@@ -31,7 +31,7 @@
# Copyright © 2020 R Veera Kumar <vkor@vkten.in>
# Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
# Copyright © 2020 Michael Rohleder <mike@rohleder.de>
-# Copyright © 2020, 2021 Felix Gruber <felgru@posteo.net>
+# Copyright © 2020, 2021, 2022 Felix Gruber <felgru@posteo.net>
# Copyright © 2020 Ryan Prior <rprior@protonmail.com>
# Copyright © 2020 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
# Copyright © 2020, 2021 Brice Waegeneire <brice@waegenei.re>
@@ -987,6 +987,8 @@ dist_patch_DATA = \
%D%/packages/patches/dbus-c++-gcc-compat.patch \
%D%/packages/patches/dbus-c++-threading-mutex.patch \
%D%/packages/patches/dbxfs-remove-sentry-sdk.patch \
+ %D%/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch \
+ %D%/packages/patches/dealii-fix-sundials.patch \
%D%/packages/patches/debops-constants-for-external-program-names.patch \
%D%/packages/patches/debops-debops-defaults-fall-back-to-less.patch \
%D%/packages/patches/dee-vapi.patch \
@@ -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, 2021 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2020–2022 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>
@@ -5268,14 +5268,16 @@ A unique design feature of Trilinos is its focus on packages.")
(define-public dealii
(package
(name "dealii")
- (version "9.3.1")
+ (version "9.3.2")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/dealii/dealii/releases/"
"download/v" version "/dealii-" version ".tar.gz"))
(sha256
- (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6"))
+ (base32 "1s0kawnljg24jj6nibwrif5gxdgg2daqfylhqqpl1lvmzmmxfhak"))
+ (patches (search-patches "dealii-fix-compiliation-with-boost-1.78.patch"
+ "dealii-fix-sundials.patch"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -5286,16 +5288,14 @@ A unique design feature of Trilinos is its focus on packages.")
(outputs '("out" "doc"))
(native-inputs
;; Required to build the documentation.
- `(("dot" ,graphviz)
- ("doxygen" ,doxygen)
- ("perl" ,perl)))
+ (list graphviz doxygen perl))
(inputs
- `(("arpack" ,arpack-ng)
- ("blas" ,openblas)
- ("gfortran" ,gfortran)
- ("lapack" ,lapack)
- ("muparser" ,muparser)
- ("zlib" ,zlib)))
+ (list arpack-ng
+ openblas
+ gfortran
+ lapack
+ muparser
+ zlib))
(propagated-inputs
;; Some scripts are installed into share/deal.II/scripts that require
;; perl and python, but they are not executable (and some are missing the
new file mode 100644
@@ -0,0 +1,40 @@
+From cbef761731627cece2a6f0276b87dacabbdc8a72 Mon Sep 17 00:00:00 2001
+From: David Wells <drwells@email.unc.edu>
+Date: Tue, 4 Jan 2022 12:46:30 -0500
+Subject: [PATCH] Fix compilation with boost 1.78.
+
+I bisected (fortunately Boost.Geometry a header-only library so adding the
+include directory sufficed) and
+https://github.com/boostorg/geometry/commit/6eb9e238bcb37e26dc31d16acf826784a2ba30f4
+is where this problem starts for us. See also
+https://github.com/boostorg/geometry/issues/792 - the easiest fix for all such
+issues is to just include the project header `boost/geometry/geometry.hpp`.
+
+In this particular case, if you look at the commit which causes grid_tools.cc
+fails to compile, its because we were relying on some implicit includes. In
+particular, we need the distance header to find the distance between points and
+boxes, but that was previously included in another file.
+
+This patch has been adapted from
+e0e76835519d122fd12b5858e16d08641a641c6a to apply to dealii 9.3.2.
+
+See https://github.com/dealii/dealii/pull/13165.
+---
+ include/deal.II/numerics/rtree.h | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/include/deal.II/numerics/rtree.h b/include/deal.II/numerics/rtree.h
+index 1b9d04dacd..1e1bfd2932 100644
+--- a/include/deal.II/numerics/rtree.h
++++ b/include/deal.II/numerics/rtree.h
+@@ -26,6 +26,7 @@
+ #include <deal.II/boost_adaptors/segment.h>
+
+ DEAL_II_DISABLE_EXTRA_DIAGNOSTICS
++#include <boost/geometry/algorithms/distance.hpp>
+ #include <boost/geometry/index/rtree.hpp>
+ #include <boost/geometry/strategies/strategies.hpp>
+ DEAL_II_ENABLE_EXTRA_DIAGNOSTICS
+--
+2.30.2
+
new file mode 100644
@@ -0,0 +1,60 @@
+From af73f368f7f9d4a00df075d1a9f50fc495f8e87a Mon Sep 17 00:00:00 2001
+From: Timo Heister <timo.heister@gmail.com>
+Date: Sat, 25 Dec 2021 12:30:45 -0500
+Subject: [PATCH] fix sundials compilation
+
+---
+ include/deal.II/sundials/n_vector.templates.h | 11 ++++++-----
+ 1 file changed, 6 insertions(+), 5 deletions(-)
+
+diff --git a/include/deal.II/sundials/n_vector.templates.h b/include/deal.II/sundials/n_vector.templates.h
+index 2b49e3efc9..746f63a03b 100644
+--- a/include/deal.II/sundials/n_vector.templates.h
++++ b/include/deal.II/sundials/n_vector.templates.h
+@@ -253,13 +253,13 @@ namespace SUNDIALS
+ template <
+ typename VectorType,
+ typename std::enable_if_t<!IsBlockVector<VectorType>::value, int> = 0>
+- MPI_Comm
++ const MPI_Comm &
+ get_communicator(N_Vector v);
+
+ template <
+ typename VectorType,
+ typename std::enable_if_t<IsBlockVector<VectorType>::value, int> = 0>
+- MPI_Comm
++ const MPI_Comm &
+ get_communicator(N_Vector v);
+
+ /**
+@@ -481,7 +481,7 @@ SUNDIALS::internal::NVectorOperations::destroy(N_Vector v)
+
+ template <typename VectorType,
+ std::enable_if_t<IsBlockVector<VectorType>::value, int>>
+-MPI_Comm
++const MPI_Comm &
+ SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v)
+ {
+ return unwrap_nvector_const<VectorType>(v)->block(0).get_mpi_communicator();
+@@ -491,7 +491,7 @@ SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v)
+
+ template <typename VectorType,
+ std::enable_if_t<!IsBlockVector<VectorType>::value, int>>
+-MPI_Comm
++const MPI_Comm &
+ SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v)
+ {
+ return unwrap_nvector_const<VectorType>(v)->get_mpi_communicator();
+@@ -519,7 +519,8 @@ SUNDIALS::internal::NVectorOperations::get_communicator_as_void_ptr(N_Vector v)
+ (void)v;
+ return nullptr;
+ # else
+- return get_communicator<VectorType>(v);
++ // We need to cast away const here, as SUNDIALS demands a pure `void *`.
++ return &(const_cast<MPI_Comm &>(get_communicator<VectorType>(v)));
+ # endif
+ }
+
+--
+2.30.2
+