diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 284 |
1 files changed, 284 insertions, 0 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index a594278341..a7931e6eeb 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -124,6 +124,7 @@ #:use-module (gnu packages m4) #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) + #:use-module (gnu packages ncurses) #:use-module (gnu packages netpbm) #:use-module (gnu packages ocaml) #:use-module (gnu packages onc-rpc) @@ -141,6 +142,7 @@ #:use-module (gnu packages ruby) #:use-module (gnu packages tbb) #:use-module (gnu packages scheme) + #:use-module (gnu packages serialization) #:use-module (gnu packages shells) #:use-module (gnu packages sphinx) #:use-module (gnu packages tcl) @@ -176,6 +178,39 @@ beginners.") (license license:gpl3+) (home-page "https://www.gnu.org/software/aris/"))) +(define-public bitwise + (package + (name "bitwise") + (version "0.42") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/mellowcandle/bitwise" + "/releases/download/v" version + "/bitwise-v" version ".tar.gz")) + (sha256 + (base32 "1lniw4bsb5qs5ybf018qllf95pzixb1q3lvybzl4k3xz8zpkrm6k")))) + (build-system gnu-build-system) + (inputs + `(("ncurses" ,ncurses) + ("readline" ,readline))) + (native-inputs + `(("cunit" ,cunit) + ("pkg-config" ,pkg-config))) + (synopsis "Terminal based bit manipulator in ncurses") + (description "Bitwise is a multi base interactive calculator supporting +dynamic base conversion and bit manipulation. It's a handy tool for low level +hackers, kernel developers and device drivers developers. + +Some of the features include: +@itemize +@item Interactive ncurses interface. +@item Command line calculator supporting all bitwise operations. +@item Individual bit manipulator. +@item Bitwise operations such as NOT, OR, AND, XOR, and shifts. +@end itemize") + (license license:gpl3+) + (home-page "https://github.com/mellowcandle/bitwise/"))) + (define-public c-graph (package (name "c-graph") @@ -4610,6 +4645,154 @@ specifications.") revised simplex and the branch-and-bound methods.") (license license:lgpl2.1+))) +;; Private Trilinos package for dealii-openmpi (similar to +;; trilinos-serial-xyce and trilinos-parallel-xyce). +;; This version is the latest known to be compatible with deal.II [1]. +;; Since the latest version of Trilinos is not necessarily supported by +;; deal.II, it may be worth keeping this package even if and when Trilinos +;; gets packaged separately for Guix (unless various versions of Trilinos are +;; packaged). +;; +;; An insightful source of information for building Trilinos for deal.II lies +;; in the Trilinos package for candi [2], which is a source-based installer +;; for deal.II and its dependencies. +;; +;; [1]: https://www.dealii.org/current/external-libs/trilinos.html +;; [2]: https://github.com/dealii/candi/blob/master/deal.II-toolchain/packages/trilinos.package +(define trilinos-for-dealii-openmpi + (package + (name "trilinos-for-dealii-openmpi") + (version "12.18.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/trilinos/Trilinos/") + (commit + (string-append "trilinos-release-" + (string-replace-substring version "." "-"))))) + (file-name (git-file-name "trilinos" version)) + (sha256 + (base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp")))) + (build-system cmake-build-system) + (native-inputs + `(("gfortran" ,gfortran) + ;; Trilinos's repository contains several C-shell scripts, but adding + ;; tcsh to the native inputs does not result in the check phase running + ;; any more tests than without it (nor is tcsh required to build + ;; Trilinos). + ;; It seems that Trilinos has replaced its use of C-shell test scripts + ;; with CMake's testing facilities. + ;; For example, + ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1] + ;; states that Zoltan's C-shell test script + ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests now + ;; performed through CMake. + ;; + ;; Perl is required for some Zoltan tests and Python 2 for one ML test. + ;; + ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html + ("perl" ,perl) + ("python" ,python-2))) + (inputs + `(("blas" ,openblas) + ("lapack" ,lapack) + ("mumps" ,mumps-openmpi) + ("scalapack" ,scalapack))) + (propagated-inputs + `(("mpi" ,openmpi))) + (arguments + `(#:build-type "Release" + #:configure-flags + `("-DBUILD_SHARED_LIBS=ON" + ;; Obtain the equivalent of RelWithDebInfo but with -O3 (the Release + ;; default) rather than -O2 (the RelWithDebInfo default), to conform + ;; to candi's trilinos.package's compilation flags, which are -g -O3. + "-DCMAKE_C_FLAGS=-g" + "-DCMAKE_CXX_FLAGS=-g" + "-DCMAKE_Fortran_FLAGS=-g" + + ;; Trilinos libraries that deal.II can interface with. + "-DTrilinos_ENABLE_Amesos=ON" + "-DTrilinos_ENABLE_AztecOO=ON" + "-DTrilinos_ENABLE_Epetra=ON" + "-DTrilinos_ENABLE_EpetraExt=ON" + "-DTrilinos_ENABLE_Ifpack=ON" + "-DTrilinos_ENABLE_ML=ON" + "-DTrilinos_ENABLE_MueLu=ON" + "-DTrilinos_ENABLE_ROL=ON" + ;; Optional; required for deal.II's GridIn::read_exodusii, but + ;; depends on netcdf. + ;; Enable if and when someone needs it. + ;;"-DTrilinos_ENABLE_SEACAS=ON" + "-DTrilinos_ENABLE_Sacado=ON" + "-DTrilinos_ENABLE_Teuchos=ON" + "-DTrilinos_ENABLE_Tpetra=ON" + "-DTrilinos_ENABLE_Zoltan=ON" + + ;; Third-party libraries (TPLs) that Trilinos can interface with. + "-DBLAS_LIBRARY_NAMES=openblas" + "-DTPL_ENABLE_MPI=ON" + "-DTPL_ENABLE_MUMPS=ON" + "-DTPL_ENABLE_SCALAPACK=ON" + + ;; Enable the tests but not the examples (which are enabled by + ;; default when enabling tests). + ;; Although some examples are run as tests, they are otherwise + ;; unnecessary since this is a private package meant for + ;; dealii-openmpi. + ;; Besides, some MueLu and ROL examples require a lot of memory to + ;; compile. + ;; + ;; (For future reference, note that some ROL and SEACAS examples + ;; require removing gfortran from CPLUS_INCLUDE_PATH as in the + ;; dune-istl, dune-localfunctions and dune-alugrid packages.) + "-DTrilinos_ENABLE_TESTS=ON" + "-DTrilinos_ENABLE_EXAMPLES=OFF" + ;; MueLu tests require considerably more time and memory to compile + ;; than the rest of the tests. + "-DMueLu_ENABLE_TESTS=OFF" + + ;; The following options were gleaned from candi's trilinos.package. + ;; (We do not enable the complex instantiations, which are anyway + ;; provided only as an option in trilinos.package, because they are + ;; costly in compilation time and memory usage, and disk space [1].) + ;; + ;; [1]: https://www.docs.trilinos.org/files/TrilinosBuildReference.html#enabling-float-and-complex-scalar-types + "-DTrilinos_ENABLE_Ifpack2=OFF" + "-DTeuchos_ENABLE_FLOAT=ON" + "-DTpetra_INST_INT_LONG=ON" + "-DTPL_ENABLE_Boost=OFF") + #:phases + (modify-phases %standard-phases + (add-after 'configure 'fix-kokkos-config + (lambda _ + ;; GNU Make 4.3 accidentally leaves the backslash preceding the + ;; number sign in strings containing a literal backslash–number + ;; sign (\#) [1, 2]. + ;; This is still an issue in Trilinos 13.0.1, but should be fixed + ;; in the following version. + ;; (The latest versions of Kokkos incorporate the fix [2].) + ;; + ;; [1]: https://github.com/GEOSX/thirdPartyLibs/issues/136 + ;; [2]: https://github.com/kokkos/kokkos/blob/3.4.00/Makefile.kokkos#L441 + (substitute* "KokkosCore_config.h" + (("\\\\#") "#")) + #t)) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) + (home-page "https://trilinos.github.io/") + (synopsis "Algorithms for engineering and scientific problems") + (description + "The Trilinos Project is an effort to develop algorithms and enabling +technologies within an object-oriented software framework for the solution of +large-scale, complex multi-physics engineering and scientific problems. +A unique design feature of Trilinos is its focus on packages.") + ;; The packages are variously licensed under more than just BSD-3 and + ;; LGPL-2.1+, but all the licenses are either BSD- or LGPL-compatible. + ;; See https://trilinos.github.io/license.html. + (license (list license:bsd-3 license:lgpl2.1+)))) + (define-public dealii (package (name "dealii") @@ -4705,6 +4888,7 @@ in finite element programs.") ("p4est" ,p4est-openmpi) ("petsc" ,petsc-openmpi) ("slepc" ,slepc-openmpi) + ("trilinos" ,trilinos-for-dealii-openmpi) ,@(alist-delete "hdf5" (package-propagated-inputs dealii)))) (arguments (substitute-keyword-arguments (package-arguments dealii) @@ -6735,3 +6919,103 @@ when an application performs repeated divisions by the same divisor.") "This header-only C++ library implements conversion to and from half-precision floating point formats.") (license license:expat)))) + +(define-public optizelle + (let ((commit "ed4160b5287518448caeb34789d92dc6a0b7e2cc")) + (package + (name "optizelle") + (version (git-version "1.3.0" "0" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/OptimoJoe/Optizelle") + (commit commit))) + (file-name (git-file-name "optizelle" commit)) + (sha256 + (base32 + "0rjrs5sdmd33a9f4xm8an7p0953aa0bxsmr4hs3ss1aad9k181vq")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Reduce the stopping tolerance in one test so that the + ;; convergence check returns the correct stopping + ;; condition. + (substitute* + "src/unit/linear_algebra/tcg_loss_of_orthogonality.cpp" + (("1e-13") "5e-14")) + ;; Skip one set of python tests. See + ;; https://github.com/OptimoJoe/Optizelle/issues/2. + (substitute* + "src/examples/inequality_scaling/CMakeLists.txt" + (("add_unit(.*)\\$\\{interfaces\\}(.*)$" all middle end) + (string-append "add_unit" middle "\"cpp\"" end))) + ;; Install the licence for Optizelle, without also + ;; including the licences for the dependencies. + (substitute* "licenses/CMakeLists.txt" + (("file.*package.*$" all) + (string-append "# " all)) + ((".*[^l].[.]txt\\)\n") "") + (("add_license.*\"\n") "")) + #t)))) + (build-system cmake-build-system) + (arguments + `(#:imported-modules ((guix build python-build-system) + ,@%cmake-build-system-modules) + #:modules (((guix build python-build-system) #:select + (python-version)) + (guix build cmake-build-system) + (guix build utils)) + #:configure-flags `("-DCMAKE_CXX_FLAGS:STRING=-pthread" + "-DENABLE_CPP_UNIT:BOOL=ON" + "-DENABLE_CPP_EXAMPLES:BOOL=ON" + "-DENABLE_PYTHON:BOOL=ON" + "-DENABLE_PYTHON_UNIT:BOOL=ON" + "-DENABLE_PYTHON_EXAMPLES:BOOL=ON" + ,(string-append "-DBLAS_LIBRARY:FILEPATH=" + (assoc-ref %build-inputs + "blas/lapack") + "/lib/libopenblas.so") + ,(string-append "-DLAPACK_LIBRARY:FILEPATH=" + (assoc-ref %build-inputs + "fortran:lib") + "/lib/libgfortran.so;" + (assoc-ref %build-inputs + "fortran:lib") + "/lib/libquadmath.so")) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-numpy-path ; Needed for the unit tests. + (lambda* (#:key inputs #:allow-other-keys) + (let* ((pyver (python-version (assoc-ref inputs "python"))) + (npdir (string-append (assoc-ref inputs "numpy") + "/lib/python" pyver + "/site-packages"))) + (substitute* "src/cmake/Modules/Optizelle.cmake" + (("PYTHONPATH=") + (string-append "LD_LIBRARY_PATH=$ENV{LIBRARY_PATH};" + "PYTHONPATH=" npdir ":")))))) + (delete 'install-license-files)))) ; LICENSE.txt is installed. + (inputs + `(("blas/lapack" ,openblas) + ("fortran:lib" ,gfortran "lib") + ("jsoncpp" ,jsoncpp) + ("numpy" ,python-numpy) + ("python" ,python))) + (native-inputs + `(("fortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "https://www.optimojoe.com/products/optizelle/") + (synopsis "Mathematical optimization library") + (description "@code{optizelle} is a software library designed to +solve nonlinear optimization problems. Four types of problem are +considered: unconstrained, equality constrained, inequality +constrained and constrained. Constraints may be applied as values of +functions or sets of partial differential equations (PDEs). + +Solution algorithms such as the preconditioned nonlinear conjugate +gradient method, sequential quadratic programming (SQP) and the +primal-dual interior-point method are made available. Interfaces are +provided for applications written in C++ and Python. Parallel +computation is supported via MPI.") + (license license:bsd-2)))) |