1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
|
# Maintainer: David Wells <drwells.aur at fastmail dot com>
# Contributor: Florian Dang <florian dot coin at gmail dot com>
pkgname=deal-ii
_realname=dealii
pkgver=9.5.1
pkgrel=1
pkgdesc="An Open Source Finite Element Differential Equations Analysis Library"
arch=("i686" "x86_64")
url="http://www.dealii.org/"
license=('LGPL')
# deal.II depends on Kokkos which is implicitly provided by Trilinos. Trilinos
# does not yet support configuration with an external copy of Kokkos so do not
# yet depend on that package.
depends=('boost' 'trilinos')
optdepends=(
# adol-c is not compatible with Trilinos - if both are installed then deal.II will use Trilinos
'adol-c: automatic differentiation library'
'arpack: Fortran77 subroutines designed to solve large scale eigenvalue problems'
'assimp: Library to import various well-known 3D model formats in an uniform manner'
'cgal: Computational Geometry Algorithms Library'
# ginkgo is not yet in the AUR
# 'ginkgo: a high-performance linear algebra library for manycore systems'
'gmsh: An automatic 3D finite element mesh generator with pre and post-processing facilities'
'gsl: A modern numerical library for C and C++ programmers'
'hdf5-openmpi: General purpose library and file format for storing scientific data'
'intel-mkl: Intel Math Kernel Library'
'lapack: Linear Algebra PACKage'
'metis: partitioning graphs, finite element meshes, fill reducing orderings for sparse matrices.'
'muparser: A fast math parser library'
'openmpi: High performance message passing library (MPI)'
'opencascade: Open CASCADE Technology, 3D modeling & numerical simulation'
'p4est-deal-ii: The parallel forest (p4est) library, built to work with deal.II'
'parmetis: A parallel graph partitioning library'
'petsc: Portable, extensible toolkit for scientific computation'
'scalapack: subset of scalable LAPACK routines redesigned for distributed memory MIMD parallel computers'
'slepc: Scalable library for Eigenvalue problem computations'
'sundials: Suite of nonlinear differential/algebraic equation solvers'
'symengine: Fast symbolic manipulation library'
'tbb: High level abstract threading library'
'suitesparse: A collection of sparse matrix libraries'
'zlib: Compression library implementing the deflate compression method found in gzip and PKZIP'
)
makedepends=('cmake')
install=deal-ii.install
source=(https://github.com/dealii/dealii/releases/download/v$pkgver/${_realname}-$pkgver.tar.gz)
sha1sums=('a94989a9e4c3b8599aceacf71d7156621c1d7426')
# where to install deal.II: change to something else (e.g., /opt/deal.II/)
# if desired.
_installation_prefix=/usr
build() {
# Since deal.II relies on a relatively large number of packages that are
# installed in nonstandard places (e.g., the PETSc AUR package is installed in
# /opt/petsc/), source their environment variable scripts in the (likely) case
# that a user installed one of these packages without logging out and logging
# back in
for package in opencascade p4est-deal-ii petsc slepc intel-mkl
do
if pacman -Qs $package >/dev/null
then
profile_file=/etc/profile.d/$package.sh
if [ -f $profile_file ]
then
source /etc/profile.d/$package.sh
fi
fi
done
rm -rf "${srcdir}/build"
mkdir "${srcdir}/build"
cd "${srcdir}/build"
# explicitly disallow bundled packages: this disables bundled copies of boost,
# intel-tbb, part of suitesparse, and muparser, which are all available in the
# standard repositories
cmake_configuration_flags=" -DDEAL_II_ALLOW_BUNDLED=OFF"
# deal.II does not use more aggressive search paths (which we need) for MPI
# unless we explicitly enable it, so check for MPI and then turn it on:
if pacman -Qs openmpi >/dev/null
then
cmake_configuration_flags+=" -DDEAL_II_WITH_MPI=ON"
fi
# See if PETSc was configured to use 64 bit indices:
if [ -n "${PETSC_DIR+x}" ]
then
if grep '^#define PETSC_USE_64BIT_INDICES 1' $PETSC_DIR/include/petscconf.h >/dev/null
then
cmake_configuration_flags+=" -DDEAL_II_WITH_64BIT_INDICES=ON"
fi
fi
# deal.II cannot find MKL unless we specify where its header is
if [ -n "${MKLROOT+x}" ]
then
cmake_configuration_flags+=" -DLAPACK_INCLUDE_DIRS=${MKLROOT}/include"
fi
# For GSL compatibility we need the full link interface, which includes
# libgslcblas, so disable --as-needed with GCC:
sed -i '/ENABLE_IF_LINKS(DEAL_II_LINKER_FLAGS "-Wl,--as-needed")/d' \
${srcdir}/${_realname}-$pkgver/cmake/setup_compiler_flags_gnu.cmake
sed -i '122ifedisableexcept(FE_INVALID);\n' \
${srcdir}/${_realname}-$pkgver/tests/quick_tests/scalapack.cc
# Also remove from LDFLAGS if necessary
LDFLAGS=$(echo $LDFLAGS | sed 's/--as-needed,//')
# Skip some warnings that appear if Trilinos uses OpenMP pragmas in headers:
extra_warning_flags=" -Wno-unknown-pragmas"
# Also skip warnings from compiling without optimizations (debug mode) and
# _FORTIFY_SOURCE:
extra_warning_flags="${extra_warning_flags} -Wno-cpp"
# the deal.II GCC flags are already well-chosen for speed (and O3 is known to
# be slightly slower than O2), so do not use flags in /etc/makepkg.conf by
# default. If you want to add more flags or disable specific packages, then
# refer to the deal.II manual.
#
# Work around a deal.II + Trilinos 14 bug by explicitly providing the Trilinos
# root directory
cmake $cmake_configuration_flags -DCMAKE_INSTALL_PREFIX=$_installation_prefix \
-DTRILINOS_DIR=/usr/ \
-DCMAKE_INSTALL_MESSAGE=NEVER -DCMAKE_CXX_FLAGS=" $extra_warning_flags" \
-DDEAL_II_SHARE_RELDIR=share/${pkgname}/ \
-DDEAL_II_EXAMPLES_RELDIR=share/${pkgname}/examples/ \
-DDEAL_II_UNITY_BUILD=ON \
-DDEAL_II_COMPONENT_DOCUMENTATION=OFF ${srcdir}/${_realname}-$pkgver
# deal.II needs about 3 GB/compilation process so use fewer jobs if your
# machine does not have the memory to support the maximum number.
make $MAKEFLAGS
cd "${srcdir}/build"
echo "export DEAL_II_DIR=$_installation_prefix" > ./deal-ii.sh
}
check() {
cd "${srcdir}/build"
# workaround a bug by setting the number of jobs to 1 (though this still
# runs in parallel)
make -j1 test
}
package() {
cd "${srcdir}/build"
make DESTDIR="${pkgdir}" install
# delete extra files that deal.II installs into the top level directory
rm "${pkgdir}/${_installation_prefix}/LICENSE.md"
rm "${pkgdir}/${_installation_prefix}/README.md"
rm "${pkgdir}/${_installation_prefix}/detailed.log"
rm "${pkgdir}/${_installation_prefix}/summary.log"
install -D -m755 "${srcdir}/build/deal-ii.sh" "${pkgdir}/etc/profile.d/deal-ii.sh"
install -D -m644 "${srcdir}/${_realname}-$pkgver/LICENSE.md" "${pkgdir}/usr/share/licenses/${_realname}-$pkgver/LICENSE.md"
}
|