diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 689 |
1 files changed, 618 insertions, 71 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e7f82341e8..7b07cb4342 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -47,6 +47,8 @@ ;;; Copyright © 2021 Philip McGrath <philip@philipmcgrath.com> ;;; Copyright © 2021 Paul A. Patience <paul@apatience.com> ;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru> +;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me> +;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -71,6 +73,7 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) + #:use-module (guix gexp) #:use-module (guix utils) #:use-module ((guix build utils) #:select (alist-replace)) #:use-module (guix build-system cmake) @@ -83,6 +86,7 @@ #:use-module (gnu packages audio) #:use-module (gnu packages autotools) #:use-module (gnu packages base) + #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages boost) #:use-module (gnu packages check) @@ -123,9 +127,11 @@ #: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) + #:use-module (gnu packages parallel) #:use-module (gnu packages pcre) #:use-module (gnu packages popt) #:use-module (gnu packages perl) @@ -139,6 +145,7 @@ #: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) @@ -164,6 +171,8 @@ (inputs `(("gtk+" ,gtk+) ("libxml2" ,libxml2))) (native-inputs `(("pkg-config" ,pkg-config))) + (arguments + `(#:configure-flags '("CFLAGS=-fcommon"))) (synopsis "Natural deduction first-order logic interface") (description "Aris is a program for performing logical proofs. It supports propositional and predicate logic, as well as Boolean algebra and @@ -174,6 +183,39 @@ 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") @@ -512,12 +554,21 @@ precision floating point numbers.") (substitute* "linalg/test.c" ((".*gsl_test\\(test_LU_decomp.*") "\n") ((".*gsl_test\\(test_LUc_decomp.*") "\n") + ((".*gsl_test\\(test_QR_decomp_r.*") "\n") ((".*gsl_test\\(test_cholesky_decomp.*") "\n") + ((".*gsl_test\\(test_pcholesky_solve.*") "\n") ((".*gsl_test\\(test_COD_lssolve2.*") "\n")) (substitute* "spmatrix/test.c" ((".*test_all.*") "\n") ((".*test_float.*") "\n") - ((".*test_complex.*") "\n")))))) + ((".*test_complex.*") "\n")) + + ;; XXX: These tests abort with: + ;; gsl: cholesky.c:645: ERROR: matrix is not positive definite + (substitute* '("multifit_nlinear/test.c" + "multilarge_nlinear/test.c") + (("gsl_ieee_env_setup.*" all) + (string-append "exit (77);\n" all))))))) (else '())))))) (home-page "https://www.gnu.org/software/gsl/") @@ -1046,6 +1097,8 @@ computations.") (arguments `(#:parallel-tests? #f #:configure-flags (list "--enable-shared" + "FCFLAGS=-fallow-argument-mismatch" + "FFLAGS=-fallow-argument-mismatch" (string-append "CPPFLAGS=-I" (assoc-ref %build-inputs "libtirpc") "/include/tirpc")) @@ -1079,7 +1132,7 @@ computations.") ;; .so-files. We truncate the hashes to avoid ;; unnecessary store references to those compilers: (substitute* "libhdf4.settings" - (("(/gnu/store/)([a-Z0-9]*)" all prefix hash) + (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash) (string-append prefix (string-take hash 10) "..."))) #t)) (add-after 'install 'provide-absolute-libjpeg-reference @@ -1625,6 +1678,13 @@ similar to MATLAB, GNU Octave or SciPy.") (sha256 (base32 "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf")) + (modules '((guix build utils))) + (snippet + ;; Make sure this variable is defined only once. Failing to do so + ;; would break builds of 'netcdf-parallel-openmpi' with a + ;; multiple-definition link error with GCC 10. + '(substitute* "ncdump/ocprint.c" + (("^int ocdebug") "static int ocdebug"))) (patches (search-patches "netcdf-date-time.patch")))) (build-system gnu-build-system) (native-inputs @@ -1658,7 +1718,7 @@ similar to MATLAB, GNU Octave or SciPy.") ;; filenames to avoid unnecessary references to the corresponding ;; store items. (substitute* "libnetcdf.settings" - (("(/gnu/store/)([a-Z0-9]*)" all prefix hash) + (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash) (string-append prefix (string-take hash 10) "..."))) #t))) @@ -1707,7 +1767,9 @@ sharing of scientific data.") "0x4acvfhbsx1q79dkkwrwbgfhm0w5ngnp4zj5kk92s1khihmqfhj")))) (build-system gnu-build-system) (arguments - `(#:parallel-tests? #f)) + `(#:configure-flags '("FCFLAGS=-fallow-argument-mismatch" + "FFLAGS=-fallow-argument-mismatch") + #:parallel-tests? #f)) (inputs `(("netcdf" ,netcdf))) (native-inputs @@ -1800,6 +1862,154 @@ large-scale nonlinear optimization. It provides C++, C, and Fortran interfaces.") (license license:epl2.0))) +(define-public nomad-optimizer + (package + (name "nomad-optimizer") + (version "4.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bbopt/nomad/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0w386d8r5ldbvnv0c0g7vz95pfpvwdxis26vaalk2amsa5akl775")))) + (build-system cmake-build-system) + (native-inputs + `(("python" ,python-wrapper) + ("python-cython" ,python-cython))) + (arguments + `(#:imported-modules ((guix build python-build-system) + ,@%cmake-build-system-modules) + #:modules (((guix build python-build-system) + #:select (python-version site-packages)) + (guix build cmake-build-system) + (guix build utils)) + #:configure-flags + '("-DBUILD_INTERFACES=ON" + "-DBUILD_TESTS=ON") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-sources-for-build + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "CMakeLists.txt" + ;; CMAKE_INSTALL_PREFIX is accidentally hardcoded. + (("set\\(CMAKE_INSTALL_PREFIX .* FORCE\\)") "") + ;; Requiring GCC version 8 or later is unwarranted. + (("message\\(FATAL_ERROR \"GCC version < 8") + "message(STATUS \"GCC version < 8")) + + (let ((out (assoc-ref outputs "out"))) + (substitute* "interfaces/PyNomad/CMakeLists.txt" + ;; We don't want to build in-place, and anyway the install + ;; command further below runs build_ext as a prerequisite. + (("COMMAND python setup_PyNomad\\.py .* build_ext --inplace\n") + "") + ;; Don't install locally. + (("COMMAND python (setup_PyNomad\\.py .* install) --user\n" + _ args) + (string-append "COMMAND ${CMAKE_COMMAND} -E env" + " CC=" ,(cc-for-target) + " CXX=" ,(cxx-for-target) + " " (which "python") + " " args + " --prefix=" out + "\n"))) + ;; Fix erroneous assumptions about the paths of the include and + ;; library directories. + (substitute* "interfaces/PyNomad/setup_PyNomad.py" + (("^( +os_include_dirs = ).*" _ prefix) + (string-append prefix "[\"../../src\"]\n")) + (("^(installed_lib_dir = ).*" _ prefix) + (string-append prefix "\"" out "/lib\"\n")))) + #t)) + + ;; Fix the tests so they run in out-of-source builds. + (add-after 'fix-sources-for-build 'fix-sources-for-tests + (lambda _ + (substitute* + (map (lambda (d) (string-append "examples/" d "/CMakeLists.txt")) + (append + (map (lambda (d) (string-append "basic/library/" d)) + '("example1" "example2" "example3" + "single_obj_parallel")) + (map (lambda (d) (string-append "advanced/library/" d)) + '("FixedVariable" "NMonly" "PSDMads" "Restart" + "c_api/example1" "c_api/example2" + "exampleSuggestAndObserve")))) + ;; The built examples are assumed to be in the source tree + ;; (which isn't the case here). + (("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)" + _ command test) + (string-append command "${CMAKE_CURRENT_BINARY_DIR}" test))) + ;; (Unrelated to support for out-of-source testing.) + (make-file-writable + "examples/advanced/library/exampleSuggestAndObserve/cache0.txt") + + (let* ((builddir (string-append (getcwd) "/../build")) + ;; The BB_EXE and SURROGATE_EXE paths are interpreted + ;; relative to the configuration file provided to NOMAD. + ;; However, the configuration files are all in the source + ;; tree rather than in the build tree (unlike the compiled + ;; executables). + (fix-exe-path (lambda* (dir #:optional + (file "param.txt") + (exe-opt "BB_EXE")) + (substitute* (string-append dir "/" file) + (((string-append "^" exe-opt " +")) + ;; The $ prevents NOMAD from prefixing + ;; the executable with the path of the + ;; parent directory of the configuration + ;; file NOMAD was provided with as + ;; argument (param.txt or some such). + (string-append exe-opt " $" + builddir "/" dir "/")))))) + (for-each + (lambda (dir) + (let ((dir (string-append "examples/" dir))) + (substitute* (string-append dir "/CMakeLists.txt") + ;; The install phase has not yet run. + (("COMMAND \\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad ") + "COMMAND ${CMAKE_BINARY_DIR}/src/nomad ")) + (fix-exe-path dir) + (when (equal? dir "examples/basic/batch/surrogate_sort") + (fix-exe-path dir "param.txt" "SURROGATE_EXE")))) + (append (map (lambda (d) (string-append "basic/batch/" d)) + '("example1" "example2" + "single_obj" "single_obj_parallel" + "surrogate_sort")) + '("advanced/batch/LHonly"))) + + (let ((dir "examples/advanced/batch/FixedVariable")) + (substitute* (string-append dir "/runFixed.sh") + ;; Hardcoded path to NOMAD executable. + (("^\\.\\./\\.\\./\\.\\./\\.\\./bin/nomad ") + (string-append builddir "/src/nomad "))) + (for-each + (lambda (f) (fix-exe-path dir f)) + '("param1.txt" "param2.txt" "param3.txt" "param10.txt")))) + #t)) + + ;; The information in the .egg-info file is not kept up to date. + (add-after 'install 'delete-superfluous-egg-info + (lambda* (#:key inputs outputs #:allow-other-keys) + (delete-file (string-append + (site-packages inputs outputs) + "PyNomad-0.0.0-py" + (python-version (assoc-ref inputs "python")) + ".egg-info")) + #t))))) + (home-page "https://www.gerad.ca/nomad/") + (synopsis "Nonlinear optimization by mesh-adaptive direct search") + (description + "NOMAD is a C++ implementation of the mesh-adaptive direct search (MADS) +algorithm, designed for difficult blackbox optimization problems. These +problems occur when the functions defining the objective and constraints are +the result of costly computer simulations.") + (license license:lgpl3+))) + (define-public cbc (package (name "cbc") @@ -3553,31 +3763,32 @@ processor cores.") (synopsis "Parallel adaptive mesh refinement on forests of octrees"))) (define-public gsegrafix + ;; This is an old and equally dead "experimental fork" of the longer-dead + ;; original. At least it no longer requires the even-deader libgnomeprint{,ui} + ;; libraries, instead rendering plots with Pango. (package (name "gsegrafix") - (version "1.0.6") + (version "1.0.7.2") (source (origin - (method url-fetch) - (uri (string-append "mirror://gnu/" name "/" name "-" - version ".tar.gz")) - (sha256 - (base32 - "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda")))) + (method url-fetch) + (uri (string-append "mirror://savannah/gsegrafix-experimental/" + "gsegrafix-experimental-" version ".tar.gz")) + (sha256 + (base32 "0fwh6719xy2zasmqlp0vdx6kzm45hn37ga88xmw5cz0yx7xw4j6f")))) (build-system gnu-build-system) (arguments - `(#:configure-flags '("LDFLAGS=-lm"))) + `(#:configure-flags + (list "--disable-static"))) (inputs - `(("libgnomecanvas" ,libgnomecanvas) - ("libbonoboui" ,libbonoboui) - ("libgnomeui" ,libgnomeui) - ("libgnomeprintui" ,libgnomeprintui) - ("popt" ,popt))) + `(("glib" ,glib) + ("gtk+" ,gtk+))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "https://www.gnu.org/software/gsegrafix/") (synopsis "GNOME application to create scientific and engineering plots") - (description "GSEGrafix is an application which produces high-quality graphical + (description + "GSEGrafix is an application which produces high-quality graphical plots for science and engineering. Plots are specified via simple ASCII parameter files and data files and are presented in an anti-aliased GNOME canvas. The program supports rectangular two-dimensional plots, histograms, @@ -3600,8 +3811,9 @@ to BMP, JPEG or PNG image formats.") (patches (search-patches "maxima-defsystem-mkdir.patch")))) (build-system gnu-build-system) (inputs - `(("gcl" ,gcl) + `(("bash" ,bash-minimal) ("gnuplot" ,gnuplot) ;for plots + ("sbcl" ,sbcl) ("sed" ,sed) ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima' (native-inputs @@ -3610,15 +3822,11 @@ to BMP, JPEG or PNG image formats.") ("python" ,python))) (arguments `(#:configure-flags - (list "--enable-gcl" - (string-append "--with-posix-shell=" - (assoc-ref %build-inputs "bash") - "/bin/sh") - (string-append "--with-wish=" - (assoc-ref %build-inputs "tk") - "/bin/wish" - (let ((v ,(package-version tk))) - (string-take v (string-index-right v #\.))))) + ,#~(list "--enable-sbcl" + (string-append "--with-sbcl=" #$sbcl "/bin/sbcl") + (string-append "--with-posix-shell=" #$bash-minimal "/bin/sh") + (string-append "--with-wish=" #$tk "/bin/wish" + #$(version-major+minor (package-version tk)))) ;; By default Maxima attempts to write temporary files to ;; '/tmp/nix-build-maxima-*', which won't exist at run time. ;; Work around that. @@ -3655,7 +3863,7 @@ to BMP, JPEG or PNG image formats.") (invoke "sh" "-c" (string-append "./maxima-local " - "--lisp=gcl " + "--lisp=sbcl " "--batch-string=\"run_testsuite();\" " "| grep -q \"No unexpected errors found\"")))) ;; Make sure the doc and emacs files are found in the @@ -4033,7 +4241,7 @@ access to BLIS implementations via traditional BLAS routine calls.") (define-public openlibm (package (name "openlibm") - (version "0.6.0") + (version "0.7.4") (source (origin (method git-fetch) @@ -4042,11 +4250,12 @@ access to BLIS implementations via traditional BLAS routine calls.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh")))) + (base32 "1azms0lpxb7vxb3bln5lyz0wpwx6jnzbffkclclpq2v5aiw8d14i")))) (build-system gnu-build-system) (arguments `(#:make-flags - (list (string-append "prefix=" (assoc-ref %outputs "out"))) + (list (string-append "prefix=" (assoc-ref %outputs "out")) + ,(string-append "CC=" (cc-for-target))) #:phases ;; no configure script (modify-phases %standard-phases (delete 'configure)) @@ -4458,43 +4667,226 @@ 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") - (version "9.2.0") + (version "9.3.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/dealii/dealii/releases/" "download/v" version "/dealii-" version ".tar.gz")) (sha256 - (base32 - "0fm4xzrnb7dfn4415j24d8v3jkh0lssi86250x2f5wgi83xq4nnh")) + (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6")) (modules '((guix build utils))) (snippet - ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost '(begin + ;; Remove bundled boost, muparser, TBB and UMFPACK. (delete-file-recursively "bundled") #t)))) (build-system cmake-build-system) + (outputs '("out" "doc")) + (native-inputs + ;; Required to build the documentation. + `(("dot" ,graphviz) + ("doxygen" ,doxygen) + ("perl" ,perl))) (inputs - `(("tbb" ,tbb) - ("zlib" ,zlib) - ("boost" ,boost) - ("p4est" ,p4est) + `(("arpack" ,arpack-ng) ("blas" ,openblas) + ("gfortran" ,gfortran) ("lapack" ,lapack) - ("arpack" ,arpack-ng) ("muparser" ,muparser) - ("gfortran" ,gfortran) - ("suitesparse" ,suitesparse))) ;for UMFPACK + ("zlib" ,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 + ;; shebang line) and therefore must be explicitly passed to the + ;; interpreter. + ;; 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. + `(("boost" ,boost) + ("hdf5" ,hdf5) + ("suitesparse" ,suitesparse) ; For UMFPACK. + ("tbb" ,tbb))) (arguments - `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease + `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease. + ;; The tests take too long and must be explicitly enabled with "make + ;; setup_tests". + ;; See https://www.dealii.org/developer/developers/testsuite.html. + ;; (They can also be run for an already installed deal.II.) + #:tests? #f #:configure-flags - ;; Work around a bug in libsuitesparseconfig linking - ;; see https://github.com/dealii/dealii/issues/4745 - '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON"))) - (home-page "https://www.dealii.org") + (let ((doc (string-append (assoc-ref %outputs "doc") + "/share/doc/" ,name "-" ,version))) + `("-DDEAL_II_COMPONENT_DOCUMENTATION=ON" + ,(string-append "-DDEAL_II_DOCREADME_RELDIR=" doc) + ,(string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html") + ;; Don't compile the examples because the source and CMakeLists.txt + ;; are installed anyway, allowing users to do so for themselves. + "-DDEAL_II_COMPILE_EXAMPLES=OFF" + ,(string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc "/examples"))) + #:phases + (modify-phases %standard-phases + (add-after 'install 'remove-build-logs + ;; These build logs leak the name of the build directory by storing + ;; the values of CMAKE_SOURCE_DIR and CMAKE_BINARY_DIR. + (lambda* (#:key outputs #:allow-other-keys) + (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))))) + (home-page "https://www.dealii.org/") (synopsis "Finite element library") (description "Deal.II is a C++ program library targeted at the computational solution @@ -4505,30 +4897,25 @@ in finite element programs.") (license license:lgpl2.1+))) (define-public dealii-openmpi - (package (inherit dealii) + (package/inherit dealii (name "dealii-openmpi") (inputs - `(("mpi" ,openmpi) - ;;Supported only with MPI: - ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate? + `(("arpack" ,arpack-ng-openmpi) + ("metis" ,metis) + ("scalapack" ,scalapack) + ,@(alist-delete "arpack" (package-inputs dealii)))) + (propagated-inputs + `(("hdf5" ,hdf5-parallel-openmpi) + ("mpi" ,openmpi) ("p4est" ,p4est-openmpi) ("petsc" ,petsc-openmpi) ("slepc" ,slepc-openmpi) - ("metis" ,metis) ;for MUMPS - ("scalapack" ,scalapack) ;for MUMPS - ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings - ("arpack" ,arpack-ng-openmpi) - ,@(fold alist-delete (package-inputs dealii) - '("p4est" "arpack")))) + ("trilinos" ,trilinos-for-dealii-openmpi) + ,@(alist-delete "hdf5" (package-propagated-inputs dealii)))) (arguments (substitute-keyword-arguments (package-arguments dealii) - ((#:configure-flags cf) - `(cons "-DDEAL_II_WITH_MPI:BOOL=ON" - ,cf)) - ((#:phases phases '%standard-phases) - `(modify-phases ,phases - (add-before 'check 'mpi-setup - ,%openmpi-setup))))) + ((#:configure-flags flags) + `(cons "-DDEAL_II_WITH_MPI=ON" ,flags)))) (synopsis "Finite element library (with MPI support)"))) (define-public flann @@ -4731,7 +5118,7 @@ set.") texlive-latex-framed texlive-latex-geometry texlive-latex-hanging - texlive-latex-hyperref + texlive-hyperref texlive-latex-multirow texlive-latex-natbib texlive-latex-needspace @@ -4743,7 +5130,7 @@ set.") texlive-latex-tocloft texlive-latex-upquote texlive-latex-varwidth - texlive-latex-wasysym + texlive-wasysym texlive-latex-wrapfig))))) (inputs `(("blas" ,openblas) @@ -4854,14 +5241,14 @@ supports compressed MAT files, as well as newer (version 7.3) MAT files.") (define-public vc (package (name "vc") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/VcDevel/Vc/releases/" "download/" version "/Vc-" version ".tar.gz")) (sha256 (base32 - "17qili8bf8r78cng65yf4qmgna8kiqjqbgcqbric6v9j6nkhkrk8")))) + "0lirdqzcxys9walz04bllsphydynk7973aimd5k1h1qbwi8z3lsh")))) (build-system cmake-build-system) (arguments '(#:configure-flags @@ -6043,7 +6430,7 @@ management via the GIMPS project's Primenet server.") (define-public nauty (package (name "nauty") - (version "2.7r1") + (version "2.7r3") (source (origin (method url-fetch) @@ -6051,7 +6438,7 @@ management via the GIMPS project's Primenet server.") "https://pallini.di.uniroma1.it/" "nauty" (string-join (string-split version #\.) "") ".tar.gz")) (sha256 - (base32 "0xsfqfcknbd6g6wzpa5l7crmmk3bf3zjh37rhylq6b20dqcmvjkn")))) + (base32 "1hl81gpf3xjf809w04jczvilq1ixy9ch1qrax8a7lgx52svna1jg")))) (build-system gnu-build-system) (outputs '("out" "lib")) (arguments @@ -6494,3 +6881,163 @@ high-performance multidimensional array containers for scientific computing.") (license (list license:artistic2.0 license:bsd-3 license:lgpl3+)))) + +(define-public fxdiv + ;; There is currently no tag in this repo. + (let ((commit "63058eff77e11aa15bf531df5dd34395ec3017c8") + (version "0.0") + (revision "1")) + (package + (name "fxdiv") + (version (git-version version revision commit)) + (home-page "https://github.com/Maratyszcza/FXdiv") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0zwzh8gmbx4m6b18s5nf13b0dk5yjkd1fs8f421bl7fz5f9gjd9f")) + (patches (search-patches "fxdiv-system-libraries.patch")))) + (build-system cmake-build-system) + (inputs + `(("googletest" ,googletest) + ("googlebenchmark" ,googlebenchmark))) + (synopsis + "C++ library for division via fixed-point multiplication by inverse") + (description + "On modern CPUs and GPUs, integer division is several times slower than +multiplication. FXdiv implements an algorithm to replace an integer division +with a multiplication and two shifts. This algorithm improves performance +when an application performs repeated divisions by the same divisor.") + (license license:expat)))) + +(define-public fp16 + ;; There is currently no tag in this repo. + (let ((commit "0a92994d729ff76a58f692d3028ca1b64b145d91") + (version "0.0") + (revision "1")) + (package + (name "fp16") + (version (git-version version revision commit)) + (home-page "https://github.com/Maratyszcza/FP16") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "05mm4vrxsac35hjf5djif9r6rdxj9ippg97ia3p6q6b8lrp7srwv")) + (patches (search-patches "fp16-system-libraries.patch")))) + (build-system cmake-build-system) + (native-inputs + `(("python-wrapper" ,python-wrapper))) + (inputs + `(("psimd" ,psimd) + ("googletest" ,googletest) + ("googlebenchmark" ,googlebenchmark))) + (synopsis "C++ library for half-precision floating point formats") + (description + "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)))) |