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-rw-r--r--gnu/packages/maths.scm512
1 files changed, 499 insertions, 13 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 602c696567..7d3ac773b3 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -749,7 +749,7 @@ incompatible with HDF5.")
(define-public hdf5
(package
(name "hdf5")
- (version "1.8.19")
+ (version "1.8.21")
(source
(origin
(method url-fetch)
@@ -759,12 +759,14 @@ incompatible with HDF5.")
version ".tar.bz2")
(string-append "https://support.hdfgroup.org/ftp/HDF5/"
"current"
- (apply string-append
- (take (string-split version #\.) 2))
+ (match (string-split version #\.)
+ ((major minor _ ...)
+ (string-append major minor)))
"/src/hdf5-" version ".tar.bz2")))
(sha256
- (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
- (patches (list (search-patch "hdf5-config-date.patch")))))
+ (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
+ (patches (search-patches "hdf5-config-date.patch"
+ "hdf5-1.8-mpi-deprecations.patch"))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)))
@@ -877,7 +879,8 @@ extremely large and complex data collections.")
"/src/hdf5-" version ".tar.bz2")))
(sha256
(base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
- (patches (list (search-patch "hdf5-config-date.patch")))))))
+ (patches (search-patches "hdf5-config-date.patch"
+ "hdf5-mpi-deprecations.patch"))))))
(define-public hdf-java
(package
@@ -2331,7 +2334,8 @@ void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
"RowPerm = NOROWPERM;"))
#t))
(patches (search-patches "superlu-dist-scotchmetis.patch"
- "superlu-dist-awpm-grid.patch"))))
+ "superlu-dist-awpm-grid.patch"
+ "superlu-dist-fix-mpi-deprecations.patch"))))
(build-system cmake-build-system)
(native-inputs
`(("tcsh" ,tcsh)))
@@ -2691,7 +2695,7 @@ to BMP, JPEG or PNG image formats.")
(define-public maxima
(package
(name "maxima")
- (version "5.42.1")
+ (version "5.42.2")
(source
(origin
(method url-fetch)
@@ -2699,7 +2703,7 @@ to BMP, JPEG or PNG image formats.")
version "-source/" name "-" version ".tar.gz"))
(sha256
(base32
- "1ka0xf70a55ndgmyrq7p5xxbd78pq7bfkqhgxsivaqdw6gn5lmcg"))
+ "0kdncy6137sg3rradirxzj10mkcvafxd892zlclwhr9sa7b12zhn"))
(patches (search-patches "maxima-defsystem-mkdir.patch"))))
(build-system gnu-build-system)
(inputs
@@ -2802,7 +2806,7 @@ point numbers.")
(define-public wxmaxima
(package
(name "wxmaxima")
- (version "18.11.4")
+ (version "19.01.3")
(source
(origin
(method git-fetch)
@@ -2812,7 +2816,7 @@ point numbers.")
(file-name (git-file-name name version))
(sha256
(base32
- "1sz8n9v23q442l7yjj67pjh0dk78rl4cbcc3j8m1bm88anlfxl9r"))))
+ "1vwahx3zxkn3qlv4z0fm7v8wh0wspvs026alrh7ff7s0c2dcy95x"))))
(build-system cmake-build-system)
(native-inputs
`(("gettext" ,gettext-minimal)))
@@ -2926,7 +2930,7 @@ parts of it.")
(define-public openblas
(package
(name "openblas")
- (version "0.3.3")
+ (version "0.3.4")
(source
(origin
(method url-fetch)
@@ -2935,7 +2939,7 @@ parts of it.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0cvlixnpc3cdvvn3f30phfvsgnqljqix6wn72ps9rj7xdhvw06jg"))))
+ "1s56lgilyyw86dzmj3jkci9zsg24n60wq4d0zri1hrxlxb6ihimj"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
@@ -4244,3 +4248,485 @@ linear algebra primitives specifically targeting graph analytics.")
license:gpl2+ ;include/psort/(funnel|sort)*.h
license:x11 ;usort and psort
license:bsd-3)))) ;CombBLAS and MersenneTwister.h
+
+(define-public dune-common
+ (package
+ (name "dune-common")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://dune-project.org/download/"
+ version "/dune-common-" version ".tar.gz"))
+ (sha256
+ (base32
+ "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw"))))
+ (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)))
+ ;; 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)))))
+ (inputs
+ `(("gmp" ,gmp)
+ ("metis" ,metis)
+ ("openmpi" ,openmpi)
+ ("openblas" ,openblas)
+ ("python" ,python)
+ ("superlu" ,superlu)))
+ (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).")
+ ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
+ (license license:gpl2)))
+
+(define-public dune-geometry
+ (package
+ (name "dune-geometry")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://dune-project.org/download/"
+ version "/dune-geometry-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn"))))
+ (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)
+ ;; Optional
+ ("openblas" ,openblas)
+ ("gmp" ,gmp)
+ ("python" ,python)))
+ (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 basic DUNE geometry classes.")
+ ;; GPL version 2 with "runtime exception"
+ (license license:gpl2)))
+
+(define-public dune-grid
+ (package
+ (name "dune-grid")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://dune-project.org/download/"
+ version "/dune-grid-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0"))))
+ (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)))
+ ;; 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)))))
+ (inputs
+ `(("dune-common" ,dune-common)
+ ("dune-geometry" ,dune-geometry)
+ ("gmp" ,gmp)
+ ("metis" ,metis)
+ ("openblas" ,openblas)
+ ("openmpi" ,openmpi)
+ ("python" ,python)))
+ (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 basic DUNE grid classes.")
+ ;; GPL version 2 with "runtime exception"
+ (license license:gpl2)))
+
+(define-public dune-istl
+ (package
+ (name "dune-istl")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://dune-project.org/download/"
+ version "/dune-istl-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w"))))
+ (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)))
+ ;; 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)))))
+ (inputs
+ `(("dune-common" ,dune-common)
+ ("openmpi" ,openmpi)
+ ;; Optional
+ ("metis" ,metis)
+ ("superlu" ,superlu)
+ ("openblas" ,openblas)
+ ("gmp" ,gmp)
+ ("python" ,python)))
+ (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.
+
+This is the iterative solver template library which provides generic sparse
+matrix/vector classes and a variety of solvers based on these classes. A
+special feature is the use of templates to exploit the recursive block
+structure of finite element matrices at compile time. Available solvers
+include Krylov methods, (block-) incomplete decompositions and
+aggregation-based algebraic multigrid.")
+ ;; GPL version 2 with "runtime exception"
+ (license license:gpl2)))
+
+(define-public dune-localfunctions
+ (package
+ (name "dune-localfunctions")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://dune-project.org/download/"
+ version "/dune-localfunctions-" version ".tar.gz"))
+ (sha256
+ (base32
+ "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl"))))
+ (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)
+ ("dune-geometry" ,dune-geometry)
+ ("openmpi" ,openmpi)
+ ;; Optional
+ ("metis" ,metis)
+ ("superlu" ,superlu)
+ ("gmp" ,gmp)))
+ (native-inputs
+ `(("gfortran" ,gfortran)
+ ("pkg-config" ,pkg-config)))
+ (home-page "https://dune-project.org/")
+ (synopsis "Distributed and Unified Numerics Environment") ; TODO
+ (description "This DUNE module provides interface and implementation for
+shape functions defined on the DUNE reference elements. In addition to the
+shape function, interpolation operators and special keys are provided which
+can be used to assemble global function spaces on finite-element grids.
+
+This package provides an interface and implementation for shape functions
+defined on the DUNE reference elements. In addition to the shape function,
+interpolation operators and special keys are provided which can be used to
+assemble global function spaces on finite-element grids.")
+ ;; GPL version 2 with "runtime exception"
+ (license license:gpl2)))
+
+(define-public dune-alugrid
+ (package
+ (name "dune-alugrid")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://dune-project.org/download/"
+ version "/dune-alugrid-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI
+ ; environment
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-include
+ (lambda _
+ (substitute* "dune/alugrid/test/test-alugrid.cc"
+ (("doc/grids/gridfactory/testgrids")
+ "doc/dune-grid/grids/gridfactory/testgrids"))
+ #t))
+ (add-after 'build 'build-tests
+ (lambda* (#:key inputs make-flags #:allow-other-keys)
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-append (assoc-ref inputs "dune-grid") "/share:"
+ (getenv "CPLUS_INCLUDE_PATH")))
+ (apply invoke "make" "build_tests" make-flags))))))
+ (inputs
+ `(("dune-common" ,dune-common)
+ ("dune-geometry" ,dune-geometry)
+ ("dune-grid" ,dune-grid)
+ ("openmpi" ,openmpi)
+ ;; Optional
+ ("metis" ,metis)
+ ("openblas" ,openblas)
+ ("python" ,python)
+ ("superlu" ,superlu)
+ ("gmp" ,gmp)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("gfortran" ,gfortran)
+ ("pkg-config" ,pkg-config)))
+ (home-page "https://dune-project.org/")
+ (synopsis "Distributed and Unified Numerics Environment")
+ (description "ALUGrid is an adaptive, loadbalancing, unstructured
+implementation of the DUNE grid interface supporting either simplices or
+cubes.")
+ (license license:gpl2+)))
+
+(define-public dune-typetree
+ (package
+ (name "dune-typetree")
+ (version "2.6.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.dune-project.org/staging/dune-typetree.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9"))))
+ (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)
+ ;; Optional
+ ("openblas" ,openblas)
+ ("python" ,python)
+ ("metis" ,metis)
+ ("superlu" ,superlu)
+ ("gmp" ,gmp)))
+ (native-inputs
+ `(("gfortran" ,gfortran)
+ ("pkg-config" ,pkg-config)))
+ (home-page "https://dune-project.org/")
+ (synopsis "Distributed and Unified Numerics Environment")
+ (description "TypeTree is a template library for constructing and
+operating on statically typed trees of objects.")
+ ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
+ (license (list license:lgpl3+ license:gpl2))))
+
+(define-public dune-functions
+ (package
+ (name "dune-functions")
+ (version "2.6.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.dune-project.org/staging/dune-functions.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
+ (build-system cmake-build-system)
+ (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid
+ (inputs
+ `(("dune-common" ,dune-common)
+ ("dune-istl" ,dune-istl)
+ ("dune-localfunctions" ,dune-localfunctions)
+ ("dune-grid" ,dune-grid)
+ ("dune-geometry" ,dune-geometry)
+ ("dune-typetree" ,dune-typetree)
+ ("openmpi" ,openmpi)
+ ("openblas" ,openblas)
+ ("metis" ,metis)
+ ("python" ,python)
+ ("superlu" ,superlu)
+ ("gmp" ,gmp)))
+ (native-inputs
+ `(("gfortran" ,gfortran)
+ ("pkg-config" ,pkg-config)))
+ (home-page "https://dune-project.org/")
+ (synopsis "Distributed and Unified Numerics Environment")
+ (description "The dune-functions module provides an abstraction layer for
+global finite element functions. Its two main concepts are functions
+implemented as callable objects, and bases of finite element spaces.")
+ ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
+ (license (list license:lgpl3+ license:gpl2))))
+
+(define-public dune-pdelab
+ (package
+ (name "dune-pdelab")
+ (version "2.6.0-rc1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v"))))
+ (build-system cmake-build-system)
+ (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
+ (inputs
+ `(("dune-common" ,dune-common)
+ ("dune-istl" ,dune-istl)
+ ("dune-localfunctions" ,dune-localfunctions)
+ ("dune-geometry" ,dune-geometry)
+ ("dune-grid" ,dune-grid)
+ ("dune-typetree" ,dune-typetree)
+ ("dune-functions" ,dune-functions)
+ ("openmpi" ,openmpi)
+ ;; Optional
+ ("openblas" ,openblas)
+ ("eigen" ,eigen)
+ ("metis" ,metis)
+ ("python" ,python)
+ ("superlu" ,superlu)
+ ("gmp" ,gmp)))
+ (native-inputs
+ `(("gfortran" ,gfortran)
+ ("pkg-config" ,pkg-config)))
+ (home-page "https://dune-project.org/")
+ (synopsis "Differential equations solver toolbox")
+ (description "PDELab is a partial differential equations solver toolbox
+built on top of DUNE, the Distributed and Unified Numerics Environment.")
+ ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
+ (license (list license:lgpl3+ license:gpl2))))
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