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dealii: add nanoflann, sundials and adol-c plus fixes on macOS (#5175)

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* expat: fix build on macOS

* nanoflann: add new package

* sundials: fix compilation on macOS with clang+gfortran

* adol-c: add 2.6.3

* dealii: add adol-c, nanoflann, sundials and 8.5.1

* sundials: minor cleanup
This commit is contained in:
Denis Davydov 2017-08-25 03:18:06 +02:00 committed by Adam J. Stewart
parent 61cc55985b
commit c0d3d33b58
5 changed files with 76 additions and 3 deletions
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1
var/spack/repos/builtin/packages/adol-c/package.py
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@ -34,6 +34,7 @@ class AdolC(AutotoolsPackage):
version('develop', git='https://gitlab.com/adol-c/adol-c.git',
branch='master')
version('2.6.3', 'f78f67f70d5874830a1ad1c0f54e54f7')
version('2.6.2', '0f9547584c99c0673e4f81cf64e8d865')
version('2.6.1', '1032b28427d6e399af4610e78c0f087b')

26
var/spack/repos/builtin/packages/dealii/package.py
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@ -36,6 +36,7 @@ class Dealii(CMakePackage):
# only add for immediate deps.
transitive_rpaths = False
version('8.5.1', '39b9ebd6ab083d63cfc9044319aaa2ee')
version('8.5.0', 'ef999cc310b007559a6343bf5b1759bc')
version('8.4.2', '84c6bd3f250d3e0681b645d24cb987a7')
version('8.4.1', 'efbaf16f9ad59cfccad62302f36c3c1d')
@ -48,12 +49,15 @@ class Dealii(CMakePackage):
variant('mpi', default=True, description='Compile with MPI')
variant('arpack', default=True,
description='Compile with Arpack and PArpack (only with MPI)')
variant('adol-c', default=False,
description='Compile with Adol-c')
variant('doc', default=False,
description='Compile with documentation')
variant('gsl', default=True, description='Compile with GSL')
variant('hdf5', default=True,
description='Compile with HDF5 (only with MPI)')
variant('metis', default=True, description='Compile with Metis')
variant('nanoflann', default=False, description='Compile with Nanoflann')
variant('netcdf', default=True,
description='Compile with Netcdf (only with MPI)')
variant('oce', default=True, description='Compile with OCE')
@ -61,6 +65,8 @@ class Dealii(CMakePackage):
description='Compile with P4est (only with MPI)')
variant('petsc', default=True,
description='Compile with Petsc (only with MPI)')
variant('sundials', default=False,
description='Compile with Sundials')
variant('slepc', default=True,
description='Compile with Slepc (only with Petsc and MPI)')
variant('trilinos', default=True,
@ -109,6 +115,7 @@ class Dealii(CMakePackage):
# optional dependencies
depends_on("mpi", when="+mpi")
depends_on("adol-c@2.6.4:", when='@9.0:+adol-c')
depends_on("arpack-ng+mpi", when='+arpack+mpi')
depends_on("doxygen+graphviz", when='+doc')
depends_on("graphviz", when='+doc')
@ -118,6 +125,7 @@ class Dealii(CMakePackage):
# but we should not need it
depends_on("metis@5:+int64+real64", when='+metis+int64')
depends_on("metis@5:~int64+real64", when='+metis~int64')
depends_on("nanoflann", when="@9.0:+nanoflann")
depends_on("netcdf+mpi", when="+netcdf+mpi")
depends_on("netcdf-cxx", when='+netcdf+mpi')
depends_on("oce", when='+oce')
@ -129,10 +137,14 @@ class Dealii(CMakePackage):
depends_on("slepc", when='+slepc+petsc+mpi')
depends_on("slepc@:3.6.3", when='@:8.4.1+slepc+petsc+mpi')
depends_on("slepc~arpack", when='+slepc+petsc+mpi+int64')
depends_on("sundials", when='@9.0:+sundials')
depends_on("trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos", when='+trilinos+mpi~int64')
depends_on("trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos~hypre", when="+trilinos+mpi+int64")
# check that the combination of variants makes sense
conflicts('+nanoflann', when='@:8.5.1')
conflicts('+sundials', when='@:8.5.1')
conflicts('+adol-c', when='@:8.5.1')
conflicts('+gsl', when='@:8.4.2')
conflicts('+python', when='@:8.4.2')
for p in ['+arpack', '+hdf5', '+netcdf', '+p4est', '+petsc',
@ -211,7 +223,8 @@ def cmake_args(self):
# Optional dependencies for which library names are the same as CMake
# variables:
for library in (
'gsl', 'hdf5', 'p4est', 'petsc', 'slepc', 'trilinos', 'metis'):
'gsl', 'hdf5', 'p4est', 'petsc', 'slepc', 'trilinos', 'metis',
'sundials', 'nanoflann'):
if library in spec:
options.extend([
'-D%s_DIR=%s' % (library.upper(), spec[library].prefix),
@ -222,6 +235,17 @@ def cmake_args(self):
'-DDEAL_II_WITH_%s:BOOL=OFF' % library.upper()
])
# adol-c
if '+adol-c' in spec:
options.extend([
'-DADOLC_DIR=%s' % spec['adol-c'].prefix,
'-DDEAL_II_WITH_ADOLC=ON'
])
else:
options.extend([
'-DDEAL_II_WITH_ADOLC=OFF'
])
# doxygen
options.extend([
'-DDEAL_II_COMPONENT_DOCUMENTATION=%s' %

3
var/spack/repos/builtin/packages/expat/package.py
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@ -23,6 +23,7 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import sys
class Expat(AutotoolsPackage):
@ -39,7 +40,7 @@ class Expat(AutotoolsPackage):
# someone's asking for an older version and also libbsd.
# In order to install an older version, you'll need to add
# `~libbsd`.
variant('libbsd', default=True,
variant('libbsd', default=sys.platform != 'darwin',
description="Use libbsd (for high quality randomness)")
depends_on('libbsd', when="@2.2.1:+libbsd")

39
var/spack/repos/builtin/packages/nanoflann/package.py Normal file
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@ -0,0 +1,39 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Nanoflann(CMakePackage):
"""a C++ header-only library for Nearest Neighbor (NN) search wih KD-trees.
"""
homepage = "https://github.com/jlblancoc/nanoflann"
url = "https://github.com/jlblancoc/nanoflann/archive/v1.2.3.tar.gz"
version('1.2.3', '92a0f44a631c41aa06f9716c51dcdb11')
def cmake_args(self):
args = ['-DBUILD_SHARED_LIBS=ON']
return args

10
var/spack/repos/builtin/packages/sundials/package.py
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@ -68,10 +68,18 @@ def on_off(varstr):
return 'ON' if varstr in self.spec else 'OFF'
cmake_args = std_cmake_args[:]
fortran_flag = self.compiler.pic_flag
if spec.satisfies('%clang platform=darwin'):
mpif77 = Executable(self.spec['mpi'].mpif77)
libgfortran = LibraryList(mpif77('--print-file-name',
'libgfortran.a', output=str))
fortran_flag += ' ' + libgfortran.ld_flags
cmake_args.extend([
'-DBUILD_SHARED_LIBS=ON',
'-DCMAKE_C_FLAGS={0}'.format(self.compiler.pic_flag),
'-DCMAKE_Fortran_FLAGS={0}'.format(self.compiler.pic_flag),
'-DCMAKE_Fortran_FLAGS={0}'.format(fortran_flag),
'-DEXAMPLES_ENABLE=ON',
'-DEXAMPLES_INSTALL=ON',
'-DFCMIX_ENABLE=ON',