gnu/packages/simulation.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
   3 ;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
   4 ;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
   5 ;;;
   6 ;;; This file is part of GNU Guix.
   7 ;;;
   8 ;;; GNU Guix is free software; you can redistribute it and/or modify it
   9 ;;; under the terms of the GNU General Public License as published by
  10 ;;; the Free Software Foundation; either version 3 of the License, or (at
  11 ;;; your option) any later version.
  12 ;;;
  13 ;;; GNU Guix is distributed in the hope that it will be useful, but
  14 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  15 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  16 ;;; GNU General Public License for more details.
  17 ;;;
  18 ;;; You should have received a copy of the GNU General Public License
  19 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  20
  21 (define-module (gnu packages simulation)
  22   #:use-module (gnu packages)
  23   #:use-module (gnu packages algebra)
  24   #:use-module (gnu packages admin)
  25   #:use-module (gnu packages base)
  26   #:use-module (gnu packages bash)
  27   #:use-module (gnu packages bison)
  28   #:use-module (gnu packages boost)
  29   #:use-module (gnu packages check)
  30   #:use-module (gnu packages cmake)
  31   #:use-module (gnu packages compression)
  32   #:use-module (gnu packages flex)
  33   #:use-module (gnu packages gettext)
  34   #:use-module (gnu packages gcc)
  35   #:use-module (gnu packages gl)
  36   #:use-module (gnu packages graphics)
  37   #:use-module (gnu packages gtk)
  38   #:use-module (gnu packages linux)
  39   #:use-module (gnu packages m4)
  40   #:use-module (gnu packages maths)
  41   #:use-module (gnu packages mpi)
  42   #:use-module (gnu packages multiprecision)
  43   #:use-module (gnu packages ncurses)
  44   #:use-module (gnu packages pkg-config)
  45   #:use-module (gnu packages python)
  46   #:use-module (gnu packages python-build)
  47   #:use-module (gnu packages python-science)
  48   #:use-module (gnu packages python-xyz)
  49   #:use-module (gnu packages readline)
  50   #:use-module (gnu packages tls)
  51   #:use-module (gnu packages version-control)
  52   #:use-module (gnu packages xml)
  53   #:use-module (gnu packages xorg)
  54   #:use-module (guix download)
  55   #:use-module (guix gexp)
  56   #:use-module (guix git-download)
  57   #:use-module (guix svn-download)
  58   #:use-module (guix build-system cmake)
  59   #:use-module (guix build-system gnu)
  60   #:use-module (guix build-system python)
  61   #:use-module ((guix licenses) #:prefix license:)
  62   #:use-module (guix packages)
  63   #:use-module (guix utils)
  64   #:use-module (ice-9 ftw)
  65   #:use-module (ice-9 regex)
  66   #:use-module (srfi srfi-1))
  67
  68 (define-public openfoam
  69   (package
  70     (name "openfoam")
  71     (version "4.1")
  72     (source
  73      (origin
  74        (method url-fetch)
  75        (uri (string-append
  76              "http://dl.openfoam.org/source/"
  77              (string-map (lambda (x) (if (eq? x #\.) #\- x)) version)))
  78        (file-name (string-append name "-" version ".tar.gz"))
  79        (sha256
  80         (base32 "0cgxh4h2hf50qbvvdg5miwc2nympb0nrv3md96vb3gbs9vk8vq9d"))
  81        (patches (search-patches "openfoam-4.1-cleanup.patch"))
  82        (modules '((guix build utils)))
  83        (snippet
  84         '(begin
  85            ;; Include <sys/sysmacros.h>, which is where glibc >= 2.28 provides
  86            ;; 'major' and 'minor'.
  87            (substitute* "src/OSspecific/POSIX/fileStat.C"
  88              (("#include <unistd\\.h>")
  89               "#include <unistd.h>\n#include <sys/sysmacros.h>\n"))
  90            #t))))
  91     (build-system gnu-build-system)
  92     (inputs
  93      `(("boost" ,boost)
  94        ("cgal" ,cgal)
  95        ("flex" ,flex)
  96        ("git" ,git)
  97        ("gmp" ,gmp)
  98        ("libxt" ,libxt)
  99        ("metis" ,metis)
 100        ("mpfr" ,mpfr)
 101        ("ncurses" ,ncurses)
 102        ("readline" ,readline)
 103        ("scotch" ,pt-scotch32)
 104        ("zlib" ,zlib)))
 105     (native-inputs
 106      (list bison))
 107     (propagated-inputs
 108      (list gzip gnuplot openmpi))
 109     (outputs '("debug"                  ;~60MB
 110                "out"))
 111     (arguments
 112      `( ;; Executable files and shared libraries are located in the 'platforms'
 113        ;; subdirectory.
 114        #:strip-directories (list (string-append
 115                                   "lib/OpenFOAM-" ,version
 116                                   "/platforms/linux64GccDPInt32Opt/bin")
 117                                  (string-append
 118                                   "lib/OpenFOAM-" ,version
 119                                   "/platforms/linux64GccDPInt32Opt/lib"))
 120        #:tests? #f                                ; no tests to run
 121
 122        #:modules ((ice-9 ftw)
 123                   (ice-9 regex)
 124                   (guix build gnu-build-system)
 125                   (guix build utils))
 126
 127        #:phases (modify-phases %standard-phases
 128                   (add-after 'unpack 'rename-build-directory
 129                     (lambda _
 130                       (chdir "..")
 131                       ;; Use 'OpenFOAM-version' convention to match the file
 132                       ;; name expectations in the build phase.
 133                       (let ((unpack-dir (string-append
 134                                          (getcwd) "/"
 135                                          (list-ref (scandir (getcwd) (lambda (name)
 136                                                                        (string-match "^OpenFOAM" name))) 0)))
 137                             (build-dir (string-append
 138                                         (getcwd) "/OpenFOAM-" ,version)))
 139                         (rename-file unpack-dir build-dir) ; rename build directory
 140                         (chdir (basename build-dir))) ; move to build directory
 141                       #t))
 142                   (delete 'configure)             ; no configure phase
 143                   (replace 'build
 144                     (lambda _
 145                       (let ((libraries '("boost" "cgal" "gmp" "metis" "mpfr" "scotch")))
 146                         ;; set variables to define store paths
 147                         (for-each (lambda (library)
 148                                     (setenv (string-append
 149                                              (string-upcase library) "_ROOT")
 150                                             (assoc-ref %build-inputs library))) libraries))
 151                       ;; set variables to define package versions
 152                       (setenv "SCOTCHVERSION" ,(package-version scotch))
 153                       (setenv "METISVERSION" ,(package-version metis))
 154                       ;; set variable to pass extra 'rpath' arguments to linker
 155                       (setenv "LDFLAGS"
 156                               (string-append
 157                                "-Wl,"
 158                                "-rpath=" %output "/lib/OpenFOAM-" ,version
 159                                "/platforms/linux64GccDPInt32Opt/lib,"
 160                                "-rpath=" %output "/lib/OpenFOAM-" ,version
 161                                "/platforms/linux64GccDPInt32Opt/lib/dummy"))
 162                       ;; compile OpenFOAM libraries and applications
 163                       (zero? (system (format #f
 164                                              "source ./etc/bashrc && ./Allwmake -j~a"
 165                                              (parallel-job-count))))))
 166                   (add-after 'build 'update-configuration-files
 167                     (lambda _
 168                       ;; record store paths and package versions in
 169                       ;; configuration files
 170                       (substitute* "etc/config.sh/CGAL"
 171                         (("$BOOST_ROOT") (getenv "BOOST_ROOT")))
 172                       (substitute* "etc/config.sh/CGAL"
 173                         (("$CGAL_ROOT") (getenv "CGAL_ROOT")))
 174                       (substitute* "etc/config.sh/metis"
 175                         (("$METIS_ROOT") (getenv "METIS_ROOT")))
 176                       (substitute* "etc/config.sh/metis"
 177                         (("$METISVERSION") (getenv "METISVERSION")))
 178                       (substitute* "etc/config.sh/scotch"
 179                         (("$SCOTCH_ROOT") (getenv "SCOTCH_ROOT")))
 180                       (substitute* "etc/config.sh/scotch"
 181                         (("$SCOTCHVERSION") (getenv "SCOTCHVERSION")))
 182                       (substitute* "etc/config.sh/settings"
 183                         (("$GMP_ROOT") (getenv "GMP_ROOT")))
 184                       (substitute* "etc/config.sh/settings"
 185                         (("$MPFR_ROOT") (getenv "MPFR_ROOT")))
 186                       ;; reset lockDir variable to refer to write-enabled
 187                       ;; directory
 188                       (substitute* "wmake/wmake"
 189                         (("        lockDir=.*$")
 190                          "        lockDir=$HOME/.$WM_PROJECT/.wmake\n"))
 191                       (substitute* "wmake/wmakeScheduler"
 192                         (("lockDir=.*$")
 193                          "lockDir=$HOME/.$WM_PROJECT/.wmake\n"))
 194                       (substitute* "wmake/wmakeSchedulerUptime"
 195                         (("lockDir=.*$")
 196                          "lockDir=$HOME/.$WM_PROJECT/.wmake\n"))
 197                       #t))
 198                   (add-after 'build 'cleanup
 199                     ;; Avoid unncessary, voluminous object and dep files.
 200                     (lambda _
 201                       (delete-file-recursively
 202                        "platforms/linux64GccDPInt32Opt/src")
 203                       (delete-file-recursively
 204                        "platforms/linux64GccDPInt32OptSYSTEMOPENMPI")
 205                       (for-each delete-file (find-files "." "\\.o$"))
 206                       #t))
 207                   (replace 'install
 208                     (lambda _
 209                       ;; use 'OpenFOAM-version' convention
 210                       (let ((install-dir (string-append
 211                                           %output "/lib/OpenFOAM-" ,version)))
 212                         (mkdir-p install-dir)     ; create install directory
 213                         ;; move contents of build directory to install directory
 214                         (copy-recursively "." install-dir))))
 215                   (add-after 'install 'add-symbolic-link
 216                     (lambda _
 217                       ;; add symbolic link for standard 'bin' directory
 218                       (symlink
 219                        (string-append "./lib/OpenFOAM-" ,version
 220                                       "/platforms/linux64GccDPInt32Opt/bin")
 221                        (string-append %output "/bin"))
 222                       #t)))))
 223     ;; Note:
 224     ;;  Tutorial files are installed read-only in /gnu/store.
 225     ;;  To allow write permissions on files copied from the store a
 226     ;;  'chmod' step is needed before running the applications.  For
 227     ;;  example, from a user's login:
 228     ;;  $ source $GUIX_PROFILE/lib/OpenFOAM-4.1/etc/bashrc
 229     ;;  $ mkdir -p $FOAM_RUN
 230     ;;  $ cd $FOAM_RUN
 231     ;;  $ cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzDaily .
 232     ;;  $ cd pitzDaily
 233     ;;  $ chmod -R u+w .
 234     ;;  $ blockMesh
 235     (synopsis "Framework for numerical simulation of fluid flow")
 236     (description "OpenFOAM provides a set of solvers and methods for tackling
 237 problems in the field of Computational Fluid Dynamics (CFD).  It is written in
 238 C++.  Governing equations such as the Navier-Stokes equations can be solved in
 239 integral form.  Physical processes such as phase change, droplet transport and
 240 chemical reaction can be modelled.  Numerical methods are included to deal with
 241 sharp gradients, such as those encountered in flows with shock waves and flows
 242 with gas/liquid interfaces.  Large problems may be split into smaller, connected
 243 problems for efficient solution on parallel systems.")
 244     (license license:gpl3+)
 245     (home-page "https://openfoam.org")))
 246
 247 (define-public python-fenics-dijitso
 248   (package
 249     (name "python-fenics-dijitso")
 250     (version "2019.1.0")
 251     (source
 252       (origin
 253         (method url-fetch)
 254         (uri (pypi-uri "fenics-dijitso" version))
 255         (sha256
 256           (base32
 257             "0lhqsq8ypdak0ahr2jnyvg07yrqp6wicjxi6k56zx24wp3qg60sc"))))
 258     (build-system python-build-system)
 259     (inputs
 260      (list openmpi python-numpy))
 261     (native-inputs
 262      (list python-pytest-cov))
 263     (propagated-inputs
 264      (list python-mpi4py))
 265     (arguments
 266      `(#:phases
 267        (modify-phases %standard-phases
 268          (add-after 'build 'mpi-setup
 269            ,%openmpi-setup)
 270          (replace 'check
 271            (lambda _
 272              (setenv "HOME" "/tmp")
 273              (with-directory-excursion "test"
 274                ;; Disable parallel tests to avoid race condition.  See
 275                ;; https://github.com/pytest-dev/pytest-cov/issues/237.
 276                (substitute* "runtests.sh"
 277                  (("for p in 1 4 8 16; do")
 278                   "for p in 1; do"))
 279                (invoke "./runtests.sh")))))))
 280     (home-page "https://bitbucket.org/fenics-project/dijitso/")
 281     (synopsis "Distributed just-in-time building of shared libraries")
 282     (description
 283       "Dijitso provides a core component of the @code{FEniCS} framework,
 284 namely the just-in-time compilation of C++ code that is generated from
 285 Python modules.  It is called from within a C++ library, using ctypes
 286 to import the dynamic shared library directly.
 287
 288 As long as the compiled code can provide a simple factory function to
 289 a class implementing a predefined C++ interface, there is no limit to
 290 the complexity of that interface.  Parallel support depends on the
 291 @code{mpi4py} interface.")
 292     (license license:lgpl3+)))
 293
 294 (define-public python-fenics-ufl
 295   (package
 296     (name "python-fenics-ufl")
 297     (version "2019.1.0")
 298     (source
 299       (origin
 300         (method url-fetch)
 301         (uri (pypi-uri "fenics-ufl" version))
 302         (sha256
 303           (base32
 304             "10dz8x3lm68x2w3kkqcjask38h0zkhhak26jdbkppr8g9y8wny7p"))))
 305     (build-system python-build-system)
 306     (inputs
 307      (list python-numpy))
 308     (native-inputs
 309      (list python-pytest))
 310     (arguments
 311      '(#:phases
 312        (modify-phases %standard-phases
 313          (replace 'check
 314            (lambda _
 315              (invoke "py.test" "test"))))))
 316     (home-page "https://bitbucket.org/fenics-project/ufl/")
 317     (synopsis "Unified language for form-compilers")
 318     (description "The Unified Form Language (UFL) is a domain specific
 319 language for declaration of finite element discretizations of
 320 variational forms.  More precisely, it defines a flexible interface
 321 for choosing finite element spaces and defining expressions for weak
 322 forms in a notation close to mathematical notation.
 323
 324 UFL is part of the FEniCS Project.")
 325     (license license:lgpl3+)))
 326
 327 (define-public python-fenics-fiat
 328   (package
 329     (name "python-fenics-fiat")
 330     (version "2019.1.0")
 331     (source
 332       (origin
 333         (method url-fetch)
 334         (uri (pypi-uri "fenics-fiat" version))
 335         (sha256
 336           (base32
 337             "13sc7lma3d2mh43an7i4kkdbbk4cmvxjk45wi43xnjd7qc38zg4b"))))
 338     (build-system python-build-system)
 339     (native-inputs
 340      (list python-pytest))
 341     (propagated-inputs
 342      (list python-numpy python-sympy))
 343     (arguments
 344      '(#:phases
 345        (modify-phases %standard-phases
 346          (replace 'check
 347            (lambda _
 348              (with-directory-excursion "test"
 349                ;; FIXME: three FIAT test modules are known to fail
 350                ;; with recent versions of pytest (>= 4).  These are
 351                ;; skipped for FIAT version 2019.1.0 pending an
 352                ;; upstream pull request. For details see request #59
 353                ;; at https://bitbucket.org/fenics-project/fiat/.
 354                (invoke "py.test" "unit/"
 355                        "--ignore=unit/test_fiat.py"
 356                        "--ignore=unit/test_quadrature.py"
 357                        "--ignore=unit/test_reference_element.py")))))))
 358     (home-page "https://bitbucket.org/fenics-project/fiat/")
 359     (synopsis "Tabulation of finite element function spaces")
 360     (description
 361       "The FInite element Automatic Tabulator (FIAT) supports
 362 generation of arbitrary order instances of the Lagrange elements on
 363 lines, triangles, and tetrahedra.  It is also capable of generating
 364 arbitrary order instances of Jacobi-type quadrature rules on the same
 365 element shapes.  Further, H(div) and H(curl) conforming finite element
 366 spaces such as the families of Raviart-Thomas, Brezzi-Douglas-Marini
 367 and Nedelec are supported on triangles and tetrahedra.  Upcoming
 368 versions will also support Hermite and nonconforming elements.
 369
 370 FIAT is part of the FEniCS Project.")
 371     (license license:lgpl3+)))
 372
 373 (define-public python-fenics-ffc
 374   (package
 375     (name "python-fenics-ffc")
 376     (version "2019.1.0.post0")
 377     (source
 378       (origin
 379         (method url-fetch)
 380         (uri (pypi-uri "fenics-ffc" version))
 381         (sha256
 382           (base32
 383             "1f2a44ha65fg3a1prrbrsz4dgvibsv0j5c3pi2m52zi93bhwwgg9"))))
 384     (build-system python-build-system)
 385     (native-inputs
 386      (list python-pytest))
 387     (propagated-inputs
 388      (list python-fenics-dijitso python-fenics-fiat python-fenics-ufl))
 389     (arguments
 390      '(#:phases
 391        (modify-phases %standard-phases
 392          (replace 'check
 393            (lambda _
 394              (setenv "HOME" (getcwd))
 395              (with-directory-excursion "test"
 396                ;; FIXME: the tests in subdirectory
 397                ;; 'unit/ufc/finite_element' require the ffc_factory
 398                ;; extension module.  This module, located in the 'libs'
 399                ;; subdirectory, needs to be built and made accessible
 400                ;; prior to running the tests.
 401                (invoke "py.test" "unit/" "--ignore=unit/ufc/")
 402                (with-directory-excursion "uflacs"
 403                  (invoke "py.test" "unit/")))
 404              #t)))))
 405     (home-page "https://bitbucket.org/fenics-project/ffc/")
 406     (synopsis "Compiler for finite element variational forms")
 407     (description "The FEniCS Form Compiler (FFC) is a compiler for
 408 finite element variational forms.  From a high-level description of
 409 the form, it generates efficient low-level C++ code that can be used
 410 to assemble the corresponding discrete operator (tensor).  In
 411 particular, a bilinear form may be assembled into a matrix and a
 412 linear form may be assembled into a vector.  FFC may be used either
 413 from the command line (by invoking the @code{ffc} command) or as a
 414 Python module (@code{import ffc}).
 415
 416 FFC is part of the FEniCS Project.")
 417     ;; There are two files released with a public domain licence;
 418     ;; ufc.h and ufc_geometry.h, in subdirectory 'ffc/backends/ufc'.
 419     (license (list license:public-domain license:lgpl3+))))
 420
 421 (define-public fenics-dolfin
 422   (package
 423     (name "fenics-dolfin")
 424     (version "2019.1.0.post0")
 425     (source
 426       (origin
 427         (method url-fetch)
 428         (uri (string-append
 429               "https://bitbucket.org/fenics-project/dolfin/get/"
 430               version ".tar.gz"))
 431         (file-name (string-append name "-" version ".tar.gz"))
 432         (sha256
 433           (base32
 434            "1m91hwcq5gfj4qqswp8l8kj58nia48f0n4kq13w0xqj4biq7rla0"))
 435         (patches (search-patches "fenics-dolfin-algorithm.patch"
 436                                  "fenics-dolfin-demo-init.patch"
 437                                  "fenics-dolfin-boost.patch"
 438                                  "fenics-dolfin-config-slepc.patch"))
 439         (modules '((guix build utils)))
 440         (snippet
 441          '(begin
 442             ;; Make sure we don't use the bundled test framework.
 443             (delete-file-recursively "test/unit/cpp/catch")
 444             (substitute* "test/unit/cpp/main.cpp"
 445               ;; Use standard search paths for 'catch' header file.
 446               (("#include.*")
 447                "#include <catch.hpp>\n"))
 448             (substitute* "test/unit/cpp/CMakeLists.txt"
 449               ;; Specify directory to find the header file.
 450               (("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back)
 451                (string-append front
 452                               "$ENV{CATCH_DIR}/include" back "\n")))))))
 453     (build-system cmake-build-system)
 454     (inputs
 455      `(("blas" ,openblas)
 456        ("boost" ,boost)
 457        ("eigen" ,eigen)
 458        ("hdf5" ,hdf5-parallel-openmpi)
 459        ("lapack" ,lapack)
 460        ("libxml2" ,libxml2)
 461        ("openmpi" ,openmpi)
 462        ("python" ,python-3)
 463        ("scotch" ,pt-scotch32)
 464        ("suitesparse" ,suitesparse)
 465        ("sundials" ,sundials-openmpi)
 466        ("zlib" ,zlib)))
 467     (native-inputs
 468      `(("catch" ,catch-framework2-1)
 469        ("pkg-config" ,pkg-config)))
 470     (propagated-inputs
 471      `(("ffc" ,python-fenics-ffc)
 472        ("petsc" ,petsc-openmpi)
 473        ("slepc" ,slepc-openmpi)))
 474     (arguments
 475      `(#:configure-flags
 476        `("-DDOLFIN_ENABLE_DOCS:BOOL=OFF"
 477          "-DDOLFIN_ENABLE_HDF5:BOOL=ON"
 478          "-DDOLFIN_ENABLE_MPI:BOOL=ON"
 479          "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
 480          "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
 481          "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
 482          "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
 483        #:phases
 484        (modify-phases %standard-phases
 485          (add-after 'patch-usr-bin-file 'mpi-setup
 486            ,%openmpi-setup)
 487          (add-after 'patch-source-shebangs 'set-paths
 488            (lambda _
 489              ;; Define paths to store locations.
 490              (setenv "BLAS_DIR" (assoc-ref %build-inputs "blas"))
 491              (setenv "CATCH_DIR" (assoc-ref %build-inputs "catch"))
 492              (setenv "LAPACK_DIR" (assoc-ref %build-inputs "lapack"))
 493              (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
 494              (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
 495              (setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch"))
 496              (setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials"))
 497              (setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse"))))
 498          (add-before 'check 'pre-check
 499            (lambda _
 500              ;; The Dolfin repository uses git-lfs, whereby web links are
 501              ;; substituted for large files.  Guix does not currently support
 502              ;; git-lfs, so only the links are downloaded.  The tests that
 503              ;; require the absent meshes cannot run and are skipped.
 504              ;;
 505              ;; One serial test fails and is skipped.
 506              ;; i) demo_multimesh-stokes_serial:
 507              ;;   Warning: Found no facets matching domain for boundary
 508              ;;   condition.
 509              ;;
 510              ;; One mpi test fails and is skipped.
 511              ;; i) demo_stokes-iterative_mpi:
 512              ;;   The MPI_Comm_rank() function was called before MPI_INIT was
 513              ;;   invoked
 514              (call-with-output-file "CTestCustom.cmake"
 515                (lambda (port)
 516                  (display
 517                    (string-append
 518                     "set(CTEST_CUSTOM_TESTS_IGNORE "
 519                     "demo_bcs_serial "
 520                     "demo_bcs_mpi "
 521                     "demo_eigenvalue_serial "
 522                     "demo_eigenvalue_mpi "
 523                     "demo_navier-stokes_serial "
 524                     "demo_navier-stokes_mpi "
 525                     "demo_stokes-taylor-hood_serial "
 526                     "demo_stokes-taylor-hood_mpi "
 527                     "demo_subdomains_serial "
 528                     "demo_advection-diffusion_serial "
 529                     "demo_advection-diffusion_mpi "
 530                     "demo_auto-adaptive-navier-stokes_serial "
 531                     "demo_contact-vi-snes_serial "
 532                     "demo_contact-vi-snes_mpi "
 533                     "demo_contact-vi-tao_serial "
 534                     "demo_contact-vi-tao_mpi "
 535                     "demo_curl-curl_serial "
 536                     "demo_curl-curl_mpi "
 537                     "demo_dg-advection-diffusion_serial "
 538                     "demo_dg-advection-diffusion_mpi "
 539                     "demo_elasticity_serial "
 540                     "demo_elasticity_mpi "
 541                     "demo_elastodynamics_serial "
 542                     "demo_elastodynamics_mpi "
 543                     "demo_lift-drag_serial "
 544                     "demo_lift-drag_mpi "
 545                     "demo_mesh-quality_serial "
 546                     "demo_mesh-quality_mpi "
 547                     "demo_multimesh-stokes_serial "
 548                     ")\n") port)))))
 549          (replace 'check
 550            (lambda* (#:key tests? #:allow-other-keys)
 551              (when tests?
 552                (invoke "make" "unittests")
 553                (invoke "make" "demos")
 554                (invoke "ctest" "-R" "unittests")
 555                (invoke "ctest" "-R" "demo" "-R" "serial")
 556                (invoke "ctest" "-R" "demo" "-R" "mpi")))))))
 557     (home-page "https://bitbucket.org/fenics-project/dolfin/")
 558     (synopsis "Problem solving environment for differential equations")
 559     (description
 560       "DOLFIN is a computational framework for finding numerical
 561 solutions to problems described by differential equations.  Numerical
 562 models in DOLFIN are constructed using general families of finite
 563 elements.  Data structures are provided for discretizing the governing
 564 system on a computational mesh.  A compact syntax, similar to
 565 mathematical notation, is made available for defining function spaces
 566 and expressing variational forms.  Interfaces to specialized matrix
 567 solvers are provided for solving the resultant linear systems.
 568
 569 @code{fenics-dolfin} is part of the FEniCS project.  It is the C++
 570 user interface to the FEniCS core components and external libraries.")
 571     ;; The source code for the DOLFIN C++ library is licensed under the
 572     ;; GNU Lesser General Public License, version 3 or later, with the
 573     ;; following exceptions:
 574     ;;
 575     ;; public-domain: dolfin/geometry/predicates.cpp
 576     ;;                dolfin/geometry/predicates.h
 577     ;;
 578     ;; zlib:          dolfin/io/base64.cpp
 579     ;;                dolfin/io/base64.h
 580     ;;
 581     ;; expat:         dolfin/io/pugiconfig.hpp
 582     ;;                dolfin/io/pugixml.cpp
 583     ;;                dolfin/io/pugixml.hpp
 584     (license (list license:public-domain
 585                    license:zlib
 586                    license:expat
 587                    license:lgpl3+))))
 588
 589 (define-public fenics
 590   (package/inherit fenics-dolfin
 591     (name "fenics")
 592     (build-system python-build-system)
 593     (inputs
 594      `(("pybind11" ,pybind11)
 595        ("python-matplotlib" ,python-matplotlib)
 596        ,@(alist-delete "python" (package-inputs fenics-dolfin))))
 597     (native-inputs
 598      `(("cmake" ,cmake-minimal)
 599        ("ply" ,python-ply)
 600        ("pytest" ,python-pytest)
 601        ("python-decorator" ,python-decorator)
 602        ("python-pkgconfig" ,python-pkgconfig)
 603        ,@(package-native-inputs fenics-dolfin)))
 604     (propagated-inputs
 605      `(("dolfin" ,fenics-dolfin)
 606        ("petsc4py" ,python-petsc4py)
 607        ("slepc4py" ,python-slepc4py)))
 608     (arguments
 609      `(#:phases
 610        (modify-phases %standard-phases
 611          (add-after 'unpack 'relax-requirements
 612            (lambda _
 613              (substitute* "python/setup.py"
 614                (("pybind11==") "pybind11>="))))
 615          (add-after 'patch-source-shebangs 'set-paths
 616            (lambda _
 617              ;; Define paths to store locations.
 618              (setenv "PYBIND11_DIR" (assoc-ref %build-inputs "pybind11"))
 619              ;; Move to python sub-directory.
 620              (chdir "python")))
 621          (add-after 'build 'mpi-setup
 622            ,%openmpi-setup)
 623          (add-before 'check 'pre-check
 624            (lambda _
 625              ;; Exclude three tests that generate
 626              ;; 'NotImplementedError' in matplotlib version 3.1.2.
 627              ;; See
 628              ;; <https://github.com/matplotlib/matplotlib/issues/15382>.
 629              ;; Also exclude tests that require meshes supplied by
 630              ;; git-lfs.
 631              (substitute* "demo/test.py"
 632                (("(.*stem !.*)" line)
 633                 (string-append
 634                  line "\n"
 635                  "excludeList = [\n"
 636                  "'built-in-meshes', \n"
 637                  "'hyperelasticity', \n"
 638                  "'elasticity', \n"
 639                  "'multimesh-quadrature', \n"
 640                  "'multimesh-marking', \n"
 641                  "'mixed-poisson-sphere', \n"
 642                  "'mesh-quality', \n"
 643                  "'lift-drag', \n"
 644                  "'elastodynamics', \n"
 645                  "'dg-advection-diffusion', \n"
 646                  "'curl-curl', \n"
 647                  "'contact-vi-tao', \n"
 648                  "'contact-vi-snes', \n"
 649                  "'collision-detection', \n"
 650                  "'buckling-tao', \n"
 651                  "'auto-adaptive-navier-stokes', \n"
 652                  "'advection-diffusion', \n"
 653                  "'subdomains', \n"
 654                  "'stokes-taylor-hood', \n"
 655                  "'stokes-mini', \n"
 656                  "'navier-stokes', \n"
 657                  "'eigenvalue']\n"
 658                  "demos = ["
 659                  "d for d in demos if d[0].stem not in "
 660                  "excludeList]\n")))
 661              (setenv "HOME" (getcwd))
 662              ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
 663              (setenv "OPENBLAS_NUM_THREADS" "1")))
 664          (replace 'check
 665            (lambda* (#:key tests? #:allow-other-keys)
 666              (when tests?
 667                (with-directory-excursion "test"
 668                  (invoke
 669                   "pytest" "unit"
 670                   ;; The test test_snes_set_from_options() in the file
 671                   ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
 672                   "--ignore" "unit/nls/test_PETScSNES_solver.py"
 673                   ;; Fails with a segfault.
 674                   "--ignore" "unit/io/test_XDMF.py")))))
 675          (add-after 'install 'install-demo-files
 676            (lambda* (#:key outputs #:allow-other-keys)
 677              (let* ((demos (string-append
 678                             (assoc-ref outputs "out")
 679                             "/share/python-dolfin/demo")))
 680                (mkdir-p demos)
 681                (with-directory-excursion "demo"
 682                  (for-each (lambda (file)
 683                              (let* ((dir (dirname file))
 684                                     (tgt-dir (string-append demos "/" dir)))
 685                                (unless (equal? "." dir)
 686                                  (mkdir-p tgt-dir)
 687                                  (install-file file tgt-dir))))
 688                            (find-files "." ".*\\.(py|gz|xdmf)$")))))))))
 689     (home-page "https://fenicsproject.org/")
 690     (synopsis "High-level environment for solving differential equations")
 691     (description
 692       "@code{fenics} is a computing platform for solving general classes of
 693 problems that involve differential equations.  @code{fenics} facilitates
 694 access to efficient methods for dealing with ordinary differential
 695 equations (ODEs) and partial differential equations (PDEs).  Systems of
 696 equations such as these are commonly encountered in areas of engineering,
 697 mathematics and the physical sciences.  It is particularly well-suited to
 698 problems that can be solved using the Finite Element Method (FEM).
 699
 700 @code{fenics} is the top level of the set of packages that are developed
 701 within the FEniCS project.  It provides the python user interface to the
 702 FEniCS core components and external libraries.")
 703     (license license:lgpl3+)))
 704
 705 (define-public fullswof-2d
 706   (let ((revision 505)
 707         (release "1.09.01"))
 708     (package
 709       (name "fullswof-2d")
 710       (version release)
 711       (source (origin
 712                (method svn-fetch)
 713                (uri (svn-reference
 714                      (url (string-append "https://subversion.renater.fr/"
 715                                          "anonscm/svn/fullswof-2d/tags/"
 716                                          "release-" version))
 717                      (revision revision)))
 718                (file-name (string-append "fullswof-2d-" version "-checkout"))
 719                (sha256
 720                 (base32
 721                  "16v08dx7h7n4wyddzbwimazwyj74ynis12mpjfkay4243npy44b8"))))
 722       (build-system gnu-build-system)
 723       (native-inputs
 724        (list inetutils)) ; for 'hostname', used in the check phase
 725       (arguments
 726        `(#:phases
 727          (modify-phases %standard-phases
 728            (delete 'configure)     ; no configure script
 729            (add-after 'build 'build-tools
 730              (lambda _
 731                (with-directory-excursion "Tools/ConvertFormat"
 732                  (invoke "make" "../../bin/asc2xyz")
 733                  (invoke "make" "../../bin/xyz2asc"))
 734                (with-directory-excursion "Tools/ExtractWindow"
 735                  (invoke "make" "../../bin/cropxyz"))
 736                #t))
 737            (replace 'check         ; no check target
 738              (lambda _
 739                (invoke "make" "benchref")))
 740            (replace 'install       ; no install target
 741              (lambda* (#:key outputs #:allow-other-keys)
 742                (let* ((out (assoc-ref outputs "out"))
 743                       (bin (string-append out "/bin"))
 744                       (doc (string-append
 745                             out "/share/doc/" ,name "-" ,version))
 746                       (examples (string-append doc "/Examples")))
 747                  (with-directory-excursion "bin"
 748                    (for-each (lambda (binary) (install-file binary bin))
 749                              (list "asc2xyz" "xyz2asc" "cropxyz"
 750                                    "FullSWOF_2D")))
 751                  (with-directory-excursion "doc"
 752                    (for-each (lambda (pdf) (install-file pdf doc))
 753                              (list "Documentation.pdf" "refman.pdf")))
 754                  (with-directory-excursion "Tools"
 755                    (for-each (lambda (dir)
 756                                (copy-file
 757                                 (string-append dir "/README.txt")
 758                                 (string-append doc "/README_" dir ".txt")))
 759                              (list "ConvertFormat" "ExtractWindow")))
 760                  (copy-recursively "Examples" examples)
 761                  #t))))))
 762       (home-page "https://www.idpoisson.fr/fullswof/")
 763       (synopsis "Two dimensional flow solver for flood modelling")
 764       (description "@code{FullSWOF_2d} is a numerical tool for solving
 765 the shallow water equations on structured grids.  The name FullSWOF
 766 refers to the Full form of the Shallow Water equations for Overland
 767 Flow.  The discretized system of equations is solved using the finite
 768 volume method.  A choice of shock-capturing methods is available to
 769 locate the transition boundaries between the wet areas and the dry
 770 areas in the model.  A semi-implicit method is used to advance the
 771 solution in time.  The tool is typically applied to the modelling of
 772 river flooding.")
 773       (license license:cecill))))
 774
 775 (define-public python-meshio
 776   (package
 777     (name "python-meshio")
 778     (version "5.3.4")
 779     (source
 780      (origin
 781        (method url-fetch)
 782        (uri (pypi-uri "meshio" version))
 783        (sha256
 784         (base32
 785          "1w39qcg0rw5kb04j7sa45fnqd6k20fsdgrf62cmw2ygjgwnnjh72"))
 786        (snippet
 787         '(let ((file (open-file "setup.py" "a")))
 788            (display "from setuptools import setup\nsetup()" file)
 789            (close-port file)))))
 790     (build-system python-build-system)
 791     (inputs
 792      (list python-h5py
 793            python-netcdf4))
 794     (native-inputs
 795      (list python-pytest))
 796     (propagated-inputs
 797      (list python-importlib-metadata
 798            python-numpy
 799            python-rich))
 800     (arguments
 801      '(#:phases
 802        (modify-phases %standard-phases
 803          (replace 'check
 804            (lambda* (#:key tests? #:allow-other-keys)
 805              (when tests?
 806                (invoke "python" "-m" "pytest" "-v" "tests")))))))
 807     (home-page "https://github.com/nschloe/meshio")
 808     (synopsis "I/O for mesh files")
 809     (description "There are various file formats available for
 810 representing unstructured meshes and mesh data.  The @code{meshio}
 811 package is able to read and write mesh files in many formats and to
 812 convert files from one format to another.  Formats such as cgns, h5m,
 813 gmsh, xdmf and vtk are supported.  The package provides command-line
 814 tools and a collection of Python modules for programmatic use.")
 815     (license license:expat)))
 816
 817 (define-public python-pygmsh
 818   (package
 819     (name "python-pygmsh")
 820     (version "7.1.17")
 821     (source
 822      (origin
 823        (method git-fetch)
 824        (uri (git-reference
 825              (url "https://github.com/nschloe/pygmsh")
 826              (commit (string-append "v" version))))
 827        (file-name (git-file-name name version))
 828        (sha256
 829         (base32
 830          "11flp2c4ynk1fhanf4mqyzrpd0gjbnv6afrwwc7xi3mb6ms69lr0"))))
 831     (build-system python-build-system)
 832     (arguments
 833      (list
 834       #:phases
 835       #~(modify-phases %standard-phases
 836           (add-after 'unpack 'workaround-gmsh-detection-failure
 837             (lambda _
 838               ;; Due to lack of metadata, the gmsh Python package is not
 839               ;; detected although importable.
 840               (substitute* "pyproject.toml"
 841                 (("\"gmsh\",") ""))))
 842           ;; XXX: PEP 517 manual build copied from python-isort.
 843           (replace 'build
 844             (lambda _
 845               (invoke "python" "-m" "build" "--wheel" "--no-isolation" ".")))
 846           (replace 'check
 847             (lambda* (#:key tests? #:allow-other-keys)
 848               (when tests?
 849                 (invoke "pytest" "-v" "tests"))))
 850           (replace 'install
 851             (lambda _
 852               (let ((whl (car (find-files "dist" "\\.whl$"))))
 853                 (invoke "pip" "--no-cache-dir" "--no-input"
 854                         "install" "--no-deps" "--prefix" #$output whl)))))))
 855     (native-inputs (list python-pypa-build python-flit-core python-pytest))
 856     (propagated-inputs (list gmsh python-meshio python-numpy))
 857     (home-page "https://github.com/nschloe/pygmsh")
 858     (synopsis "Python frontend for Gmsh")
 859     (description "The goal of @code{pygmsh} is to combine the power of
 860 Gmsh with the versatility of Python.  The package generalises many of
 861 the methods and functions that comprise the Gmsh Python API.  In this
 862 way the meshing of complex geometries using high-level abstractions is
 863 made possible.  The package provides a Python library together with a
 864 command-line utility for mesh optimisation.")
 865     (license license:gpl3+)))
 866
 867 (define-public python-dolfin-adjoint
 868   (package
 869     (name "python-dolfin-adjoint")
 870     (version "2019.1.0")
 871     (source
 872       (origin
 873         (method git-fetch)
 874         (uri (git-reference
 875               (url "https://github.com/dolfin-adjoint/pyadjoint")
 876               (commit version)))
 877         (file-name (git-file-name name version))
 878         (sha256
 879           (base32
 880            "0xhy76a5f33hz94wc9g2mc5qmwkxfccbbc6yxl7psm130afp8lhn"))
 881         (modules '((guix build utils)))
 882         (snippet
 883          '(begin
 884             ;; One of the migration tests attempts to call openmpi
 885             ;; recursively and fails.  See
 886             ;; https://bitbucket.org/mpi4py/mpi4py/issues/95.  Run the
 887             ;; test sequentially instead.
 888             (with-directory-excursion "tests/migration/optimal_control_mms"
 889               (substitute* "test_optimal_control_mms.py"
 890                 (("\\\"mpirun\\\", \\\"-n\\\", \\\"2\\\", ") "")))
 891             ;; Result files are regenerated in the check phase.
 892             (delete-file-recursively
 893              "tests/migration/viscoelasticity/test-results")
 894             #t))))
 895     (build-system python-build-system)
 896     (inputs
 897      (list fenics openmpi pybind11))
 898     (native-inputs
 899      (list pkg-config
 900            python-coverage
 901            python-decorator
 902            python-flake8
 903            python-pkgconfig
 904            python-pytest))
 905     (propagated-inputs
 906      `(("scipy" ,python-scipy)))
 907     (arguments
 908      `(#:phases
 909        (modify-phases %standard-phases
 910          (add-after 'build 'mpi-setup
 911                     ,%openmpi-setup)
 912          (add-after 'install 'install-doc
 913            (lambda* (#:key outputs #:allow-other-keys)
 914              (let* ((doc (string-append (assoc-ref outputs "out")
 915                                         "/share/doc/" ,name "-"
 916                                         ,version))
 917                     (examples (string-append doc "/examples")))
 918                (mkdir-p examples)
 919                (copy-recursively "examples" examples))
 920              #t))
 921          (replace 'check
 922            (lambda* (#:key inputs outputs tests? #:allow-other-keys)
 923              (when tests?
 924                (add-installed-pythonpath inputs outputs)
 925                (setenv "HOME" (getcwd))
 926                (and (invoke "py.test" "-v" "tests/fenics_adjoint")
 927                     (invoke "py.test" "-v" "tests/migration")
 928                     (invoke "py.test" "-v" "tests/pyadjoint")))
 929              #t)))))
 930     (home-page "http://www.dolfin-adjoint.org")
 931     (synopsis "Automatic differentiation library")
 932     (description "@code{python-dolfin-adjoint} is a solver of
 933 differential equations associated with a governing system and a
 934 functional of interest.  Working from the forward model the solver
 935 automatically derives the discrete adjoint and tangent linear models.
 936 These additional models are key ingredients in many algorithms such as
 937 data assimilation, optimal control, sensitivity analysis, design
 938 optimisation and error estimation.  The dolfin-adjoint project
 939 provides the necessary tools and data structures for cases where the
 940 forward model is implemented in @code{fenics} or
 941 @url{https://firedrakeproject.org,firedrake}.")
 942     (license license:lgpl3)))