From dfc8b3ff2ddcd48ea983c423f9979563f2d81994 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Tue, 2 Apr 2024 17:41:04 +0000 Subject: gnu: Add mfem. * 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 --- gnu/local.mk | 2 + gnu/packages/maths.scm | 170 ++++++++++++++++++++- gnu/packages/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 ccff8648be..d8fd0166b4 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1700,6 +1700,8 @@ 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 cc42ce7902..e64fc40929 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -45,7 +45,7 @@ ;;; Copyright © 2021 Gerd Heber ;;; Copyright © 2021 Franck Pérignon ;;; Copyright © 2021 Philip McGrath -;;; Copyright © 2021, 2022 Paul A. Patience +;;; Copyright © 2021-2024 Paul A. Patience ;;; Copyright © 2021 Ivan Gankevich ;;; Copyright © 2021 Jean-Baptiste Volatier ;;; Copyright © 2021, 2023 Guillaume Le Vaillant @@ -152,6 +152,7 @@ #: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) @@ -6896,6 +6897,173 @@ in finite element programs.") (delete 'unset-cpath))))) (synopsis "Finite element library (with MPI support)"))) +(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 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=" #$(this-package-input "hdf5"))) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'clean-mpi-references + (lambda _ + (substitute* "config/config.mk.in" + (("(MFEM_MPIEXEC += ).*" _ prefix) + ;; Set to non-empty value, to avoid running unexpected + ;; commands. + (string-append prefix (which "false") "\n")) + (("(MFEM_MPIEXEC_NP +=).*" _ prefix) + (string-append prefix "\n")) + (("(MFEM_MPI_NP +=).*" _ prefix) + (string-append prefix "\n"))))) + (add-after 'unpack 'clean-local-references + (lambda _ + (substitute* "config/config.mk.in" + (("(MFEM_BUILD_TAG += ).*" _ prefix) + (string-append prefix "(none)\n"))))) + (add-before 'check 'build-tests + (lambda _ + (invoke "cmake" "--build" "." "--target" "tests"))) + (add-after 'check 'build-doc + (lambda _ + (setenv "HOME" "/tmp") ; Writable cache for fontconfig + (invoke "cmake" "--build" "." "--target" "doc"))) + (add-after 'install 'remove-examples + (lambda _ + (delete-file-recursively + (string-append #$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)) + ;; 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 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 + -- cgit v1.2.3