new package: Percept (#6636)

This also adds the 'exception' boost library to the set of default
libraries built by boost.

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

@@ -91,6 +91,7 @@ class Boost(Package):
     default_install_libs = set(['atomic',
                                 'chrono',
                                 'date_time',
+                                'exception',
                                 'filesystem',
                                 'graph',
                                 'iostreams',
@@ -339,6 +340,8 @@ def install(self, spec, prefix):
             withLibs.remove('chrono')
         if not spec.satisfies('@1.43.0:'):
             withLibs.remove('random')
+        if not spec.satisfies('@1.39.0:'):
+            withLibs.remove('exception')
         if '+graph' in spec and '+mpi' in spec:
             withLibs.append('graph_parallel')
 

var/spack/repos/builtin/packages/percept/fix_cmakelists.patch

@@ -0,0 +1,54 @@
+--- percept.orig/CMakeLists.txt	2017-12-08 09:16:41.572819000 -0700
++++ percept/CMakeLists.txt	2017-12-08 09:17:25.028818000 -0700
+@@ -97,13 +97,6 @@
+     SET (INSTALL_PERCEPT TRUE)
+ ENDIF()
+ 
+-IF (INSTALL_PERCEPT)
+-  set(BINARY_INSTALL_DIR bin)
+-  set(INCLUDE_INSTALL_DIR include)
+-  set(LIB_INSTALL_DIR lib)
+-  INCLUDE(CMakePackageConfigHelpers)
+-ENDIF ()
+-
+ MESSAGE("Setting and checking of compilers:")
+ SET(CMAKE_CXX_COMPILER ${Trilinos_CXX_COMPILER} )
+ SET(CMAKE_C_COMPILER ${Trilinos_C_COMPILER} )
+@@ -269,6 +262,8 @@
+ FILE (GLOB ADAPT_SOURCE src/adapt/main/*.cpp)
+ MESSAGE("-- ADAPT_SOURCE = ${ADAPT_SOURCE}")
+ 
++file(GLOB TRANSFER_SOURCE src/percept/mesh_transfer/*.cpp)
++
+ FILE (GLOB PERCEPT_UTEST_SOURCE test/unit_tests/*.cpp)
+ MESSAGE("-- PERCEPT_UTEST_SOURCE = ${PERCEPT_UTEST_SOURCE}")
+ 
+@@ -330,8 +325,11 @@
+   TARGET_LINK_LIBRARIES(${percept_lib_name} ${Trilinos_LIBRARIES} ${YAML_LIBRARY} ${OPENNURBS_LIBRARY} ${BOOST_LIBRARIES})
+ #  TARGET_LINK_LIBRARIES(${percept_lib_name} ${GTEST_LIBRARY})
+ 
++  add_executable(mesh_transfer ${TRANSFER_SOURCE})
++  target_link_libraries(mesh_transfer ${percept_lib_name})
++
+   SET_PROPERTY(
+-    TARGET ${percept_lib_name} ${adapt_ex_name} ${percept_utest_name} ${percept_rtest_name}
++    TARGET ${percept_lib_name} mesh_transfer ${adapt_ex_name} ${percept_utest_name} ${percept_rtest_name}
+     PROPERTY COMPILE_DEFINITIONS STK_PERCEPT_LITE=0 STK_PERCEPT_HAS_GEOMETRY STK_PERCEPT_USE_INTREPID
+   )
+ 
+@@ -342,5 +340,15 @@
+ 
+ ENDIF()
+ 
++IF (INSTALL_PERCEPT)
++  install(TARGETS ${percept_ex_name} ${adapt_ex_name}
++          ${percept_htest_name} ${percept_rtest_name} ${percept_utest_name}
++          mesh_transfer percept
++          RUNTIME DESTINATION bin
++          ARCHIVE DESTINATION lib
++          LIBRARY DESTINATION lib)
++  #install(DIRECTORY include/ DESTINATION include)
++  include(CMakePackageConfigHelpers)
++ENDIF ()
+ 
+ MESSAGE("\nAnd CMake says...:")

var/spack/repos/builtin/packages/percept/fix_header.patch

@@ -0,0 +1,19 @@
+--- percept.orig/src/percept/MeshType.hpp	2017-12-08 09:16:42.080818000 -0700
++++ percept/src/percept/MeshType.hpp	2017-12-08 09:17:25.568819000 -0700
+@@ -11,6 +11,7 @@
+ #include <percept/Percept.hpp>
+ 
+ #include <array>
++#include <memory>
+ #include <stk_mesh/base/Field.hpp>
+ #include <stk_mesh/base/Entity.hpp>
+ #include <stk_mesh/base/Bucket.hpp>
+@@ -62,7 +63,7 @@
+       typedef Kokkos::LayoutRight   SecondaryDataLayout;
+ #endif
+ 
+-	#elif KOKKOS_HAVE_OPENMP
++	#elif defined(KOKKOS_HAVE_OPENMP)
+   	  typedef Kokkos::OpenMP     ExecSpace;
+   	  typedef Kokkos::OpenMP     MemSpace;
+   	  typedef Kokkos::LayoutLeft DataLayout;

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

@@ -0,0 +1,75 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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/spack/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 Percept(CMakePackage):
+    """Parallel mesh refinement and adaptivity tools for the finite
+    element method.
+    """
+
+    homepage = "https://github.com/PerceptTools/percept"
+    url      = "https://github.com/PerceptTools/percept.git"
+
+    # This package file was created at percept
+    # commit dc1c8ec0175213146ac139946beca185a84c22e8
+    version('develop',
+            git='https://github.com/PerceptTools/percept.git', branch='master')
+
+    depends_on('googletest')
+    depends_on('opennurbs@percept')
+    depends_on('boost+graph+mpi')
+    depends_on('yaml-cpp+pic~shared@0.5.3:')
+    # Percept was initially tested against Trilinos 12.12.1
+    depends_on('trilinos~shared+exodus+tpetra+epetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf+aztec+sacado~openmp+shards+intrepid+cgns@master,12.12.1:')
+
+    patch('fix_cmakelists.patch')
+    patch('fix_header.patch')
+
+    def cmake_args(self):
+        spec = self.spec
+        options = []
+
+        options.extend([
+            '-DSTK_PERCEPT_LITE:BOOL=OFF',
+            '-DSTK_ADAPT_HAVE_YAML_CPP:BOOL=ON',
+            '-DTrilinos_DIR:PATH=%s' %
+            spec['trilinos'].prefix,
+            '-DYAML_DIR:PATH=%s' %
+            spec['yaml-cpp'].prefix,
+            '-DBOOST_DIR:PATH=%s' %
+            spec['boost'].prefix,
+            '-DOPENNURBS_DIR:PATH=%s' %
+            spec['opennurbs'].prefix,
+            '-DOPENNURBS_INCLUDE_DIR:PATH=%s' %
+            spec['opennurbs'].prefix.include,
+            '-DOPENNURBS_LIBRARY_DIR:PATH=%s' %
+            spec['opennurbs'].prefix.lib,
+            '-DPERCEPT_TPLS_INSTALL_DIR:PATH=%s' %
+            spec['googletest'].prefix,
+            '-DENABLE_INSTALL:BOOL=ON'
+        ])
+
+        return options