gnu: dealii: Update to 9.3.2.
* gnu/packages/maths.scm (dealii): Update to 9.3.2. [source]: Add dealii-fix-compiliation-with-boost-1.78.patch and dealii-fix-sundials.patch. [inputs]: Use simplified format. [native-inputs]: Use simplified format. * gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch: New file. * gnu/packages/patches/dealii-fix-sundials.patch: New file. * gnu/local.mk: Add new patch files. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
This commit is contained in:
Felix Gruber
Nicolas Goaziou
parent
f499f62941
commit
80f616139c
4 changed files with 115 additions and 13 deletions
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@ -31,7 +31,7 @@
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# Copyright © 2020 R Veera Kumar <vkor@vkten.in>
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# Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
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# Copyright © 2020 Michael Rohleder <mike@rohleder.de>
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# Copyright © 2020, 2021 Felix Gruber <felgru@posteo.net>
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# Copyright © 2020, 2021, 2022 Felix Gruber <felgru@posteo.net>
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# Copyright © 2020 Ryan Prior <rprior@protonmail.com>
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# Copyright © 2020 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
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# Copyright © 2020, 2021 Brice Waegeneire <brice@waegenei.re>
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@ -980,6 +980,8 @@ dist_patch_DATA = \
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%D%/packages/patches/dbus-c++-gcc-compat.patch \
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%D%/packages/patches/dbus-c++-threading-mutex.patch \
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%D%/packages/patches/dbxfs-remove-sentry-sdk.patch \
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%D%/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch \
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%D%/packages/patches/dealii-fix-sundials.patch \
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%D%/packages/patches/debops-constants-for-external-program-names.patch \
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%D%/packages/patches/debops-debops-defaults-fall-back-to-less.patch \
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%D%/packages/patches/dee-vapi.patch \
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@ -34,7 +34,7 @@
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;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
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;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
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;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
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;;; Copyright © 2020, 2021 Felix Gruber <felgru@posteo.net>
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;;; Copyright © 2020–2022 Felix Gruber <felgru@posteo.net>
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;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
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;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
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;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
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@ -5268,14 +5268,16 @@ A unique design feature of Trilinos is its focus on packages.")
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(define-public dealii
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(package
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(name "dealii")
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(version "9.3.1")
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(version "9.3.2")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "https://github.com/dealii/dealii/releases/"
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"download/v" version "/dealii-" version ".tar.gz"))
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(sha256
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(base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6"))
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(base32 "1s0kawnljg24jj6nibwrif5gxdgg2daqfylhqqpl1lvmzmmxfhak"))
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(patches (search-patches "dealii-fix-compiliation-with-boost-1.78.patch"
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"dealii-fix-sundials.patch"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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@ -5286,16 +5288,14 @@ A unique design feature of Trilinos is its focus on packages.")
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(outputs '("out" "doc"))
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(native-inputs
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;; Required to build the documentation.
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`(("dot" ,graphviz)
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("doxygen" ,doxygen)
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("perl" ,perl)))
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(list graphviz doxygen perl))
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(inputs
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`(("arpack" ,arpack-ng)
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("blas" ,openblas)
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("gfortran" ,gfortran)
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("lapack" ,lapack)
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("muparser" ,muparser)
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("zlib" ,zlib)))
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(list arpack-ng
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openblas
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gfortran
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lapack
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muparser
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zlib))
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(propagated-inputs
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;; Some scripts are installed into share/deal.II/scripts that require
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;; perl and python, but they are not executable (and some are missing the
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@ -0,0 +1,40 @@
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From cbef761731627cece2a6f0276b87dacabbdc8a72 Mon Sep 17 00:00:00 2001
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From: David Wells <drwells@email.unc.edu>
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Date: Tue, 4 Jan 2022 12:46:30 -0500
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Subject: [PATCH] Fix compilation with boost 1.78.
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I bisected (fortunately Boost.Geometry a header-only library so adding the
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include directory sufficed) and
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https://github.com/boostorg/geometry/commit/6eb9e238bcb37e26dc31d16acf826784a2ba30f4
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is where this problem starts for us. See also
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https://github.com/boostorg/geometry/issues/792 - the easiest fix for all such
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issues is to just include the project header `boost/geometry/geometry.hpp`.
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In this particular case, if you look at the commit which causes grid_tools.cc
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fails to compile, its because we were relying on some implicit includes. In
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particular, we need the distance header to find the distance between points and
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boxes, but that was previously included in another file.
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This patch has been adapted from
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e0e76835519d122fd12b5858e16d08641a641c6a to apply to dealii 9.3.2.
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See https://github.com/dealii/dealii/pull/13165.
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---
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include/deal.II/numerics/rtree.h | 1 +
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1 file changed, 1 insertion(+)
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diff --git a/include/deal.II/numerics/rtree.h b/include/deal.II/numerics/rtree.h
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index 1b9d04dacd..1e1bfd2932 100644
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--- a/include/deal.II/numerics/rtree.h
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+++ b/include/deal.II/numerics/rtree.h
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@@ -26,6 +26,7 @@
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#include <deal.II/boost_adaptors/segment.h>
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DEAL_II_DISABLE_EXTRA_DIAGNOSTICS
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+#include <boost/geometry/algorithms/distance.hpp>
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#include <boost/geometry/index/rtree.hpp>
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#include <boost/geometry/strategies/strategies.hpp>
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DEAL_II_ENABLE_EXTRA_DIAGNOSTICS
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--
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2.30.2
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60
gnu/packages/patches/dealii-fix-sundials.patch
Normal file
60
gnu/packages/patches/dealii-fix-sundials.patch
Normal file
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@ -0,0 +1,60 @@
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From af73f368f7f9d4a00df075d1a9f50fc495f8e87a Mon Sep 17 00:00:00 2001
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From: Timo Heister <timo.heister@gmail.com>
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Date: Sat, 25 Dec 2021 12:30:45 -0500
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Subject: [PATCH] fix sundials compilation
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---
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include/deal.II/sundials/n_vector.templates.h | 11 ++++++-----
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1 file changed, 6 insertions(+), 5 deletions(-)
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diff --git a/include/deal.II/sundials/n_vector.templates.h b/include/deal.II/sundials/n_vector.templates.h
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index 2b49e3efc9..746f63a03b 100644
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--- a/include/deal.II/sundials/n_vector.templates.h
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+++ b/include/deal.II/sundials/n_vector.templates.h
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@@ -253,13 +253,13 @@ namespace SUNDIALS
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template <
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typename VectorType,
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typename std::enable_if_t<!IsBlockVector<VectorType>::value, int> = 0>
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- MPI_Comm
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+ const MPI_Comm &
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get_communicator(N_Vector v);
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template <
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typename VectorType,
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typename std::enable_if_t<IsBlockVector<VectorType>::value, int> = 0>
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- MPI_Comm
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+ const MPI_Comm &
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get_communicator(N_Vector v);
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/**
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@@ -481,7 +481,7 @@ SUNDIALS::internal::NVectorOperations::destroy(N_Vector v)
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template <typename VectorType,
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std::enable_if_t<IsBlockVector<VectorType>::value, int>>
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-MPI_Comm
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+const MPI_Comm &
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SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v)
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{
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return unwrap_nvector_const<VectorType>(v)->block(0).get_mpi_communicator();
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@@ -491,7 +491,7 @@ SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v)
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template <typename VectorType,
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std::enable_if_t<!IsBlockVector<VectorType>::value, int>>
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-MPI_Comm
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+const MPI_Comm &
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SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v)
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{
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return unwrap_nvector_const<VectorType>(v)->get_mpi_communicator();
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@@ -519,7 +519,8 @@ SUNDIALS::internal::NVectorOperations::get_communicator_as_void_ptr(N_Vector v)
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(void)v;
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return nullptr;
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# else
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- return get_communicator<VectorType>(v);
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+ // We need to cast away const here, as SUNDIALS demands a pure `void *`.
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+ return &(const_cast<MPI_Comm &>(get_communicator<VectorType>(v)));
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# endif
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}
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--
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2.30.2
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