[PATCH 00/11] gnu: maths: dune-*: Update to version 2.9.0

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3 participants
  • Felix Gruber
  • Ludovic Courtès
  • Ludovic Courtès
Owner
unassigned
Submitted by
Felix Gruber
Severity
normal
F
F
Felix Gruber wrote on 14 Apr 2023 21:25
(address . guix-patches@gnu.org)(name . Felix Gruber)(address . felgru@posteo.net)
20230414192518.41188-1-felgru@posteo.net
This patchset updates all packages belonging to the Dune finite element
library to the latest release 2.9.0.

Felix Gruber (11):
gnu: dune-common: Update to 2.9.0.
gnu: dune-geometry: Update to 2.9.0.
gnu: dune-uggrid: Update to 2.9.0.
gnu: dune-grid: Update to 2.9.0.
gnu: dune-istl: Update to 2.9.0.
gnu: dune-localfunctions: Update to 2.9.0.
gnu: dune-alugrid: Update to 2.9.0.
gnu: dune-subgrid: Update to 2.9.0-1-e83f3f9.
gnu: dune-typetree: Update to 2.9.0.
gnu: dune-functions: Update to 2.9.0.
gnu: dune-pdelab: Update to 2.8.0-0.d5dddb6.

gnu/local.mk | 2 +
gnu/packages/maths.scm | 161 +++++++++---------
...une-grid-add-missing-include-cassert.patch | 24 +++
.../dune-istl-fix-solver-playground.patch | 61 +++++++
4 files changed, 168 insertions(+), 80 deletions(-)
create mode 100644 gnu/packages/patches/dune-grid-add-missing-include-cassert.patch
create mode 100644 gnu/packages/patches/dune-istl-fix-solver-playground.patch

--
2.39.2
F
F
Felix Gruber wrote on 14 Apr 2023 21:27
[PATCH 01/11] gnu: dune-common: Update to 2.9.0.
(address . 62842@debbugs.gnu.org)(name . Felix Gruber)(address . felgru@posteo.net)
20230414192736.41322-1-felgru@posteo.net
* gnu/packages/maths.scm (dune-common): Update to 2.9.0.
---
gnu/packages/maths.scm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)

Toggle diff (33 lines)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index c10fc8075c..f20126479b 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -34,7 +34,7 @@
;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
;;; Copyright © 2020 Jakub K?dzio?ka <kuba@kadziolka.net>
-;;; Copyright © 2020–2022 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2020–2023 Felix Gruber <felgru@posteo.net>
;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
@@ -6780,7 +6780,7 @@ (define-public combinatorial-blas
(define-public dune-common
(package
(name "dune-common")
- (version "2.7.1")
+ (version "2.9.0")
(source
(origin
(method url-fetch)
@@ -6788,7 +6788,7 @@ (define-public dune-common
version "/dune-common-" version ".tar.gz"))
(sha256
(base32
- "0sidwdkyrrqjkqhpvrlc991pzi5xzlvxk91s2n7qk3widwy7fch2"))))
+ "04pzk8q0bibci8z5xlwndhh3y3vs63mw7kad62lbzfwrr5121hrd"))))
(build-system cmake-build-system)
(arguments
`(#:phases
--
2.39.2
F
F
Felix Gruber wrote on 14 Apr 2023 21:27
[PATCH 02/11] gnu: dune-geometry: Update to 2.9.0.
(address . 62842@debbugs.gnu.org)(name . Felix Gruber)(address . felgru@posteo.net)
20230414192736.41322-2-felgru@posteo.net
* gnu/packages/maths.scm (dune-geometry): Update to 2.9.0.
---
gnu/packages/maths.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (24 lines)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index f20126479b..7a1578164b 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6817,7 +6817,7 @@ (define-public dune-common
(define-public dune-geometry
(package
(name "dune-geometry")
- (version "2.7.1")
+ (version "2.9.0")
(source
(origin
(method url-fetch)
@@ -6825,7 +6825,7 @@ (define-public dune-geometry
version "/dune-geometry-" version ".tar.gz"))
(sha256
(base32
- "068mh3fd110xl27rwxqlqy4d9cpqw2vqm2pzfrripiaqscb3byfy"))))
+ "1bl1abipcf7zysmyyy2ikfx0nip55kasrb1bbkh11ghdilxrwwqy"))))
(build-system cmake-build-system)
(arguments
`(#:phases
--
2.39.2
F
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Felix Gruber wrote on 14 Apr 2023 21:27
[PATCH 03/11] gnu: dune-uggrid: Update to 2.9.0.
(address . 62842@debbugs.gnu.org)(name . Felix Gruber)(address . felgru@posteo.net)
20230414192736.41322-3-felgru@posteo.net
* gnu/packages/maths.scm (dune-uggrid): Update to 2.9.0.
---
gnu/packages/maths.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (24 lines)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 7a1578164b..7177f8c60d 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6858,7 +6858,7 @@ (define-public dune-geometry
(define-public dune-uggrid
(package
(name "dune-uggrid")
- (version "2.7.1")
+ (version "2.9.0")
(source
(origin
(method git-fetch)
@@ -6868,7 +6868,7 @@ (define-public dune-uggrid
(file-name (git-file-name name version))
(sha256
(base32
- "11qz52g9d5k96fqik2lyi80xryw174rnny074pj70ardl6zzz83p"))))
+ "1xwmiabb25nydi0yzhd64vq6fm3razix6k87afhq88q0ywzll65x"))))
(build-system cmake-build-system)
(arguments
`(#:phases
--
2.39.2
F
F
Felix Gruber wrote on 14 Apr 2023 21:27
[PATCH 04/11] gnu: dune-grid: Update to 2.9.0.
(address . 62842@debbugs.gnu.org)(name . Felix Gruber)(address . felgru@posteo.net)
20230414192736.41322-4-felgru@posteo.net
* gnu/packages/maths.scm (dune-grid): Update to 2.9.0.
[source](patches): Add patch to fix build.
* gnu/packages/patches/dune-grid-add-missing-include-cassert.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
gnu/local.mk | 1 +
gnu/packages/maths.scm | 6 +++--
...une-grid-add-missing-include-cassert.patch | 24 +++++++++++++++++++
3 files changed, 29 insertions(+), 2 deletions(-)
create mode 100644 gnu/packages/patches/dune-grid-add-missing-include-cassert.patch

Toggle diff (68 lines)
diff --git a/gnu/local.mk b/gnu/local.mk
index 8088e8170b..96d5aad909 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1056,6 +1056,7 @@ dist_patch_DATA = \
%D%/packages/patches/dovecot-trees-support-dovecot-2.3.patch \
%D%/packages/patches/dstat-fix-crash-when-specifying-delay.patch \
%D%/packages/patches/dstat-skip-devices-without-io.patch \
+ %D%/packages/patches/dune-grid-add-missing-include-cassert.patch \
%D%/packages/patches/dvd+rw-tools-add-include.patch \
%D%/packages/patches/dynaconf-unvendor-deps.patch \
%D%/packages/patches/efivar-211.patch \
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 7177f8c60d..95e2eb3ef7 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6898,7 +6898,7 @@ (define-public dune-uggrid
(define-public dune-grid
(package
(name "dune-grid")
- (version "2.7.1")
+ (version "2.9.0")
(source
(origin
(method url-fetch)
@@ -6906,7 +6906,9 @@ (define-public dune-grid
version "/dune-grid-" version ".tar.gz"))
(sha256
(base32
- "15iws03hkbmr4a4rqqb0rriz1m8szl96wdr7gw0jmrcnlzbdbbx5"))))
+ "17l2vlr8q3rfifxv80r3jlzamx478xn0vfjkrl3ns1akk7miycq8"))
+ (patches (search-patches
+ "dune-grid-add-missing-include-cassert.patch"))))
(build-system cmake-build-system)
(arguments
`(#:phases
diff --git a/gnu/packages/patches/dune-grid-add-missing-include-cassert.patch b/gnu/packages/patches/dune-grid-add-missing-include-cassert.patch
new file mode 100644
index 0000000000..7462b11934
--- /dev/null
+++ b/gnu/packages/patches/dune-grid-add-missing-include-cassert.patch
@@ -0,0 +1,24 @@
+From ef843b1a66308247ba4d2e2c116ff5517421a91b Mon Sep 17 00:00:00 2001
+From: Simon Praetorius <simon.praetorius@tu-dresden.de>
+Date: Tue, 6 Dec 2022 13:39:44 +0100
+Subject: [PATCH] Add missing include <cassert>
+
+---
+ dune/grid/test/yasp/test-yaspgrid-partitioner.cc | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/dune/grid/test/yasp/test-yaspgrid-partitioner.cc b/dune/grid/test/yasp/test-yaspgrid-partitioner.cc
+index 93ae042b0..9a4530201 100644
+--- a/dune/grid/test/yasp/test-yaspgrid-partitioner.cc
++++ b/dune/grid/test/yasp/test-yaspgrid-partitioner.cc
+@@ -6,6 +6,7 @@
+ #include <config.h>
+
+ #include <array>
++#include <cassert>
+ #include <iostream>
+
+ #include <dune/common/filledarray.hh>
+--
+2.39.2
+
--
2.39.2
F
F
Felix Gruber wrote on 14 Apr 2023 21:27
[PATCH 05/11] gnu: dune-istl: Update to 2.9.0.
(address . 62842@debbugs.gnu.org)(name . Felix Gruber)(address . felgru@posteo.net)
20230414192736.41322-5-felgru@posteo.net
* gnu/packages/maths.scm (dune-istl): Update to 2.9.0.
[source](patches): Add patch to fix test phase.
* gnu/packages/patches/dune-istl-fix-solver-playground.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
gnu/local.mk | 1 +
gnu/packages/maths.scm | 5 +-
.../dune-istl-fix-solver-playground.patch | 61 +++++++++++++++++++
3 files changed, 65 insertions(+), 2 deletions(-)
create mode 100644 gnu/packages/patches/dune-istl-fix-solver-playground.patch

Toggle diff (104 lines)
diff --git a/gnu/local.mk b/gnu/local.mk
index 96d5aad909..37bef69b4d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1057,6 +1057,7 @@ dist_patch_DATA = \
%D%/packages/patches/dstat-fix-crash-when-specifying-delay.patch \
%D%/packages/patches/dstat-skip-devices-without-io.patch \
%D%/packages/patches/dune-grid-add-missing-include-cassert.patch \
+ %D%/packages/patches/dune-istl-fix-solver-playground.patch \
%D%/packages/patches/dvd+rw-tools-add-include.patch \
%D%/packages/patches/dynaconf-unvendor-deps.patch \
%D%/packages/patches/efivar-211.patch \
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 95e2eb3ef7..ad50b65cae 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6946,7 +6946,7 @@ (define-public dune-grid
(define-public dune-istl
(package
(name "dune-istl")
- (version "2.7.1")
+ (version "2.9.0")
(source
(origin
(method url-fetch)
@@ -6954,7 +6954,8 @@ (define-public dune-istl
version "/dune-istl-" version ".tar.gz"))
(sha256
(base32
- "1cy69s1266hvnh8blznlvvkrf8i2g640rc3mf7kp872wgvdz4nb9"))))
+ "0smghqr400xl84j0laabgwaj2p5jlj3n3s85bm7qp9m2vjz6rav6"))
+ (patches (search-patches "dune-istl-fix-solver-playground.patch"))))
(build-system cmake-build-system)
(arguments
`(#:phases
diff --git a/gnu/packages/patches/dune-istl-fix-solver-playground.patch b/gnu/packages/patches/dune-istl-fix-solver-playground.patch
new file mode 100644
index 0000000000..b3df4b6ffa
--- /dev/null
+++ b/gnu/packages/patches/dune-istl-fix-solver-playground.patch
@@ -0,0 +1,61 @@
+From fe929f17e98b577171f58ca520b5145be41730ea Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Christoph=20Gr=C3=BCninger?= <gruenich@dune-project.org>
+Date: Thu, 16 Mar 2023 19:48:40 +0100
+Subject: [PATCH] Adjust sequential and both parallel cases in
+ istl-solver-playground
+
+Do same thing, independent of paralellel, distributed, or
+sequential.
+This fixes the test in the sequential case.
+---
+ src/istl-solver-playground.hh | 22 ++++++++++++++++------
+ 1 file changed, 16 insertions(+), 6 deletions(-)
+
+diff --git a/src/istl-solver-playground.hh b/src/istl-solver-playground.hh
+index 0ff3abd5..11693cf5 100644
+--- a/src/istl-solver-playground.hh
++++ b/src/istl-solver-playground.hh
+@@ -66,7 +66,11 @@ std::shared_ptr<OOCOMM> loadSystem(std::shared_ptr<Mat>& m,
+ std::shared_ptr<OOCOMM> oocomm;
+ if(distributed){
+ oocomm = std::make_shared<OOCOMM>(MPI_COMM_WORLD);
+- loadMatrixMarket(*m, matrixfilename, *oocomm);
++ if(matrixfilename != "laplacian"){
++ loadMatrixMarket(*m, matrixfilename, *oocomm);
++ }else{
++ setupLaplacian(*m, config.get("N", 20));
++ }
+ if(config.get("random_rhs", false)){
+ rhs->resize(m->N());
+ srand(42);
+@@ -98,16 +102,22 @@ template<class Mat, class Vec>
+ void loadSystem(std::shared_ptr<Mat>& m,
+ std::shared_ptr<Vec>& rhs,
+ const Dune::ParameterTree& config){
+- std::string matrixfilename = config.get<std::string>("matrix");
++ // generate Laplacian or load matrix
++ std::string matrixfilename = config.get<std::string>("matrix", "laplacian");
++ if(matrixfilename == "laplacian"){
++ setupLaplacian(*m, config.get("N", 20));
++ }else{
++ loadMatrixMarket(*m, matrixfilename);
++ }
++ // use random values or load right-hand side
+ std::string rhsfilename;
+- if(!config.get("random_rhs", false))
+- rhsfilename = config.get<std::string>("rhs");
+- loadMatrixMarket(*m, matrixfilename);
+ if(config.get("random_rhs", false)){
+ rhs->resize(m->N());
+ fillRandom(*rhs);
+- }else
++ }else{
++ rhsfilename = config.get<std::string>("rhs");
+ loadMatrixMarket(*rhs, rhsfilename);
++ }
+ }
+ #endif
+
+--
+2.39.2
+
--
2.39.2
F
F
Felix Gruber wrote on 14 Apr 2023 21:27
[PATCH 06/11] gnu: dune-localfunctions: Update to 2.9.0.
(address . 62842@debbugs.gnu.org)(name . Felix Gruber)(address . felgru@posteo.net)
20230414192736.41322-6-felgru@posteo.net
* gnu/packages/maths.scm (dune-localfunctions): Update to 2.9.0.
---
gnu/packages/maths.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (24 lines)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index ad50b65cae..020f599f70 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -7008,7 +7008,7 @@ (define-public dune-istl
(define-public dune-localfunctions
(package
(name "dune-localfunctions")
- (version "2.7.1")
+ (version "2.9.0")
(source
(origin
(method url-fetch)
@@ -7016,7 +7016,7 @@ (define-public dune-localfunctions
version "/dune-localfunctions-" version ".tar.gz"))
(sha256
(base32
- "031i42anrhi0ngpvp42rdjbkic7v3008fwild9xg7flffwvnpshg"))))
+ "02zl49q40ifmic221fxlhi8zj9pybdyjavzvgn1zwh636ysgjbsp"))))
(build-system cmake-build-system)
(arguments
`(#:phases
--
2.39.2
F
F
Felix Gruber wrote on 14 Apr 2023 21:27
[PATCH 07/11] gnu: dune-alugrid: Update to 2.9.0.
(address . 62842@debbugs.gnu.org)(name . Felix Gruber)(address . felgru@posteo.net)
20230414192736.41322-7-felgru@posteo.net
* gnu/packages/maths.scm (dune-alugrid): Update to 2.9.0.
---
gnu/packages/maths.scm | 101 ++++++++++++++++++++---------------------
1 file changed, 49 insertions(+), 52 deletions(-)

Toggle diff (116 lines)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 020f599f70..34fb239c73 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -7064,60 +7064,57 @@ (define-public dune-localfunctions
(license license:gpl2)))
(define-public dune-alugrid
- ;; This was the last commit on the releases/2.7 branch as of 2021-12-17,
- ;; 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 parallel-build? #:allow-other-keys)
- (setenv "CPLUS_INCLUDE_PATH"
- (string-append (assoc-ref inputs "dune-grid") "/share"))
- (apply invoke "make" "build_tests"
- `(,@(if parallel-build?
- `("-j" ,(number->string (parallel-job-count)))
- '())
- ,@make-flags)))))))
- (inputs
- (list dune-common
- dune-geometry
- dune-grid
- ;; Optional
- metis
- openblas
- python
- superlu
- gmp
- zlib))
- (native-inputs
- (list gfortran pkg-config))
- (home-page "https://dune-project.org/")
- (synopsis "Distributed and Unified Numerics Environment")
- (description "ALUGrid is an adaptive, loadbalancing, unstructured
+ (package
+ (name "dune-alugrid")
+ (version "2.9.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.dune-project.org/extensions/dune-alugrid.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0s41jinsfpm56nx41vkmyv3y9n072ssw9hxjm7di64zcszgpjmzd"))))
+ (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 parallel-build? #:allow-other-keys)
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-append (assoc-ref inputs "dune-grid") "/share"))
+ (apply invoke "make" "build_tests"
+ `(,@(if parallel-build?
+ `("-j" ,(number->string (parallel-job-count)))
+ '())
+ ,@make-flags)))))))
+ (inputs
+ (list dune-common
+ dune-geometry
+ dune-grid
+ ;; Optional
+ metis
+ openblas
+ python
+ superlu
+ gmp
+ zlib))
+ (native-inputs
+ (list gfortran 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
;; This was the last commit on the releases/2.7 branch as of 2021-12-17.
--
2.39.2
F
F
Felix Gruber wrote on 14 Apr 2023 21:27
[PATCH 08/11] gnu: dune-subgrid: Update to 2.9.0-1-e83f3f9.
(address . 62842@debbugs.gnu.org)(name . Felix Gruber)(address . felgru@posteo.net)
20230414192736.41322-8-felgru@posteo.net
* gnu/packages/maths.scm (dune-subgrid): Update to 2.9.0-1-e83f3f9.
[source]: Update URL of dune-subgrid's Git repository.
---
gnu/packages/maths.scm | 13 +++++++------
1 file changed, 7 insertions(+), 6 deletions(-)

Toggle diff (36 lines)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 34fb239c73..d00570788c 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -7117,22 +7117,23 @@ (define-public dune-alugrid
(license license:gpl2+)))
(define-public dune-subgrid
- ;; This was the last commit on the releases/2.7 branch as of 2021-12-17.
- ;; Unfortunately the dune-subgrid repository contains no release tags.
- (let ((commit "45d1ee9f3f711e209695deee97912f4954f7f280"))
+ ; dune-subgrid does not tag its releases.
+ ; The following commit is a few commits past the releases/2.9 branch
+ ; to include some additional commits fixing compatibility with dune-uggrid.
+ (let ((commit "e83f3f919c2602425467ed767f279bc9c356c436"))
(package
(name "dune-subgrid")
- (version (git-version "2.7.1" "0" commit))
+ (version (git-version "2.9.0" "1" commit))
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid")
+ (url "https://gitlab.dune-project.org/extensions/dune-subgrid")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
- "0xjf7865wil7kzym608kv3nc3ff3m3nlqich4k9wjyvy3lz6panh"))))
+ "1dv4zg5j17bldpgg02ycg9fbfmnc1kffixgzbkkz86f2dmwgh2b6"))))
(build-system cmake-build-system)
(arguments
`(#:phases
--
2.39.2
F
F
Felix Gruber wrote on 14 Apr 2023 21:27
[PATCH 09/11] gnu: dune-typetree: Update to 2.9.0.
(address . 62842@debbugs.gnu.org)(name . Felix Gruber)(address . felgru@posteo.net)
20230414192736.41322-9-felgru@posteo.net
* gnu/packages/maths.scm (dune-typetree): Update to 2.9.0.
---
gnu/packages/maths.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (24 lines)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index d00570788c..d65be7f087 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -7166,7 +7166,7 @@ (define-public dune-subgrid
(define-public dune-typetree
(package
(name "dune-typetree")
- (version "2.7.1")
+ (version "2.9.0")
(source
(origin
(method git-fetch)
@@ -7176,7 +7176,7 @@ (define-public dune-typetree
(file-name (git-file-name name version))
(sha256
(base32
- "1kx9k8i7pdw6l6ny6nq85v5p1nd6yxldzaj8k3nizaz3q1j407pv"))))
+ "1qcnl8giivnn8zprszdwrqw4q29sv3c2pr8dlrz616j10i4r8p18"))))
(build-system cmake-build-system)
(arguments
`(#:phases
--
2.39.2
F
F
Felix Gruber wrote on 14 Apr 2023 21:27
[PATCH 10/11] gnu: dune-functions: Update to 2.9.0.
(address . 62842@debbugs.gnu.org)(name . Felix Gruber)(address . felgru@posteo.net)
20230414192736.41322-10-felgru@posteo.net
* gnu/packages/maths.scm (dune-functions): Update to 2.9.0.
---
gnu/packages/maths.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (24 lines)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index d65be7f087..b9d305c101 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -7208,7 +7208,7 @@ (define-public dune-typetree
(define-public dune-functions
(package
(name "dune-functions")
- (version "2.7.1")
+ (version "2.9.0")
(source
(origin
(method git-fetch)
@@ -7218,7 +7218,7 @@ (define-public dune-functions
(file-name (git-file-name name version))
(sha256
(base32
- "04dhr4asnl38bf1gp8hrk31maav33m7q71lhl2n5yk1q1x6i77nw"))))
+ "0pmi9vk0pdq9qp3xvknsndg8l6f2xkjr1rwbfbzsl9aj0qv9rn2p"))))
(build-system cmake-build-system)
(arguments
`(#:phases
--
2.39.2
F
F
Felix Gruber wrote on 14 Apr 2023 21:27
[PATCH 11/11] gnu: dune-pdelab: Update to 2.8.0-0.d5dddb6.
(address . 62842@debbugs.gnu.org)(name . Felix Gruber)(address . felgru@posteo.net)
20230414192736.41322-11-felgru@posteo.net
* gnu/packages/maths.scm (dune-pdelab): Update to 2.8.0-0.d5dddb6.
---
gnu/packages/maths.scm | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)

Toggle diff (32 lines)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index b9d305c101..9c910a43c3 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -7259,12 +7259,12 @@ (define-public dune-functions
(license (list license:lgpl3+ license:gpl2))))
(define-public dune-pdelab
- ;; This was the last commit on the releases/2.7 branch as of 2021-12-17,
- ;; unfortunately there was no tag for any 2.7 release.
- (let ((commit "09aef74d95661d18a7789d2f517ae77797eec738"))
+ ;; This was the last commit on the releases/2.8 branch as of 2023-04-12,
+ ;; unfortunately there was no tag for any 2.8 release.
+ (let ((commit "d5dddb6b1c21b95e867ff53cca159ad676689f5c"))
(package
(name "dune-pdelab")
- (version (git-version "2.7.1" "0" commit))
+ (version (git-version "2.8.0" "0" commit))
(source
(origin
(method git-fetch)
@@ -7274,7 +7274,7 @@ (define-public dune-pdelab
(file-name (git-file-name name version))
(sha256
(base32
- "0nv69ayr4gln9m1s94z9zkrxqi8nzar3z6awnvgqz595nmjf82ac"))))
+ "0l2idjp59a6x46vdd30xhhsnv7chql0z7msdsyra2h6pqm6xiqxk"))))
(build-system cmake-build-system)
(arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
(inputs
--
2.39.2
L
L
Ludovic Courtès wrote on 2 May 2023 12:13
Re: bug#62842: [PATCH 00/11] gnu: maths: dune-*: Update to version 2.9.0
(name . Felix Gruber)(address . felgru@posteo.net)(address . 62842-done@debbugs.gnu.org)
87bkj382il.fsf@gnu.org
Hi Felix,

Felix Gruber <felgru@posteo.net> skribis:

Toggle quote (12 lines)
> gnu: dune-common: Update to 2.9.0.
> gnu: dune-geometry: Update to 2.9.0.
> gnu: dune-uggrid: Update to 2.9.0.
> gnu: dune-grid: Update to 2.9.0.
> gnu: dune-istl: Update to 2.9.0.
> gnu: dune-localfunctions: Update to 2.9.0.
> gnu: dune-alugrid: Update to 2.9.0.
> gnu: dune-subgrid: Update to 2.9.0-1-e83f3f9.
> gnu: dune-typetree: Update to 2.9.0.
> gnu: dune-functions: Update to 2.9.0.
> gnu: dune-pdelab: Update to 2.8.0-0.d5dddb6.

Applied!

We have a green light from qa.guix:
https://qa.guix.gnu.org/issue/62842. That was pre-core-updates, but
I’m assuming things are still fine (‘dune-common’ builds fine for me on
x86_64-linux).

Thank you!

Ludo’.
Closed
L
L
Ludovic Courtès wrote on 2 May 2023 15:01
(name . Felix Gruber)(address . felgru@posteo.net)(address . 62842@debbugs.gnu.org)
877ctq99ay.fsf@gnu.org
Felix Gruber <felgru@posteo.net> skribis:

Toggle quote (3 lines)
> This patchset updates all packages belonging to the Dune finite element
> library to the latest release 2.9.0.

There’s one test failure on aarch64-linux:

Toggle snippet (14 lines)
99/106 Test #99: eigenvaluestest ........................Subprocess aborted***Exception: 1.24 sec
Eigenvalues of Rosser matrix: (-1020.05,0) (0.0980486,0) (-1.05342e-14,0) (1020.05,0) (1020,0) (1019.9,0) (1000,0) (1000,0)
Eigenvalues of Rosser matrix: (-1020.05,0) (0.0980486,0) (-1.05342e-14,0) (1020.05,0) (1020,0) (1019.9,0) (1000,0) (1000,0)
Eigenvalues of Rosser matrix: (-1020.05,0) (0.0980486,0) (-1.05342e-14,0) (1020.05,0) (1020,0) (1019.9,0) (1000,0) (1000,0)
terminate called after throwing an instance of 'Dune::MathError'
what(): MathError [testSymmetricFieldMatrix:/tmp/guix-build-dune-common-2.9.0.drv-0/dune-common-2.9.0/dune/common/test/eigenvaluestest.cc:143]: Vector computed by FMatrixHelp::eigenValuesVectors is not an eigenvector

[…]
The following tests FAILED:
99 - eigenvaluestest (Subprocess aborted)
Errors while running CTest
make: *** [Makefile:74: test] Error 8


Could you take a look and/or report it upstream?

Thanks,
Ludo’.
L
L
Ludovic Courtès wrote on 2 May 2023 15:02
(name . Felix Gruber)(address . felgru@posteo.net)(address . 62842@debbugs.gnu.org)
87354e9997.fsf@gnu.org
Felix Gruber <felgru@posteo.net> skribis:

Toggle quote (3 lines)
> This patchset updates all packages belonging to the Dune finite element
> library to the latest release 2.9.0.

Well, there are additional failures actually:


Ludo’.
F
F
Felix Gruber wrote on 2 May 2023 22:18
(name . Ludovic Courtès)(address . ludovic.courtes@inria.fr)(address . 62842@debbugs.gnu.org)
cdfb119e-1794-a470-c6aa-836013bc51c8@posteo.net
Hi Ludo’,

On 5/2/23 15:01, Ludovic Courtès wrote:
Toggle quote (26 lines)
> Felix Gruber <felgru@posteo.net> skribis:
>
>> This patchset updates all packages belonging to the Dune finite element
>> library to the latest release 2.9.0.
>
> There’s one test failure on aarch64-linux:
>
> --8<---------------cut here---------------start------------->8---
> 99/106 Test #99: eigenvaluestest ........................Subprocess aborted***Exception: 1.24 sec
> Eigenvalues of Rosser matrix: (-1020.05,0) (0.0980486,0) (-1.05342e-14,0) (1020.05,0) (1020,0) (1019.9,0) (1000,0) (1000,0)
> Eigenvalues of Rosser matrix: (-1020.05,0) (0.0980486,0) (-1.05342e-14,0) (1020.05,0) (1020,0) (1019.9,0) (1000,0) (1000,0)
> Eigenvalues of Rosser matrix: (-1020.05,0) (0.0980486,0) (-1.05342e-14,0) (1020.05,0) (1020,0) (1019.9,0) (1000,0) (1000,0)
> terminate called after throwing an instance of 'Dune::MathError'
> what(): MathError [testSymmetricFieldMatrix:/tmp/guix-build-dune-common-2.9.0.drv-0/dune-common-2.9.0/dune/common/test/eigenvaluestest.cc:143]: Vector computed by FMatrixHelp::eigenValuesVectors is not an eigenvector
>
> […]
> The following tests FAILED:
> 99 - eigenvaluestest (Subprocess aborted)
> Errors while running CTest
> make: *** [Makefile:74: test] Error 8
> --8<---------------cut here---------------end--------------->8---
>
> From <https://ci.guix.gnu.org/build/1228281/details>.
>
> Could you take a look and/or report it upstream?

Thanks for letting me know. I've looked into upstream issues/fixes for
this problem and it seems that these aarch64 test failures are a known
issue [1]. This bugreport mentions build failures in dune-common's
Debian package, which nowadays seems to be patched to disable the
failing tests [2].

[2]:

I've prepared a patch to apply Debian's patch for disabling the failing
tests to our dune-common package. You can find it attached to this
email. Can you test if it fixes the aarch64-linux builds (I don't have
access to an aarch64 machine)?
I hope that this would also fix the build failures for the other dune-*
packages on aarch64-linux, which are currently all failing because they
depend on the broken dune-common package.

Kind regards,
Felix
From 1001e15623108e6f92b89a1a2daacd43b5e2a123 Mon Sep 17 00:00:00 2001
From: Felix Gruber <felgru@posteo.net>
Date: Tue, 2 May 2023 21:59:30 +0200
Subject: [PATCH] gnu: dune-common: Fix build on aarch64-linux.

* gnu/packages/maths.scm (dune-common)[source]: Add patch to disable
tests that are failing on aarch64-linux.
* gnu/packages/patches/dune-common-disable-long-double-eigenvalue-checks.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Register it.
---
gnu/local.mk | 1 +
gnu/packages/maths.scm | 4 ++-
...isable-long-double-eigenvalue-checks.patch | 28 +++++++++++++++++++
3 files changed, 32 insertions(+), 1 deletion(-)
create mode 100644 gnu/packages/patches/dune-common-disable-long-double-eigenvalue-checks.patch

Toggle diff (63 lines)
diff --git a/gnu/local.mk b/gnu/local.mk
index 1476c730ba..68a40e7c6c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1056,6 +1056,7 @@ dist_patch_DATA = \
%D%/packages/patches/dovecot-trees-support-dovecot-2.3.patch \
%D%/packages/patches/dstat-fix-crash-when-specifying-delay.patch \
%D%/packages/patches/dstat-skip-devices-without-io.patch \
+ %D%/packages/patches/dune-common-disable-long-double-eigenvalue-checks.patch \
%D%/packages/patches/dune-grid-add-missing-include-cassert.patch \
%D%/packages/patches/dune-istl-fix-solver-playground.patch \
%D%/packages/patches/dvd+rw-tools-add-include.patch \
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index d7e2719b70..31ae3796fc 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6805,7 +6805,9 @@ (define-public dune-common
version "/dune-common-" version ".tar.gz"))
(sha256
(base32
- "04pzk8q0bibci8z5xlwndhh3y3vs63mw7kad62lbzfwrr5121hrd"))))
+ "04pzk8q0bibci8z5xlwndhh3y3vs63mw7kad62lbzfwrr5121hrd"))
+ (patches (search-patches
+ "dune-common-disable-long-double-eigenvalue-checks.patch"))))
(build-system cmake-build-system)
(arguments
`(#:phases
diff --git a/gnu/packages/patches/dune-common-disable-long-double-eigenvalue-checks.patch b/gnu/packages/patches/dune-common-disable-long-double-eigenvalue-checks.patch
new file mode 100644
index 0000000000..cdab27b933
--- /dev/null
+++ b/gnu/packages/patches/dune-common-disable-long-double-eigenvalue-checks.patch
@@ -0,0 +1,28 @@
+--- a/dune/common/test/eigenvaluestest.cc
++++ b/dune/common/test/eigenvaluestest.cc
+@@ -340,20 +340,20 @@
+ testSymmetricFieldMatrix<double,200>();
+ testSymmetricFieldMatrix<float,4>();
+ testSymmetricFieldMatrix<float,200>();
+- testSymmetricFieldMatrix<long double,4>();
+- testSymmetricFieldMatrix<long double,200>();
++// testSymmetricFieldMatrix<long double,4>();
++// testSymmetricFieldMatrix<long double,200>();
+ #endif // HAVE_LAPACK
+
+ testSymmetricFieldMatrix<double,2>();
+ testSymmetricFieldMatrix<double,3>();
+ testSymmetricFieldMatrix<float,2>();
+ testSymmetricFieldMatrix<float,3>();
+- testSymmetricFieldMatrix<long double,2>();
+- testSymmetricFieldMatrix<long double,3>();
++// testSymmetricFieldMatrix<long double,2>();
++// testSymmetricFieldMatrix<long double,3>();
+
+ checkMultiplicity<double>();
+ checkMultiplicity<float>();
+- checkMultiplicity<long double>();
++// checkMultiplicity<long double>();
+
+ return 0;
+ }
--
2.39.2
L
L
Ludovic Courtès wrote on 4 May 2023 11:35
(name . Felix Gruber)(address . felgru@posteo.net)(address . 62842@debbugs.gnu.org)
87sfcctp65.fsf@inria.fr
Hi,

Felix Gruber <felgru@posteo.net> skribis:

Toggle quote (11 lines)
> From 1001e15623108e6f92b89a1a2daacd43b5e2a123 Mon Sep 17 00:00:00 2001
> From: Felix Gruber <felgru@posteo.net>
> Date: Tue, 2 May 2023 21:59:30 +0200
> Subject: [PATCH] gnu: dune-common: Fix build on aarch64-linux.
>
> * gnu/packages/maths.scm (dune-common)[source]: Add patch to disable
> tests that are failing on aarch64-linux.
> * gnu/packages/patches/dune-common-disable-long-double-eigenvalue-checks.patch:
> New file.
> * gnu/local.mk (dist_patch_DATA): Register it.

I confirmed that it solves the problem on AArch64.

I tweaked it, in particular adding a comment at the top of the patch,
and committed.

Thanks,
Ludo’.
?
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