diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 170 |
1 files changed, 169 insertions, 1 deletions
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 <gerd.heber@gmail.com> ;;; Copyright © 2021 Franck Pérignon <franck.perignon@univ-grenoble-alpes.fr> ;;; Copyright © 2021 Philip McGrath <philip@philipmcgrath.com> -;;; Copyright © 2021, 2022 Paul A. Patience <paul@apatience.com> +;;; Copyright © 2021-2024 Paul A. Patience <paul@apatience.com> ;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru> ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me> ;;; Copyright © 2021, 2023 Guillaume Le Vaillant <glv@posteo.net> @@ -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") |