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

* 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

var/spack/repos/builtin/packages/adol-c/package.py

@@ -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')
 

var/spack/repos/builtin/packages/dealii/package.py

@@ -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' %

var/spack/repos/builtin/packages/expat/package.py

@@ -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")
 

var/spack/repos/builtin/packages/nanoflann/package.py

@@ -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

var/spack/repos/builtin/packages/sundials/package.py

@@ -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',