[bug#62842] [PATCH 00/11] gnu: maths: dune-*: Update to version 2.9.0

[bug#62842] [PATCH 00/11] gnu: maths: dune-*: Update to version 2.9.0

[Felix Gruber]

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

[bug#62842] [PATCH 01/11] gnu: dune-common: Update to 2.9.0.

[Felix Gruber]

* gnu/packages/maths.scm (dune-common): Update to 2.9.0.
---
 gnu/packages/maths.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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 Kądziołka <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

[bug#62842] [PATCH 02/11] gnu: dune-geometry: Update to 2.9.0.

[Felix Gruber]

* gnu/packages/maths.scm (dune-geometry): Update to 2.9.0.
---
 gnu/packages/maths.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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

[bug#62842] [PATCH 03/11] gnu: dune-uggrid: Update to 2.9.0.

[Felix Gruber]

* gnu/packages/maths.scm (dune-uggrid): Update to 2.9.0.
---
 gnu/packages/maths.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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

[bug#62842] [PATCH 04/11] gnu: dune-grid: Update to 2.9.0.

[Felix Gruber]

* 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

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

[bug#62842] [PATCH 05/11] gnu: dune-istl: Update to 2.9.0.

[Felix Gruber]

* 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

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

[bug#62842] [PATCH 06/11] gnu: dune-localfunctions: Update to 2.9.0.

[Felix Gruber]

* gnu/packages/maths.scm (dune-localfunctions): Update to 2.9.0.
---
 gnu/packages/maths.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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

[bug#62842] [PATCH 07/11] gnu: dune-alugrid: Update to 2.9.0.

[Felix Gruber]

* gnu/packages/maths.scm (dune-alugrid): Update to 2.9.0.
---
 gnu/packages/maths.scm | 101 ++++++++++++++++++++---------------------
 1 file changed, 49 insertions(+), 52 deletions(-)

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

[bug#62842] [PATCH 08/11] gnu: dune-subgrid: Update to 2.9.0-1-e83f3f9.

[Felix Gruber]

* 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(-)

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

[bug#62842] [PATCH 09/11] gnu: dune-typetree: Update to 2.9.0.

[Felix Gruber]

* gnu/packages/maths.scm (dune-typetree): Update to 2.9.0.
---
 gnu/packages/maths.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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

[bug#62842] [PATCH 10/11] gnu: dune-functions: Update to 2.9.0.

[Felix Gruber]

* gnu/packages/maths.scm (dune-functions): Update to 2.9.0.
---
 gnu/packages/maths.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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

[bug#62842] [PATCH 11/11] gnu: dune-pdelab: Update to 2.8.0-0.d5dddb6.

[Felix Gruber]

* 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(-)

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

bug#62842: [PATCH 00/11] gnu: maths: dune-*: Update to version 2.9.0

[Ludovic Courtès]

Hi Felix,

Felix Gruber <felgru@posteo.net> skribis:

>   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’.

[bug#62842] [PATCH 00/11] gnu: maths: dune-*: Update to version 2.9.0

[Ludovic Courtès]

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,
Ludo’.

[bug#62842] [PATCH 00/11] gnu: maths: dune-*: Update to version 2.9.0

[Ludovic Courtès]

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.

Well, there are additional failures actually:

  https://ci.guix.gnu.org/eval/442046?status=failed

Ludo’.

[bug#62842] [PATCH 00/11] gnu: maths: dune-*: Update to version 2.9.0

[Felix Gruber]

[-- Attachment #1: Type: text/plain, Size: 2386 bytes --]

Hi Ludo’,

On 5/2/23 15:01, Ludovic Courtès wrote:
> 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].

[1]: https://gitlab.dune-project.org/core/dune-common/-/issues/262
[2]: 
https://sources.debian.org/src/dune-common/2.9.0-2/debian/patches/disable-long-double-eigenvalue-checks.patch/

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

[-- Attachment #2: 0001-gnu-dune-common-Fix-build-on-aarch64-linux.patch --]
[-- Type: text/x-patch, Size: 3397 bytes --]

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

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

[bug#62842] [PATCH 00/11] gnu: maths: dune-*: Update to version 2.9.0

[Ludovic Courtès]

Hi,

Felix Gruber <felgru@posteo.net> skribis:

> 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’.