From unknown Sun Aug 10 09:46:24 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#33059 <33059@debbugs.gnu.org> To: bug#33059 <33059@debbugs.gnu.org> Subject: Status: [PATCH 00/10] Add the FEniCS Project Reply-To: bug#33059 <33059@debbugs.gnu.org> Date: Sun, 10 Aug 2025 16:46:24 +0000 retitle 33059 [PATCH 00/10] Add the FEniCS Project reassign 33059 guix-patches submitter 33059 Paul Garlick severity 33059 normal tag 33059 moreinfo patch thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 16 05:18:33 2018 Received: (at submit) by debbugs.gnu.org; 16 Oct 2018 09:18:33 +0000 Received: from localhost ([127.0.0.1]:51795 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLUm-0002wA-QT for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:18:32 -0400 Received: from eggs.gnu.org ([208.118.235.92]:44582) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLUl-0002vy-D3 for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:18:31 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gCLUe-0002bv-FR for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:18:25 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.0 required=5.0 tests=BAYES_40 autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:38607) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1gCLUd-0002bU-I1 for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:18:24 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:54185) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gCLUc-0002ht-Gw for guix-patches@gnu.org; Tue, 16 Oct 2018 05:18:23 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gCLUX-0002SZ-Nt for guix-patches@gnu.org; Tue, 16 Oct 2018 05:18:21 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:58260) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1gCLUV-0002K8-W9 for guix-patches@gnu.org; Tue, 16 Oct 2018 05:18:17 -0400 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gCLUP-0001xT-6M; Tue, 16 Oct 2018 10:18:10 +0100 From: Paul Garlick To: guix-patches@gnu.org Subject: [PATCH 00/10] Add the FEniCS Project Date: Tue, 16 Oct 2018 10:17:08 +0100 Message-Id: <1539681428-6399-1-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x (no timestamps) [generic] [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: submit Cc: Paul Garlick 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: -6.0 (------) Hi Guix, This set of patches adds definitions and dependencies for the FEniCS Project. FEniCS provides a problem-solving environment for general classes of problems that involve differential equations. It is particularly well-suited to problems that can be solved using the Finite Element Method. There are two main packages; i) fenics-dolfin: C++ library plus interface ii) python-fenics-dolfin: Python interface There are four FEniCS dependencies: i) python-fenics-ffc ii) python-fenics-fiat iii) python-fenics-ufl iv) python-fenics-dijitso There are three external dependencies: i) python-slepc4py ii) python-petsc4py iii) python-mpi4py There is an extra package 'fenics' that inherits its defintion from python-fenics-dolfin. This is to provide a sensible default for users expecting to find a package of this name. Best regards, Paul. Paul Garlick (10): gnu: Add python-mpi4py. gnu: Add python-petsc4py. gnu: Add python-slepc4py. gnu: Add python-fenics-dijitso. gnu: Add python-fenics-ufl. gnu: Add python-fenics-fiat. gnu: Add python-fenics-ffc. gnu: Add fenics-dolfin. gnu: Add python-fenics-dolfin. gnu: Add fenics. gnu/packages/simulation.scm | 688 +++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 687 insertions(+), 1 deletion(-) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 16 05:32:18 2018 Received: (at 33059) by debbugs.gnu.org; 16 Oct 2018 09:32:18 +0000 Received: from localhost ([127.0.0.1]:51801 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLi6-0003H1-3A for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:18 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:19720) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLi4-0003Go-NE for 33059@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:17 -0400 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gCLhy-0004Oh-Au; Tue, 16 Oct 2018 10:32:10 +0100 From: Paul Garlick To: 33059@debbugs.gnu.org Subject: [PATCH 01/10] gnu: Add python-mpi4py. Date: Tue, 16 Oct 2018 10:31:15 +0100 Message-Id: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (python-mpi4py): New variable. --- gnu/packages/simulation.scm | 45 ++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 44 insertions(+), 1 deletion(-) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index a5b661e..857d856 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017 Paul Garlick +;;; Copyright © 2017, 2018 Paul Garlick ;;; ;;; This file is part of GNU Guix. ;;; @@ -36,6 +36,7 @@ #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) #:use-module (gnu packages readline) + #:use-module (gnu packages ssh) #:use-module (gnu packages tls) #:use-module (gnu packages version-control) #:use-module (gnu packages xml) @@ -43,6 +44,7 @@ #:use-module (guix download) #:use-module (guix build utils) #:use-module (guix build-system gnu) + #:use-module (guix build-system python) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix utils) @@ -221,3 +223,44 @@ with gas/liquid interfaces. Large problems may be split into smaller, connected problems for efficient solution on parallel systems.") (license license:gpl3+) (home-page "https://openfoam.org"))) + +(define-public python-mpi4py + (package + (name "python-mpi4py") + (version "3.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "mpi4py" version)) + (sha256 + (base32 + "1mzgd26dfv4vwbci8gq77ss9f0x26i9aqzq9b9vs9ndxhlnv0mxl")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'mpi-setup + ,%openmpi-setup) + (add-before 'check 'pre-check + (lambda _ + ;; Skip BaseTestSpawn class (causes error 'ompi_dpm_dyn_init() + ;; failed --> Returned "Unreachable"' in chroot environment). + (substitute* "test/test_spawn.py" + (("unittest.skipMPI\\('openmpi\\(<3.0.0\\)'\\)") + "unittest.skipMPI('openmpi')")) + #t))))) + (inputs + `(("openmpi" ,openmpi))) + (home-page + "https://bitbucket.org/mpi4py/mpi4py/") + (synopsis "Python bindings for the Message Passing Interface standard") + (description "MPI for Python (mpi4py) provides bindings of the Message +Passing Interface (MPI) standard for the Python programming language, allowing +any Python program to exploit multiple processors. + +mpi4py is constructed on top of the MPI-1/MPI-2 specification and provides an +object oriented interface which closely follows MPI-2 C++ bindings. It +supports point-to-point and collective communications of any picklable Python +object as well as optimized communications of Python objects (such as NumPy +arrays) that expose a buffer interface.") + (license license:bsd-3))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 16 05:32:29 2018 Received: (at 33059) by debbugs.gnu.org; 16 Oct 2018 09:32:29 +0000 Received: from localhost ([127.0.0.1]:51804 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLiH-0003HQ-Dy for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:29 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:19824) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLiG-0003HD-9D for 33059@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:28 -0400 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gCLiA-0004Oh-BU; Tue, 16 Oct 2018 10:32:22 +0100 From: Paul Garlick To: 33059@debbugs.gnu.org Subject: [PATCH 02/10] gnu: Add python-petsc4py. Date: Tue, 16 Oct 2018 10:31:16 +0100 Message-Id: <1539682284-6446-2-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (python-petsc4py): New variable. --- gnu/packages/simulation.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 857d856..3f6b73f 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -35,6 +35,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) + #:use-module (gnu packages python) #:use-module (gnu packages readline) #:use-module (gnu packages ssh) #:use-module (gnu packages tls) @@ -264,3 +265,40 @@ supports point-to-point and collective communications of any picklable Python object as well as optimized communications of Python objects (such as NumPy arrays) that expose a buffer interface.") (license license:bsd-3))) + +(define-public python-petsc4py + (package + (name "python-petsc4py") + (version "3.9.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "petsc4py" version)) + (sha256 + (base32 + "1f8zd1ac9irsgkyqmzq30d9kl10fy1nh6zk312dhs43g449fkkhc")))) + (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)))) + (inputs + `(("petsc" ,petsc-openmpi) + ("python-numpy" ,python-numpy))) + (home-page + "https://bitbucket.org/petsc/petsc4py/") + (synopsis "Python bindings for PETSc") + (description "PETSc, the Portable, Extensible Toolkit for +Scientific Computation, is a suite of data structures and routines for +the scalable (parallel) solution of scientific applications modeled by +partial differential equations. It employs the MPI standard for all +message-passing communication. @code{petsc4py} provides Python +bindings to almost all functions of PETSc.") + (license license:bsd-3))) + -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 16 05:32:35 2018 Received: (at 33059) by debbugs.gnu.org; 16 Oct 2018 09:32:36 +0000 Received: from localhost ([127.0.0.1]:51807 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLiN-0003Hj-Me for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:35 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:19900) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLiM-0003HP-1T for 33059@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:34 -0400 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gCLiG-0004Oh-B1; Tue, 16 Oct 2018 10:32:28 +0100 From: Paul Garlick To: 33059@debbugs.gnu.org Subject: [PATCH 03/10] gnu: Add python-slepc4py. Date: Tue, 16 Oct 2018 10:31:17 +0100 Message-Id: <1539682284-6446-3-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (python-slepc4py): New variable. --- gnu/packages/simulation.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 3f6b73f..72528c0 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -302,3 +302,41 @@ message-passing communication. @code{petsc4py} provides Python bindings to almost all functions of PETSc.") (license license:bsd-3))) +(define-public python-slepc4py + (package + (name "python-slepc4py") + (version "3.9.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "slepc4py" version)) + (sha256 + (base32 + "02xr0vndgibgkz3rgprqk05n3mk5mpgqw550sr4681vcsgz4zvb7")))) + (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))) + (home-page + "https://bitbucket.org/slepc/slepc4py/") + (synopsis "Python bindings for SLEPc") + (description "SLEPc, the Scalable Library for Eigenvalue Problem +Computations, is based on PETSc, the Portable, Extensible Toolkit for +Scientific Computation. It employs the MPI standard for all +message-passing communication. @code{slepc4py} provides Python +bindings to almost all functions of SLEPc.") + (license license:bsd-3))) + -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 16 05:32:43 2018 Received: (at 33059) by debbugs.gnu.org; 16 Oct 2018 09:32:43 +0000 Received: from localhost ([127.0.0.1]:51811 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLiV-0003I4-0g for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:43 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:20002) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLiT-0003Hq-E5 for 33059@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:41 -0400 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gCLiN-0004Oh-B7; Tue, 16 Oct 2018 10:32:36 +0100 From: Paul Garlick To: 33059@debbugs.gnu.org Subject: [PATCH 04/10] gnu: Add python-fenics-dijitso. Date: Tue, 16 Oct 2018 10:31:18 +0100 Message-Id: <1539682284-6446-4-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (python-fenics-dijitso): New varaible. --- gnu/packages/simulation.scm | 51 ++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 50 insertions(+), 1 deletion(-) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 72528c0..8bbf435 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -22,6 +22,7 @@ #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages boost) + #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages flex) #:use-module (gnu packages gettext) @@ -339,4 +340,52 @@ Scientific Computation. It employs the MPI standard for all message-passing communication. @code{slepc4py} provides Python bindings to almost all functions of SLEPc.") (license license:bsd-3))) - + +(define-public python-fenics-dijitso + (package + (name "python-fenics-dijitso") + (version "2018.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fenics-dijitso" version)) + (sha256 + (base32 + "1qax2f52qsjbd1h5lk5i5shp448qlakxabjjybrfc1w823p0yql9")))) + (build-system python-build-system) + (inputs + `(("openmpi" ,openmpi) + ("python-numpy" ,python-numpy))) + (native-inputs + `(("python-pytest-cov" ,python-pytest-cov))) + (propagated-inputs + `(("python-mpi4py" ,python-mpi4py))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'mpi-setup + ,%openmpi-setup) + (replace 'check + (lambda _ + (setenv "HOME" "/tmp") + (setenv "PYTHONPATH" + (string-append (getcwd) ":" (getenv "PYTHONPATH"))) + (chdir "test") + (invoke "./runtests.sh") + (chdir "..") + #t))))) + (home-page + "https://bitbucket.org/fenics-project/dijitso/") + (synopsis + "Distributed just-in-time building of shared libraries") + (description + "Dijitso provides a core component of the @code{FEniCS} framework, +namely the just-in-time compilation of C++ code that is generated from +Python modules. It is called from within a C++ library, using ctypes +to import the dynamic shared library directly. + +As long as the compiled code can provide a simple factory function to +a class implementing a predefined C++ interface, there is no limit to +the complexity of that interface. Parallel support depends on the +@code{mpi4py} interface.") + (license license:lgpl3+))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 16 05:32:47 2018 Received: (at 33059) by debbugs.gnu.org; 16 Oct 2018 09:32:47 +0000 Received: from localhost ([127.0.0.1]:51814 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLiZ-0003IL-BD for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:47 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:20080) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLiX-0003Hw-JH for 33059@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:45 -0400 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gCLiR-0004Oh-Cg; Tue, 16 Oct 2018 10:32:40 +0100 From: Paul Garlick To: 33059@debbugs.gnu.org Subject: [PATCH 05/10] gnu: Add python-fenics-ufl. Date: Tue, 16 Oct 2018 10:31:19 +0100 Message-Id: <1539682284-6446-5-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (python-fenics-ufl): New variable. --- gnu/packages/simulation.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 8bbf435..214a834 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -389,3 +389,42 @@ a class implementing a predefined C++ interface, there is no limit to the complexity of that interface. Parallel support depends on the @code{mpi4py} interface.") (license license:lgpl3+))) + +(define-public python-fenics-ufl + (package + (name "python-fenics-ufl") + (version "2018.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fenics-ufl" version)) + (sha256 + (base32 + "1fq8yc86s1s3c8c0b1rc2vf265q0hrkzg57100fg1nghcz0p4vla")))) + (build-system python-build-system) + (inputs + `(("python-numpy" ,python-numpy))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) ":" (getenv "PYTHONPATH"))) + (chdir "test") + (invoke "py.test") + (chdir "..") + #t))))) + (home-page + "https://bitbucket.org/fenics-project/ufl/") + (synopsis "Unified language for form-compilers") + (description "The Unified Form Language (UFL) is a domain specific +language for declaration of finite element discretizations of +variational forms. More precisely, it defines a flexible interface +for choosing finite element spaces and defining expressions for weak +forms in a notation close to mathematical notation. + +UFL is part of the FEniCS Project.") + (license license:lgpl3+))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 16 05:32:52 2018 Received: (at 33059) by debbugs.gnu.org; 16 Oct 2018 09:32:52 +0000 Received: from localhost ([127.0.0.1]:51817 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLie-0003Ie-JG for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:52 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:20144) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLic-0003IE-VQ for 33059@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:51 -0400 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gCLiX-0004Oh-Aa; Tue, 16 Oct 2018 10:32:45 +0100 From: Paul Garlick To: 33059@debbugs.gnu.org Subject: [PATCH 06/10] gnu: Add python-fenics-fiat. Date: Tue, 16 Oct 2018 10:31:20 +0100 Message-Id: <1539682284-6446-6-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (python-fenics-fiat): New variable. --- gnu/packages/simulation.scm | 44 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 214a834..3a5e6cb 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -428,3 +428,47 @@ forms in a notation close to mathematical notation. UFL is part of the FEniCS Project.") (license license:lgpl3+))) + +(define-public python-fenics-fiat + (package + (name "python-fenics-fiat") + (version "2018.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fenics-fiat" version)) + (sha256 + (base32 + "0fmjd93r6bwf6xs8csw86qzphrnr66xwv7f372w59gmq8mg6rljc")))) + (build-system python-build-system) + (native-inputs + `(("python-pytest" ,python-pytest))) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-sympy" ,python-sympy))) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) ":" (getenv "PYTHONPATH"))) + (chdir "test") + (invoke "py.test" "unit/") + (chdir "..") + #t))))) + (home-page + "https://bitbucket.org/fenics-project/fiat/") + (synopsis "Tabulation of finite element function spaces") + (description + "The FInite element Automatic Tabulator (FIAT) supports +generation of arbitrary order instances of the Lagrange elements on +lines, triangles, and tetrahedra. It is also capable of generating +arbitrary order instances of Jacobi-type quadrature rules on the same +element shapes. Further, H(div) and H(curl) conforming finite element +spaces such as the families of Raviart-Thomas, Brezzi-Douglas-Marini +and Nedelec are supported on triangles and tetrahedra. Upcoming +versions will also support Hermite and nonconforming elements. + +FIAT is part of the FEniCS Project.") + (license license:lgpl3+))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 16 05:32:55 2018 Received: (at 33059) by debbugs.gnu.org; 16 Oct 2018 09:32:55 +0000 Received: from localhost ([127.0.0.1]:51820 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLig-0003It-Ri for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:55 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:20172) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLif-0003IU-Tt for 33059@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:54 -0400 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gCLia-0004Oh-AE; Tue, 16 Oct 2018 10:32:48 +0100 From: Paul Garlick To: 33059@debbugs.gnu.org Subject: [PATCH 07/10] gnu: Add python-fenics-ffc. Date: Tue, 16 Oct 2018 10:31:21 +0100 Message-Id: <1539682284-6446-7-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (python-fenics-ffc): New variable. --- gnu/packages/simulation.scm | 54 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 3a5e6cb..f6ad966 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -472,3 +472,57 @@ versions will also support Hermite and nonconforming elements. FIAT is part of the FEniCS Project.") (license license:lgpl3+))) + +(define-public python-fenics-ffc + (package + (name "python-fenics-ffc") + (version "2018.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fenics-ffc" version)) + (sha256 + (base32 + "1b2ia5vlkw298x7rf0k2p3ihlpwkwgc98p3s6sbpds3hqmfrzdz9")))) + (build-system python-build-system) + (native-inputs + `(("python-pytest" ,python-pytest))) + (propagated-inputs + `(("python-fenics-dijitso" ,python-fenics-dijitso) + ("python-fenics-fiat" ,python-fenics-fiat) + ("python-fenics-ufl" ,python-fenics-ufl))) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "HOME" (getcwd)) + (setenv "PYTHONPATH" + (string-append (getcwd) ":" (getenv "PYTHONPATH"))) + (chdir "test") + ;; FIXME: the tests in subdirectory + ;; 'unit/ufc/finite_element' require the ffc_factory + ;; extension module. This module, located in the 'libs' + ;; subdirectory, needs to be built and made accessible + ;; prior to running the tests. + (invoke "py.test" "unit/" "--ignore=unit/ufc/") + (chdir "uflacs") + (invoke "py.test" "unit/") + (chdir "../..") + #t))))) + (home-page + "https://bitbucket.org/fenics-project/ffc/") + (synopsis "Compiler for finite element variational forms") + (description "The FEniCS Form Compiler (FFC) is a compiler for +finite element variational forms. From a high-level description of +the form, it generates efficient low-level C++ code that can be used +to assemble the corresponding discrete operator (tensor). In +particular, a bilinear form may be assembled into a matrix and a +linear form may be assembled into a vector. FFC may be used either +from the command line (by invoking the @code{ffc} command) or as a +Python module (@code{import ffc}). + +FFC is part of the FEniCS Project.") + ;; There are two files released with a public domain licence; + ;; ufc.h and ufc_geometry.h, in subdirectory 'ffc/backends/ufc'. + (license (list license:public-domain license:lgpl3+)))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 16 05:33:00 2018 Received: (at 33059) by debbugs.gnu.org; 16 Oct 2018 09:33:00 +0000 Received: from localhost ([127.0.0.1]:51823 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLim-0003JC-6K for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:33:00 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:20220) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLik-0003Ik-2O for 33059@debbugs.gnu.org; Tue, 16 Oct 2018 05:32:58 -0400 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gCLid-0004Oh-CF; Tue, 16 Oct 2018 10:32:52 +0100 From: Paul Garlick To: 33059@debbugs.gnu.org Subject: [PATCH 08/10] gnu: Add fenics-dolfin. Date: Tue, 16 Oct 2018 10:31:22 +0100 Message-Id: <1539682284-6446-8-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (fenics-dolfin): New variable. --- gnu/packages/simulation.scm | 228 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 228 insertions(+) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index f6ad966..3594f07 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -18,11 +18,13 @@ (define-module (gnu packages simulation) #:use-module (gnu packages) + #:use-module (gnu packages algebra) #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages boost) #:use-module (gnu packages check) + #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages flex) #:use-module (gnu packages gettext) @@ -36,6 +38,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages readline) #:use-module (gnu packages ssh) @@ -45,6 +48,7 @@ #:use-module (gnu packages xorg) #:use-module (guix download) #:use-module (guix build utils) + #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system python) #:use-module ((guix licenses) #:prefix license:) @@ -526,3 +530,227 @@ FFC is part of the FEniCS Project.") ;; There are two files released with a public domain licence; ;; ufc.h and ufc_geometry.h, in subdirectory 'ffc/backends/ufc'. (license (list license:public-domain license:lgpl3+)))) + +(define-public fenics-dolfin + (package + (name "fenics-dolfin") + (version "2018.1.0.post1") + (source + (origin + (method url-fetch) + (uri (string-append + "https://bitbucket.org/fenics-project/dolfin/get/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "12zkk8j3xsg6l8p0ggwsl03084vlcivw4h99b7z9kndg7k89b3ya")))) + (build-system cmake-build-system) + (inputs + `(("blas" ,openblas) + ("boost" ,boost) + ("eigen" ,eigen) + ("hdf5" ,hdf5-parallel-openmpi) + ("lapack" ,lapack) + ("libxml2" ,libxml2) + ("openmpi" ,openmpi) + ("python" ,python-3) + ("scotch" ,pt-scotch32) + ("suitesparse" ,suitesparse) + ("sundials" ,sundials-openmpi) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (propagated-inputs + `(("ffc" ,python-fenics-ffc) + ("petsc" ,petsc-openmpi) + ("slepc" ,slepc-openmpi))) + (arguments + `(#:configure-flags + `("-DDOLFIN_ENABLE_DOCS:BOOL=OFF" + "-DDOLFIN_ENABLE_HDF5:BOOL=ON" + "-DDOLFIN_ENABLE_MPI:BOOL=ON" + "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF" + "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON" + "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON" + "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF") + #:phases + (modify-phases %standard-phases + (add-after 'patch-usr-bin-file 'mpi-setup + ,%openmpi-setup) + (add-after 'patch-source-shebangs 'set-paths + (lambda _ + ;; Define paths to store locations. + (setenv "BLAS_DIR" (assoc-ref %build-inputs "blas")) + (setenv "LAPACK_DIR" (assoc-ref %build-inputs "lapack")) + (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) + (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc")) + (setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch")) + (setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials")) + (setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse")) + #t)) + (add-before 'configure 'pre-configure + (lambda _ + (use-modules (ice-9 regex) + (ice-9 rdelim) + (guix build utils) + (rnrs io ports)) + ;; Add extra include directories required by the unit tests. + (with-atomic-file-replacement "test/unit/cpp/CMakeLists.txt" + (let ((rx (make-regexp "target_link_libraries"))) + (lambda (in out) + (let loop () + (let ((line (read-line in 'concat))) + (if (eof-object? line) + #t + (begin + (display line out) + (when (regexp-exec rx line) + (display + (string-append + "target_include_directories(" + "unittests PRIVATE " + "${DOLFIN_SOURCE_DIR} " + "${DOLFIN_SOURCE_DIR}/dolfin " + "${DOLFIN_BINARY_DIR})\n") out)) + (loop)))))))) + ;; Add extra include directories required by the demo tests. + (with-atomic-file-replacement "demo/CMakeLists.txt" + (let ((rx (make-regexp "find_package"))) + (lambda (in out) + (let loop () + (let ((line (read-line in 'concat))) + (if (eof-object? line) + #t + (begin + (display line out) + (when (regexp-exec rx line) + (display + (string-append + "include_directories(" + "${DOLFIN_SOURCE_DIR} " + "${DOLFIN_SOURCE_DIR}/dolfin " + "${DOLFIN_BINARY_DIR})\n") out)) + (loop)))))))))) + (add-before 'check 'pre-check + (lambda _ + ;; The Dolfin repository uses git-lfs, whereby web links are + ;; substituted for large files. Guix does not currently support + ;; git-lfs, so only the links are downloaded. The tests that + ;; require the absent meshes cannot run and are skipped. + ;; + ;; Two other serial tests fail and are skipped. + ;; i) demo_stokes-iterative_serial, + ;; The MPI_Comm_rank() function was called before MPI_INIT was + ;; invoked + ;; ii) demo_multimesh-stokes_serial: + ;; Warning: Found no facets matching domain for boundary + ;; condition. + ;; + ;; One mpi test fails and is skipped. + ;; i) demo_stokes-iterative_mpi: + ;; The MPI_Comm_rank() function was called before MPI_INIT was + ;; invoked + (call-with-output-file "CTestCustom.cmake" + (lambda (port) + (display + (string-append + "set(CTEST_CUSTOM_TESTS_IGNORE " + "demo_bcs_serial " + "demo_bcs_mpi " + "demo_eigenvalue_serial " + "demo_eigenvalue_mpi " + "demo_navier-stokes_serial " + "demo_navier-stokes_mpi " + "demo_stokes-taylor-hood_serial " + "demo_stokes-taylor-hood_mpi " + "demo_subdomains_serial " + "demo_advection-diffusion_serial " + "demo_advection-diffusion_mpi " + "demo_auto-adaptive-navier-stokes_serial " + "demo_contact-vi-snes_serial " + "demo_contact-vi-snes_mpi " + "demo_contact-vi-tao_serial " + "demo_contact-vi-tao_mpi " + "demo_curl-curl_serial " + "demo_curl-curl_mpi " + "demo_dg-advection-diffusion_serial " + "demo_dg-advection-diffusion_mpi " + "demo_elasticity_serial " + "demo_elasticity_mpi " + "demo_elastodynamics_serial " + "demo_elastodynamics_mpi " + "demo_lift-drag_serial " + "demo_lift-drag_mpi " + "demo_mesh-quality_serial " + "demo_mesh-quality_mpi " + "demo_multimesh-stokes_serial " + "demo_stokes-iterative_serial " + "demo_stokes-iterative_mpi " + ")\n") port))) + #t)) + (replace 'check + (lambda _ + (and (invoke "make" "unittests") + (invoke "make" "demos") + (invoke "ctest" "-R" "unittests") + (invoke "ctest" "-R" "demo" "-R" "serial") + (invoke "ctest" "-R" "demo" "-R" "mpi"))))))) + (home-page + "https://bitbucket.org/fenics-project/dolfin/") + (synopsis + "Problem solving environment for differential equations") + (description + "DOLFIN is a computational framework for finding numerical +solutions to problems described by differential equations. Numerical +models in DOLFIN are constructed using general families of finite +elements. Data structures are provided for discretizing the governing +system on a computational mesh. A compact syntax, similar to +mathematical notation, is made available for defining function spaces +and expressing variational forms. Interfaces to specialized matrix +solvers are provided for solving the resultant linear systems. + +@code{fenics-dolfin} is part of the FEniCS project. It is the C++ +user interface to the FEniCS core components and external libraries.") + ;; The source code files for the DOLFIN C++ library are licensed under the + ;; GNU Lesser General Public License, version 3 or later, with the + ;; following exceptions: + ;; + ;; bsd-2: cmake/modules/FindAMD.cmake + ;; cmake/modules/FindBLASHeader.cmake + ;; cmake/modules/FindCHOLMOD.cmake + ;; cmake/modules/FindEigen3.cmake + ;; cmake/modules/FindMPFR.cmake + ;; cmake/modules/FindNumPy.cmake + ;; cmake/modules/FindPETSc.cmake + ;; cmake/modules/FindPETSc4py.cmake + ;; cmake/modules/FindParMETIS.cmake + ;; cmake/modules/FindSCOTCH.cmake + ;; cmake/modules/FindSLEPc.cmake + ;; cmake/modules/FindSLEPc4py.cmake + ;; cmake/modules/FindSphinx.cmake + ;; cmake/modules/FindSUNDIALS.cmake + ;; cmake/modules/FindUFC.cmake + ;; + ;; bsd-3: cmake/modules/FindBLAS.cmake + ;; cmake/modules/FindLAPACK.cmake + ;; cmake/modules/FindMPI.cmake + ;; + ;; public-domain: dolfin/geometry/predicates.cpp + ;; dolfin/geometry/predicates.h + ;; + ;; zlib: dolfin/io/base64.cpp + ;; dolfin/io/base64.h + ;; + ;; expat: dolfin/io/pugiconfig.hpp + ;; dolfin/io/pugixml.cpp + ;; dolfin/io/pugixml.hpp + ;; + ;; boost1.0: test/unit/cpp/catch/catch.hpp + (license (list license:bsd-2 + license:bsd-3 + license:public-domain + license:zlib + license:expat + license:boost1.0 + license:lgpl3+)))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 16 05:33:10 2018 Received: (at 33059) by debbugs.gnu.org; 16 Oct 2018 09:33:10 +0000 Received: from localhost ([127.0.0.1]:51829 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLip-0003Ju-Ly for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:33:10 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:20246) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLin-0003J2-QU for 33059@debbugs.gnu.org; Tue, 16 Oct 2018 05:33:02 -0400 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gCLih-0004Oh-Bo; Tue, 16 Oct 2018 10:32:56 +0100 From: Paul Garlick To: 33059@debbugs.gnu.org Subject: [PATCH 09/10] gnu: Add python-fenics-dolfin. Date: Tue, 16 Oct 2018 10:31:23 +0100 Message-Id: <1539682284-6446-9-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (python-fenics-dolfin): New variable. --- gnu/packages/simulation.scm | 147 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 147 insertions(+) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 3594f07..c0617b3 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -754,3 +754,150 @@ user interface to the FEniCS core components and external libraries.") license:expat license:boost1.0 license:lgpl3+)))) + +(define-public python-fenics-dolfin + (package (inherit fenics-dolfin) + (name "python-fenics-dolfin") + (build-system python-build-system) + (inputs + `(("pybind11" ,pybind11) + ("python-matplotlib" ,python-matplotlib) + ,@(alist-delete "python" (package-inputs fenics-dolfin)))) + (native-inputs + `(("cmake" ,cmake) + ("ply" ,python-ply) + ("pytest" ,python-pytest) + ("python-decorator" ,python-decorator) + ("python-pkgconfig" ,python-pkgconfig) + ,@(package-native-inputs fenics-dolfin))) + (propagated-inputs + `(("dolfin" ,fenics-dolfin) + ("petsc4py" ,python-petsc4py) + ("slepc4py" ,python-slepc4py))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'patch-source-shebangs 'set-paths + (lambda _ + ;; Define paths to store locations. + (setenv "PYBIND11_DIR" (assoc-ref %build-inputs "pybind11")) + ;; Move to python sub-directory. + (chdir "python") + #t)) + (add-after 'build 'mpi-setup + ,%openmpi-setup) + (add-before 'check 'pre-check + (lambda _ + (use-modules (ice-9 regex) + (ice-9 rdelim) + (guix build utils) + (rnrs io ports)) + ;; Exclude tests that require meshes supplied by git-lfs. + (with-atomic-file-replacement "demo/test.py" + (let ((rx (make-regexp "stem !"))) + (lambda (in out) + (let loop () + (let ((line (read-line in 'concat))) + (if (eof-object? line) + #t + (begin + (display line out) + (when (regexp-exec rx line) + (display + (string-append + "excludeList = [\n" + "'multimesh-quadrature', \n" + "'multimesh-marking', \n" + "'mixed-poisson-sphere', \n" + "'mesh-quality', \n" + "'lift-drag', \n" + "'elastodynamics', \n" + "'dg-advection-diffusion', \n" + "'contact-vi-tao', \n" + "'contact-vi-snes', \n" + "'collision-detection', \n" + "'buckling-tao', \n" + "'auto-adaptive-navier-stokes', \n" + "'advection-diffusion', \n" + "'subdomains', \n" + "'stokes-taylor-hood', \n" + "'stokes-mini', \n" + "'navier-stokes', \n" + "'eigenvalue']\n" + "demos = [" + "d for d in demos if d[0].stem not in " + "excludeList]\n") out)) + (loop)))))))) + (setenv "HOME" (getcwd)) + (setenv "PYTHONPATH" + (string-append + (getcwd) "/build/lib.linux-x86_64-" + ,(version-major+minor (package-version python)) ":" + (getenv "PYTHONPATH"))) + ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP. + (setenv "OPENBLAS_NUM_THREADS" "1") + #t)) + (replace 'check + (lambda _ + (chdir "test") + ;; Note: The test test_snes_set_from_options() in the file + ;; unit/nls/test_PETScSNES_solver.py fails and is ignored. + (and (invoke "py.test" "unit" + "--ignore" "unit/nls/test_PETScSNES_solver.py") + (invoke "mpirun" "-np" "3" "python" "-B" "-m" "pytest" "unit" + "--ignore" "unit/nls/test_PETScSNES_solver.py")) + (chdir "../demo") + ;; Check demos. + (invoke "python" "generate-demo-files.py") + (and (invoke "python" "-m" "pytest" "-v" "test.py") + (invoke "python" "-m" "pytest" "-v" "test.py" + "--mpiexec=mpiexec" "--num-proc=3")) + (chdir "..") + #t)) + (add-after 'install 'install-demo-files + (lambda* (#:key outputs #:allow-other-keys) + (let* ((demos (string-append (assoc-ref outputs "out") + "/share/python-dolfin/demo"))) + (mkdir-p demos) + (with-directory-excursion "demo" + (for-each (lambda (file) + (let* ((dir (dirname file)) + (tgt-dir (string-append demos "/" dir))) + (unless (equal? "." dir) + (mkdir-p tgt-dir) + (install-file file tgt-dir)))) + (find-files "." ".*\\.(py|gz|xdmf)$")))) + #t))))) + (home-page + "https://bitbucket.org/fenics-project/dolfin/") + (synopsis + "High-level problem solving environment for differential equations") + (description + "DOLFIN is a computational framework for finding numerical +solutions to problems described by differential equations. Numerical +models in DOLFIN are constructed using general families of finite +elements. Data structures are provided for discretizing the governing +system on a computational mesh. A compact syntax, similar to +mathematical notation, is made available for defining function spaces +and expressing variational forms. Interfaces to specialized matrix +solvers are provided for solving the resultant linear systems. + +@code{python-fenics-dolfin} is part of the FEniCS project. It is the +python user interface to the FEniCS core components and external +libraries.") + ;; The python files in DOLFIN are licensed under the GNU Lesser + ;; General Public License, version 3 or later, with the following + ;; exceptions: + ;; + ;; bsd-2: python/cmake/FindPETSc4py.cmake + ;; + ;; bsd-3: site-packages/dolfin_utils/cppparser/CppHeaderParser.py + ;; + ;; expat: site-packages/dolfin_utils/ordereddict.py + ;; + ;; gpl2+: utils/pylit/pylit.py + (license (list license:bsd-2 + license:bsd-3 + license:expat + license:gpl2+ + license:lgpl3+)))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 16 05:33:10 2018 Received: (at 33059) by debbugs.gnu.org; 16 Oct 2018 09:33:10 +0000 Received: from localhost ([127.0.0.1]:51837 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLiw-0003Kt-Ep for submit@debbugs.gnu.org; Tue, 16 Oct 2018 05:33:10 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:20266) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCLir-0003JB-1U for 33059@debbugs.gnu.org; Tue, 16 Oct 2018 05:33:05 -0400 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gCLil-0004Oh-At; Tue, 16 Oct 2018 10:32:59 +0100 From: Paul Garlick To: 33059@debbugs.gnu.org Subject: [PATCH 10/10] gnu: Add fenics. Date: Tue, 16 Oct 2018 10:31:24 +0100 Message-Id: <1539682284-6446-10-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (fenics): New variable. --- gnu/packages/simulation.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index c0617b3..2e47067 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -901,3 +901,9 @@ libraries.") license:expat license:gpl2+ license:lgpl3+)))) + +;; The FEniCS Project. +(define-public fenics + (package + (inherit python-fenics-dolfin) + (name "fenics"))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 16 14:31:05 2018 Received: (at 33059) by debbugs.gnu.org; 16 Oct 2018 18:31:06 +0000 Received: from localhost ([127.0.0.1]:53936 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCU7V-0006vn-Jq for submit@debbugs.gnu.org; Tue, 16 Oct 2018 14:31:05 -0400 Received: from flashner.co.il ([178.62.234.194]:42756) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gCU7U-0006vI-H4 for 33059@debbugs.gnu.org; Tue, 16 Oct 2018 14:31:04 -0400 Received: from localhost (unknown [141.226.10.13]) by flashner.co.il (Postfix) with ESMTPSA id 75A3A40027; Tue, 16 Oct 2018 18:30:58 +0000 (UTC) Date: Tue, 16 Oct 2018 21:30:57 +0300 From: Efraim Flashner To: Paul Garlick Subject: Re: [bug#33059] [PATCH 04/10] gnu: Add python-fenics-dijitso. Message-ID: <20181016183057.GB12881@macbook41> References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-4-git-send-email-pgarlick@tourbillion-technology.com> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="zx4FCpZtqtKETZ7O" Content-Disposition: inline In-Reply-To: <1539682284-6446-4-git-send-email-pgarlick@tourbillion-technology.com> User-Agent: Mutt/1.10.1 (2018-07-13) X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -1.0 (-) --zx4FCpZtqtKETZ7O Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Tue, Oct 16, 2018 at 10:31:18AM +0100, Paul Garlick wrote: > + (chdir "test") > + (invoke "./runtests.sh") > + (chdir "..") >=20 for this part you may want to look into 'with-directory-excursion' --=20 Efraim Flashner =D7=90=D7=A4=D7=A8=D7=99=D7=9D = =D7=A4=D7=9C=D7=A9=D7=A0=D7=A8 GPG key =3D A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted --zx4FCpZtqtKETZ7O Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCgAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAlvGLmEACgkQQarn3Mo9 g1Gj9A/+IU6gnxB9FxcC/yZUB5qHT5zlsA7VQqLEb2g0N/+vbNgpEJ58Pjcf8ewn 5T/JyPDXJrX6q8G70YFbhk2HBegAmbjL92CymWcqfzkQdmD9HzvZBGMWtNIDn0V4 ZbogBxLzXnvIyUMZqC8buRLG1zUltZAGHlS/SEq8yItWOCfXuv09xSX4pm2G7wZg nM1AlOzQxb+FuPlKeR5mlX1z+9sklrut3oVBKBw9kyxpaDfcSC2MQPZxOvMr1P5+ a4uRNij/CuQ7ZKhBCck/9vXpnh58ZkCeq1sS6KL5zsmCGI69ji3tTvvfGjqFgN4q zWT4VJG1d35zr5sZB9vKkjEaD6zoVzgFwVuhXBvMdGYN2SxdNM76Z7PI5+aComPb n1xiew20sAViCMNGZ2e1CFn+9bYc41ylQP2SnXfluKIhZPMhzwjNXsAzkQ9273KT Hg36MtiQqClpc6pvZOxOwrCatiqWZcFCUa5gCBl+OwMZNyQFCCDRzXScuWuVlCa3 mCQHOjXW8sZ5aIuaFRLDpIzh2LiXLJePdU6WlkwfcqWdKaxp97/0rxlKjMleZhQ1 AxWwE4ug5hP8wt98P4Myx5lxHDGo0wWmyNKo7JBLS3bzFJSP/PnN77amqFKuo599 0+/qmE3VGEUE6wVMIfPtosecaOhLzM9oGHdMhTNnU3lZI5/8XpU= =aChx -----END PGP SIGNATURE----- --zx4FCpZtqtKETZ7O-- From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 17 05:09:58 2018 Received: (at 33059) by debbugs.gnu.org; 17 Oct 2018 09:09:58 +0000 Received: from localhost ([127.0.0.1]:54366 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gChq2-0000Xa-7t for submit@debbugs.gnu.org; Wed, 17 Oct 2018 05:09:58 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:43570) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gChq1-0000XM-9M for 33059@debbugs.gnu.org; Wed, 17 Oct 2018 05:09:57 -0400 Received: from [79.123.23.187] (helo=pancake.local) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gChpv-0007lg-9q; Wed, 17 Oct 2018 10:09:51 +0100 Message-ID: <1539767389.2698.6.camel@tourbillion-technology.com> Subject: Re: [bug#33059] [PATCH 04/10] gnu: Add python-fenics-dijitso. From: Paul Garlick To: Efraim Flashner Date: Wed, 17 Oct 2018 10:09:49 +0100 In-Reply-To: <20181016183057.GB12881@macbook41> References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-4-git-send-email-pgarlick@tourbillion-technology.com> <20181016183057.GB12881@macbook41> Content-Type: text/plain; charset="UTF-8" X-Mailer: Evolution 3.18.5.2-0ubuntu3.2 Mime-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -1.7 (-) Hi Efraim, > > +             (chdir "test") > > +             (invoke "./runtests.sh") > > +             (chdir "..") > > > for this part you may want to look into 'with-directory-excursion' Thanks.  Will do. In fact, in these patches there is a need to change directories a few times, so I will unify the treatment throughout with 'with-directory- excursion'. Best regards, Paul. From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 19 12:03:46 2018 Received: (at 33059) by debbugs.gnu.org; 19 Oct 2018 16:03:46 +0000 Received: from localhost ([127.0.0.1]:59676 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gDXFZ-0005Fd-Uv for submit@debbugs.gnu.org; Fri, 19 Oct 2018 12:03:46 -0400 Received: from mail.onyx.syn-alias.com ([206.152.134.66]:58588 helo=smtp.centurylink.net) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gDXFW-0005FO-4s for 33059@debbugs.gnu.org; Fri, 19 Oct 2018 12:03:44 -0400 DKIM-Signature: v=1; a=rsa-sha1; d=centurylink.net; s=ctl201402; c=relaxed/simple; q=dns/txt; i=@centurylink.net; t=1539965016; h=From:Subject:Date:To:MIME-Version:Content-Type; bh=2jKcVsBCM264rMWaJzx4qaQZht4=; b=GzrxxMC6Zl9Yu4pTUs2fbGEuWNnB7t8Wh9jtXyIOAjD4Dv/HH/qdeZUq3yL28ohw K43NVHQ778wR8orX+s/Lxa22O3WWZBVLp3G8jRkIlA5KoXazC9meCG4BfeahmbOs JpKoLcoOsUkbZstiykvLIaihZNmfZH0CqrNmlxAiNwhr3hNOfIr9urDJ7oSD8Qz2 B6nRlRWl2gDMmQJsMw2APCvO+ygYbMYkWzpuR4u0unqZCsCDjpRioxtLW5m5uzV+ m0xA9Sl556hlBhPs0uSdv40oAjCA0id0cjqVJ7PqhNA4jfSe5YZKtYw03duVs0HF Jfww3XwoPdR9Lq/74+jIgg==; X_CMAE_Category: , , X-CNFS-Analysis: v=2.2 cv=cr/ZqBwi c=1 sm=1 tr=0 a=MhzntBxPsQQsyKet5jur4A==:117 a=MhzntBxPsQQsyKet5jur4A==:17 a=KGjhK52YXX0A:10 a=smKx5t2vBNcA:10 a=zSv6zi-ZgakA:10 a=v9CA4rZzAAAA:8 a=k3KT-WtySNv1_5x4LBkA:9 a=CjuIK1q_8ugA:10 a=tayxmWxdKBXgLeo3m4UA:9 a=vvO3zLalzpCLnPWG-uKa:22 X-CM-Score: 0 X-Scanned-by: Cloudmark Authority Engine X-Authed-Username: ZXJpY2JhdmllckBjZW50dXJ5bGluay5uZXQ= Authentication-Results: smtp03.onyx.dfw.sync.lan smtp.user=ericbavier@centurylink.net; auth=pass (LOGIN) Received: from [97.116.181.145] ([97.116.181.145:50402] helo=localhost) by smtp.centurylink.net (envelope-from ) (ecelerity 3.6.25.56547 r(Core:3.6.25.0)) with ESMTPSA (cipher=AES256-GCM-SHA384) id DC/36-05142-8500ACB5; Fri, 19 Oct 2018 12:03:36 -0400 Date: Fri, 19 Oct 2018 11:03:34 -0500 From: Eric Bavier To: Paul Garlick Subject: Re: [bug#33059] [PATCH 01/10] gnu: Add python-mpi4py. Message-ID: <20181019110334.776232e9@centurylink.net> In-Reply-To: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> References: <1539681428-6399-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: Claws Mail 3.17.1 (GTK+ 2.24.32; x86_64-unknown-linux-gnu) MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; boundary="Sig_/K53fWJTjPcnY_Dm7QztMQcH"; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -1.0 (-) --Sig_/K53fWJTjPcnY_Dm7QztMQcH Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: quoted-printable On Tue, 16 Oct 2018 10:31:15 +0100 Paul Garlick wrote: > * gnu/packages/simulation.scm (python-mpi4py): New variable. > --- > gnu/packages/simulation.scm | 45 +++++++++++++++++++++++++++++++++++++++= +++++- > 1 file changed, 44 insertions(+), 1 deletion(-) I haven't done a proper review yet, but... Would this package be better put in (gnu packages mpi). Same with the petsc4py and slepc4py, in (gnu packages maths). `~Eric --Sig_/K53fWJTjPcnY_Dm7QztMQcH Content-Type: application/pgp-signature Content-Description: OpenPGP digital signature -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEoMXjUi7471xkzbfw/XPKxxnTJWYFAlvKAFYACgkQ/XPKxxnT JWYG5w/+LciVY83m8tVz1yX4vI7U5SBjGjCJq0aX2zBalZx+ARS5pzhJz5HYCGe1 rTbmTAkE83fJS5OXwTpazoKnuLpQ0widkBTxoMakPn/P8h9uagfdUNmHREuaboDR +5nJroDL5auiLx3XDNkd1s7IWUynkFdD+D3NrKkj88ihTeNxtTux5RX5m2+6lwKT C5c7+Kb7EDE7+OLFlWx9Nzq+f3EwvCMpsMmq5UT5kUKh8LQvdH75q0SMD3X/xzeA 8qNQsRhaRHwaKRtAPFTkzZSJY86ad2MS7OjtZBUgjpzyWNd16gkvIrjfA75G9AjL Hlsbfg3RJ4JcjECx7gJKEpKA+RsVuULSIsd3LuJ6pXZ7QSeHrJLeSKOxiGOKZqGG nCuxraoChUCE6lb4eLO1pEE29cvBBqZ1fbPcoSE4XigufoxxLYfgG2SGLm5wfHvG NRIFIaMwDmBnfFLxclh/HmK+jrg2J0tmieJjbpTA/4hQXpkb0dtYaaWslIkj5e+L UemqFr/XA6kKGUg31oiS7zWZMEOlqx2LxOHjpXqT5xehgSrUe3Hjve8q8eAHutDl fYFygNMEuKo/oIHVJ8Cfwm2J/QYXjZ/eSK0vAgld5WUAFwjuZMDRkJpq/AHPenHF sZSszgooWzf83kCvoLDYYTUprCc712iQifDZB2sfbXrvcJwrb4w= =hoYw -----END PGP SIGNATURE----- --Sig_/K53fWJTjPcnY_Dm7QztMQcH-- From debbugs-submit-bounces@debbugs.gnu.org Mon Oct 22 04:52:02 2018 Received: (at 33059) by debbugs.gnu.org; 22 Oct 2018 08:52:02 +0000 Received: from localhost ([127.0.0.1]:35104 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gEVwQ-0006je-Go for submit@debbugs.gnu.org; Mon, 22 Oct 2018 04:52:02 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:25742) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gEVwO-0006j8-Au for 33059@debbugs.gnu.org; Mon, 22 Oct 2018 04:52:01 -0400 Received: from [79.123.23.187] (helo=pancake.local) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gEVwH-0006Z3-Aj; Mon, 22 Oct 2018 09:51:53 +0100 Message-ID: <1540198312.4645.12.camel@tourbillion-technology.com> Subject: Re: [bug#33059] [PATCH 01/10] gnu: Add python-mpi4py. From: Paul Garlick To: Eric Bavier Date: Mon, 22 Oct 2018 09:51:52 +0100 In-Reply-To: <20181019110334.776232e9@centurylink.net> References: <1539681428-6399-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> <20181019110334.776232e9@centurylink.net> Content-Type: text/plain; charset="UTF-8" X-Mailer: Evolution 3.18.5.2-0ubuntu3.2 Mime-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -1.7 (-) Hi Eric, > Would this package be better > put in (gnu packages mpi).  Same with the petsc4py and slepc4py, in > (gnu packages maths). Yes, good idea.  These three dependencies are 'external', in the sense that their development is independent of the FEniCS project.  They could be used as dependencies of future packages that may not go in (gnu packages simulation). Also, the versions of petsc4py and slepc4py keep track of petsc and slepc.  So version 3.9.1 of petsc4py, for example, depends on version 3.9 of petsc.  Keeping the package definitions near to each other in the same module will be a useful 'aide memoire'. I shall wait a little longer for any more comments, then move these three definitions in the way you suggest and re-submit as 'v2'. patches. Best regards, Paul. From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 24 17:44:21 2018 Received: (at 33059) by debbugs.gnu.org; 24 Oct 2018 21:44:21 +0000 Received: from localhost ([127.0.0.1]:40857 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFQwv-0000sN-3L for submit@debbugs.gnu.org; Wed, 24 Oct 2018 17:44:21 -0400 Received: from eggs.gnu.org ([208.118.235.92]:34693) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFQwt-0000sB-7G for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:44:19 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gFQwi-00036N-V1 for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:44:13 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:56391) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gFQwi-00035l-15; Wed, 24 Oct 2018 17:44:08 -0400 Received: from 50.135.159.77.rev.sfr.net ([77.159.135.50]:33662 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gFQwh-0005z2-NQ; Wed, 24 Oct 2018 17:44:07 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Paul Garlick Subject: Re: [bug#33059] [PATCH 01/10] gnu: Add python-mpi4py. References: <1539681428-6399-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 3 Brumaire an 227 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: Wed, 24 Oct 2018 23:44:05 +0200 In-Reply-To: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> (Paul Garlick's message of "Tue, 16 Oct 2018 10:31:15 +0100") Message-ID: <8736svyq8q.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -6.0 (------) Hi Paul, Paul Garlick skribis: > * gnu/packages/simulation.scm (python-mpi4py): New variable. I agree with Eric=E2=80=99s suggestion but otherwise LGTM. Thanks, Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 24 17:45:50 2018 Received: (at 33059) by debbugs.gnu.org; 24 Oct 2018 21:45:50 +0000 Received: from localhost ([127.0.0.1]:40861 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFQyM-0001YF-Ds for submit@debbugs.gnu.org; Wed, 24 Oct 2018 17:45:50 -0400 Received: from eggs.gnu.org ([208.118.235.92]:35067) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFQyL-0001T9-7k for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:45:49 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gFQyF-0004Nm-HF for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:45:44 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:56404) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gFQyF-0004Na-DJ; Wed, 24 Oct 2018 17:45:43 -0400 Received: from 50.135.159.77.rev.sfr.net ([77.159.135.50]:33664 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gFQyF-0006G5-3P; Wed, 24 Oct 2018 17:45:43 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Paul Garlick Subject: Re: [bug#33059] [PATCH 02/10] gnu: Add python-petsc4py. References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-2-git-send-email-pgarlick@tourbillion-technology.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 3 Brumaire an 227 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: Wed, 24 Oct 2018 23:45:41 +0200 In-Reply-To: <1539682284-6446-2-git-send-email-pgarlick@tourbillion-technology.com> (Paul Garlick's message of "Tue, 16 Oct 2018 10:31:16 +0100") Message-ID: <87y3anxblm.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -6.0 (------) Paul Garlick skribis: > * gnu/packages/simulation.scm (python-petsc4py): New variable. Should it be in maths.scm? Your call! :-) Apart from that it LGTM. Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 24 17:46:38 2018 Received: (at 33059) by debbugs.gnu.org; 24 Oct 2018 21:46:38 +0000 Received: from localhost ([127.0.0.1]:40870 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFQz7-00028b-Da for submit@debbugs.gnu.org; Wed, 24 Oct 2018 17:46:37 -0400 Received: from eggs.gnu.org ([208.118.235.92]:35205) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFQz4-00023C-Vb for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:46:35 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gFQyv-0004tp-Uc for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:46:29 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:56411) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gFQyv-0004tj-RD; Wed, 24 Oct 2018 17:46:25 -0400 Received: from 50.135.159.77.rev.sfr.net ([77.159.135.50]:33674 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gFQyv-0006LT-Hl; Wed, 24 Oct 2018 17:46:25 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Paul Garlick Subject: Re: [bug#33059] [PATCH 03/10] gnu: Add python-slepc4py. References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-3-git-send-email-pgarlick@tourbillion-technology.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 3 Brumaire an 227 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: Wed, 24 Oct 2018 23:46:23 +0200 In-Reply-To: <1539682284-6446-3-git-send-email-pgarlick@tourbillion-technology.com> (Paul Garlick's message of "Tue, 16 Oct 2018 10:31:17 +0100") Message-ID: <87tvlbxbkg.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -6.0 (------) Paul Garlick skribis: > * gnu/packages/simulation.scm (python-slepc4py): New variable. LGTM. From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 24 17:48:22 2018 Received: (at 33059) by debbugs.gnu.org; 24 Oct 2018 21:48:22 +0000 Received: from localhost ([127.0.0.1]:40886 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFR0o-00033X-Jo for submit@debbugs.gnu.org; Wed, 24 Oct 2018 17:48:22 -0400 Received: from eggs.gnu.org ([208.118.235.92]:35656) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFR0n-00033L-A3 for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:48:21 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gFR0d-0006cq-V5 for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:48:15 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:56426) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gFR0b-0006af-VH; Wed, 24 Oct 2018 17:48:10 -0400 Received: from 50.135.159.77.rev.sfr.net ([77.159.135.50]:33684 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gFR0b-0006Xn-LV; Wed, 24 Oct 2018 17:48:09 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Paul Garlick Subject: Re: [bug#33059] [PATCH 04/10] gnu: Add python-fenics-dijitso. References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-4-git-send-email-pgarlick@tourbillion-technology.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 3 Brumaire an 227 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: Wed, 24 Oct 2018 23:48:07 +0200 In-Reply-To: <1539682284-6446-4-git-send-email-pgarlick@tourbillion-technology.com> (Paul Garlick's message of "Tue, 16 Oct 2018 10:31:18 +0100") Message-ID: <87pnvzxbhk.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -6.0 (------) Paul Garlick skribis: > * gnu/packages/simulation.scm (python-fenics-dijitso): New varaible. I agree with Efraim=E2=80=99s suggestion to use =E2=80=98with-directory-exc= ursion=E2=80=99. Nitpick: > + (home-page > + "https://bitbucket.org/fenics-project/dijitso/") Indentation is off. > + (synopsis > + "Distributed just-in-time building of shared libraries") Please keep =E2=80=98home-page=E2=80=99 and =E2=80=98synopsis=E2=80=99 on a= single line each. Otherwise LGTM, thanks! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 24 17:52:54 2018 Received: (at 33059) by debbugs.gnu.org; 24 Oct 2018 21:52:54 +0000 Received: from localhost ([127.0.0.1]:40895 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFR5C-0003Ak-6M for submit@debbugs.gnu.org; Wed, 24 Oct 2018 17:52:54 -0400 Received: from eggs.gnu.org ([208.118.235.92]:36758) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFR5B-0003AY-9t for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:52:53 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gFR4z-0002Ex-Qz for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:52:47 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:56542) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gFR4w-0002Ck-Io; Wed, 24 Oct 2018 17:52:39 -0400 Received: from 50.135.159.77.rev.sfr.net ([77.159.135.50]:33702 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gFR4w-00077K-9W; Wed, 24 Oct 2018 17:52:38 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Paul Garlick Subject: Re: [bug#33059] [PATCH 05/10] gnu: Add python-fenics-ufl. References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-5-git-send-email-pgarlick@tourbillion-technology.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 3 Brumaire an 227 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: Wed, 24 Oct 2018 23:52:32 +0200 In-Reply-To: <1539682284-6446-5-git-send-email-pgarlick@tourbillion-technology.com> (Paul Garlick's message of "Tue, 16 Oct 2018 10:31:19 +0100") Message-ID: <87lg6nxba7.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -6.0 (------) Paul Garlick skribis: > * gnu/packages/simulation.scm (python-fenics-ufl): New variable. [...] > + (chdir "test") > + (invoke "py.test") > + (chdir "..") Also =E2=80=98with-directory-excursion=E2=80=99 here. > + (home-page > + "https://bitbucket.org/fenics-project/ufl/") Single line please. :-) Otherwise LGTM! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 24 17:53:41 2018 Received: (at 33059) by debbugs.gnu.org; 24 Oct 2018 21:53:41 +0000 Received: from localhost ([127.0.0.1]:40902 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFR5w-0003CQ-QF for submit@debbugs.gnu.org; Wed, 24 Oct 2018 17:53:41 -0400 Received: from eggs.gnu.org ([208.118.235.92]:37007) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFR5v-0003CD-JX for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:53:39 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gFR5h-0002ih-0W for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:53:30 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:56564) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gFR5f-0002hi-OF; Wed, 24 Oct 2018 17:53:24 -0400 Received: from 50.135.159.77.rev.sfr.net ([77.159.135.50]:33704 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gFR5b-0007Bi-Kg; Wed, 24 Oct 2018 17:53:23 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Paul Garlick Subject: Re: [bug#33059] [PATCH 06/10] gnu: Add python-fenics-fiat. References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-6-git-send-email-pgarlick@tourbillion-technology.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 3 Brumaire an 227 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: Wed, 24 Oct 2018 23:53:18 +0200 In-Reply-To: <1539682284-6446-6-git-send-email-pgarlick@tourbillion-technology.com> (Paul Garlick's message of "Tue, 16 Oct 2018 10:31:20 +0100") Message-ID: <87h8hbxb8x.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -6.0 (------) Paul Garlick skribis: > * gnu/packages/simulation.scm (python-fenics-fiat): New variable. [...] > + (chdir "test") > + (invoke "py.test" "unit/") > + (chdir "..") > + #t))))) > + (home-page > + "https://bitbucket.org/fenics-project/fiat/") Same here, but otherwise LGTM. From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 24 17:55:45 2018 Received: (at 33059) by debbugs.gnu.org; 24 Oct 2018 21:55:45 +0000 Received: from localhost ([127.0.0.1]:40908 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFR7x-0003G2-DK for submit@debbugs.gnu.org; Wed, 24 Oct 2018 17:55:45 -0400 Received: from eggs.gnu.org ([208.118.235.92]:37526) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFR7v-0003Fp-D5 for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:55:43 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gFR7m-0004K9-Ac for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 17:55:38 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:56695) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gFR7l-0004Ju-Sl; Wed, 24 Oct 2018 17:55:34 -0400 Received: from 50.135.159.77.rev.sfr.net ([77.159.135.50]:33714 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gFR7l-0007PJ-Ig; Wed, 24 Oct 2018 17:55:33 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Paul Garlick Subject: Re: [bug#33059] [PATCH 07/10] gnu: Add python-fenics-ffc. References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-7-git-send-email-pgarlick@tourbillion-technology.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 3 Brumaire an 227 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: Wed, 24 Oct 2018 23:55:32 +0200 In-Reply-To: <1539682284-6446-7-git-send-email-pgarlick@tourbillion-technology.com> (Paul Garlick's message of "Tue, 16 Oct 2018 10:31:21 +0100") Message-ID: <87d0rzxb57.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -6.0 (------) Paul Garlick skribis: > * gnu/packages/simulation.scm (python-fenics-ffc): New variable. [...] > + (chdir "test") > + ;; FIXME: the tests in subdirectory > + ;; 'unit/ufc/finite_element' require the ffc_factory > + ;; extension module. This module, located in the 'libs' > + ;; subdirectory, needs to be built and made accessible > + ;; prior to running the tests. > + (invoke "py.test" "unit/" "--ignore=unit/ufc/") > + (chdir "uflacs") > + (invoke "py.test" "unit/") > + (chdir "../..") > + #t))))) > + (home-page > + "https://bitbucket.org/fenics-project/ffc/") Same! :-) From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 24 18:12:39 2018 Received: (at 33059) by debbugs.gnu.org; 24 Oct 2018 22:12:39 +0000 Received: from localhost ([127.0.0.1]:40951 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFROJ-0005m8-6H for submit@debbugs.gnu.org; Wed, 24 Oct 2018 18:12:39 -0400 Received: from eggs.gnu.org ([208.118.235.92]:42873) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFROH-0005lq-19 for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 18:12:37 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gFRO7-0007I5-KZ for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 18:12:31 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:56975) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gFRO3-0007F7-H7; Wed, 24 Oct 2018 18:12:24 -0400 Received: from 50.135.159.77.rev.sfr.net ([77.159.135.50]:33796 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gFRO3-00083a-0X; Wed, 24 Oct 2018 18:12:23 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Paul Garlick Subject: Re: [bug#33059] [PATCH 08/10] gnu: Add fenics-dolfin. References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-8-git-send-email-pgarlick@tourbillion-technology.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 3 Brumaire an 227 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: Thu, 25 Oct 2018 00:12:19 +0200 In-Reply-To: <1539682284-6446-8-git-send-email-pgarlick@tourbillion-technology.com> (Paul Garlick's message of "Tue, 16 Oct 2018 10:31:22 +0100") Message-ID: <87va5rvvss.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -6.0 (------) Paul Garlick skribis: > * gnu/packages/simulation.scm (fenics-dolfin): New variable. [...] > + (add-before 'configure 'pre-configure > + (lambda _ > + (use-modules (ice-9 regex) > + (ice-9 rdelim) > + (guix build utils) > + (rnrs io ports)) Please use #:modules instead of an inner =E2=80=98use-modules=E2=80=99 form= (which may or may not work in future Guile versions.) > + ;; Add extra include directories required by the unit tests. > + (with-atomic-file-replacement "test/unit/cpp/CMakeLists.txt" > + (let ((rx (make-regexp "target_link_libraries"))) > + (lambda (in out) > + (let loop () > + (let ((line (read-line in 'concat))) > + (if (eof-object? line) > + #t > + (begin > + (display line out) > + (when (regexp-exec rx line) > + (display > + (string-append > + "target_include_directories(" > + "unittests PRIVATE " > + "${DOLFIN_SOURCE_DIR} " > + "${DOLFIN_SOURCE_DIR}/dolfin " > + "${DOLFIN_BINARY_DIR})\n") out)) > + (loop)))))))) Could this be achieved with a single =E2=80=98substitute*=E2=80=99? It loo= ks like that would be more compact. Also, perhaps this should be done in a =E2=80=98snippet=E2=80=99? > + ;; Add extra include directories required by the demo tests. > + (with-atomic-file-replacement "demo/CMakeLists.txt" > + (let ((rx (make-regexp "find_package"))) > + (lambda (in out) > + (let loop () > + (let ((line (read-line in 'concat))) > + (if (eof-object? line) > + #t > + (begin > + (display line out) > + (when (regexp-exec rx line) > + (display > + (string-append > + "include_directories(" > + "${DOLFIN_SOURCE_DIR} " > + "${DOLFIN_SOURCE_DIR}/dolfin " > + "${DOLFIN_BINARY_DIR})\n") out)) > + (loop)))))))))) Same question here. > + (call-with-output-file "CTestCustom.cmake" > + (lambda (port) > + (display > + (string-append > + "set(CTEST_CUSTOM_TESTS_IGNORE " > + "demo_bcs_serial " > + "demo_bcs_mpi " > + "demo_eigenvalue_serial " > + "demo_eigenvalue_mpi " > + "demo_navier-stokes_serial " Could we avoid listing all the files here? I=E2=80=99m thinking about some= thing like =E2=80=98scandir=E2=80=99 + =E2=80=98delete=E2=80=99. > + ;; The source code files for the DOLFIN C++ library are licensed und= er the > + ;; GNU Lesser General Public License, version 3 or later, with the > + ;; following exceptions: > + ;; > + ;; bsd-2: cmake/modules/FindAMD.cmake > + ;; cmake/modules/FindBLASHeader.cmake > + ;; cmake/modules/FindCHOLMOD.cmake > + ;; cmake/modules/FindEigen3.cmake > + ;; cmake/modules/FindMPFR.cmake > + ;; cmake/modules/FindNumPy.cmake > + ;; cmake/modules/FindPETSc.cmake > + ;; cmake/modules/FindPETSc4py.cmake > + ;; cmake/modules/FindParMETIS.cmake > + ;; cmake/modules/FindSCOTCH.cmake > + ;; cmake/modules/FindSLEPc.cmake > + ;; cmake/modules/FindSLEPc4py.cmake > + ;; cmake/modules/FindSphinx.cmake > + ;; cmake/modules/FindSUNDIALS.cmake > + ;; cmake/modules/FindUFC.cmake > + ;; > + ;; bsd-3: cmake/modules/FindBLAS.cmake > + ;; cmake/modules/FindLAPACK.cmake > + ;; cmake/modules/FindMPI.cmake > + ;; > + ;; public-domain: dolfin/geometry/predicates.cpp > + ;; dolfin/geometry/predicates.h > + ;; > + ;; zlib: dolfin/io/base64.cpp > + ;; dolfin/io/base64.h > + ;; > + ;; expat: dolfin/io/pugiconfig.hpp > + ;; dolfin/io/pugixml.cpp > + ;; dolfin/io/pugixml.hpp > + ;; > + ;; boost1.0: test/unit/cpp/catch/catch.hpp Thanks for the detailed licensing review! IMO we don=E2=80=99t need to list the license of the .cmake files, which are just build files (likewise, we usually ignore M4 files and shell scripts found in Autotools-based projects.) I wonder if we could use our =E2=80=98catch=E2=80=99 package and remove =E2= =80=98catch.hpp=E2=80=99. That=E2=80=99s it! From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 24 18:15:17 2018 Received: (at 33059) by debbugs.gnu.org; 24 Oct 2018 22:15:17 +0000 Received: from localhost ([127.0.0.1]:40956 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFRQq-00065b-Ou for submit@debbugs.gnu.org; Wed, 24 Oct 2018 18:15:17 -0400 Received: from eggs.gnu.org ([208.118.235.92]:43676) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFRQp-0005zG-6W for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 18:15:15 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gFRQg-0000eE-L1 for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 18:15:09 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:57022) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gFRQg-0000e2-Fk; Wed, 24 Oct 2018 18:15:06 -0400 Received: from 50.135.159.77.rev.sfr.net ([77.159.135.50]:33808 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gFRQf-0008JG-ES; Wed, 24 Oct 2018 18:15:06 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Paul Garlick Subject: Re: [bug#33059] [PATCH 09/10] gnu: Add python-fenics-dolfin. In-Reply-To: <1539682284-6446-9-git-send-email-pgarlick@tourbillion-technology.com> (Paul Garlick's message of "Tue, 16 Oct 2018 10:31:23 +0100") References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-9-git-send-email-pgarlick@tourbillion-technology.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 4 Brumaire an 227 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: Thu, 25 Oct 2018 00:15:04 +0200 Message-ID: <87pnvzvvo7.fsf@gnu.org> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -6.0 (------) Paul Garlick skribis: > * gnu/packages/simulation.scm (python-fenics-dolfin): New variable. [...] > + (lambda _ > + (use-modules (ice-9 regex) > + (ice-9 rdelim) > + (guix build utils) > + (rnrs io ports)) Rather #:modules. > + ;; Exclude tests that require meshes supplied by git-lfs. > + (with-atomic-file-replacement "demo/test.py" > + (let ((rx (make-regexp "stem !"))) > + (lambda (in out) > + (let loop () Same question as before about using =E2=80=98substitute*=E2=80=99. > + (chdir "../demo") > + ;; Check demos. > + (invoke "python" "generate-demo-files.py") > + (and (invoke "python" "-m" "pytest" "-v" "test.py") > + (invoke "python" "-m" "pytest" "-v" "test.py" > + "--mpiexec=3Dmpiexec" "--num-proc=3D3")) > + (chdir "..") Rather =E2=80=98with-directory-excursion=E2=80=99. > + (home-page > + "https://bitbucket.org/fenics-project/dolfin/") > + (synopsis > + "High-level problem solving environment for differential equations= ") Single line. :-) From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 24 18:18:04 2018 Received: (at 33059) by debbugs.gnu.org; 24 Oct 2018 22:18:04 +0000 Received: from localhost ([127.0.0.1]:40960 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFRTW-0007wl-Ai for submit@debbugs.gnu.org; Wed, 24 Oct 2018 18:18:03 -0400 Received: from eggs.gnu.org ([208.118.235.92]:44489) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gFRTS-0007wP-Pu for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 18:18:00 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gFRTI-0002tL-KS for 33059@debbugs.gnu.org; Wed, 24 Oct 2018 18:17:53 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:57062) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gFRTI-0002tB-Fr; Wed, 24 Oct 2018 18:17:48 -0400 Received: from 50.135.159.77.rev.sfr.net ([77.159.135.50]:33818 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gFRTI-00005G-6v; Wed, 24 Oct 2018 18:17:48 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Paul Garlick Subject: Re: [bug#33059] [PATCH 10/10] gnu: Add fenics. References: <1539682284-6446-1-git-send-email-pgarlick@tourbillion-technology.com> <1539682284-6446-10-git-send-email-pgarlick@tourbillion-technology.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 4 Brumaire an 227 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: Thu, 25 Oct 2018 00:17:46 +0200 In-Reply-To: <1539682284-6446-10-git-send-email-pgarlick@tourbillion-technology.com> (Paul Garlick's message of "Tue, 16 Oct 2018 10:31:24 +0100") Message-ID: <87k1m7vvjp.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 33059 Cc: 33059@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: -6.0 (------) Paul Garlick skribis: > * gnu/packages/simulation.scm (fenics): New variable. [...] > +;; The FEniCS Project. > +(define-public fenics > + (package > + (inherit python-fenics-dolfin) > + (name "fenics"))) Would it make sense to simply rename =E2=80=9Cpython-fenics-dolfin=E2=80=9D= to =E2=80=9Cfenics=E2=80=9D? I don=E2=80=99t know about Eric but for myself I don=E2=80=99t have anythin= g to add. Perhaps you can prepare a v2? Thank you for the big patch series! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Thu Nov 08 04:23:58 2018 Received: (at control) by debbugs.gnu.org; 8 Nov 2018 09:23:58 +0000 Received: from localhost ([127.0.0.1]:40292 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gKgXe-00016v-72 for submit@debbugs.gnu.org; Thu, 08 Nov 2018 04:23:58 -0500 Received: from eggs.gnu.org ([208.118.235.92]:42952) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gKgXb-00016e-T9 for control@debbugs.gnu.org; Thu, 08 Nov 2018 04:23:56 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gKgXV-00046m-Q5 for control@debbugs.gnu.org; Thu, 08 Nov 2018 04:23:50 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:48640) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gKgXV-00046a-Ja for control@debbugs.gnu.org; Thu, 08 Nov 2018 04:23:49 -0500 Received: from [2001:660:6102:320:e120:2c8f:8909:cdfe] (port=59016 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gKgXV-0004dW-7p for control@debbugs.gnu.org; Thu, 08 Nov 2018 04:23:49 -0500 Date: Thu, 08 Nov 2018 10:23:47 +0100 Message-Id: <87efbv6hy4.fsf@gnu.org> To: control@debbugs.gnu.org From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) Subject: control message for bug #33059 MIME-version: 1.0 Content-type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: control 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: -6.0 (------) tags 33059 moreinfo From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 12 11:02:30 2018 Received: (at 33059) by debbugs.gnu.org; 12 Nov 2018 16:02:30 +0000 Received: from localhost ([127.0.0.1]:48231 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEfV-0000uv-Sc for submit@debbugs.gnu.org; Mon, 12 Nov 2018 11:02:30 -0500 Received: from smtp.hosts.co.uk ([85.233.160.19]:62502) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEfT-0000uf-Cy for 33059@debbugs.gnu.org; Mon, 12 Nov 2018 11:02:27 -0500 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gMEfM-000500-9S; Mon, 12 Nov 2018 16:02:21 +0000 From: Paul Garlick To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , =?UTF-8?q?Ludovic=20Court=C3=A8s?= Subject: [PATCH v2 0/9] Add the FEniCS Project, v2 patches Date: Mon, 12 Nov 2018 16:00:32 +0000 Message-Id: <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <87k1m7vvjp.fsf@gnu.org> References: <87k1m7vvjp.fsf@gnu.org> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) Hi Efraim, Hi Eric, Hi Ludo, Thank you for your comments on the patch series for the FEniCS Project packages. I have been able to make changes to address all of the suggestions with one exception, noted below. The main differences between the original and v2 patches are: i) python-mpi4py is now part of (gnu packages mpi) ii) python-petsc4py is now part of (gnu packages maths) iii) python-slepc4py is now part of (gnu packages maths) iv) temporary directory changes use 'with-directory-excursion' v) 'substitute*' is used in preference to 'with-atomic-file-replacement' vi) the Guix 'catch' package is used in preference to the bundled version vii) the 'python-fenics-dolfin' package has been renamed 'fenics' viii) the 'fenics' package has an updated home-page and synopsis The remaining suggestion was in the 'fenics-dolfin' package: > + (string-append > + "set(CTEST_CUSTOM_TESTS_IGNORE " > + "demo_bcs_serial " > + "demo_bcs_mpi " > + "demo_eigenvalue_serial " > + "demo_eigenvalue_mpi " > + "demo_navier-stokes_serial " > Could we avoid listing all the files here? I tried a few ideas to avoid listing the demos to ignore. These are the ones with the 'git-lfs' links. However, this proved to be awkward. The source code lists the demos that cmake expects to be present. So, one may either make a list of demos to ignore (as in the original patch) or delete the same members from a list to include (plus delete the subdirectories themselves). Simply deleting the subdirectories from the build directory does not work. Since they exist as Makefile targets they are re-created by the 'make demos' step. I think the original method is preferable. An advantage is that users may readily access the demos if they are using Guix on a host system that has a git-lfs package available. Best regards, Paul. Paul Garlick (9): gnu: Add python-mpi4py. gnu: Add python-petsc4py. gnu: Add python-slepc4py. gnu: Add python-fenics-dijitso. gnu: Add python-fenics-ufl. gnu: Add python-fenics-fiat. gnu: Add python-fenics-ffc. gnu: Add fenics-dolfin. gnu: Add fenics. gnu/packages/maths.scm | 72 +++++++ gnu/packages/mpi.scm | 42 ++++ gnu/packages/simulation.scm | 490 +++++++++++++++++++++++++++++++++++++++++++- 3 files changed, 603 insertions(+), 1 deletion(-) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 12 11:03:10 2018 Received: (at 33059) by debbugs.gnu.org; 12 Nov 2018 16:03:10 +0000 Received: from localhost ([127.0.0.1]:48235 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEg6-0000wF-8A for submit@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:10 -0500 Received: from smtp.hosts.co.uk ([85.233.160.19]:62686) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEg1-0000vW-5P for 33059@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:04 -0500 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gMEfv-000500-6s; Mon, 12 Nov 2018 16:02:55 +0000 From: Paul Garlick To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , =?UTF-8?q?Ludovic=20Court=C3=A8s?= Subject: [PATCH v2 1/9] gnu: Add python-mpi4py. Date: Mon, 12 Nov 2018 16:00:33 +0000 Message-Id: <1542038441-5738-2-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> References: <87k1m7vvjp.fsf@gnu.org> <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/mpi.scm (python-mpi4py): New variable. --- gnu/packages/mpi.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm index fc8aade..f08a7f5 100644 --- a/gnu/packages/mpi.scm +++ b/gnu/packages/mpi.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2017 Dave Love ;;; Copyright © 2017 Efraim Flashner ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018 Paul Garlick ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,6 +30,7 @@ #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system gnu) + #:use-module (guix build-system python) #:use-module (gnu packages) #:use-module (gnu packages gcc) #:use-module (gnu packages linux) @@ -263,3 +265,43 @@ only provides @code{MPI_THREAD_FUNNELED}."))) ;; in the build environment than the package wants while testing. (setenv "OMPI_MCA_rmaps_base_oversubscribe" "yes") #t)) + +(define-public python-mpi4py + (package + (name "python-mpi4py") + (version "3.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "mpi4py" version)) + (sha256 + (base32 + "1mzgd26dfv4vwbci8gq77ss9f0x26i9aqzq9b9vs9ndxhlnv0mxl")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'mpi-setup + ,%openmpi-setup) + (add-before 'check 'pre-check + (lambda _ + ;; Skip BaseTestSpawn class (causes error 'ompi_dpm_dyn_init() + ;; failed --> Returned "Unreachable"' in chroot environment). + (substitute* "test/test_spawn.py" + (("unittest.skipMPI\\('openmpi\\(<3.0.0\\)'\\)") + "unittest.skipMPI('openmpi')")) + #t))))) + (inputs + `(("openmpi" ,openmpi))) + (home-page "https://bitbucket.org/mpi4py/mpi4py/") + (synopsis "Python bindings for the Message Passing Interface standard") + (description "MPI for Python (mpi4py) provides bindings of the Message +Passing Interface (MPI) standard for the Python programming language, allowing +any Python program to exploit multiple processors. + +mpi4py is constructed on top of the MPI-1/MPI-2 specification and provides an +object oriented interface which closely follows MPI-2 C++ bindings. It +supports point-to-point and collective communications of any picklable Python +object as well as optimized communications of Python objects (such as NumPy +arrays) that expose a buffer interface.") + (license bsd-3))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 12 11:03:11 2018 Received: (at 33059) by debbugs.gnu.org; 12 Nov 2018 16:03:11 +0000 Received: from localhost ([127.0.0.1]:48238 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgA-0000wT-QV for submit@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:11 -0500 Received: from smtp.hosts.co.uk ([85.233.160.19]:62740) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEg9-0000w4-6E for 33059@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:09 -0500 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gMEg3-000500-7S; Mon, 12 Nov 2018 16:03:03 +0000 From: Paul Garlick To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , =?UTF-8?q?Ludovic=20Court=C3=A8s?= Subject: [PATCH v2 2/9] gnu: Add python-petsc4py. Date: Mon, 12 Nov 2018 16:00:34 +0000 Message-Id: <1542038441-5738-3-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> References: <87k1m7vvjp.fsf@gnu.org> <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/maths.scm (python-petsc4py): New variable. --- gnu/packages/maths.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 0d040bf..e36a574 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1808,6 +1808,41 @@ scientific applications modeled by partial differential equations.") ,@(delete "--with-mpi=0" ,cf))))) (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) +(define-public python-petsc4py + (package + (name "python-petsc4py") + (version "3.9.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "petsc4py" version)) + (sha256 + (base32 + "1f8zd1ac9irsgkyqmzq30d9kl10fy1nh6zk312dhs43g449fkkhc")))) + (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)))) + (inputs + `(("petsc" ,petsc-openmpi) + ("python-numpy" ,python-numpy))) + (home-page "https://bitbucket.org/petsc/petsc4py/") + (synopsis "Python bindings for PETSc") + (description "PETSc, the Portable, Extensible Toolkit for +Scientific Computation, is a suite of data structures and routines for +the scalable (parallel) solution of scientific applications modeled by +partial differential equations. It employs the MPI standard for all +message-passing communication. @code{petsc4py} provides Python +bindings to almost all functions of PETSc.") + (license license:bsd-3))) + (define-public python-kiwisolver (package (name "python-kiwisolver") -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 12 11:03:19 2018 Received: (at 33059) by debbugs.gnu.org; 12 Nov 2018 16:03:19 +0000 Received: from localhost ([127.0.0.1]:48241 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgI-0000wr-4N for submit@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:18 -0500 Received: from smtp.hosts.co.uk ([85.233.160.19]:62792) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgF-0000wP-UJ for 33059@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:16 -0500 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gMEgA-000500-6m; Mon, 12 Nov 2018 16:03:10 +0000 From: Paul Garlick To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , =?UTF-8?q?Ludovic=20Court=C3=A8s?= Subject: [PATCH v2 3/9] gnu: Add python-slepc4py. Date: Mon, 12 Nov 2018 16:00:35 +0000 Message-Id: <1542038441-5738-4-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> References: <87k1m7vvjp.fsf@gnu.org> <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/maths.scm (python-slepc4py): New variable. --- gnu/packages/maths.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e36a574..b1cddfd 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1974,6 +1974,43 @@ arising after the discretization of partial differential equations.") ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi)))) (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)"))) +(define-public python-slepc4py + (package + (name "python-slepc4py") + (version "3.9.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "slepc4py" version)) + (sha256 + (base32 + "02xr0vndgibgkz3rgprqk05n3mk5mpgqw550sr4681vcsgz4zvb7")))) + (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))) + (home-page "https://bitbucket.org/slepc/slepc4py/") + (synopsis "Python bindings for SLEPc") + (description "SLEPc, the Scalable Library for Eigenvalue Problem +Computations, is based on PETSc, the Portable, Extensible Toolkit for +Scientific Computation. It employs the MPI standard for all +message-passing communication. @code{slepc4py} provides Python +bindings to almost all functions of SLEPc.") + (license license:bsd-3))) + (define-public mumps (package (name "mumps") -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 12 11:03:27 2018 Received: (at 33059) by debbugs.gnu.org; 12 Nov 2018 16:03:27 +0000 Received: from localhost ([127.0.0.1]:48244 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgP-0000xE-0Q for submit@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:27 -0500 Received: from smtp.hosts.co.uk ([85.233.160.19]:62868) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgN-0000ws-IK for 33059@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:24 -0500 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gMEgH-000500-8Z; Mon, 12 Nov 2018 16:03:18 +0000 From: Paul Garlick To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , =?UTF-8?q?Ludovic=20Court=C3=A8s?= Subject: [PATCH v2 4/9] gnu: Add python-fenics-dijitso. Date: Mon, 12 Nov 2018 16:00:36 +0000 Message-Id: <1542038441-5738-5-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> References: <87k1m7vvjp.fsf@gnu.org> <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (python-fenics-dijitso): New varaible. --- gnu/packages/simulation.scm | 51 ++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 50 insertions(+), 1 deletion(-) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index a5b661e..86b1aba 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017 Paul Garlick +;;; Copyright © 2017, 2018 Paul Garlick ;;; ;;; This file is part of GNU Guix. ;;; @@ -22,6 +22,7 @@ #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages boost) + #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages flex) #:use-module (gnu packages gettext) @@ -35,6 +36,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) + #:use-module (gnu packages python) #:use-module (gnu packages readline) #:use-module (gnu packages tls) #:use-module (gnu packages version-control) @@ -43,6 +45,7 @@ #:use-module (guix download) #:use-module (guix build utils) #:use-module (guix build-system gnu) + #:use-module (guix build-system python) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix utils) @@ -221,3 +224,49 @@ with gas/liquid interfaces. Large problems may be split into smaller, connected problems for efficient solution on parallel systems.") (license license:gpl3+) (home-page "https://openfoam.org"))) + +(define-public python-fenics-dijitso + (package + (name "python-fenics-dijitso") + (version "2018.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fenics-dijitso" version)) + (sha256 + (base32 + "1qax2f52qsjbd1h5lk5i5shp448qlakxabjjybrfc1w823p0yql9")))) + (build-system python-build-system) + (inputs + `(("openmpi" ,openmpi) + ("python-numpy" ,python-numpy))) + (native-inputs + `(("python-pytest-cov" ,python-pytest-cov))) + (propagated-inputs + `(("python-mpi4py" ,python-mpi4py))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'mpi-setup + ,%openmpi-setup) + (replace 'check + (lambda _ + (setenv "HOME" "/tmp") + (setenv "PYTHONPATH" + (string-append (getcwd) ":" (getenv "PYTHONPATH"))) + (with-directory-excursion "test" + (invoke "./runtests.sh")) + #t))))) + (home-page "https://bitbucket.org/fenics-project/dijitso/") + (synopsis "Distributed just-in-time building of shared libraries") + (description + "Dijitso provides a core component of the @code{FEniCS} framework, +namely the just-in-time compilation of C++ code that is generated from +Python modules. It is called from within a C++ library, using ctypes +to import the dynamic shared library directly. + +As long as the compiled code can provide a simple factory function to +a class implementing a predefined C++ interface, there is no limit to +the complexity of that interface. Parallel support depends on the +@code{mpi4py} interface.") + (license license:lgpl3+))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 12 11:03:32 2018 Received: (at 33059) by debbugs.gnu.org; 12 Nov 2018 16:03:32 +0000 Received: from localhost ([127.0.0.1]:48247 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgW-0000xZ-6E for submit@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:32 -0500 Received: from smtp.hosts.co.uk ([85.233.160.19]:62926) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgU-0000xD-27 for 33059@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:31 -0500 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gMEgO-000500-78; Mon, 12 Nov 2018 16:03:24 +0000 From: Paul Garlick To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , =?UTF-8?q?Ludovic=20Court=C3=A8s?= Subject: [PATCH v2 5/9] gnu: Add python-fenics-ufl. Date: Mon, 12 Nov 2018 16:00:37 +0000 Message-Id: <1542038441-5738-6-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> References: <87k1m7vvjp.fsf@gnu.org> <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (python-fenics-ufl): New variable. --- gnu/packages/simulation.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 86b1aba..7165fb5 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -270,3 +270,40 @@ a class implementing a predefined C++ interface, there is no limit to the complexity of that interface. Parallel support depends on the @code{mpi4py} interface.") (license license:lgpl3+))) + +(define-public python-fenics-ufl + (package + (name "python-fenics-ufl") + (version "2018.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fenics-ufl" version)) + (sha256 + (base32 + "1fq8yc86s1s3c8c0b1rc2vf265q0hrkzg57100fg1nghcz0p4vla")))) + (build-system python-build-system) + (inputs + `(("python-numpy" ,python-numpy))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) ":" (getenv "PYTHONPATH"))) + (with-directory-excursion "test" + (invoke "py.test")) + #t))))) + (home-page "https://bitbucket.org/fenics-project/ufl/") + (synopsis "Unified language for form-compilers") + (description "The Unified Form Language (UFL) is a domain specific +language for declaration of finite element discretizations of +variational forms. More precisely, it defines a flexible interface +for choosing finite element spaces and defining expressions for weak +forms in a notation close to mathematical notation. + +UFL is part of the FEniCS Project.") + (license license:lgpl3+))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 12 11:03:41 2018 Received: (at 33059) by debbugs.gnu.org; 12 Nov 2018 16:03:41 +0000 Received: from localhost ([127.0.0.1]:48250 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgf-0000xz-G9 for submit@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:41 -0500 Received: from smtp.hosts.co.uk ([85.233.160.19]:63024) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgc-0000xh-TQ for 33059@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:39 -0500 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gMEgW-000500-9e; Mon, 12 Nov 2018 16:03:33 +0000 From: Paul Garlick To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , =?UTF-8?q?Ludovic=20Court=C3=A8s?= Subject: [PATCH v2 6/9] gnu: Add python-fenics-fiat. Date: Mon, 12 Nov 2018 16:00:38 +0000 Message-Id: <1542038441-5738-7-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> References: <87k1m7vvjp.fsf@gnu.org> <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (python-fenics-fiat): New variable. --- gnu/packages/simulation.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 7165fb5..ecdb2b2 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -307,3 +307,45 @@ forms in a notation close to mathematical notation. UFL is part of the FEniCS Project.") (license license:lgpl3+))) + +(define-public python-fenics-fiat + (package + (name "python-fenics-fiat") + (version "2018.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fenics-fiat" version)) + (sha256 + (base32 + "0fmjd93r6bwf6xs8csw86qzphrnr66xwv7f372w59gmq8mg6rljc")))) + (build-system python-build-system) + (native-inputs + `(("python-pytest" ,python-pytest))) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-sympy" ,python-sympy))) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) ":" (getenv "PYTHONPATH"))) + (with-directory-excursion "test" + (invoke "py.test" "unit/")) + #t))))) + (home-page "https://bitbucket.org/fenics-project/fiat/") + (synopsis "Tabulation of finite element function spaces") + (description + "The FInite element Automatic Tabulator (FIAT) supports +generation of arbitrary order instances of the Lagrange elements on +lines, triangles, and tetrahedra. It is also capable of generating +arbitrary order instances of Jacobi-type quadrature rules on the same +element shapes. Further, H(div) and H(curl) conforming finite element +spaces such as the families of Raviart-Thomas, Brezzi-Douglas-Marini +and Nedelec are supported on triangles and tetrahedra. Upcoming +versions will also support Hermite and nonconforming elements. + +FIAT is part of the FEniCS Project.") + (license license:lgpl3+))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 12 11:03:48 2018 Received: (at 33059) by debbugs.gnu.org; 12 Nov 2018 16:03:48 +0000 Received: from localhost ([127.0.0.1]:48253 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgl-0000yM-QC for submit@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:48 -0500 Received: from smtp.hosts.co.uk ([85.233.160.19]:63096) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgj-0000xx-Mn for 33059@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:46 -0500 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gMEgd-000500-94; Mon, 12 Nov 2018 16:03:40 +0000 From: Paul Garlick To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , =?UTF-8?q?Ludovic=20Court=C3=A8s?= Subject: [PATCH v2 7/9] gnu: Add python-fenics-ffc. Date: Mon, 12 Nov 2018 16:00:39 +0000 Message-Id: <1542038441-5738-8-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> References: <87k1m7vvjp.fsf@gnu.org> <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (python-fenics-ffc): New variable. --- gnu/packages/simulation.scm | 52 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index ecdb2b2..d1a5e46 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -349,3 +349,55 @@ versions will also support Hermite and nonconforming elements. FIAT is part of the FEniCS Project.") (license license:lgpl3+))) + +(define-public python-fenics-ffc + (package + (name "python-fenics-ffc") + (version "2018.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fenics-ffc" version)) + (sha256 + (base32 + "1b2ia5vlkw298x7rf0k2p3ihlpwkwgc98p3s6sbpds3hqmfrzdz9")))) + (build-system python-build-system) + (native-inputs + `(("python-pytest" ,python-pytest))) + (propagated-inputs + `(("python-fenics-dijitso" ,python-fenics-dijitso) + ("python-fenics-fiat" ,python-fenics-fiat) + ("python-fenics-ufl" ,python-fenics-ufl))) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "HOME" (getcwd)) + (setenv "PYTHONPATH" + (string-append (getcwd) ":" (getenv "PYTHONPATH"))) + (with-directory-excursion "test" + ;; FIXME: the tests in subdirectory + ;; 'unit/ufc/finite_element' require the ffc_factory + ;; extension module. This module, located in the 'libs' + ;; subdirectory, needs to be built and made accessible + ;; prior to running the tests. + (invoke "py.test" "unit/" "--ignore=unit/ufc/") + (with-directory-excursion "uflacs" + (invoke "py.test" "unit/"))) + #t))))) + (home-page "https://bitbucket.org/fenics-project/ffc/") + (synopsis "Compiler for finite element variational forms") + (description "The FEniCS Form Compiler (FFC) is a compiler for +finite element variational forms. From a high-level description of +the form, it generates efficient low-level C++ code that can be used +to assemble the corresponding discrete operator (tensor). In +particular, a bilinear form may be assembled into a matrix and a +linear form may be assembled into a vector. FFC may be used either +from the command line (by invoking the @code{ffc} command) or as a +Python module (@code{import ffc}). + +FFC is part of the FEniCS Project.") + ;; There are two files released with a public domain licence; + ;; ufc.h and ufc_geometry.h, in subdirectory 'ffc/backends/ufc'. + (license (list license:public-domain license:lgpl3+)))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 12 11:03:54 2018 Received: (at 33059) by debbugs.gnu.org; 12 Nov 2018 16:03:54 +0000 Received: from localhost ([127.0.0.1]:48256 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgs-0000yf-3a for submit@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:54 -0500 Received: from smtp.hosts.co.uk ([85.233.160.19]:63162) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgp-0000yK-MH for 33059@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:52 -0500 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gMEgj-000500-7B; Mon, 12 Nov 2018 16:03:46 +0000 From: Paul Garlick To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , =?UTF-8?q?Ludovic=20Court=C3=A8s?= Subject: [PATCH v2 8/9] gnu: Add fenics-dolfin. Date: Mon, 12 Nov 2018 16:00:40 +0000 Message-Id: <1542038441-5738-9-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> References: <87k1m7vvjp.fsf@gnu.org> <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (fenics-dolfin): New variable. --- gnu/packages/simulation.scm | 191 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 191 insertions(+) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index d1a5e46..bd139d3 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -18,11 +18,13 @@ (define-module (gnu packages simulation) #:use-module (gnu packages) + #:use-module (gnu packages algebra) #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages boost) #:use-module (gnu packages check) + #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages flex) #:use-module (gnu packages gettext) @@ -36,6 +38,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages readline) #:use-module (gnu packages tls) @@ -44,6 +47,7 @@ #:use-module (gnu packages xorg) #:use-module (guix download) #:use-module (guix build utils) + #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system python) #:use-module ((guix licenses) #:prefix license:) @@ -401,3 +405,190 @@ FFC is part of the FEniCS Project.") ;; There are two files released with a public domain licence; ;; ufc.h and ufc_geometry.h, in subdirectory 'ffc/backends/ufc'. (license (list license:public-domain license:lgpl3+)))) + +(define-public fenics-dolfin + (package + (name "fenics-dolfin") + (version "2018.1.0.post1") + (source + (origin + (method url-fetch) + (uri (string-append + "https://bitbucket.org/fenics-project/dolfin/get/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "12zkk8j3xsg6l8p0ggwsl03084vlcivw4h99b7z9kndg7k89b3ya")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Make sure we don't use the bundled test framework. + (delete-file-recursively "test/unit/cpp/catch") + (substitute* "test/unit/cpp/main.cpp" + ;; Use standard search paths for 'catch' header file. + (("#include.*") + "#include \n")) + (substitute* "test/unit/cpp/CMakeLists.txt" + ;; Add extra include directories required by the unit tests. + (("(^target_link_libraries.*)" line) + (string-append line "\n" + "target_include_directories(" + "unittests PRIVATE " + "${DOLFIN_SOURCE_DIR} " + "${DOLFIN_SOURCE_DIR}/dolfin " + "${DOLFIN_BINARY_DIR})\n")) + (("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back) + (string-append front + "$ENV{CATCH_DIR}" + "/include" back "\n"))) + (substitute* "demo/CMakeLists.txt" + ;; Add extra include directories required by the demo tests. + (("(^#find_package.*)" line) + (string-append line "\n" + "include_directories(" + "${DOLFIN_SOURCE_DIR} " + "${DOLFIN_SOURCE_DIR}/dolfin " + "${DOLFIN_BINARY_DIR})\n"))) + #t)))) + (build-system cmake-build-system) + (inputs + `(("blas" ,openblas) + ("boost" ,boost) + ("eigen" ,eigen) + ("hdf5" ,hdf5-parallel-openmpi) + ("lapack" ,lapack) + ("libxml2" ,libxml2) + ("openmpi" ,openmpi) + ("python" ,python-3) + ("scotch" ,pt-scotch32) + ("suitesparse" ,suitesparse) + ("sundials" ,sundials-openmpi) + ("zlib" ,zlib))) + (native-inputs + `(("catch" ,catch-framework2) + ("pkg-config" ,pkg-config))) + (propagated-inputs + `(("ffc" ,python-fenics-ffc) + ("petsc" ,petsc-openmpi) + ("slepc" ,slepc-openmpi))) + (arguments + `(#:configure-flags + `("-DDOLFIN_ENABLE_DOCS:BOOL=OFF" + "-DDOLFIN_ENABLE_HDF5:BOOL=ON" + "-DDOLFIN_ENABLE_MPI:BOOL=ON" + "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF" + "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON" + "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON" + "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF") + #:phases + (modify-phases %standard-phases + (add-after 'patch-usr-bin-file 'mpi-setup + ,%openmpi-setup) + (add-after 'patch-source-shebangs 'set-paths + (lambda _ + ;; Define paths to store locations. + (setenv "BLAS_DIR" (assoc-ref %build-inputs "blas")) + (setenv "CATCH_DIR" (assoc-ref %build-inputs "catch")) + (setenv "LAPACK_DIR" (assoc-ref %build-inputs "lapack")) + (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) + (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc")) + (setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch")) + (setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials")) + (setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse")) + #t)) + (add-before 'check 'pre-check + (lambda _ + ;; The Dolfin repository uses git-lfs, whereby web links are + ;; substituted for large files. Guix does not currently support + ;; git-lfs, so only the links are downloaded. The tests that + ;; require the absent meshes cannot run and are skipped. + ;; + ;; Two other serial tests fail and are skipped. + ;; i) demo_stokes-iterative_serial, + ;; The MPI_Comm_rank() function was called before MPI_INIT was + ;; invoked + ;; ii) demo_multimesh-stokes_serial: + ;; Warning: Found no facets matching domain for boundary + ;; condition. + ;; + ;; One mpi test fails and is skipped. + ;; i) demo_stokes-iterative_mpi: + ;; The MPI_Comm_rank() function was called before MPI_INIT was + ;; invoked + (call-with-output-file "CTestCustom.cmake" + (lambda (port) + (display + (string-append + "set(CTEST_CUSTOM_TESTS_IGNORE " + "demo_bcs_serial " + "demo_bcs_mpi " + "demo_eigenvalue_serial " + "demo_eigenvalue_mpi " + "demo_navier-stokes_serial " + "demo_navier-stokes_mpi " + "demo_stokes-taylor-hood_serial " + "demo_stokes-taylor-hood_mpi " + "demo_subdomains_serial " + "demo_advection-diffusion_serial " + "demo_advection-diffusion_mpi " + "demo_auto-adaptive-navier-stokes_serial " + "demo_contact-vi-snes_serial " + "demo_contact-vi-snes_mpi " + "demo_contact-vi-tao_serial " + "demo_contact-vi-tao_mpi " + "demo_curl-curl_serial " + "demo_curl-curl_mpi " + "demo_dg-advection-diffusion_serial " + "demo_dg-advection-diffusion_mpi " + "demo_elasticity_serial " + "demo_elasticity_mpi " + "demo_elastodynamics_serial " + "demo_elastodynamics_mpi " + "demo_lift-drag_serial " + "demo_lift-drag_mpi " + "demo_mesh-quality_serial " + "demo_mesh-quality_mpi " + "demo_multimesh-stokes_serial " + "demo_stokes-iterative_serial " + "demo_stokes-iterative_mpi " + ")\n") port))) + #t)) + (replace 'check + (lambda _ + (and (invoke "make" "unittests") + (invoke "make" "demos") + (invoke "ctest" "-R" "unittests") + (invoke "ctest" "-R" "demo" "-R" "serial") + (invoke "ctest" "-R" "demo" "-R" "mpi"))))))) + (home-page "https://bitbucket.org/fenics-project/dolfin/") + (synopsis "Problem solving environment for differential equations") + (description + "DOLFIN is a computational framework for finding numerical +solutions to problems described by differential equations. Numerical +models in DOLFIN are constructed using general families of finite +elements. Data structures are provided for discretizing the governing +system on a computational mesh. A compact syntax, similar to +mathematical notation, is made available for defining function spaces +and expressing variational forms. Interfaces to specialized matrix +solvers are provided for solving the resultant linear systems. + +@code{fenics-dolfin} is part of the FEniCS project. It is the C++ +user interface to the FEniCS core components and external libraries.") + ;; The source code for the DOLFIN C++ library is licensed under the + ;; GNU Lesser General Public License, version 3 or later, with the + ;; following exceptions: + ;; + ;; public-domain: dolfin/geometry/predicates.cpp + ;; dolfin/geometry/predicates.h + ;; + ;; zlib: dolfin/io/base64.cpp + ;; dolfin/io/base64.h + ;; + ;; expat: dolfin/io/pugiconfig.hpp + ;; dolfin/io/pugixml.cpp + ;; dolfin/io/pugixml.hpp + (license (list license:public-domain + license:zlib + license:expat + license:lgpl3+)))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 12 11:03:57 2018 Received: (at 33059) by debbugs.gnu.org; 12 Nov 2018 16:03:58 +0000 Received: from localhost ([127.0.0.1]:48259 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgv-0000yx-J8 for submit@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:57 -0500 Received: from smtp.hosts.co.uk ([85.233.160.19]:63214) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gMEgu-0000yX-Ef for 33059@debbugs.gnu.org; Mon, 12 Nov 2018 11:03:56 -0500 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1gMEgo-000500-7G; Mon, 12 Nov 2018 16:03:50 +0000 From: Paul Garlick To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , =?UTF-8?q?Ludovic=20Court=C3=A8s?= Subject: [PATCH v2 9/9] gnu: Add fenics. Date: Mon, 12 Nov 2018 16:00:41 +0000 Message-Id: <1542038441-5738-10-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 In-Reply-To: <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> References: <87k1m7vvjp.fsf@gnu.org> <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 33059 Cc: Paul Garlick 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 (-) * gnu/packages/simulation.scm (fenics): New variable. --- gnu/packages/simulation.scm | 117 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 117 insertions(+) diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index bd139d3..6144e23 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -592,3 +592,120 @@ user interface to the FEniCS core components and external libraries.") license:zlib license:expat license:lgpl3+)))) + +(define-public fenics + (package (inherit fenics-dolfin) + (name "fenics") + (build-system python-build-system) + (inputs + `(("pybind11" ,pybind11) + ("python-matplotlib" ,python-matplotlib) + ,@(alist-delete "python" (package-inputs fenics-dolfin)))) + (native-inputs + `(("cmake" ,cmake) + ("ply" ,python-ply) + ("pytest" ,python-pytest) + ("python-decorator" ,python-decorator) + ("python-pkgconfig" ,python-pkgconfig) + ,@(package-native-inputs fenics-dolfin))) + (propagated-inputs + `(("dolfin" ,fenics-dolfin) + ("petsc4py" ,python-petsc4py) + ("slepc4py" ,python-slepc4py))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'patch-source-shebangs 'set-paths + (lambda _ + ;; Define paths to store locations. + (setenv "PYBIND11_DIR" (assoc-ref %build-inputs "pybind11")) + ;; Move to python sub-directory. + (chdir "python") + #t)) + (add-after 'build 'mpi-setup + ,%openmpi-setup) + (add-before 'check 'pre-check + (lambda _ + ;; Exclude tests that require meshes supplied by git-lfs. + (substitute* "demo/test.py" + (("(.*stem !.*)" line) + (string-append + line "\n" + "excludeList = [\n" + "'multimesh-quadrature', \n" + "'multimesh-marking', \n" + "'mixed-poisson-sphere', \n" + "'mesh-quality', \n" + "'lift-drag', \n" + "'elastodynamics', \n" + "'dg-advection-diffusion', \n" + "'contact-vi-tao', \n" + "'contact-vi-snes', \n" + "'collision-detection', \n" + "'buckling-tao', \n" + "'auto-adaptive-navier-stokes', \n" + "'advection-diffusion', \n" + "'subdomains', \n" + "'stokes-taylor-hood', \n" + "'stokes-mini', \n" + "'navier-stokes', \n" + "'eigenvalue']\n" + "demos = [" + "d for d in demos if d[0].stem not in " + "excludeList]\n"))) + (setenv "HOME" (getcwd)) + (setenv "PYTHONPATH" + (string-append + (getcwd) "/build/lib.linux-x86_64-" + ,(version-major+minor (package-version python)) ":" + (getenv "PYTHONPATH"))) + ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP. + (setenv "OPENBLAS_NUM_THREADS" "1") + #t)) + (replace 'check + (lambda _ + (with-directory-excursion "test" + ;; Note: The test test_snes_set_from_options() in the file + ;; unit/nls/test_PETScSNES_solver.py fails and is ignored. + (and (invoke "py.test" "unit" "--ignore" + "unit/nls/test_PETScSNES_solver.py") + (invoke "mpirun" "-np" "3" "python" "-B" "-m" + "pytest" "unit" "--ignore" + "unit/nls/test_PETScSNES_solver.py"))) + (with-directory-excursion "demo" + ;; Check demos. + (invoke "python" "generate-demo-files.py") + (and (invoke "python" "-m" "pytest" "-v" "test.py") + (invoke "python" "-m" "pytest" "-v" "test.py" + "--mpiexec=mpiexec" "--num-proc=3"))) + #t)) + (add-after 'install 'install-demo-files + (lambda* (#:key outputs #:allow-other-keys) + (let* ((demos (string-append + (assoc-ref outputs "out") + "/share/python-dolfin/demo"))) + (mkdir-p demos) + (with-directory-excursion "demo" + (for-each (lambda (file) + (let* ((dir (dirname file)) + (tgt-dir (string-append demos "/" dir))) + (unless (equal? "." dir) + (mkdir-p tgt-dir) + (install-file file tgt-dir)))) + (find-files "." ".*\\.(py|gz|xdmf)$")))) + #t))))) + (home-page "https://fenicsproject.org/") + (synopsis "High-level environment for solving differential equations") + (description + "@code{fenics} is a computing platform for solving general classes of +problems that involve differential equations. @code{fenics} facilitates +access to efficient methods for dealing with ordinary differential +equations (ODEs) and partial differential equations (PDEs). Systems of +equations such as these are commonly encountered in areas of engineering, +mathematics and the physical sciences. It is particularly well-suited to +problems that can be solved using the Finite Element Method (FEM). + +@code{fenics} is the top level of the set of packages that are developed +within the FEniCS project. It provides the python user interface to the +FEniCS core components and external libraries.") + (license license:lgpl3+))) -- 1.8.3.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 14 15:39:25 2018 Received: (at 33059-done) by debbugs.gnu.org; 14 Nov 2018 20:39:25 +0000 Received: from localhost ([127.0.0.1]:52620 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gN1wb-00045L-Gu for submit@debbugs.gnu.org; Wed, 14 Nov 2018 15:39:25 -0500 Received: from eggs.gnu.org ([208.118.235.92]:49654) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gN1wZ-000459-5W for 33059-done@debbugs.gnu.org; Wed, 14 Nov 2018 15:39:23 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gN1wS-0003CN-Ua for 33059-done@debbugs.gnu.org; Wed, 14 Nov 2018 15:39:17 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:46159) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gN1w3-0002nk-NW; Wed, 14 Nov 2018 15:38:54 -0500 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=39070 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gN1w2-00043k-IA; Wed, 14 Nov 2018 15:38:51 -0500 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Paul Garlick Subject: Re: [PATCH v2 0/9] Add the FEniCS Project, v2 patches References: <87k1m7vvjp.fsf@gnu.org> <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 24 Brumaire an 227 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: Wed, 14 Nov 2018 21:38:48 +0100 In-Reply-To: <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> (Paul Garlick's message of "Mon, 12 Nov 2018 16:00:32 +0000") Message-ID: <87zhubcs2v.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 33059-done Cc: Eric Bavier , 33059-done@debbugs.gnu.org, Efraim Flashner 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: -6.0 (------) Hello Paul and all, Paul Garlick skribis: > Hi Efraim, Hi Eric, Hi Ludo, > > Thank you for your comments on the patch series for the FEniCS Project > packages. I have been able to make changes to address all of the > suggestions with one exception, noted below. > > The main differences between the original and v2 patches are: > > i) python-mpi4py is now part of (gnu packages mpi) > ii) python-petsc4py is now part of (gnu packages maths) > iii) python-slepc4py is now part of (gnu packages maths) > iv) temporary directory changes use 'with-directory-excursion' > v) 'substitute*' is used in preference to 'with-atomic-file-replacement' > vi) the Guix 'catch' package is used in preference to the bundled version > vii) the 'python-fenics-dolfin' package has been renamed 'fenics' > viii) the 'fenics' package has an updated home-page and synopsis > > The remaining suggestion was in the 'fenics-dolfin' package: > >> + (string-append >> + "set(CTEST_CUSTOM_TESTS_IGNORE " >> + "demo_bcs_serial " >> + "demo_bcs_mpi " >> + "demo_eigenvalue_serial " >> + "demo_eigenvalue_mpi " >> + "demo_navier-stokes_serial " > >> Could we avoid listing all the files here? > > I tried a few ideas to avoid listing the demos to ignore. These are the = ones > with the 'git-lfs' links. However, this proved to be awkward. > > The source code lists the demos that cmake expects to be present. So, one > may either make a list of demos to ignore (as in the original patch) or d= elete > the same members from a list to include (plus delete the subdirectories > themselves). Simply deleting the subdirectories from the build directory= does > not work. Since they exist as Makefile targets they are re-created by the > 'make demos' step. > > I think the original method is preferable. An advantage is that users may > readily access the demos if they are using Guix on a host system that has > a git-lfs package available. Thanks a lot for taking the time to address the comments we made on this patch series. I=E2=80=99ve applied the whole series on =E2=80=98master=E2= =80=99; everything lints and builds for me on x86_64-linux (there are new versions of the PETSc and SLEPSc bindings available, BTW.) Thank you! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 14 16:11:51 2018 Received: (at 33059) by debbugs.gnu.org; 14 Nov 2018 21:11:51 +0000 Received: from localhost ([127.0.0.1]:52639 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gN2Rz-0004ua-IO for submit@debbugs.gnu.org; Wed, 14 Nov 2018 16:11:51 -0500 Received: from eggs.gnu.org ([208.118.235.92]:58018) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gN2Rx-0004uO-V5 for 33059@debbugs.gnu.org; Wed, 14 Nov 2018 16:11:50 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gN2Rl-0005Y9-6U for 33059@debbugs.gnu.org; Wed, 14 Nov 2018 16:11:40 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:46960) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gN2RX-0005Lz-V2; Wed, 14 Nov 2018 16:11:25 -0500 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=39304 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gN2RW-0001ky-9z; Wed, 14 Nov 2018 16:11:22 -0500 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Paul Garlick Subject: Re: [PATCH v2 6/9] gnu: Add python-fenics-fiat. References: <87k1m7vvjp.fsf@gnu.org> <1542038441-5738-1-git-send-email-pgarlick@tourbillion-technology.com> <1542038441-5738-7-git-send-email-pgarlick@tourbillion-technology.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 24 Brumaire an 227 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: Wed, 14 Nov 2018 22:11:20 +0100 In-Reply-To: <1542038441-5738-7-git-send-email-pgarlick@tourbillion-technology.com> (Paul Garlick's message of "Mon, 12 Nov 2018 16:00:38 +0000") Message-ID: <87r2fnbc07.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 33059 Cc: 33059@debbugs.gnu.org, Efraim Flashner , 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: -6.0 (------) Paul Garlick skribis: > * gnu/packages/simulation.scm (python-fenics-fiat): New variable. Apparently this one has a test failure on i686-linux: https://berlin.guixsd.org/build/623722/log/raw It=E2=80=99s not uncommon for numerical software tests to break on 32-bit platforms. Perhaps you could ask upstream what they think about it? Thanks, Ludo=E2=80=99. From unknown Sun Aug 10 09:46:24 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Thu, 13 Dec 2018 12:24:04 +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