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-rw-r--r--gnu/packages/maths.scm207
1 files changed, 106 insertions, 101 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 263f80f246..e694a5b187 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4593,36 +4593,8 @@ linear algebra primitives specifically targeting graph analytics.")
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
(apply invoke "make" "build_tests" make-flags)))
- ;; These tests fail because they require a fully functional MPI
- ;; environment.
- (add-after 'unpack 'disable-failing-tests
- (lambda _
- (setenv "ARGS"
- (string-append "--exclude-regex '("
- (string-join
- (list
- "remoteindicestest"
- "remoteindicestest-mpi-2"
- "syncertest"
- "syncertest-mpi-2"
- "variablesizecommunicatortest"
- "variablesizecommunicatortest-mpi-2"
- "arithmetictestsuitetest"
- "assertandreturntest"
- "assertandreturntest_ndebug"
- "concept"
- "debugaligntest"
- "mpicollectivecommunication"
- "mpicollectivecommunication-mpi-2"
- "mpiguardtest"
- "mpiguardtest-mpi-2"
- "mpihelpertest"
- "mpihelpertest-mpi-2"
- "mpihelpertest2"
- "mpihelpertest2-mpi-2")
- "|")
- ")'"))
- #t)))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(inputs
`(("gmp" ,gmp)
("metis" ,metis)
@@ -4684,6 +4656,42 @@ This package contains the basic DUNE geometry classes.")
;; GPL version 2 with "runtime exception"
(license license:gpl2)))
+(define-public dune-uggrid
+ (package
+ (name "dune-uggrid")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://dune-project.org/download/"
+ version "/dune-uggrid-" version ".tar.gz"))
+ (sha256
+ (base32
+ "05l7a1gb78mny49anyxk6rjvn66rhgm30y72v5cjg0m5kfgr1a1f"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'build 'build-tests
+ (lambda* (#:key make-flags #:allow-other-keys)
+ (apply invoke "make" "build_tests" make-flags))))))
+ (inputs
+ `(("dune-common" ,dune-common)
+ ("openmpi" ,openmpi)))
+ (native-inputs
+ `(("gfortran" ,gfortran)
+ ("pkg-config" ,pkg-config)))
+ (home-page "https://dune-project.org/")
+ (synopsis "Distributed and Unified Numerics Environment")
+ (description "DUNE, the Distributed and Unified Numerics Environment is a
+modular toolbox for solving @dfn{partial differential equations} (PDEs) with
+grid-based methods. It supports the easy implementation of methods like
+@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
+Differences} (FD).
+
+This package contains the DUNE UG grid classes.")
+ (license license:lgpl2.1)))
+
(define-public dune-grid
(package
(name "dune-grid")
@@ -4703,54 +4711,8 @@ This package contains the basic DUNE geometry classes.")
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
(apply invoke "make" "build_tests" make-flags)))
- ;; These tests fail because they require a fully functional MPI
- ;; environment.
- (add-after 'unpack 'disable-failing-tests
- (lambda _
- (setenv "ARGS"
- (string-append "--exclude-regex '("
- (string-join
- (list
- "scsgmappertest"
- "conformvolumevtktest"
- "gnuplottest"
- "nonconformboundaryvtktest"
- "subsamplingvtktest"
- "vtktest"
- "vtktest-mpi-2"
- "vtksequencetest"
- "gmshtest-onedgrid"
- "test-dgf-yasp"
- "test-dgf-yasp-offset"
- "test-dgf-oned"
- "test-geogrid-yaspgrid"
- "test-gridinfo"
- "test-identitygrid"
- "testiteratorranges"
- "test-hierarchicsearch"
- "test-parallel-ug-mpi-2"
- "test-yaspgrid-backuprestore-equidistant"
- "test-yaspgrid-backuprestore-equidistant-mpi-2"
- "test-yaspgrid-backuprestore-equidistantoffset"
- "test-yaspgrid-backuprestore-equidistantoffset-mpi-2"
- "test-yaspgrid-backuprestore-tensor"
- "test-yaspgrid-backuprestore-tensor-mpi-2"
- "test-yaspgrid-tensorgridfactory"
- "test-yaspgrid-tensorgridfactory-mpi-2"
- "test-yaspgrid-yaspfactory-1d"
- "test-yaspgrid-yaspfactory-1d-mpi-2"
- "test-yaspgrid-yaspfactory-2d"
- "test-yaspgrid-yaspfactory-2d-mpi-2"
- "test-yaspgrid-yaspfactory-3d"
- "test-yaspgrid-yaspfactory-3d-mpi-2"
- "globalindexsettest"
- "persistentcontainertest"
- "structuredgridfactorytest"
- "tensorgridfactorytest"
- "vertexordertest")
- "|")
- ")'"))
- #t)))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
@@ -4759,6 +4721,8 @@ This package contains the basic DUNE geometry classes.")
("openblas" ,openblas)
("openmpi" ,openmpi)
("python" ,python)))
+ (propagated-inputs
+ `(("dune-uggrid" ,dune-uggrid)))
(native-inputs
`(("gfortran" ,gfortran)
("pkg-config" ,pkg-config)))
@@ -4793,29 +4757,14 @@ This package contains the basic DUNE grid classes.")
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
(apply invoke "make" "build_tests" make-flags)))
- ;; These tests fail because they require a fully functional MPI
- ;; environment.
- (add-after 'unpack 'disable-failing-tests
- (lambda _
- (setenv "ARGS"
- (string-append "--exclude-regex '("
- (string-join
- (list
- "galerkintest"
- "hierarchytest"
- "pamgtest"
- "pamg_comm_repart_test"
- "matrixredisttest"
- "vectorcommtest"
- "matrixmarkettest")
- "|")
- ")'"))
- #t)))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(inputs
`(("dune-common" ,dune-common)
("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
+ ("suitesparse" ,suitesparse)
("superlu" ,superlu)
("openblas" ,openblas)
("gmp" ,gmp)
@@ -4896,9 +4845,7 @@ assemble global function spaces on finite-element grids.")
"1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
(build-system cmake-build-system)
(arguments
- `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI
- ; environment
- #:phases
+ `(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-include
(lambda _
@@ -4910,7 +4857,9 @@ assemble global function spaces on finite-element grids.")
(lambda* (#:key inputs make-flags #:allow-other-keys)
(setenv "CPLUS_INCLUDE_PATH"
(string-append (assoc-ref inputs "dune-grid") "/share"))
- (apply invoke "make" "build_tests" make-flags))))))
+ (apply invoke "make" "build_tests" make-flags)))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
@@ -4933,6 +4882,49 @@ implementation of the DUNE grid interface supporting either simplices or
cubes.")
(license license:gpl2+)))
+(define-public dune-subgrid
+ (package
+ (name "dune-subgrid")
+ (version "2.6.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid")
+ (commit "releases/2.6-1")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1gcv35rx3knqd54r4pp9rzd639db4j8w2r2ibq43w1mgwdcqhs64"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'build 'build-tests
+ (lambda* (#:key make-flags #:allow-other-keys)
+ (apply invoke "make" "build_tests" make-flags)))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
+ (inputs
+ `(("dune-common" ,dune-common)
+ ("dune-geometry" ,dune-geometry)
+ ("dune-grid" ,dune-grid)
+ ("openmpi" ,openmpi)
+ ;; Optional
+ ("metis" ,metis)
+ ("openblas" ,openblas)
+ ("gmp" ,gmp)))
+ (native-inputs
+ `(("gfortran" ,gfortran)
+ ("pkg-config" ,pkg-config)))
+ (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php")
+ (synopsis "Distributed and Unified Numerics Environment")
+ (description "The dune-subgrid module allows to mark elements of
+another hierarchical dune grid. The set of marked elements can then be
+accessed as a hierarchical dune grid in its own right. Dune-Subgrid
+provides the full grid interface including adaptive mesh refinement.")
+ (license license:gpl2+)))
+
(define-public dune-typetree
(package
(name "dune-typetree")
@@ -4988,7 +4980,20 @@ operating on statically typed trees of objects.")
(base32
"1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
(build-system cmake-build-system)
- (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'disable-failing-tests
+ (lambda _
+ (setenv "ARGS"
+ ;; unable to load GMSH file in this test
+ "--exclude-regex gridviewfunctionspacebasistest")
+ #t))
+ (add-after 'build 'build-tests
+ (lambda* (#:key make-flags #:allow-other-keys)
+ (apply invoke "make" "build_tests" make-flags)))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(inputs
`(("dune-common" ,dune-common)
("dune-istl" ,dune-istl)
generated by cgit v1.2.3 (git 2.25.4) at 2024-05-19 10:34:34 +0000