From patchwork Mon Nov 12 16:00:33 2018 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Paul Garlick X-Patchwork-Id: 188 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id B7EAC167F7; Mon, 12 Nov 2018 16:04:47 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.9 required=5.0 tests=BAYES_00,RCVD_IN_DNSWL_HI, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:4830:134:3::11]) by mira.cbaines.net (Postfix) with ESMTPS id 5BE04167F5 for ; Mon, 12 Nov 2018 16:04:47 +0000 (GMT) Received: from localhost ([::1]:49373 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhi-0004ab-7I for patchwork@mira.cbaines.net; Mon, 12 Nov 2018 11:04:46 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:36623) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhE-0004LJ-Le for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:19 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gMEh5-0004ih-Mv for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:16 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:44001) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gMEh0-0004ex-2r for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1gMEgz-0000zG-V8 for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#33059] [PATCH v2 1/9] gnu: Add python-mpi4py. Resent-From: Paul Garlick Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Nov 2018 16:04:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33059 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: moreinfo patch To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , Ludovic =?utf-8?q?Court=C3=A8s?= Received: via spool by 33059-submit@debbugs.gnu.org id=B33059.15420385903627 (code B ref 33059); Mon, 12 Nov 2018 16:04:01 +0000 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 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 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 208.118.235.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: Paul Garlick Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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))) From patchwork Mon Nov 12 16:00:34 2018 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Paul Garlick X-Patchwork-Id: 183 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 9BD4F167F7; Mon, 12 Nov 2018 16:04:24 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.9 required=5.0 tests=BAYES_00,RCVD_IN_DNSWL_HI, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:4830:134:3::11]) by mira.cbaines.net (Postfix) with ESMTPS id 543D9167F5 for ; Mon, 12 Nov 2018 16:04:24 +0000 (GMT) Received: from localhost ([::1]:49364 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhL-0004Mg-Gm for patchwork@mira.cbaines.net; Mon, 12 Nov 2018 11:04:23 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:36540) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEh8-0004Hk-Vd for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:12 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gMEh5-0004ir-Nj for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:10 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:44002) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gMEh0-0004fF-Iq for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1gMEh0-0000zO-Dv for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#33059] [PATCH v2 2/9] gnu: Add python-petsc4py. Resent-From: Paul Garlick Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Nov 2018 16:04:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33059 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: moreinfo patch To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , Ludovic =?utf-8?q?Court=C3=A8s?= Received: via spool by 33059-submit@debbugs.gnu.org id=B33059.15420385913633 (code B ref 33059); Mon, 12 Nov 2018 16:04:02 +0000 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 208.118.235.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: Paul Garlick Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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") From patchwork Mon Nov 12 16:00:35 2018 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Paul Garlick X-Patchwork-Id: 182 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 3E2FB167F7; Mon, 12 Nov 2018 16:04:19 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.9 required=5.0 tests=BAYES_00,RCVD_IN_DNSWL_HI, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:4830:134:3::11]) by mira.cbaines.net (Postfix) with ESMTPS id DD30E167F5 for ; Mon, 12 Nov 2018 16:04:18 +0000 (GMT) Received: from localhost ([::1]:49363 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhF-0004K0-RD for patchwork@mira.cbaines.net; Mon, 12 Nov 2018 11:04:17 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:36541) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEh8-0004Hl-Vd for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:12 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gMEh6-0004jP-J6 for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:10 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:44003) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gMEh1-0004fj-4w for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:05 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1gMEh1-0000zV-0A for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#33059] [PATCH v2 3/9] gnu: Add python-slepc4py. Resent-From: Paul Garlick Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Nov 2018 16:04:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33059 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: moreinfo patch To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , Ludovic =?utf-8?q?Court=C3=A8s?= Received: via spool by 33059-submit@debbugs.gnu.org id=B33059.15420385993655 (code B ref 33059); Mon, 12 Nov 2018 16:04:02 +0000 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 208.118.235.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: Paul Garlick Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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") From patchwork Mon Nov 12 16:00:36 2018 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Paul Garlick X-Patchwork-Id: 187 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 7C791167F7; Mon, 12 Nov 2018 16:04:38 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.9 required=5.0 tests=BAYES_00,RCVD_IN_DNSWL_HI, URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:4830:134:3::11]) by mira.cbaines.net (Postfix) with ESMTPS id EC7EE167F5 for ; Mon, 12 Nov 2018 16:04:37 +0000 (GMT) Received: from localhost ([::1]:49371 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhZ-0004X9-A6 for patchwork@mira.cbaines.net; Mon, 12 Nov 2018 11:04:37 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:36616) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhE-0004LG-Jd for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:19 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gMEh8-0004kc-Nd for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:13 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:44004) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gMEh1-0004g0-MW for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:06 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1gMEh1-0000zd-Hi for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#33059] [PATCH v2 4/9] gnu: Add python-fenics-dijitso. Resent-From: Paul Garlick Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Nov 2018 16:04:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33059 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: moreinfo patch To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , Ludovic =?utf-8?q?Court=C3=A8s?= Received: via spool by 33059-submit@debbugs.gnu.org id=B33059.15420386073678 (code B ref 33059); Mon, 12 Nov 2018 16:04:03 +0000 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 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 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 208.118.235.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: Paul Garlick Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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+))) From patchwork Mon Nov 12 16:00:37 2018 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Paul Garlick X-Patchwork-Id: 190 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id EEC26167F7; Mon, 12 Nov 2018 16:04:57 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.9 required=5.0 tests=BAYES_00,RCVD_IN_DNSWL_HI, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:4830:134:3::11]) by mira.cbaines.net (Postfix) with ESMTPS id ADA95167F5 for ; Mon, 12 Nov 2018 16:04:57 +0000 (GMT) Received: from localhost ([::1]:49376 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhs-0004fa-QW for patchwork@mira.cbaines.net; Mon, 12 Nov 2018 11:04:56 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:36614) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhE-0004LF-Jb for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:26 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gMEh8-0004kn-OX for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:13 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:44005) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gMEh2-0004g8-4L for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:06 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1gMEh1-0000zk-W9 for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#33059] [PATCH v2 5/9] gnu: Add python-fenics-ufl. Resent-From: Paul Garlick Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Nov 2018 16:04:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33059 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: moreinfo patch To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , Ludovic =?utf-8?q?Court=C3=A8s?= Received: via spool by 33059-submit@debbugs.gnu.org id=B33059.15420386123697 (code B ref 33059); Mon, 12 Nov 2018 16:04:03 +0000 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 208.118.235.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: Paul Garlick Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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+))) From patchwork Mon Nov 12 16:00:38 2018 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Paul Garlick X-Patchwork-Id: 185 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id C489F167F8; Mon, 12 Nov 2018 16:04:30 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.9 required=5.0 tests=BAYES_00,RCVD_IN_DNSWL_HI, URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:4830:134:3::11]) by mira.cbaines.net (Postfix) with ESMTPS id 6D271167F6 for ; Mon, 12 Nov 2018 16:04:30 +0000 (GMT) Received: from localhost ([::1]:49370 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhR-0004UN-Oi for patchwork@mira.cbaines.net; Mon, 12 Nov 2018 11:04:29 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:36618) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhE-0004LH-K5 for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:19 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gMEh8-0004ke-NR for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:13 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:44006) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gMEh2-0004gT-MZ for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:06 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1gMEh2-0000zs-Ho for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#33059] [PATCH v2 6/9] gnu: Add python-fenics-fiat. Resent-From: Paul Garlick Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Nov 2018 16:04:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33059 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: moreinfo patch To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , Ludovic =?utf-8?q?Court=C3=A8s?= Received: via spool by 33059-submit@debbugs.gnu.org id=B33059.15420386213723 (code B ref 33059); Mon, 12 Nov 2018 16:04:04 +0000 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 208.118.235.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: Paul Garlick Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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+))) From patchwork Mon Nov 12 16:00:39 2018 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Paul Garlick X-Patchwork-Id: 184 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id BD6CF167F7; Mon, 12 Nov 2018 16:04:27 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.9 required=5.0 tests=BAYES_00,RCVD_IN_DNSWL_HI, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:4830:134:3::11]) by mira.cbaines.net (Postfix) with ESMTPS id 73C0D167F5 for ; Mon, 12 Nov 2018 16:04:27 +0000 (GMT) Received: from localhost ([::1]:49365 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhO-0004OF-PJ for patchwork@mira.cbaines.net; Mon, 12 Nov 2018 11:04:26 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:36612) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhE-0004LE-J4 for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:19 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gMEh8-0004ku-Pj for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:13 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:44007) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gMEh3-0004gb-6S for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:07 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1gMEh3-0000zz-24 for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#33059] [PATCH v2 7/9] gnu: Add python-fenics-ffc. Resent-From: Paul Garlick Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Nov 2018 16:04:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33059 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: moreinfo patch To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , Ludovic =?utf-8?q?Court=C3=A8s?= Received: via spool by 33059-submit@debbugs.gnu.org id=B33059.15420386283746 (code B ref 33059); Mon, 12 Nov 2018 16:04:05 +0000 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 208.118.235.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: Paul Garlick Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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+)))) From patchwork Mon Nov 12 16:00:40 2018 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Paul Garlick X-Patchwork-Id: 189 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id C8BF6167F7; Mon, 12 Nov 2018 16:04:49 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.9 required=5.0 tests=BAYES_00,RCVD_IN_DNSWL_HI, URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:4830:134:3::11]) by mira.cbaines.net (Postfix) with ESMTPS id 3F5D8167F5 for ; Mon, 12 Nov 2018 16:04:49 +0000 (GMT) Received: from localhost ([::1]:49374 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhk-0004cy-Co for patchwork@mira.cbaines.net; Mon, 12 Nov 2018 11:04:48 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:36608) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhE-0004LB-I7 for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:19 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gMEh8-0004l1-QT for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:15 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:44008) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gMEh3-0004gt-Mz for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:07 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1gMEh3-000107-If for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#33059] [PATCH v2 8/9] gnu: Add fenics-dolfin. Resent-From: Paul Garlick Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Nov 2018 16:04:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33059 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: moreinfo patch To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , Ludovic =?utf-8?q?Court=C3=A8s?= Received: via spool by 33059-submit@debbugs.gnu.org id=B33059.15420386343766 (code B ref 33059); Mon, 12 Nov 2018 16:04:05 +0000 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 208.118.235.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: Paul Garlick Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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+)))) From patchwork Mon Nov 12 16:00:41 2018 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Paul Garlick X-Patchwork-Id: 186 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 73C63167F7; Mon, 12 Nov 2018 16:04:32 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.9 required=5.0 tests=BAYES_00,RCVD_IN_DNSWL_HI, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:4830:134:3::11]) by mira.cbaines.net (Postfix) with ESMTPS id 158BA167F5 for ; Mon, 12 Nov 2018 16:04:32 +0000 (GMT) Received: from localhost ([::1]:49368 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhT-0004S6-ET for patchwork@mira.cbaines.net; Mon, 12 Nov 2018 11:04:31 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:36609) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gMEhE-0004LC-IH for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:19 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gMEh8-0004lM-Tl for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:15 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:44009) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gMEh4-0004hd-7s for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:07 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1gMEh4-00010E-1Q for guix-patches@gnu.org; Mon, 12 Nov 2018 11:04:06 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#33059] [PATCH v2 9/9] gnu: Add fenics. Resent-From: Paul Garlick Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Nov 2018 16:04:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33059 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: moreinfo patch To: 33059@debbugs.gnu.org, Efraim Flashner , Eric Bavier , Ludovic =?utf-8?q?Court=C3=A8s?= Received: via spool by 33059-submit@debbugs.gnu.org id=B33059.15420386383783 (code B ref 33059); Mon, 12 Nov 2018 16:04:05 +0000 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 208.118.235.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: Paul Garlick Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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+)))