnpypzshaPkpF cmW/nmekGi5R4iSZC+8ywWol49Z2nChAhJ2jgduZiMAUP+DAs7ckbjU/mTN/67EB5a Gxh32zGHIV/xZxA51eiTcmUtew77UBhp1Tv14NkGdDEJo1ySUI4nyCqpLtlC/XWT8m eWUB+bhIn/5zg+Z9btM9/c9soNTilbvtAabRHXWJefmh5zpNOUuguelxBQTVC7d4wc kXmORjSAnCCU3gWz2+Jm/84GAnEKKwLWihvgZdcfmqh3mptPtWccMUWAOowVA+ZYCl mwE6Lovn+9YLg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4X005B04BPz9rxL; Thu, 5 Sep 2024 15:07:25 +0200 (CEST) MIME-Version: 1.0 Date: Thu, 05 Sep 2024 13:07:25 +0000 From: Eric Bavier In-Reply-To: <87seue8qg8.fsf@gnu.org> References: <87seue8qg8.fsf@gnu.org> Message-ID: <692205d6c164d7e3e339068c65a43db4@posteo.net> Content-Type: text/plain; charset=UTF-8; format=flowed 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 (---) On 05.09.2024 03:17, Ludovic Court=C3=A8s wrote: > Hi, >=20 > Ludovic Court=C3=A8s skribis: >=20 >> gnu: petsc: Update to 3.21.4. >> gnu: python-petsc4py: Update to 3.21.4. >> gnu: slepc: Update to 3.21.1. >> gnu: python-slepc4py: Update to 3.21.1. >> gnu: petsc: Make =E2=80=98petscvariables=E2=80=99 reproducible. >> gnu: sundials: Upgrade to 7.1.1. >> gnu: sundials, sundials-openmpi: Use gexps. >> gnu: dealii: Update to 9.6.0. >=20 > Pushed as 993d6d2e7be4dac738629c76a51058f4dc5bc449 after re-testing > locally. Thank you for this series, it looks great! I finally got a chance to look through it just before you pushed. My=20 only note is that I noticed this in the output of petsc's "check" phase: # ------------- # Summary # ------------- # FAILED vec_pf_impls_string_tests-ex1_1 diff-snes_tutorials-ex78_2 # success 5721/10154 tests (56.3%) # failed 2/10154 tests (0.0%) # todo 240/10154 tests (2.4%) # skip 4191/10154 tests (41.3%) but the 'check' phase doesn't fail. I wonder if the `make check` invocation does not return a failure code when the tests fail. These=20 test failures in particular look mostly harmless, but maybe other more catastrophic=20 failures might not be caught if `check` is not detecting failures. --=20 `~Eric From unknown Sat Jun 21 10:43:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#72877] [PATCH 0/8] Upgrade PETSc, SLEPc, SUNDIALS, and DealII Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 05 Sep 2024 14:56:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 72877 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Eric Bavier Cc: 72877-done@debbugs.gnu.org, Andreas Enge , Sharlatan Hellseher Received: via spool by 72877-done@debbugs.gnu.org id=D72877.172554811230296 (code D ref 72877); Thu, 05 Sep 2024 14:56:03 +0000 Received: (at 72877-done) by debbugs.gnu.org; 5 Sep 2024 14:55:12 +0000 Received: from localhost ([127.0.0.1]:37827 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1smDt9-0007sW-9I for submit@debbugs.gnu.org; Thu, 05 Sep 2024 10:55:12 -0400 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:14584) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1smDgK-0006zL-M1 for 72877-done@debbugs.gnu.org; Thu, 05 Sep 2024 10:42:00 -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:content-transfer-encoding; bh=MljfRCtMSyFvFfV/2kflVplFTymKuAYFZCEOuyQma1o=; b=Ci7BrBQJD4tvbtbZ/1mQ0YGJtZp2DnoARdO06pe9BthxsZ/wAlGmsAgY nsDeX8k2Bel57xvT7CK+4jC4KFIBR84PjErGQsxO6X+VNrabhl+M0GzIe XENhX58oUN1br7VtuNhOpxgtC1jhiCRoDt/REq/fWe6Moe3Lpb21BcsN2 w=; 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="6.10,205,1719871200"; d="scan'208";a="181710203" Received: from 91-160-117-201.subs.proxad.net (HELO ribbon) ([91.160.117.201]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 05 Sep 2024 16:40:45 +0200 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= In-Reply-To: <692205d6c164d7e3e339068c65a43db4@posteo.net> (Eric Bavier's message of "Thu, 05 Sep 2024 13:07:25 +0000") References: <87seue8qg8.fsf@gnu.org> <692205d6c164d7e3e339068c65a43db4@posteo.net> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: =?UTF-8?Q?D=C3=A9cadi?= 20 Fructidor an 232 de la =?UTF-8?Q?R=C3=A9volution,?= jour de la Hotte 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: Thu, 05 Sep 2024 16:40:44 +0200 Message-ID: <87a5gm6u4z.fsf@inria.fr> User-Agent: Gnus/5.13 (Gnus v5.13) 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 Eric, Thanks for taking the time to look into it. (I rushed the patch series more than usual because the whole stack was broken since the =E2=80=98core-updates=E2=80=99 merge.) Eric Bavier skribis: > I finally got a chance to look through it just before you pushed. My > only > note is that I noticed this in the output of petsc's "check" phase: > > # ------------- > # Summary > # ------------- > # FAILED vec_pf_impls_string_tests-ex1_1 diff-snes_tutorials-ex78_2 > # success 5721/10154 tests (56.3%) > # failed 2/10154 tests (0.0%) > # todo 240/10154 tests (2.4%) > # skip 4191/10154 tests (41.3%) > > but the 'check' phase doesn't fail. I wonder if the `make check` > invocation does not return a failure code when the tests fail. These > test failures > in particular look mostly harmless, but maybe other more catastrophic > failures > might not be caught if `check` is not detecting failures. Oh. I was told in the meantime that we might want to use =E2=80=98make tes= t=E2=80=99 instead, so perhaps we should followup on this update with a switch to =E2=80=98make test=E2=80=99 and see if problems as shown above still appear: https://gitlab.com/petsc/petsc/-/issues/1634#note_2070200322 Ludo=E2=80=99.