Package: guix-patches;
Reported by: Felix Gruber <felgru <at> posteo.net>
Date: Thu, 4 Mar 2021 19:55:02 UTC
Severity: normal
Tags: patch
Done: Ludovic Courtès <ludovic.courtes <at> inria.fr>
Bug is archived. No further changes may be made.
Message #8 received at 46929 <at> debbugs.gnu.org (full text, mbox):
From: Felix Gruber <felgru <at> posteo.net> To: 46929 <at> debbugs.gnu.org Cc: Felix Gruber <felgru <at> posteo.net> Subject: [PATCH v2] gnu: maths: dune-*: Update to version 2.7.1 Date: Thu, 20 May 2021 22:06:03 +0000
* gnu/packages/maths.scm (dune-alugrid, dune-common, dune-functions,
dune-geometry, dune-grid, dune-istl, dune-localfunctions, dune-pdelab,
dune-subgrid, dune-typetree, dune-uggrid): Update to version 2.7.1.
(dune-istl)[source](patches) Remove patch that is no longer needed.
(dune-alugrid, dune-subgrid, dune-pdelab)[version]: Use `git-version` to
compute the version string.
* gnu/packages/patches/dune-istl-2.7-fix-non-mpi-tests.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove above patch.
---
Since v1 of the patch, I've made the following changes:
* Use git-version to generate versions.
* Add comments to explain that some of the packages didn't have a recent
release tag.
* Update dune-alugrid to use the latest commit from the releases/2.7
branch.
(The simd tests in dune-common take ages to complete, I wonder if I
should disable them to significantly cut down the build time.)
gnu/local.mk | 1 -
gnu/packages/maths.scm | 280 +++++++++---------
.../dune-istl-2.7-fix-non-mpi-tests.patch | 82 -----
3 files changed, 144 insertions(+), 219 deletions(-)
delete mode 100644 gnu/packages/patches/dune-istl-2.7-fix-non-mpi-tests.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index dd68bb5957..0d676dcf69 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -955,7 +955,6 @@ dist_patch_DATA = \
%D%/packages/patches/doxygen-1.8.17-runtests.patch \
%D%/packages/patches/dstat-fix-crash-when-specifying-delay.patch \
%D%/packages/patches/dstat-skip-devices-without-io.patch \
- %D%/packages/patches/dune-istl-2.7-fix-non-mpi-tests.patch \
%D%/packages/patches/dvd+rw-tools-add-include.patch \
%D%/packages/patches/ecl-16-format-directive-limit.patch \
%D%/packages/patches/ecl-16-ignore-stderr-write-error.patch \
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 6b3f5cf41c..65ae445efb 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5346,7 +5346,7 @@ linear algebra primitives specifically targeting graph analytics.")
(define-public dune-common
(package
(name "dune-common")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method url-fetch)
@@ -5354,7 +5354,7 @@ linear algebra primitives specifically targeting graph analytics.")
version "/dune-common-" version ".tar.gz"))
(sha256
(base32
- "140q1zh44cr5yrjwg4b5ga803rkqv55vk30l2cqm29aklj1wb0rw"))))
+ "0sidwdkyrrqjkqhpvrlc991pzi5xzlvxk91s2n7qk3widwy7fch2"))))
(build-system cmake-build-system)
(arguments
`(#:phases
@@ -5384,7 +5384,7 @@ Differences} (FD).")
(define-public dune-geometry
(package
(name "dune-geometry")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method url-fetch)
@@ -5392,7 +5392,7 @@ Differences} (FD).")
version "/dune-geometry-" version ".tar.gz"))
(sha256
(base32
- "1cicvlwbyyw76npicnblxckyvhbfn3ip8isydiv3hlrlz8zcg5nr"))))
+ "068mh3fd110xl27rwxqlqy4d9cpqw2vqm2pzfrripiaqscb3byfy"))))
(build-system cmake-build-system)
(arguments
`(#:phases
@@ -5424,7 +5424,7 @@ This package contains the basic DUNE geometry classes.")
(define-public dune-uggrid
(package
(name "dune-uggrid")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method git-fetch)
@@ -5434,7 +5434,7 @@ This package contains the basic DUNE geometry classes.")
(file-name (git-file-name name version))
(sha256
(base32
- "192miqgmfj6jwk969gydzpbv9ki7jg5nky3ydnrwa2nq29b5xkh0"))))
+ "11qz52g9d5k96fqik2lyi80xryw174rnny074pj70ardl6zzz83p"))))
(build-system cmake-build-system)
(arguments
`(#:phases
@@ -5461,7 +5461,7 @@ This package contains the DUNE UG grid classes.")
(define-public dune-grid
(package
(name "dune-grid")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method url-fetch)
@@ -5469,7 +5469,7 @@ This package contains the DUNE UG grid classes.")
version "/dune-grid-" version ".tar.gz"))
(sha256
(base32
- "17fjz30qazjgl11sryyxnw9klai4yz1ji4bs68013xcxc5hdv27s"))))
+ "15iws03hkbmr4a4rqqb0rriz1m8szl96wdr7gw0jmrcnlzbdbbx5"))))
(build-system cmake-build-system)
(arguments
`(#:phases
@@ -5504,7 +5504,7 @@ This package contains the basic DUNE grid classes.")
(define-public dune-istl
(package
(name "dune-istl")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method url-fetch)
@@ -5512,8 +5512,7 @@ This package contains the basic DUNE grid classes.")
version "/dune-istl-" version ".tar.gz"))
(sha256
(base32
- "0gl3wgz5rs6sb4m83440ny45sbx7z7lnbi3gx6r9nm3rvy5j33f9"))
- (patches (search-patches "dune-istl-2.7-fix-non-mpi-tests.patch"))))
+ "1cy69s1266hvnh8blznlvvkrf8i2g640rc3mf7kp872wgvdz4nb9"))))
(build-system cmake-build-system)
(arguments
`(#:phases
@@ -5563,7 +5562,7 @@ aggregation-based algebraic multigrid.")
(define-public dune-localfunctions
(package
(name "dune-localfunctions")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method url-fetch)
@@ -5571,7 +5570,7 @@ aggregation-based algebraic multigrid.")
version "/dune-localfunctions-" version ".tar.gz"))
(sha256
(base32
- "1yih59h6vngii696bx1c2vil02lriij4kz0nc583mjn9kiaqxfqd"))))
+ "031i42anrhi0ngpvp42rdjbkic7v3008fwild9xg7flffwvnpshg"))))
(build-system cmake-build-system)
(arguments
`(#:phases
@@ -5616,99 +5615,105 @@ assemble global function spaces on finite-element grids.")
(license license:gpl2)))
(define-public dune-alugrid
- (package
- (name "dune-alugrid")
- (version "2.7.0-git-81d35682")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://gitlab.dune-project.org/extensions/dune-alugrid.git")
- (commit "81d356827c84454b971937db02c02b90bbcd7fe5")))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0z54lwfp53prcrs94k8gwh047l9z642jll3l56xlyfr69z0b2zz1"))))
- (build-system cmake-build-system)
- (arguments
- `(#: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"))
- (apply invoke "make" "build_tests" make-flags))))))
- (inputs
- `(("dune-common" ,dune-common)
- ("dune-geometry" ,dune-geometry)
- ("dune-grid" ,dune-grid)
- ;; 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
+ ;; This was the last commit on the releases/2.7 branch as of 2021-05-20,
+ ;; unfortunately there was no tag for any 2.7 release.
+ (let ((commit "51bde29a2dfa7cfac4fb73d40ffd42b9c1eb1d3d"))
+ (package
+ (name "dune-alugrid")
+ (version (git-version "2.7.1" "0" commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.dune-project.org/extensions/dune-alugrid.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0z16wg6llzxs7vjg2yilg31vwnkz8k050j6bspg3blbym0razy15"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#: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"))
+ (apply invoke "make" "build_tests" make-flags))))))
+ (inputs
+ `(("dune-common" ,dune-common)
+ ("dune-geometry" ,dune-geometry)
+ ("dune-grid" ,dune-grid)
+ ;; 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+)))
+ (license license:gpl2+))))
(define-public dune-subgrid
- (package
- (name "dune-subgrid")
- (version "2.7.0-git-2103a363")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid")
- (commit "2103a363f32e8d7b60e66eee7ddecf969f6cf762")))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1wsjlypd3835c3arqjkw836cxx5q67zy447wa65q634lf6f6v9ia"))))
- (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)
- ("dune-grid" ,dune-grid)
- ;; 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 marks elements of
+ ;; This was the last commit on the releases/2.7 branch as of 2021-05-20.
+ ;; Unfortunately the dune-subgrid repository contains no release tags.
+ (let ((commit "45d1ee9f3f711e209695deee97912f4954f7f280"))
+ (package
+ (name "dune-subgrid")
+ (version (git-version "2.7.1" "0" commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0xjf7865wil7kzym608kv3nc3ff3m3nlqich4k9wjyvy3lz6panh"))))
+ (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)
+ ("dune-grid" ,dune-grid)
+ ;; 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 marks 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+)))
+ (license license:gpl2+))))
(define-public dune-typetree
(package
(name "dune-typetree")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method git-fetch)
@@ -5718,7 +5723,7 @@ provides the full grid interface including adaptive mesh refinement.")
(file-name (git-file-name name version))
(sha256
(base32
- "1rhv25yg0q1hw50c8wlfqhgwrjl4mh62zq9v14ilwgzbfgxmpiy7"))))
+ "1kx9k8i7pdw6l6ny6nq85v5p1nd6yxldzaj8k3nizaz3q1j407pv"))))
(build-system cmake-build-system)
(arguments
`(#:phases
@@ -5747,7 +5752,7 @@ operating on statically typed trees of objects.")
(define-public dune-functions
(package
(name "dune-functions")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method git-fetch)
@@ -5757,7 +5762,7 @@ operating on statically typed trees of objects.")
(file-name (git-file-name name version))
(sha256
(base32
- "1na4gcih0kin37ksj2xj07ds04v7zx53pjdhm1hzy55jjfqdjk8h"))))
+ "04dhr4asnl38bf1gp8hrk31maav33m7q71lhl2n5yk1q1x6i77nw"))))
(build-system cmake-build-system)
(arguments
`(#:phases
@@ -5795,45 +5800,48 @@ implemented as callable objects, and bases of finite element spaces.")
(license (list license:lgpl3+ license:gpl2))))
(define-public dune-pdelab
- (package
- (name "dune-pdelab")
- (version "2.7.0-git-476fe437")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
- (commit "476fe43763fa6f459c5e4658e2a2b4b5582db834")))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0cs36piqzn6rq0j2ih3ab3q3q9yg199wk72k5qi86pkzh7i7fdn1"))))
- (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)
- ;; 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
+ ;; This was the last commit on the releases/2.7 branch as of 2021-05-20,
+ ;; unfortunately there was no tag for any 2.7 release.
+ (let ((commit "3435f7f1f4d05e3f6e8d9fe8a06a09569c7244be"))
+ (package
+ (name "dune-pdelab")
+ (version (git-version "2.7.1" "0" commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0akllyj4qh686h1xs53n102vf70ydxa7g6ha5gj3wdlig2ny4vik"))))
+ (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)
+ ;; 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))))
+ ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
+ (license (list license:lgpl3+ license:gpl2)))))
(define add-openmpi-to-dune-package
(let ((dune-package?
diff --git a/gnu/packages/patches/dune-istl-2.7-fix-non-mpi-tests.patch b/gnu/packages/patches/dune-istl-2.7-fix-non-mpi-tests.patch
deleted file mode 100644
index ee2bb8f676..0000000000
--- a/gnu/packages/patches/dune-istl-2.7-fix-non-mpi-tests.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-Fix build of dune-istl's tests
-
-Patch copied from upstream source repository:
-
-https://gitlab.dune-project.org/core/dune-istl/-/commit/9eee3462df5a64881c08574f9291e76db398de0a
-
-From 9eee3462df5a64881c08574f9291e76db398de0a Mon Sep 17 00:00:00 2001
-From: Felix Gruber <felgru <at> posteo.net>
-Date: Sat, 4 Apr 2020 15:27:09 +0200
-Subject: [PATCH] make tests succeed when MPI is disabled
-
-When MPI is not available or explicitly disabled with the CMake build
-option -DCMAKE_IDSABLE_FIND_PACKAGE_MPI=TRUE, some tests were unable to
-build.
-
-The tests created from solverfactorytest.cc.in and part of
-scalarproductstest.cc use Dune::OwnerOverlapCopyCommunication which is
-defined behind `#if HAVE_MPI` and is thus not available in a non-MPI
-build. I've thus disabled those tests when MPI is unavailable.
-
-The matrixmarkettest did not work without MPI, as it contained some code
-using the wrong template parameters when HAVE_MPI was not set. Those
-template paramters have been fixed now.
-
-I've confirmed, that after my changes `make build_tests` succeeds to
-build all tests and that those tests run without failure.
----
- dune/istl/test/CMakeLists.txt | 3 ++-
- dune/istl/test/matrixmarkettest.cc | 2 +-
- dune/istl/test/scalarproductstest.cc | 2 ++
- 3 files changed, 5 insertions(+), 2 deletions(-)
-
-diff --git a/dune/istl/test/CMakeLists.txt b/dune/istl/test/CMakeLists.txt
-index ffd87969..2c7b2387 100644
---- a/dune/istl/test/CMakeLists.txt
-+++ b/dune/istl/test/CMakeLists.txt
-@@ -77,7 +77,8 @@ set(DUNE_TEST_FACTORY_BLOCK_SIZES
- function(add_factory_test BLOCK)
- STRING(REGEX REPLACE "[^a-zA-Z0-9]" "" BLOCK_CLEAN ${BLOCK})
- configure_file(solverfactorytest.cc.in solverfactorytest_${BLOCK_CLEAN}.cc)
-- dune_add_test(SOURCES ${CMAKE_CURRENT_BINARY_DIR}/solverfactorytest_${BLOCK_CLEAN}.cc)
-+ dune_add_test(SOURCES ${CMAKE_CURRENT_BINARY_DIR}/solverfactorytest_${BLOCK_CLEAN}.cc
-+ CMAKE_GUARD HAVE_MPI)
- endfunction(add_factory_test)
-
- foreach(FIELD_TYPE ${DUNE_TEST_FACTORY_FIELD_TYPES})
-diff --git a/dune/istl/test/matrixmarkettest.cc b/dune/istl/test/matrixmarkettest.cc
-index b335afe6..ce30e8ae 100644
---- a/dune/istl/test/matrixmarkettest.cc
-+++ b/dune/istl/test/matrixmarkettest.cc
-@@ -52,7 +52,7 @@ int testMatrixMarket(int N)
- storeMatrixMarket(mat, std::string("testmat"), comm);
- storeMatrixMarket(bv, std::string("testvec"), comm, false);
- #else
-- typedef Dune::MatrixAdapter<BCRSMat,BVector,BVector> Operator;
-+ typedef Dune::MatrixAdapter<Matrix,Vector,Vector> Operator;
- Operator op(mat);
- op.apply(bv, cv);
-
-diff --git a/dune/istl/test/scalarproductstest.cc b/dune/istl/test/scalarproductstest.cc
-index 452b1d89..f46ce2a9 100644
---- a/dune/istl/test/scalarproductstest.cc
-+++ b/dune/istl/test/scalarproductstest.cc
-@@ -115,6 +115,7 @@ int main(int argc, char** argv)
- scalarProductTest<ScalarProduct, Vector>(scalarProduct,numBlocks);
- }
-
-+#if HAVE_MPI
- // Test the ParallelScalarProduct class
- {
- using Vector = BlockVector<FieldVector<double,BlockSize> >;
-@@ -139,6 +140,7 @@ int main(int argc, char** argv)
- ScalarProduct scalarProduct(communicator,SolverCategory::nonoverlapping);
- scalarProductTest<ScalarProduct, Vector>(scalarProduct,numBlocks);
- }
-+#endif
-
- return t.exit();
- }
---
-2.25.1
-
--
2.30.2
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.