;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
+;;; Copyright © 2017, 2018
, 2019, 2020 Paul Garlick <pgarlick@tourbillion-technology.com>
;;;
;;; This file is part of GNU Guix.
;;;
(define-module (gnu packages simulation)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
+ #:use-module (gnu packages admin)
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages bison)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-xyz)
#:use-module (gnu packages readline)
#:use-module (gnu packages tls)
#:use-module (gnu packages version-control)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (guix download)
- #:use-module (guix build utils)
+ #:use-module (guix svn-download)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "0cgxh4h2hf50qbvvdg5miwc2nympb0nrv3md96vb3gbs9vk8vq9d"))
- (patches (search-patches "openfoam-4.1-cleanup.patch"))))
+ (patches (search-patches "openfoam-4.1-cleanup.patch"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Include <sys/sysmacros.h>, which is where glibc >= 2.28 provides
+ ;; 'major' and 'minor'.
+ (substitute* "src/OSspecific/POSIX/fileStat.C"
+ (("#include <unistd\\.h>")
+ "#include <unistd.h>\n#include <sys/sysmacros.h>\n"))
+ #t))))
(build-system gnu-build-system)
(inputs
`(("boost" ,boost)
(define-public python-fenics-dijitso
(package
(name "python-fenics-dijitso")
- (version "2018.1.0")
+ (version "2019.1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "fenics-dijitso" version))
(sha256
(base32
- "1qax2f52qsjbd1h5lk5i5shp448qlakxabjjybrfc1w823p0yql9"))))
+ "0lhqsq8ypdak0ahr2jnyvg07yrqp6wicjxi6k56zx24wp3qg60sc"))))
(build-system python-build-system)
(inputs
`(("openmpi" ,openmpi)
(setenv "PYTHONPATH"
(string-append (getcwd) ":" (getenv "PYTHONPATH")))
(with-directory-excursion "test"
+ ;; Disable parallel tests to avoid race condition. See
+ ;; https://github.com/pytest-dev/pytest-cov/issues/237.
+ (substitute* "runtests.sh"
+ (("for p in 1 4 8 16; do")
+ "for p in 1; do"))
(invoke "./runtests.sh"))
#t)))))
(home-page "https://bitbucket.org/fenics-project/dijitso/")
(define-public python-fenics-ufl
(package
(name "python-fenics-ufl")
- (version "2018.1.0")
+ (version "2019.1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "fenics-ufl" version))
(sha256
(base32
- "1fq8yc86s1s3c8c0b1rc2vf265q0hrkzg57100fg1nghcz0p4vla"))))
+ "10dz8x3lm68x2w3kkqcjask38h0zkhhak26jdbkppr8g9y8wny7p"))))
(build-system python-build-system)
(inputs
`(("python-numpy" ,python-numpy)))
(define-public python-fenics-fiat
(package
(name "python-fenics-fiat")
- (version "2018.1.0")
+ (version "2019.1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "fenics-fiat" version))
(sha256
(base32
- "0fmjd93r6bwf6xs8csw86qzphrnr66xwv7f372w59gmq8mg6rljc"))))
+ "13sc7lma3d2mh43an7i4kkdbbk4cmvxjk45wi43xnjd7qc38zg4b"))))
(build-system python-build-system)
(native-inputs
`(("python-pytest" ,python-pytest)))
(setenv "PYTHONPATH"
(string-append (getcwd) ":" (getenv "PYTHONPATH")))
(with-directory-excursion "test"
- (invoke "py.test" "unit/"))
+ ;; FIXME: three FIAT test modules are known to fail
+ ;; with recent versions of pytest (>= 4). These are
+ ;; skipped for FIAT version 2019.1.0 pending an
+ ;; upstream pull request. For details see request #59
+ ;; at https://bitbucket.org/fenics-project/fiat/.
+ (invoke "py.test" "unit/"
+ "--ignore=unit/test_fiat.py"
+ "--ignore=unit/test_quadrature.py"
+ "--ignore=unit/test_reference_element.py"))
#t)))))
(home-page "https://bitbucket.org/fenics-project/fiat/")
(synopsis "Tabulation of finite element function spaces")
(define-public python-fenics-ffc
(package
(name "python-fenics-ffc")
- (version "2018.1.0")
+ (version "2019.1.0.post0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "fenics-ffc" version))
(sha256
(base32
- "1b2ia5vlkw298x7rf0k2p3ihlpwkwgc98p3s6sbpds3hqmfrzdz9"))))
+ "1f2a44ha65fg3a1prrbrsz4dgvibsv0j5c3pi2m52zi93bhwwgg9"))))
(build-system python-build-system)
(native-inputs
`(("python-pytest" ,python-pytest)))
(define-public fenics-dolfin
(package
(name "fenics-dolfin")
- (version "2018.1.0.post1")
+ (version "2019.1.0.post0")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "12zkk8j3xsg6l8p0ggwsl03084vlcivw4h99b7z9kndg7k89b3ya"))
+ "1m91hwcq5gfj4qqswp8l8kj58nia48f0n4kq13w0xqj4biq7rla0"))
(modules '((guix build utils)))
(snippet
'(begin
(("#include.*")
"#include <catch.hpp>\n"))
(substitute* "test/unit/cpp/CMakeLists.txt"
- ;; Add extra include directories required by the unit tests.
- (("(^target_link_libraries.*)" line)
- (string-append line "\n"
- "target_include_directories("
- "unittests PRIVATE "
- "${DOLFIN_SOURCE_DIR} "
- "${DOLFIN_SOURCE_DIR}/dolfin "
- "${DOLFIN_BINARY_DIR})\n"))
+ ;; Specify directory to find the header file.
(("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back)
(string-append front
- "$ENV{CATCH_DIR}"
- "/include" back "\n")))
- (substitute* "demo/CMakeLists.txt"
- ;; Add extra include directories required by the demo tests.
- (("(^#find_package.*)" line)
- (string-append line "\n"
- "include_directories("
- "${DOLFIN_SOURCE_DIR} "
- "${DOLFIN_SOURCE_DIR}/dolfin "
- "${DOLFIN_BINARY_DIR})\n")))
+ "$ENV{CATCH_DIR}/include" back "\n")))
#t))))
(build-system cmake-build-system)
(inputs
("sundials" ,sundials-openmpi)
("zlib" ,zlib)))
(native-inputs
- `(("catch" ,catch-framework2)
+ `(("catch" ,catch-framework2-1)
("pkg-config" ,pkg-config)))
(propagated-inputs
`(("ffc" ,python-fenics-ffc)
("python-matplotlib" ,python-matplotlib)
,@(alist-delete "python" (package-inputs fenics-dolfin))))
(native-inputs
- `(("cmake" ,cmake)
+ `(("cmake" ,cmake-minimal)
("ply" ,python-ply)
("pytest" ,python-pytest)
("python-decorator" ,python-decorator)
,%openmpi-setup)
(add-before 'check 'pre-check
(lambda _
- ;; Exclude tests that require meshes supplied by git-lfs.
+ ;; Exclude three tests that generate
+ ;; 'NotImplementedError' in matplotlib version 3.1.2.
+ ;; See
+ ;; <https://github.com/matplotlib/matplotlib/issues/15382>.
+ ;; Also exclude tests that require meshes supplied by
+ ;; git-lfs.
(substitute* "demo/test.py"
(("(.*stem !.*)" line)
(string-append
line "\n"
"excludeList = [\n"
+ "'built-in-meshes', \n"
+ "'hyperelasticity', \n"
+ "'elasticity', \n"
"'multimesh-quadrature', \n"
"'multimesh-marking', \n"
"'mixed-poisson-sphere', \n"
"'lift-drag', \n"
"'elastodynamics', \n"
"'dg-advection-diffusion', \n"
+ "'curl-curl', \n"
"'contact-vi-tao', \n"
"'contact-vi-snes', \n"
"'collision-detection', \n"
(with-directory-excursion "test"
;; Note: The test test_snes_set_from_options() in the file
;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
- (and (invoke "py.test" "unit" "--ignore"
- "unit/nls/test_PETScSNES_solver.py")
- (invoke "mpirun" "-np" "3" "python" "-B" "-m"
- "pytest" "unit" "--ignore"
- "unit/nls/test_PETScSNES_solver.py")))
- (with-directory-excursion "demo"
- ;; Check demos.
- (invoke "python" "generate-demo-files.py")
- (and (invoke "python" "-m" "pytest" "-v" "test.py")
- (invoke "python" "-m" "pytest" "-v" "test.py"
- "--mpiexec=mpiexec" "--num-proc=3")))
+ ;; Limit the number of jobs to 3 as 500 MiB of memory is used
+ ;; per process.
+ (invoke "mpirun" "-np" (number->string
+ (min 3 (parallel-job-count)))
+ "python" "-B" "-m"
+ "pytest" "unit" "--ignore"
+ "unit/nls/test_PETScSNES_solver.py"))
#t))
(add-after 'install 'install-demo-files
(lambda* (#:key outputs #:allow-other-keys)
within the FEniCS project. It provides the python user interface to the
FEniCS core components and external libraries.")
(license license:lgpl3+)))
+
+(define-public fullswof-2d
+ (let ((revision 505)
+ (release "1.09.01"))
+ (package
+ (name "fullswof-2d")
+ (version release)
+ (source (origin
+ (method svn-fetch)
+ (uri (svn-reference
+ (url (string-append "https://subversion.renater.fr/"
+ "anonscm/svn/fullswof-2d/tags/"
+ "release-" version))
+ (revision revision)))
+ (file-name (string-append "fullswof-2d-" version "-checkout"))
+ (sha256
+ (base32
+ "16v08dx7h7n4wyddzbwimazwyj74ynis12mpjfkay4243npy44b8"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("inetutils" ,inetutils))) ; for 'hostname', used in the check phase
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; no configure script
+ (add-after 'build 'build-tools
+ (lambda _
+ (with-directory-excursion "Tools/ConvertFormat"
+ (invoke "make" "../../bin/asc2xyz")
+ (invoke "make" "../../bin/xyz2asc"))
+ (with-directory-excursion "Tools/ExtractWindow"
+ (invoke "make" "../../bin/cropxyz"))
+ #t))
+ (replace 'check ; no check target
+ (lambda _
+ (invoke "make" "benchref")))
+ (replace 'install ; no install target
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (doc (string-append
+ out "/share/doc/" ,name "-" ,version))
+ (examples (string-append doc "/Examples")))
+ (with-directory-excursion "bin"
+ (for-each (lambda (binary) (install-file binary bin))
+ (list "asc2xyz" "xyz2asc" "cropxyz"
+ "FullSWOF_2D")))
+ (with-directory-excursion "doc"
+ (for-each (lambda (pdf) (install-file pdf doc))
+ (list "Documentation.pdf" "refman.pdf")))
+ (with-directory-excursion "Tools"
+ (for-each (lambda (dir)
+ (copy-file
+ (string-append dir "/README.txt")
+ (string-append doc "/README_" dir ".txt")))
+ (list "ConvertFormat" "ExtractWindow")))
+ (copy-recursively "Examples" examples)
+ #t))))))
+ (home-page "https://www.idpoisson.fr/fullswof/")
+ (synopsis "Two dimensional flow solver for flood modelling")
+ (description "@code{FullSWOF_2d} is a numerical tool for solving
+the shallow water equations on structured grids. The name FullSWOF
+refers to the Full form of the Shallow Water equations for Overland
+Flow. The discretized system of equations is solved using the finite
+volume method. A choice of shock-capturing methods is available to
+locate the transition boundaries between the wet areas and the dry
+areas in the model. A semi-implicit method is used to advance the
+solution in time. The tool is typically applied to the modelling of
+river flooding.")
+ (license license:cecill))))
HCoop / jackhill / guix / guix.git / blobdiff