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References: In-Reply-To: Resent-From: "Paul A. Patience" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 02 Apr 2024 17:42:02 +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=B70056.17120796932232 (code B ref 70056); Tue, 02 Apr 2024 17:42:02 +0000 Received: (at 70056) by debbugs.gnu.org; 2 Apr 2024 17:41:33 +0000 Received: from localhost ([127.0.0.1]:56161 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rri8Z-0000Zt-UF for submit@debbugs.gnu.org; Tue, 02 Apr 2024 13:41:32 -0400 Received: from mail-4323.proton.ch ([185.70.43.23]:47343) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rri8S-0000Yg-SZ for 70056@debbugs.gnu.org; Tue, 02 Apr 2024 13:41:29 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=apatience.com; s=protonmail3; t=1712079671; x=1712338871; bh=07mlSf0aHmNEEPreA2PLRaw7t3UGGgF+Z1wOgTbp5Uc=; h=Date:To:From:Cc:Subject:Message-ID:Feedback-ID:From:To:Cc:Date: Subject:Reply-To:Feedback-ID:Message-ID:BIMI-Selector; b=vAaNehZQP9f3bG+D6XyEjzvkfkxy7VMRElNkqAePnr8B780Vh2K7pn79NJkMe1C/S qMrQHoNkKJ/gBagG9eWBq406EFv/5y9TglMkqjKLIbaVyjFnZEpbf3Spa/cFA+Hfov S8D7C1ojzx1bB18EFkV9DRkGlDISDESW7/LeGKE+VS9+swIGg+sPsVVqi765SUIO/h OKUJdVkjOxTtF4+DlfWPIEtR4IFt05FqGov39BNLn9BpPUKDbxpO+L4MM+mHo1vSik tx3VCuHExZaX5e7rEi6EFzE7tohEzQnDkgoCxXsp0KE8baw7K8ndJhAYI1kvTbYryH n79rNNYU56fVw== Date: Tue, 02 Apr 2024 17:41:04 +0000 From: "Paul A. Patience" Message-ID: Feedback-ID: 19227857:user:proton MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable 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+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN X-Spam-Score: -1.35 X-Migadu-Queue-Id: E1B6112B72 X-Migadu-Scanner: mx13.migadu.com X-Migadu-Spam-Score: -1.35 X-TUID: we2WxRzNRxTw * 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 --- Hi, After updating guix-daemon as Ludo suggested, cloning the Git repository works. The only minor thing that can be improved, in my opinion, is possibly enabl= ing MFEM_USE_SIMD only if the package is tuned (see the TODO in the patch), but I've been using MFEM for a few days with MFEM_USE_SIMD enabled and without tuning, so it should work regardless. And I don't know how practical that is to accomplish; I didn't see any othe= r cases of conditional configure flags based on the package being tuned. I updated the copyright header to include 2023 too, since I made some chang= es then. Best regards, Paul gnu/local.mk | 2 + gnu/packages/maths.scm | 170 +++++++++++++++++- .../patches/mfem-fix-mk-file-export.patch | 29 +++ .../patches/mfem-remove-source-dir-refs.patch | 101 +++++++++++ 4 files changed, 301 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/mfem-fix-mk-file-export.patch create mode 100644 gnu/packages/patches/mfem-remove-source-dir-refs.patch 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 =3D=09=09=09=09=09=09\ %D%/packages/patches/memtest86+-build-reproducibly.patch=09\ %D%/packages/patches/mercurial-hg-extension-path.patch=09\ %D%/packages/patches/mercurial-openssl-compat.patch=09=09\ + %D%/packages/patches/mfem-fix-mk-file-export.patch=09=09\ + %D%/packages/patches/mfem-remove-source-dir-refs.patch=09\ %D%/packages/patches/mhash-keygen-test-segfault.patch=09=09\ %D%/packages/patches/mia-fix-boost-headers.patch=09=09\ %D%/packages/patches/mia-vtk9.patch=09=09=09=09\ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 1b4d325649..1838b289e2 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -45,7 +45,7 @@ ;;; Copyright =C2=A9 2021 Gerd Heber ;;; Copyright =C2=A9 2021 Franck P=C3=A9rignon ;;; Copyright =C2=A9 2021 Philip McGrath -;;; Copyright =C2=A9 2021, 2022 Paul A. Patience +;;; Copyright =C2=A9 2021-2024 Paul A. Patience ;;; Copyright =C2=A9 2021 Ivan Gankevich ;;; Copyright =C2=A9 2021 Jean-Baptiste Volatier ;;; Copyright =C2=A9 2021, 2023 Guillaume Le Vaillant @@ -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 +6891,173 @@ (define-public dealii-openmpi (delete 'unset-cpath))))) (synopsis "Finite element library (with MPI support)"))) =20 +(define-public mfem + (package + (name "mfem") + (version "4.6") + (source + (origin + (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 "0vr3s110bc42r81s1hi9brwwaz01d60l6mbdlsrfxxinpnzxq7ax")) + (patches (search-patches "mfem-remove-source-dir-refs.patch" + "mfem-fix-mk-file-export.patch")))) + (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 exhaust= ive + ;; list than config/defaults.cmake. + #~(list "-DBUILD_SHARED_LIBS=3DON" + "-DMFEM_USE_MPI=3DOFF" + "-DMFEM_USE_METIS=3DOFF" ; MPI only + "-DMFEM_USE_METIS_5=3DOFF" + "-DMFEM_PRECISION=3Ddouble" ; For versions beyond 4.6 + "-DMFEM_DEBUG=3DOFF" + "-DMFEM_USE_EXCEPTIONS=3DON" + "-DMFEM_USE_ZLIB=3DON" + "-DMFEM_USE_LIBUNWIND=3DON" + "-DMFEM_USE_LAPACK=3DON" + "-DMFEM_THREAD_SAFE=3DOFF" + "-DMFEM_USE_OPENMP=3DON" + "-DMFEM_USE_LEGACY_OPENMP=3DOFF" + "-DMFEM_USE_MEMALLOC=3DON" + "-DMFEM_TIMER_TYPE=3D2" + "-DMFEM_USE_SUNDIALS=3DON" + "-DMFEM_USE_SUITESPARSE=3DON" + "-DMFEM_USE_SUPERLU=3DOFF" ; MPI only + "-DMFEM_USE_SUPERLU5=3DOFF" + "-DMFEM_USE_MUMPS=3DOFF" ; MPI only + "-DMFEM_USE_STRUMPACK=3DOFF" ; Missing dep, MPI only + "-DMFEM_USE_GINKGO=3DOFF" ; Missing dep + "-DMFEM_USE_AMGX=3DOFF" ; CUDA library + "-DMFEM_USE_GNUTLS=3DON" + "-DMFEM_USE_NETCDF=3DON" + "-DMFEM_USE_PETSC=3DOFF" ; MPI only + "-DMFEM_USE_SLEPC=3DOFF" ; MPI only + "-DMFEM_USE_MPFR=3DON" + "-DMFEM_USE_SIDRE=3DOFF" ; Missing dep + "-DMFEM_USE_FMS=3DOFF" ; Missing dep + "-DMFEM_USE_CONDUIT=3DOFF" ; Missing dep + "-DMFEM_USE_PUMI=3DOFF" ; Missing dep, MPI only + "-DMFEM_USE_HIOP=3DOFF" ; Missing dep + "-DMFEM_USE_GSLIB=3DOFF" ; Missing dep + "-DMFEM_USE_CUDA=3DOFF" + "-DMFEM_USE_HIP=3DOFF" ; GPU library + "-DMFEM_USE_RAJA=3DOFF" ; Missing dep + "-DMFEM_USE_OCCA=3DOFF" ; Missing dep + "-DMFEM_USE_CEED=3DOFF" ; Missing dep + "-DMFEM_USE_CALIPER=3DOFF" ; Missing dep + "-DMFEM_USE_ALGOIM=3DOFF" ; Missing dep + "-DMFEM_USE_UMPIRE=3DOFF" ; Missing dep + "-DMFEM_USE_SIMD=3DON" + "-DMFEM_USE_ADIOS2=3DOFF" ; Missing dep + "-DMFEM_USE_MKL_CPARDISO=3DOFF" ; Intel MKL + "-DMFEM_USE_MKL_PARDISO=3DOFF" + "-DMFEM_USE_MOONOLITH=3DOFF" ; Missing dep + "-DMFEM_USE_ADFORWARD=3DOFF" + "-DMFEM_USE_CODIPACK=3DOFF" ; Missing dep + "-DMFEM_USE_BENCHMARK=3DOFF" ; Only for benchmarks + "-DMFEM_USE_PARELAG=3DOFF" ; Missing dep, only for mi= niapps + "-DMFEM_USE_ENZYME=3DOFF" ; Missing dep, requires Cl= ang + "-DMFEM_ENABLE_TESTING=3DON" + "-DMFEM_ENABLE_EXAMPLES=3DON" + "-DMFEM_ENABLE_MINIAPPS=3DON" ; Used in some tests + "-DMFEM_ENABLE_GOOGLE_BENCHMARKS=3DOFF" + (string-append "-DHDF5_DIR=3D" #$(this-package-input "h= df5"))) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'clean-mpi-references + (lambda _ + (substitute* "config/config.mk.in" + (("(MFEM_MPIEXEC +=3D ).*" _ prefix) + ;; Set to non-empty value, to avoid running unexpect= ed + ;; commands. + (string-append prefix (which "false") "\n")) + (("(MFEM_MPIEXEC_NP +=3D).*" _ prefix) + (string-append prefix "\n")) + (("(MFEM_MPI_NP +=3D).*" _ prefix) + (string-append prefix "\n"))))) + (add-after 'unpack 'clean-local-references + (lambda _ + (substitute* "config/config.mk.in" + (("(MFEM_BUILD_TAG +=3D ).*" _ prefix) + (string-append prefix "(none)\n"))))) + (add-before 'check 'build-tests + (lambda _ + (invoke "cmake" "--build" "." "--target" "tests"))) + (add-after 'check 'build-doc + (lambda _ + (setenv "HOME" "/tmp") ; Writable cache for fontconfig + (invoke "cmake" "--build" "." "--target" "doc"))) + (add-after 'install 'remove-examples + (lambda _ + (delete-file-recursively + (string-append #$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.c= make") + ((";mpfr;") + (string-append ";" mpfr "/lib/libmpfr.so;")) + ((";unwind;") + (string-append ";" libunwind "/lib/libunwind.so;")= )) + (substitute* (string-append #$output "/share/mfem/con= fig.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 an= d + ;; 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)) + ;; TODO: Enable MFEM_USE_SIMD only if tuned? + (properties '((tunable? . #t))) + (home-page "https://mfem.org/") + (synopsis "Finite element library") + (description "MFEM is a modular parallel C++ library for finite elemen= t +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/packa= ges/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_US= E_CUDA + MFEM_USE_HIP MFEM_USE_RAJA MFEM_USE_OCCA MFEM_USE_CEED MFEM_USE_CAL= IPER + MFEM_USE_UMPIRE MFEM_USE_SIMD MFEM_USE_ADIOS2 MFEM_USE_MKL_CPARDISO +- MFEM_USE_ADFORWARD MFEM_USE_CODIPACK MFEM_USE_BENCHMARK MFEM_USE_PA= RELAG +- 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_ALG= OIM ++ MFEM_USE_ENZYME) + foreach(var ${CONFIG_MK_BOOL_VARS}) + if (${var}) + set(${var} YES) +--=20 +2.41.0 + diff --git a/gnu/packages/patches/mfem-remove-source-dir-refs.patch b/gnu/p= ackages/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) +=20 +-// MFEM source directory. +-#define MFEM_SOURCE_DIR "@MFEM_SOURCE_DIR@" +- + // MFEM install directory. + #define MFEM_INSTALL_DIR "@MFEM_INSTALL_DIR@" +=20 +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) +=20 +-// 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@" +=20 +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 =3D @MFEM_VERSION@ + MFEM_VERSION_STRING =3D @MFEM_VERSION_STRING@ +-MFEM_SOURCE_DIR =3D @MFEM_SOURCE_DIR@ + MFEM_INSTALL_DIR =3D @MFEM_INSTALL_DIR@ + MFEM_GIT_STRING =3D @MFEM_GIT_STRING@ + MFEM_USE_MPI =3D @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 =3D MFEM_INSTALL_DIR "/include/mfem/fem/cee= d"; +- const char *source_dir =3D MFEM_SOURCE_DIR "/fem/ceed"; + struct_stat m_stat; + if (stat(install_dir, &m_stat) =3D=3D 0 && S_ISDIR(m_stat.st_mode)) + { + ceed_path =3D install_dir; + } +- else if (stat(source_dir, &m_stat) =3D=3D 0 && S_ISDIR(m_stat.st_mo= de)) +- { +- ceed_path =3D 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 =3D MFEM_INSTALL_DIR "/include/mfem/"; + } +- else if (occa::io::exists(MFEM_SOURCE_DIR)) +- { +- mfemDir =3D MFEM_SOURCE_DIR; +- } + else + { +- MFEM_ABORT("Cannot find OCCA kernels in MFEM_INSTALL_DIR or MFEM_SO= URCE_DIR"); ++ MFEM_ABORT("Cannot find OCCA kernels in MFEM_INSTALL_DIR"); + } +=20 + occa::io::addLibraryPath("mfem", mfemDir); +--=20 +2.41.0 + base-commit: fb9549164520ad993c2fbbaedc899844d57baabc --=20 2.41.0