From patchwork Fri Mar 29 04:40:43 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: "Paul A. Patience" X-Patchwork-Id: 62347 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 8086A27BBE2; Fri, 29 Mar 2024 04:42:19 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id BF20227BBE9 for ; Fri, 29 Mar 2024 04:42:16 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rq444-0007Gu-Bi; Fri, 29 Mar 2024 00:42:04 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1rq441-0007AS-O2 for guix-patches@gnu.org; Fri, 29 Mar 2024 00:42:01 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rq441-0008V1-Fx for guix-patches@gnu.org; Fri, 29 Mar 2024 00:42:01 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rq442-0003CW-4L for guix-patches@gnu.org; Fri, 29 Mar 2024 00:42:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#70056] [RFC PATCH v2] gnu: Add mfem. References: In-Reply-To: Resent-From: "Paul A. Patience" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 29 Mar 2024 04:42:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 70056 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 70056@debbugs.gnu.org Cc: "Paul A. Patience" Received: via spool by 70056-submit@debbugs.gnu.org id=B70056.171168726512190 (code B ref 70056); Fri, 29 Mar 2024 04:42:02 +0000 Received: (at 70056) by debbugs.gnu.org; 29 Mar 2024 04:41:05 +0000 Received: from localhost ([127.0.0.1]:41424 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rq435-0003AX-Vd for submit@debbugs.gnu.org; Fri, 29 Mar 2024 00:41:04 -0400 Received: from mail-4323.proton.ch ([185.70.43.23]:31397) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rq431-00039j-2z for 70056@debbugs.gnu.org; Fri, 29 Mar 2024 00:41:02 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=apatience.com; s=protonmail3; t=1711687249; x=1711946449; bh=Fgaf4CMsxAFyPTQYY+knjXLoXfb3kw5NOuhpxVJrD4w=; h=Date:To:From:Cc:Subject:Message-ID:Feedback-ID:From:To:Cc:Date: Subject:Reply-To:Feedback-ID:Message-ID:BIMI-Selector; b=d1KITf553pFblywUxDCMoPrQT6U35kBS2ECHWXbDMss8WKusMaj0pFuMJ1BlsTbSF W/Rfx1qAras6h3OHFlmljcaOoj/jSDIGb7w3YU0FKDHMI9yJP0Ol1XdmeFG4TDEb/6 yDp1BPDJcnYutAmVu0mnPS4ju/cOgWNsfJQhbKWUisHzyBt7LfxfPN2lhq35dP9N2Z Vi7C4OCSTfCGK8MRU0hiGUqJLnIToFC3zmYIgj2vxA7NCInfUnZuY7DSmlKvpLQXg4 SodmWMDIKnjino3z7wy0JyQ0XAJuRvD0beTHf57a1qQ8eOgPWtCx/C52ciP0+AyHf/ pEnJAxYcUQv0w== Date: Fri, 29 Mar 2024 04:40:43 +0000 From: "Paul A. Patience" Message-ID: <5a802d6de248452445b9a7671b2e28eef8259471.1711686959.git.paul@apatience.com> Feedback-ID: 19227857:user:proton MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/maths.scm (mfem): New variable. * gnu/packages/patches/mfem-fix-mk-file-export.patch: New file. * gnu/packages/patches/mfem-remove-source-dir-refs.patch: Same. * gnu/local.mk (dist_patch_DATA): Register them. Change-Id: Ida81f2b081a016e91426b68437909653020976f5 --- The package is basically ready now, except for the suspicious ownership mentioned in the previous patch. I've tested it on a local copy of MFEM. (The OpenMPI version is trickier to compile.) gnu/local.mk | 2 + gnu/packages/maths.scm | 171 ++++++++++++++++++ .../patches/mfem-fix-mk-file-export.patch | 29 +++ .../patches/mfem-remove-source-dir-refs.patch | 101 +++++++++++ 4 files changed, 303 insertions(+) create mode 100644 gnu/packages/patches/mfem-fix-mk-file-export.patch create mode 100644 gnu/packages/patches/mfem-remove-source-dir-refs.patch base-commit: fb9549164520ad993c2fbbaedc899844d57baabc diff --git a/gnu/local.mk b/gnu/local.mk index 5429dc498c..dcedef5f99 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1682,6 +1682,8 @@ dist_patch_DATA = \ %D%/packages/patches/memtest86+-build-reproducibly.patch \ %D%/packages/patches/mercurial-hg-extension-path.patch \ %D%/packages/patches/mercurial-openssl-compat.patch \ + %D%/packages/patches/mfem-fix-mk-file-export.patch \ + %D%/packages/patches/mfem-remove-source-dir-refs.patch \ %D%/packages/patches/mhash-keygen-test-segfault.patch \ %D%/packages/patches/mia-fix-boost-headers.patch \ %D%/packages/patches/mia-vtk9.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 1b4d325649..2191b5e2da 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -151,6 +151,7 @@ (define-module (gnu packages maths) #:use-module (gnu packages xorg) #:use-module (gnu packages gl) #:use-module (gnu packages imagemagick) + #:use-module (gnu packages libunwind) #:use-module (gnu packages m4) #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) @@ -6890,6 +6891,176 @@ (define-public dealii-openmpi (delete 'unset-cpath))))) (synopsis "Finite element library (with MPI support)"))) +(define-public mfem + (package + (name "mfem") + (version "4.6") + ;; (source + ;; (origin + ;; ;; (method url-fetch) + ;; ;; (uri (string-append "https://github.com/mfem/mfem/archive/refs/tags/v" + ;; ;; version ".tar.gz")) + ;; ;; (file-name (string-append name "-" version ".tar.gz")) + ;; (method git-fetch) + ;; (uri (git-reference + ;; (url "https://github.com/mfem/mfem") + ;; (commit (string-append "v" version)))) + ;; (file-name (git-file-name name version)) + ;; (sha256 + ;; (base32 "0m57j5kd7glc8lfp5bdmmx4az4fs6lkqjwd970w4fx8gylxff3n9")) + ;; (patches (search-patches "mfem-remove-source-dir-refs.patch" + ;; "mfem-fix-mk-file-export.patch")))) + (source (local-file "/tmp/mfem" #:recursive? #t)) + (outputs '("out" "doc")) ; 338 MiB of documentation + (build-system cmake-build-system) + (arguments + (list #:configure-flags + ;; Follow order of config/defaults.mk, which has a more exhaustive + ;; list than config/defaults.cmake. + #~(list "-DBUILD_SHARED_LIBS=ON" + "-DMFEM_USE_MPI=OFF" + "-DMFEM_USE_METIS=OFF" ; MPI only + "-DMFEM_USE_METIS_5=OFF" + "-DMFEM_PRECISION=double" ; For versions beyond 4.6 + "-DMFEM_DEBUG=OFF" + "-DMFEM_USE_EXCEPTIONS=ON" + "-DMFEM_USE_ZLIB=ON" + "-DMFEM_USE_LIBUNWIND=ON" + "-DMFEM_USE_LAPACK=ON" + "-DMFEM_THREAD_SAFE=OFF" + "-DMFEM_USE_OPENMP=ON" + "-DMFEM_USE_LEGACY_OPENMP=OFF" + "-DMFEM_USE_MEMALLOC=ON" + "-DMFEM_TIMER_TYPE=2" + "-DMFEM_USE_SUNDIALS=ON" + "-DMFEM_USE_SUITESPARSE=ON" + "-DMFEM_USE_SUPERLU=OFF" ; MPI only + "-DMFEM_USE_SUPERLU5=OFF" + "-DMFEM_USE_MUMPS=OFF" ; MPI only + "-DMFEM_USE_STRUMPACK=OFF" ; Missing dep, MPI only + "-DMFEM_USE_GINKGO=OFF" ; Missing dep + "-DMFEM_USE_AMGX=OFF" ; CUDA library + "-DMFEM_USE_GNUTLS=ON" + "-DMFEM_USE_NETCDF=ON" + "-DMFEM_USE_PETSC=OFF" ; MPI only + "-DMFEM_USE_SLEPC=OFF" ; MPI only + "-DMFEM_USE_MPFR=ON" + "-DMFEM_USE_SIDRE=OFF" ; Missing dep + "-DMFEM_USE_FMS=OFF" ; Missing dep + "-DMFEM_USE_CONDUIT=OFF" ; Missing dep + "-DMFEM_USE_PUMI=OFF" ; Missing dep, MPI only + "-DMFEM_USE_HIOP=OFF" ; Missing dep + "-DMFEM_USE_GSLIB=OFF" ; Missing dep + "-DMFEM_USE_CUDA=OFF" + "-DMFEM_USE_HIP=OFF" ; GPU library + "-DMFEM_USE_RAJA=OFF" ; Missing dep + "-DMFEM_USE_OCCA=OFF" ; Missing dep + "-DMFEM_USE_CEED=OFF" ; Missing dep + "-DMFEM_USE_CALIPER=OFF" ; Missing dep + "-DMFEM_USE_ALGOIM=OFF" ; Missing dep + "-DMFEM_USE_UMPIRE=OFF" ; Missing dep + "-DMFEM_USE_SIMD=ON" + "-DMFEM_USE_ADIOS2=OFF" ; Missing dep + "-DMFEM_USE_MKL_CPARDISO=OFF" ; Intel MKL + "-DMFEM_USE_MKL_PARDISO=OFF" + "-DMFEM_USE_MOONOLITH=OFF" ; Missing dep + "-DMFEM_USE_ADFORWARD=OFF" + "-DMFEM_USE_CODIPACK=OFF" ; Missing dep + "-DMFEM_USE_BENCHMARK=OFF" ; Only for benchmarks + "-DMFEM_USE_PARELAG=OFF" ; Missing dep, only for miniapps + "-DMFEM_USE_ENZYME=OFF" ; Missing dep, requires Clang + "-DMFEM_ENABLE_TESTING=ON" + "-DMFEM_ENABLE_EXAMPLES=ON" + "-DMFEM_ENABLE_MINIAPPS=ON" ; Used in some tests + "-DMFEM_ENABLE_GOOGLE_BENCHMARKS=OFF" + (string-append "-DHDF5_DIR=" #$(this-package-input "hdf5"))) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'clean-mpi-references + (lambda _ + (substitute* (string-append "config/config.mk.in") + (("(MFEM_MPIEXEC += ).*" _ prefix) + ;; Set and non-empty, to avoid running unexpected + ;; commands. + (string-append prefix (which "false") "\n")) + (("(MFEM_MPIEXEC_NP +=).*" _ prefix) + (string-append prefix "\n")) + (("(MFEM_MPI_NP +=).*" _ prefix) + (string-append prefix "\n"))))) + (add-after 'unpack 'clean-local-references + (lambda _ + (substitute* (string-append "config/config.mk.in") + (("(MFEM_BUILD_TAG += ).*" _ prefix) + (string-append prefix "(none)\n"))))) + (add-before 'check 'build-tests + (lambda _ + (invoke "cmake" "--build" "." "--target" "tests"))) + (add-after 'check 'build-doc + (lambda _ + (setenv "HOME" "/tmp") ; Writable cache for fontconfig + (invoke "cmake" "--build" "." "--target" "doc"))) + (add-after 'install 'remove-examples + (lambda _ + (delete-file-recursively + (string-append #$output "/examples")))) + (add-after 'install 'install-doc + (lambda _ + (let ((docdir (string-append #$output:doc "/share/doc/" + #$name "-" #$version))) + (install-file "doc/CodeDocumentation.html" docdir) + (copy-recursively + "doc/CodeDocumentation" + (string-append docdir "/CodeDocumentation"))))) + (add-after 'install 'fix-library-paths + (let ((mpfr #$(this-package-input "mpfr")) + (libunwind #$(this-package-input "libunwind"))) + (lambda _ + (substitute* (string-append + #$output "/lib/cmake/mfem/MFEMTargets.cmake") + ((";mpfr;") + (string-append ";" mpfr "/lib/libmpfr.so;")) + ((";unwind;") + (string-append ";" libunwind "/lib/libunwind.so;"))) + (substitute* (string-append #$output "/share/mfem/config.mk") + ((" mpfr ") + (string-append " -Wl,-rpath," mpfr "/lib" + " -L" mpfr "/lib" + " -lmpfr ")) + ((" unwind ") + (string-append " -Wl,-rpath," libunwind "/lib" + " -L" libunwind "/lib" + " -lunwind "))))))))) + (native-inputs + (list doxygen graphviz perl)) ; For documentation + ;; No propagated inputs necessary because the installed CMake files and + ;; share/mfem/config.mk provide the full list of include directories. + (inputs + (list gnutls + hdf5 ; For NetCDF + lapack + libunwind + metis-suitesparse ; For SuiteSparse + mpfr + netcdf + suitesparse-amd + suitesparse-btf + suitesparse-camd + suitesparse-ccolamd + suitesparse-cholmod + suitesparse-colamd + suitesparse-config + suitesparse-klu + suitesparse-umfpack + sundials + zlib)) + (home-page "https://mfem.org/") + (synopsis "Finite element library") + (description "MFEM is a modular parallel C++ library for finite element +methods. Its goal is to enable high-performance scalable finite element +discretization research and application development on a wide variety of +platforms, ranging from laptops to supercomputers.") + (license license:bsd-3))) + (define-public flann (package (name "flann") diff --git a/gnu/packages/patches/mfem-fix-mk-file-export.patch b/gnu/packages/patches/mfem-fix-mk-file-export.patch new file mode 100644 index 0000000000..fbd35a029a --- /dev/null +++ b/gnu/packages/patches/mfem-fix-mk-file-export.patch @@ -0,0 +1,29 @@ +From ccba86c0259c2ae56ad44a53d5d5a2a40822cbe3 Mon Sep 17 00:00:00 2001 +From: "Paul A. Patience" +Date: Thu, 28 Mar 2024 13:28:49 -0400 +Subject: [PATCH 2/2] Add forgotten variable to mfem_export_mk_files + +MFEM_USE_MKL_PARDISO was missing. +--- + config/cmake/modules/MfemCmakeUtilities.cmake | 5 +++-- + 1 file changed, 3 insertions(+), 2 deletions(-) + +diff --git a/config/cmake/modules/MfemCmakeUtilities.cmake b/config/cmake/modules/MfemCmakeUtilities.cmake +index 204b7d87f..217f4eec7 100644 +--- a/config/cmake/modules/MfemCmakeUtilities.cmake ++++ b/config/cmake/modules/MfemCmakeUtilities.cmake +@@ -851,8 +851,9 @@ function(mfem_export_mk_files) + MFEM_USE_CONDUIT MFEM_USE_PUMI MFEM_USE_HIOP MFEM_USE_GSLIB MFEM_USE_CUDA + MFEM_USE_HIP MFEM_USE_RAJA MFEM_USE_OCCA MFEM_USE_CEED MFEM_USE_CALIPER + MFEM_USE_UMPIRE MFEM_USE_SIMD MFEM_USE_ADIOS2 MFEM_USE_MKL_CPARDISO +- MFEM_USE_ADFORWARD MFEM_USE_CODIPACK MFEM_USE_BENCHMARK MFEM_USE_PARELAG +- MFEM_USE_MOONOLITH MFEM_USE_ALGOIM MFEM_USE_ENZYME) ++ MFEM_USE_MKL_PARDISO MFEM_USE_ADFORWARD MFEM_USE_CODIPACK ++ MFEM_USE_BENCHMARK MFEM_USE_PARELAG MFEM_USE_MOONOLITH MFEM_USE_ALGOIM ++ MFEM_USE_ENZYME) + foreach(var ${CONFIG_MK_BOOL_VARS}) + if (${var}) + set(${var} YES) +-- +2.41.0 + diff --git a/gnu/packages/patches/mfem-remove-source-dir-refs.patch b/gnu/packages/patches/mfem-remove-source-dir-refs.patch new file mode 100644 index 0000000000..f9898748c7 --- /dev/null +++ b/gnu/packages/patches/mfem-remove-source-dir-refs.patch @@ -0,0 +1,101 @@ +From 0ad647e045e9cbe456ad0f5f3bdb6e015566e067 Mon Sep 17 00:00:00 2001 +From: "Paul A. Patience" +Date: Thu, 28 Mar 2024 13:22:48 -0400 +Subject: [PATCH 1/2] Remove references to MFEM_SOURCE_DIR + +--- + config/cmake/config.hpp.in | 3 --- + config/config.hpp.in | 3 --- + config/config.mk.in | 1 - + fem/ceed/interface/util.cpp | 8 +------- + general/device.cpp | 6 +----- + 5 files changed, 2 insertions(+), 19 deletions(-) + +diff --git a/config/cmake/config.hpp.in b/config/cmake/config.hpp.in +index 7cb2a958d..13f13c48d 100644 +--- a/config/cmake/config.hpp.in ++++ b/config/cmake/config.hpp.in +@@ -30,9 +30,6 @@ + #define MFEM_VERSION_MINOR (((MFEM_VERSION)/100)%100) + #define MFEM_VERSION_PATCH ((MFEM_VERSION)%100) + +-// MFEM source directory. +-#define MFEM_SOURCE_DIR "@MFEM_SOURCE_DIR@" +- + // MFEM install directory. + #define MFEM_INSTALL_DIR "@MFEM_INSTALL_DIR@" + +diff --git a/config/config.hpp.in b/config/config.hpp.in +index 39d7737c7..dbee1f32f 100644 +--- a/config/config.hpp.in ++++ b/config/config.hpp.in +@@ -30,9 +30,6 @@ + #define MFEM_VERSION_MINOR (((MFEM_VERSION)/100)%100) + #define MFEM_VERSION_PATCH ((MFEM_VERSION)%100) + +-// The absolute path of the MFEM source prefix. +-// #define MFEM_SOURCE_DIR "@MFEM_SOURCE_DIR@" +- + // The absolute path of the MFEM installation prefix. + // #define MFEM_INSTALL_DIR "@MFEM_INSTALL_DIR@" + +diff --git a/config/config.mk.in b/config/config.mk.in +index 303750bf5..d2f538666 100644 +--- a/config/config.mk.in ++++ b/config/config.mk.in +@@ -12,7 +12,6 @@ + # Variables corresponding to defines in config.hpp (YES, NO, or value) + MFEM_VERSION = @MFEM_VERSION@ + MFEM_VERSION_STRING = @MFEM_VERSION_STRING@ +-MFEM_SOURCE_DIR = @MFEM_SOURCE_DIR@ + MFEM_INSTALL_DIR = @MFEM_INSTALL_DIR@ + MFEM_GIT_STRING = @MFEM_GIT_STRING@ + MFEM_USE_MPI = @MFEM_USE_MPI@ +diff --git a/fem/ceed/interface/util.cpp b/fem/ceed/interface/util.cpp +index d122c2ab5..f2bc900a5 100644 +--- a/fem/ceed/interface/util.cpp ++++ b/fem/ceed/interface/util.cpp +@@ -257,20 +257,14 @@ const std::string &GetCeedPath() + if (ceed_path.empty()) + { + const char *install_dir = MFEM_INSTALL_DIR "/include/mfem/fem/ceed"; +- const char *source_dir = MFEM_SOURCE_DIR "/fem/ceed"; + struct_stat m_stat; + if (stat(install_dir, &m_stat) == 0 && S_ISDIR(m_stat.st_mode)) + { + ceed_path = install_dir; + } +- else if (stat(source_dir, &m_stat) == 0 && S_ISDIR(m_stat.st_mode)) +- { +- ceed_path = source_dir; +- } + else + { +- MFEM_ABORT("Cannot find libCEED kernels in MFEM_INSTALL_DIR or " +- "MFEM_SOURCE_DIR"); ++ MFEM_ABORT("Cannot find libCEED kernels in MFEM_INSTALL_DIR"); + } + // Could be useful for debugging: + // out << "Using libCEED dir: " << ceed_path << std::endl; +diff --git a/general/device.cpp b/general/device.cpp +index ccee71cd7..a68ba7191 100644 +--- a/general/device.cpp ++++ b/general/device.cpp +@@ -464,13 +464,9 @@ static void OccaDeviceSetup(const int dev) + { + mfemDir = MFEM_INSTALL_DIR "/include/mfem/"; + } +- else if (occa::io::exists(MFEM_SOURCE_DIR)) +- { +- mfemDir = MFEM_SOURCE_DIR; +- } + else + { +- MFEM_ABORT("Cannot find OCCA kernels in MFEM_INSTALL_DIR or MFEM_SOURCE_DIR"); ++ MFEM_ABORT("Cannot find OCCA kernels in MFEM_INSTALL_DIR"); + } + + occa::io::addLibraryPath("mfem", mfemDir); +-- +2.41.0 +