diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 229 |
1 files changed, 171 insertions, 58 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index fcd9c5482f..98e239d5bd 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -49,6 +49,7 @@ ;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru> ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me> ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net> +;;; Copyright © 2021 Pierre-Antoine Bouttier <pierre-antoine.bouttier@univ-grenoble-alpes.fr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1852,6 +1853,65 @@ sharing of scientific data.") (home-page (package-home-page netcdf)) (license (package-license netcdf)))) +(define-public n2p2 + (package + (name "n2p2") + (version "2.1.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/CompPhysVienna/n2p2") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1lw195ihpxwh08387i4gamk1glhalpq888q6nj8l5vswbgnrv1pq")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags '("MODE=shared" "-C" "src") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'post-unpack + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/makefile.gnu" + (("PROJECT_EIGEN=/usr/include/eigen3") + (string-append "PROJECT_EIGEN=" + (assoc-ref inputs "eigen") "/include/eigen3"))) + (substitute* "src/makefile.gnu" + (("-lblas") + (string-append "-L" (assoc-ref inputs "openblas") + "/lib -lopenblas")) + (("-march=native") + "")) + (substitute* "src/application/makefile" + (("LDFLAGS=") + "LDFLAGS=-Wl,-rpath='$$ORIGIN/../lib' ")))) + (delete 'configure) + (delete 'check) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bindir (string-append out "/bin")) + (libdir (string-append out "/lib")) + (incdir (string-append out "/include"))) + (for-each (lambda (f) (install-file f bindir)) + (find-files "bin" "^nnp-")) + (for-each (lambda (f) (install-file f libdir)) + (find-files "lib" "\\.so$")) + (for-each (lambda (f) (install-file f incdir)) + (find-files "include" "\\.h$")))))))) + (inputs + (list openmpi gsl openblas eigen)) + (synopsis "Neural network potentials for chemistry and physics") + (description "This package contains software that will allow you to use +existing neural network potential parameterizations to predict energies and +forces (with standalone tools but also in conjunction with the MD software +LAMMPS). In addition it is possible to train new neural network potentials +with the provided training tools.") + (home-page "https://compphysvienna.github.io/n2p2/") + (properties '((tunable? . #t))) ;to benefit from SIMD code in Eigen + (license license:gpl3+))) + (define-public nlopt (package (name "nlopt") @@ -3174,7 +3234,16 @@ scientific applications modeled by partial differential equations.") (("libptesmumps") "libesmumps") (("libptscotchparmetis") "libptscotchparmetisv3")))) (add-before 'configure 'mpi-setup - #$%openmpi-setup))))) + #$%openmpi-setup) + (add-after 'install 'patch-header-inclusions + ;; TODO: Replace with ‘patch-header-inclusions’ when (some form + ;; of) https://issues.guix.gnu.org/54780#19 is merged. + (lambda _ + (substitute* (string-append #$output "/include/petsclayouthdf5.h") + (("<(H5Ipublic.h)>" _ header) + (format #f "<~a/include/~a>" + #$(this-package-input "hdf5-parallel-openmpi") + header))))))))) (synopsis "Library to solve PDEs (with MUMPS and MPI support)"))) (define-public petsc-complex-openmpi @@ -5170,34 +5239,30 @@ A unique design feature of Trilinos is its focus on packages.") (define-public dealii (package (name "dealii") - (version "9.3.2") + (version "9.3.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/dealii/dealii/releases/" "download/v" version "/dealii-" version ".tar.gz")) (sha256 - (base32 "1s0kawnljg24jj6nibwrif5gxdgg2daqfylhqqpl1lvmzmmxfhak")) - (patches (search-patches "dealii-fix-compiliation-with-boost-1.78.patch" - "dealii-fix-sundials.patch")) + (base32 "0a8s4yxcbvzmfgv5qcg27h2ss4fcnyhrhhs35glqj59l9cbmkysx")) (modules '((guix build utils))) (snippet - '(begin - ;; Remove bundled boost, muparser, TBB and UMFPACK. - (delete-file-recursively "bundled") - #t)))) + ;; Remove bundled boost, muparser, TBB and UMFPACK. + '(delete-file-recursively "bundled")))) (build-system cmake-build-system) (outputs '("out" "doc")) (native-inputs ;; Required to build the documentation. - (list graphviz doxygen perl)) + (list graphviz doxygen perl)) (inputs - (list arpack-ng - openblas - gfortran - lapack - muparser - zlib)) + (list arpack-ng + openblas + gfortran + lapack + muparser + zlib)) (propagated-inputs ;; Some scripts are installed into share/deal.II/scripts that require ;; perl and python, but they are not executable (and some are missing the @@ -5206,7 +5271,11 @@ A unique design feature of Trilinos is its focus on packages.") ;; Anyway, they are meant to be used at build time, so rather than adding ;; the interpreters here, any package depending on them should just add ;; the requisite interpreter to its native inputs. - (list boost hdf5 suitesparse ; For UMFPACK. + (list boost + hdf5 + suitesparse ; For UMFPACK. + ;; SUNDIALS 6.0.0 and later will be supported in deal.II 9.4.0. + sundials-5 tbb)) (arguments `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease. @@ -5234,8 +5303,7 @@ A unique design feature of Trilinos is its focus on packages.") (let ((doc (string-append (assoc-ref outputs "doc") "/share/doc/" ,name "-" ,version))) (for-each delete-file (map (lambda (f) (string-append doc "/" f)) - '("detailed.log" "summary.log")))) - #t))))) + '("detailed.log" "summary.log"))))))))) (home-page "https://www.dealii.org/") (synopsis "Finite element library") (description @@ -5250,18 +5318,21 @@ in finite element programs.") (package/inherit dealii (name "dealii-openmpi") (inputs - `(("arpack" ,arpack-ng-openmpi) - ("metis" ,metis) - ("scalapack" ,scalapack) - ,@(alist-delete "arpack" (package-inputs dealii)))) + (modify-inputs (package-inputs dealii) + (delete "arpack") + (prepend arpack-ng-openmpi + metis + scalapack))) (propagated-inputs - `(("hdf5" ,hdf5-parallel-openmpi) - ("mpi" ,openmpi) - ("p4est" ,p4est-openmpi) - ("petsc" ,petsc-openmpi) - ("slepc" ,slepc-openmpi) - ("trilinos" ,trilinos-for-dealii-openmpi) - ,@(alist-delete "hdf5" (package-propagated-inputs dealii)))) + (modify-inputs (package-propagated-inputs dealii) + (delete "hdf5" "sundials") + (prepend hdf5-parallel-openmpi + openmpi + p4est-openmpi + petsc-openmpi + slepc-openmpi + sundials-openmpi-5 + trilinos-for-dealii-openmpi))) (arguments (substitute-keyword-arguments (package-arguments dealii) ((#:configure-flags flags) @@ -6116,32 +6187,34 @@ and comparisons are supported.") (define-public sundials (package (name "sundials") - (version "6.1.1") + (version "6.2.0") (source (origin (method url-fetch) - (uri (string-append "https://github.com/LLNL/sundials/releases/download/v6.1.1/" - "sundials-" version ".tar.gz")) + (uri (string-append "https://github.com/LLNL/sundials/releases/download/v" + version "/sundials-" version ".tar.gz")) (sha256 (base32 - "0327a1fy8rilwc4brsqqb71jd1ymb7mqgxsylab06crcg5xn7byg")))) + "07gk9060xk3bzfqf8v4fqlp0rcxswiwlsy887zv87i1gfy9map8r")))) (build-system cmake-build-system) (native-inputs - (list python-2)) ;for tests; syntax incompatible with python 3 + (list python-2)) ; For tests; syntax incompatible with Python 3. (inputs - (list gfortran ;for fcmix - openblas petsc suitesparse)) ;TODO: Add hypre + (list openblas suitesparse)) (arguments - `(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon" + '(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon" + + "-DSUNDIALS_INDEX_SIZE=32" + ;; Incompatible with 32-bit indices. + ;;"-DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON" + "-DEXAMPLES_ENABLE_C:BOOL=ON" "-DEXAMPLES_ENABLE_CXX:BOOL=ON" - "-DEXAMPLES_ENABLE_F77:BOOL=ON" - "-DEXAMPLES_ENABLE_F90:BOOL=ON" + ;; Requires -DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON. + ;;"-DEXAMPLES_ENABLE_F2003:BOOL=ON" "-DEXAMPLES_INSTALL:BOOL=OFF" - "-DFCMIX_ENABLE:BOOL=ON" - - "-DKLU_ENABLE:BOOL=ON" + "-DENABLE_KLU:BOOL=ON" ,(string-append "-DKLU_INCLUDE_DIR=" (assoc-ref %build-inputs "suitesparse") "/include") @@ -6159,22 +6232,56 @@ easily be incorporated into existing simulation codes.") (license license:bsd-3))) (define-public sundials-openmpi - (package - (inherit sundials) + (package/inherit sundials (name "sundials-openmpi") - (inputs - (modify-inputs (package-inputs sundials) - (delete "petsc") - (prepend openmpi petsc-openmpi))) ;support in SUNDIALS requires MPI + (propagated-inputs + (list openmpi + ;; Support for the below requires MPI. + hypre-openmpi + petsc-openmpi)) (arguments (substitute-keyword-arguments (package-arguments sundials) ((#:configure-flags flags '()) - `(cons* "-DENABLE_MPI:BOOL=ON" ,flags)) + `(cons* "-DENABLE_MPI:BOOL=ON" + "-DENABLE_HYPRE:BOOL=ON" + (string-append "-DHYPRE_INCLUDE_DIR=" + (assoc-ref %build-inputs "hypre-openmpi") + "/include") + (string-append "-DHYPRE_LIBRARY_DIR=" + (assoc-ref %build-inputs "hypre-openmpi") + "/lib") + "-DENABLE_PETSC:BOOL=ON" + (string-append "-DPETSC_DIR=" + (assoc-ref %build-inputs "petsc-openmpi")) + ,flags)) ((#:phases phases '%standard-phases) `(modify-phases ,phases (add-before 'check 'mpi-setup - ,%openmpi-setup))))) - (synopsis "SUNDIALS with OpenMPI support"))) + ,%openmpi-setup))))) + (synopsis "SUNDIALS with MPI support"))) + +(define-public sundials-5 + (package + (inherit sundials) + (name "sundials") + (version "5.8.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/LLNL/sundials/releases/download/v" + version "/sundials-" version ".tar.gz")) + (sha256 + (base32 + "04x2x0jchf9kbcw2a1c6f4h4as8sr6k2snfz8z9k897pa4rl1vfl")))))) + +(define-public sundials-openmpi-5 + (package/inherit sundials-5 + (name "sundials-openmpi") + (propagated-inputs + (package-propagated-inputs sundials-openmpi)) + (arguments + (package-arguments sundials-openmpi)) + (synopsis (package-synopsis sundials-openmpi)))) (define-public sundials-julia (package @@ -6193,13 +6300,19 @@ easily be incorporated into existing simulation codes.") "0nx4sqhmi126m14myzm7syv2053harav9snl0a247wnkcgs5rxrv")))) (inputs (modify-inputs (package-inputs sundials) - (prepend lapack))) + (prepend gfortran lapack))) (arguments - (substitute-keyword-arguments (package-arguments sundials) - ((#:configure-flags flags '()) - `(cons* "-DLAPACK_ENABLE:BOOL=ON" - ,flags)))) - (synopsis "SUNDIALS with lapack support as required by julia-sundials-jll"))) + '(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon" + "-DSUNDIALS_INDEX_SIZE=32" + "-DKLU_ENABLE:BOOL=ON" + ,(string-append "-DKLU_INCLUDE_DIR=" + (assoc-ref %build-inputs "suitesparse") + "/include") + ,(string-append "-DKLU_LIBRARY_DIR=" + (assoc-ref %build-inputs "suitesparse") + "/lib") + "-DLAPACK_ENABLE:BOOL=ON"))) + (synopsis "SUNDIALS with LAPACK support as required by julia-sundials-jll"))) (define-public combinatorial-blas (package |