Merge branch 'master' into feature/APE-forcing

# Conflicts:
#	CHANGELOG.md

.clang-format

@@ -13,4 +13,4 @@ AllowShortLoopsOnASingleLine: false
 IndentCaseLabels: true
 Standard: Cpp03
 AccessModifierOffset: -4
-BinPackParameters: false
+BinPackParameters: true

CHANGELOG.md

@@ -3,9 +3,11 @@ Changelog
 
 v4.4.0
 ------
-**Library:**
+**Library**:
 - Add support for variable polynomial order for 3D simulations with continuous
   Galerkin discretisation (!604)
+- Bump version of gsmpi to suppress autotuning output unless `--verbose` is
+  specified (!652)
 - Add support for variable polynomial order with periodic boundary conditions
   (!658)
 - Statistics are now printed for lowest level of multi-level static condensation
@@ -15,8 +17,15 @@ v4.4.0
 - New FieldUtils library allows support for most `FieldConvert` post-processing
   operations during simulation using a new filter (!589)
 - Adjust CMake dependencies to reduce compile time (!671)
+- Homogeneous1D dealiasing improvements (!622)
+- Add support for HDF5 as an alternative output to XML-based output, including
+  refactoring of FieldIO, improvements to MPI interface and added communicators
+  to boundary conditions (!615)
 - Update Body/Field forces at each timestep (!665)
 
+**ADRSolver:**
+- Add a projection equation system for C^0 projections (!675)
+
 **APESolver:**
 - Use a continuous basefield projection and revert to constant c formulation (!664)
 - Added ability to compute CFL number (!664)
@@ -25,14 +34,30 @@ v4.4.0
 
 **IncNavierStokesSolver:**
 - Add ability to simulate additional scalar fields (!624)
+- Improve performance when using homogeneous dealiasing (!622)
+
+**FieldConvert:**
+- Allow equi-spaced output for 1D and 2DH1D fields (!613)
 
 **NekMesh:**
 - Modify curve module to allow for spline input (!628)
+- Add STL surface writer module (!668)
+- New module for inserting an alternate high-order surface into the working
+  mesh (!669)
+- Improvements to mesh linearisation module (!659)
+- Add support for Gmsh high-order output (!679)
 
 **FieldConvert:**
 - Move all modules to a new library, FieldUtils, to support post-processing
   during simulations (!589)
 - Add module to stretch homogeneous direction (!609)
+- Add module to add composite ID of elements as a field (!674)
+
+v4.3.4
+------
+**Library:**
+- Fix performance issue with `v_ExtractDataToCoeffs` for post-processing of large
+  simulations (!672)
 
 v4.3.3
 ------

CMakeLists.txt

@@ -178,6 +178,7 @@ ENDIF ()
 INCLUDE (ThirdPartyTinyxml)
 INCLUDE (ThirdPartyLoki)
 INCLUDE (ThirdPartyMetis)
+INCLUDE (ThirdPartyHDF5)
 INCLUDE (ThirdPartyScotch)
 INCLUDE (ThirdPartyZlib)
 INCLUDE (ThirdPartyBoost)

cmake/FindHDF5.cmake

+#.rst:
+# FindHDF5
+# --------
+#
+# Find HDF5, a library for reading and writing self describing array data.
+#
+#
+#
+# This module invokes the HDF5 wrapper compiler that should be installed
+# alongside HDF5.  Depending upon the HDF5 Configuration, the wrapper
+# compiler is called either h5cc or h5pcc.  If this succeeds, the module
+# will then call the compiler with the -show argument to see what flags
+# are used when compiling an HDF5 client application.
+#
+# The module will optionally accept the COMPONENTS argument.  If no
+# COMPONENTS are specified, then the find module will default to finding
+# only the HDF5 C library.  If one or more COMPONENTS are specified, the
+# module will attempt to find the language bindings for the specified
+# components.  The only valid components are C, CXX, Fortran, HL, and
+# Fortran_HL.  If the COMPONENTS argument is not given, the module will
+# attempt to find only the C bindings.
+#
+# On UNIX systems, this module will read the variable
+# HDF5_USE_STATIC_LIBRARIES to determine whether or not to prefer a
+# static link to a dynamic link for HDF5 and all of it's dependencies.
+# To use this feature, make sure that the HDF5_USE_STATIC_LIBRARIES
+# variable is set before the call to find_package.
+#
+# To provide the module with a hint about where to find your HDF5
+# installation, you can set the environment variable HDF5_ROOT.  The
+# Find module will then look in this path when searching for HDF5
+# executables, paths, and libraries.
+#
+# Both the serial and parallel HDF5 wrappers are considered and the first
+# directory to contain either one will be used.  In the event that both appear
+# in the same directory the serial version is preferentially selected. This
+# behavior can be reversed by setting the variable HDF5_PREFER_PARALLEL to
+# true.
+#
+# In addition to finding the includes and libraries required to compile
+# an HDF5 client application, this module also makes an effort to find
+# tools that come with the HDF5 distribution that may be useful for
+# regression testing.
+#
+# This module will define the following variables:
+#
+# ::
+#
+#   HDF5_INCLUDE_DIRS - Location of the hdf5 includes
+#   HDF5_INCLUDE_DIR - Location of the hdf5 includes (deprecated)
+#   HDF5_DEFINITIONS - Required compiler definitions for HDF5
+#   HDF5_C_LIBRARIES - Required libraries for the HDF5 C bindings.
+#   HDF5_CXX_LIBRARIES - Required libraries for the HDF5 C++ bindings
+#   HDF5_Fortran_LIBRARIES - Required libraries for the HDF5 Fortran bindings
+#   HDF5_HL_LIBRARIES - Required libraries for the HDF5 high level API
+#   HDF5_Fortran_HL_LIBRARIES - Required libraries for the high level Fortran
+#                               bindings.
+#   HDF5_LIBRARIES - Required libraries for all requested bindings
+#   HDF5_FOUND - true if HDF5 was found on the system
+#   HDF5_VERSION - HDF5 version in format Major.Minor.Release
+#   HDF5_LIBRARY_DIRS - the full set of library directories
+#   HDF5_IS_PARALLEL - Whether or not HDF5 was found with parallel IO support
+#   HDF5_C_COMPILER_EXECUTABLE - the path to the HDF5 C wrapper compiler
+#   HDF5_CXX_COMPILER_EXECUTABLE - the path to the HDF5 C++ wrapper compiler
+#   HDF5_Fortran_COMPILER_EXECUTABLE - the path to the HDF5 Fortran wrapper compiler
+#   HDF5_DIFF_EXECUTABLE - the path to the HDF5 dataset comparison tool
+
+#=============================================================================
+# Copyright 2015 Axel Huebl, Helmholtz-Zentrum Dresden - Rossendorf
+# Copyright 2009 Kitware, Inc.
+#
+# Distributed under the OSI-approved BSD License (the "License");
+# see accompanying file Copyright.txt for details.
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the License for more information.
+#=============================================================================
+# (To distribute this file outside of CMake, substitute the full
+#  License text for the above reference.)
+
+# This module is maintained by Will Dicharry <wdicharry@stellarscience.com>.
+
+include(SelectLibraryConfigurations)
+include(FindPackageHandleStandardArgs)
+
+# List of the valid HDF5 components
+set( HDF5_VALID_COMPONENTS
+    C
+    CXX
+    Fortran
+    HL
+    Fortran_HL
+)
+
+# Validate the list of find components.
+if( NOT HDF5_FIND_COMPONENTS )
+    set( HDF5_LANGUAGE_BINDINGS "C" )
+else()
+    # add the extra specified components, ensuring that they are valid.
+    foreach( component ${HDF5_FIND_COMPONENTS} )
+        list( FIND HDF5_VALID_COMPONENTS ${component} component_location )
+        if( ${component_location} EQUAL -1 )
+            message( FATAL_ERROR
+                "\"${component}\" is not a valid HDF5 component." )
+        else()
+            list( APPEND HDF5_LANGUAGE_BINDINGS ${component} )
+        endif()
+    endforeach()
+endif()
+
+# Determine whether to search for serial or parallel executable first
+if(HDF5_PREFER_PARALLEL)
+  set(HDF5_C_COMPILER_NAMES h5pcc h5cc)
+  set(HDF5_CXX_COMPILER_NAMES h5pc++ h5c++)
+  set(HDF5_Fortran_COMPILER_NAMES h5pfc h5fc)
+else()
+  set(HDF5_C_COMPILER_NAMES h5cc h5pcc)
+  set(HDF5_CXX_COMPILER_NAMES h5c++ h5pc++)
+  set(HDF5_Fortran_COMPILER_NAMES h5fc h5pfc)
+endif()
+
+# try to find the HDF5 wrapper compilers
+find_program( HDF5_C_COMPILER_EXECUTABLE
+    NAMES ${HDF5_C_COMPILER_NAMES}
+    HINTS ENV HDF5_ROOT
+    PATH_SUFFIXES bin Bin
+    DOC "HDF5 Wrapper compiler.  Used only to detect HDF5 compile flags." )
+mark_as_advanced( HDF5_C_COMPILER_EXECUTABLE )
+
+find_program( HDF5_CXX_COMPILER_EXECUTABLE
+    NAMES ${HDF5_CXX_COMPILER_NAMES}
+    HINTS ENV HDF5_ROOT
+    PATH_SUFFIXES bin Bin
+    DOC "HDF5 C++ Wrapper compiler.  Used only to detect HDF5 compile flags." )
+mark_as_advanced( HDF5_CXX_COMPILER_EXECUTABLE )
+
+find_program( HDF5_Fortran_COMPILER_EXECUTABLE
+    NAMES ${HDF5_Fortran_COMPILER_NAMES}
+    HINTS ENV HDF5_ROOT
+    PATH_SUFFIXES bin Bin
+    DOC "HDF5 Fortran Wrapper compiler.  Used only to detect HDF5 compile flags." )
+mark_as_advanced( HDF5_Fortran_COMPILER_EXECUTABLE )
+
+unset(HDF5_C_COMPILER_NAMES)
+unset(HDF5_CXX_COMPILER_NAMES)
+unset(HDF5_Fortran_COMPILER_NAMES)
+
+find_program( HDF5_DIFF_EXECUTABLE
+    NAMES h5diff
+    HINTS ENV HDF5_ROOT
+    PATH_SUFFIXES bin Bin
+    DOC "HDF5 file differencing tool." )
+mark_as_advanced( HDF5_DIFF_EXECUTABLE )
+
+# Invoke the HDF5 wrapper compiler.  The compiler return value is stored to the
+# return_value argument, the text output is stored to the output variable.
+macro( _HDF5_invoke_compiler language output return_value )
+    if( HDF5_${language}_COMPILER_EXECUTABLE )
+        exec_program( ${HDF5_${language}_COMPILER_EXECUTABLE}
+            ARGS -show
+            OUTPUT_VARIABLE ${output}
+            RETURN_VALUE ${return_value}
+        )
+        if( ${${return_value}} EQUAL 0 )
+            # do nothing
+        else()
+            message( STATUS
+              "Unable to determine HDF5 ${language} flags from HDF5 wrapper." )
+        endif()
+    endif()
+endmacro()
+
+# Parse a compile line for definitions, includes, library paths, and libraries.
+macro( _HDF5_parse_compile_line
+    compile_line_var
+    include_paths
+    definitions
+    library_paths
+    libraries )
+
+    # See if we are running using an MPI wrapper. If we are, then try to also
+    # add include directories from here as well.
+    string( REGEX MATCH "^mpi[^ ]+" mpi_wrapper "${${compile_line_var}}")
+    if (mpi_wrapper)
+        # Invoke MPI wrapper to search for additional include directories
+        exec_program(${mpi_wrapper}
+            ARGS -show
+            OUTPUT_VARIABLE mpi_wrapper_output
+            RETURN_VALUE mpi_wrapper_return)
+        if (${mpi_wrapper_return} EQUAL 0)
+            string( REGEX MATCHALL "-I([^\" ]+)" include_path_flags
+                "${mpi_wrapper_output}")
+            foreach( IPATH ${include_path_flags} )
+                string( REGEX REPLACE "^-I" "" IPATH ${IPATH} )
+                string( REPLACE "//" "/" IPATH ${IPATH} )
+                list( APPEND ${include_paths} ${IPATH} )
+            endforeach()
+        endif()
+    endif()
+
+    # Match the include paths
+    string( REGEX MATCHALL "-I([^\" ]+)" include_path_flags
+        "${${compile_line_var}}"
+    )
+    foreach( IPATH ${include_path_flags} )
+        string( REGEX REPLACE "^-I" "" IPATH ${IPATH} )
+        string( REPLACE "//" "/" IPATH ${IPATH} )
+        list( APPEND ${include_paths} ${IPATH} )
+    endforeach()
+
+    # Match the definitions
+    string( REGEX MATCHALL "-D[^ ]*" definition_flags "${${compile_line_var}}" )
+    foreach( DEF ${definition_flags} )
+        list( APPEND ${definitions} ${DEF} )
+    endforeach()
+
+    # Match the library paths
+    string( REGEX MATCHALL "-L([^\" ]+|\"[^\"]+\")" library_path_flags
+        "${${compile_line_var}}"
+    )
+
+    foreach( LPATH ${library_path_flags} )
+        string( REGEX REPLACE "^-L" "" LPATH ${LPATH} )
+        string( REPLACE "//" "/" LPATH ${LPATH} )
+        list( APPEND ${library_paths} ${LPATH} )
+    endforeach()
+
+    # now search for the library names specified in the compile line (match -l...)
+    # match only -l's preceded by a space or comma
+    # this is to exclude directory names like xxx-linux/
+    string( REGEX MATCHALL "[, ]-l([^\", ]+)" library_name_flags
+        "${${compile_line_var}}" )
+    # strip the -l from all of the library flags and add to the search list
+    foreach( LIB ${library_name_flags} )
+        string( REGEX REPLACE "^[, ]-l" "" LIB ${LIB} )
+        list( APPEND ${libraries} ${LIB} )
+    endforeach()
+endmacro()
+
+# Try to find HDF5 using an installed hdf5-config.cmake
+if( NOT HDF5_FOUND )
+    find_package( HDF5 QUIET NO_MODULE )
+    if( HDF5_FOUND )
+        set( HDF5_INCLUDE_DIRS ${HDF5_INCLUDE_DIR} )
+        set( HDF5_LIBRARIES )
+        set( HDF5_C_TARGET hdf5 )
+        set( HDF5_CXX_TARGET hdf5_cpp )
+        set( HDF5_HL_TARGET hdf5_hl )
+        set( HDF5_Fortran_TARGET hdf5_fortran )
+        set( HDF5_Fortran_HL_TARGET hdf5_hl_fortran )
+        foreach( _component ${HDF5_LANGUAGE_BINDINGS} )
+            list( FIND HDF5_VALID_COMPONENTS ${_component} _component_location )
+            get_target_property( _comp_location ${HDF5_${_component}_TARGET} LOCATION )
+            if( _comp_location )
+                set( HDF5_${_component}_LIBRARY ${_comp_location} CACHE PATH
+                    "HDF5 ${_component} library" )
+                mark_as_advanced( HDF5_${_component}_LIBRARY )
+                list( APPEND HDF5_LIBRARIES ${HDF5_${_component}_LIBRARY} )
+            endif()
+        endforeach()
+    endif()
+endif()
+
+if( NOT HDF5_FOUND )
+    _HDF5_invoke_compiler( C HDF5_C_COMPILE_LINE HDF5_C_RETURN_VALUE )
+    _HDF5_invoke_compiler( CXX HDF5_CXX_COMPILE_LINE HDF5_CXX_RETURN_VALUE )
+    _HDF5_invoke_compiler( Fortran HDF5_Fortran_COMPILE_LINE HDF5_Fortran_RETURN_VALUE )
+    set(HDF5_HL_COMPILE_LINE ${HDF5_C_COMPILE_LINE})
+    set(HDF5_Fortran_HL_COMPILE_LINE ${HDF5_Fortran_COMPILE_LINE})
+
+    # seed the initial lists of libraries to find with items we know we need
+    set( HDF5_C_LIBRARY_NAMES_INIT hdf5 )
+    set( HDF5_HL_LIBRARY_NAMES_INIT hdf5_hl ${HDF5_C_LIBRARY_NAMES_INIT} )
+    set( HDF5_CXX_LIBRARY_NAMES_INIT hdf5_cpp ${HDF5_C_LIBRARY_NAMES_INIT} )
+    set( HDF5_Fortran_LIBRARY_NAMES_INIT hdf5_fortran
+        ${HDF5_C_LIBRARY_NAMES_INIT} )
+    set( HDF5_Fortran_HL_LIBRARY_NAMES_INIT hdf5hl_fortran hdf5_hl
+        ${HDF5_Fortran_LIBRARY_NAMES_INIT} )
+
+    foreach( LANGUAGE ${HDF5_LANGUAGE_BINDINGS} )
+        if( HDF5_${LANGUAGE}_COMPILE_LINE )
+            _HDF5_parse_compile_line( HDF5_${LANGUAGE}_COMPILE_LINE
+                HDF5_${LANGUAGE}_INCLUDE_FLAGS
+                HDF5_${LANGUAGE}_DEFINITIONS
+                HDF5_${LANGUAGE}_LIBRARY_DIRS
+                HDF5_${LANGUAGE}_LIBRARY_NAMES
+            )
+
+            # take a guess that the includes may be in the 'include' sibling
+            # directory of a library directory.
+            foreach( dir ${HDF5_${LANGUAGE}_LIBRARY_DIRS} )
+                list( APPEND HDF5_${LANGUAGE}_INCLUDE_FLAGS ${dir}/../include )
+            endforeach()
+        endif()
+
+        # set the definitions for the language bindings.
+        list( APPEND HDF5_DEFINITIONS ${HDF5_${LANGUAGE}_DEFINITIONS} )
+
+        # find the HDF5 include directories
+        if(${LANGUAGE} MATCHES "Fortran")
+            set(HDF5_INCLUDE_FILENAME hdf5.mod)
+        else()
+            set(HDF5_INCLUDE_FILENAME hdf5.h)
+        endif()
+
+        find_path( HDF5_${LANGUAGE}_INCLUDE_DIR ${HDF5_INCLUDE_FILENAME}
+            HINTS
+                ${HDF5_${LANGUAGE}_INCLUDE_FLAGS}
+                ENV
+                    HDF5_ROOT
+            PATHS
+                $ENV{HOME}/.local/include
+            PATH_SUFFIXES
+                include
+                Include
+        )
+        mark_as_advanced( HDF5_${LANGUAGE}_INCLUDE_DIR )
+        list( APPEND HDF5_INCLUDE_DIRS ${HDF5_${LANGUAGE}_INCLUDE_DIR} )
+
+        set( HDF5_${LANGUAGE}_LIBRARY_NAMES
+            ${HDF5_${LANGUAGE}_LIBRARY_NAMES_INIT}
+            ${HDF5_${LANGUAGE}_LIBRARY_NAMES} )
+
+        # find the HDF5 libraries
+        foreach( LIB ${HDF5_${LANGUAGE}_LIBRARY_NAMES} )
+            if( UNIX AND HDF5_USE_STATIC_LIBRARIES )
+                # According to bug 1643 on the CMake bug tracker, this is the
+                # preferred method for searching for a static library.
+                # See https://cmake.org/Bug/view.php?id=1643.  We search
+                # first for the full static library name, but fall back to a
+                # generic search on the name if the static search fails.
+                set( THIS_LIBRARY_SEARCH_DEBUG lib${LIB}d.a ${LIB}d )
+                set( THIS_LIBRARY_SEARCH_RELEASE lib${LIB}.a ${LIB} )
+            else()
+                set( THIS_LIBRARY_SEARCH_DEBUG ${LIB}d )
+                set( THIS_LIBRARY_SEARCH_RELEASE ${LIB} )
+            endif()
+            find_library( HDF5_${LIB}_LIBRARY_DEBUG
+                NAMES ${THIS_LIBRARY_SEARCH_DEBUG}
+                HINTS ${HDF5_${LANGUAGE}_LIBRARY_DIRS}
+                ENV HDF5_ROOT
+                PATH_SUFFIXES lib Lib )
+            find_library( HDF5_${LIB}_LIBRARY_RELEASE
+                NAMES ${THIS_LIBRARY_SEARCH_RELEASE}
+                HINTS ${HDF5_${LANGUAGE}_LIBRARY_DIRS}
+                ENV HDF5_ROOT
+                PATH_SUFFIXES lib Lib )
+            select_library_configurations( HDF5_${LIB} )
+            list(APPEND HDF5_${LANGUAGE}_LIBRARIES ${HDF5_${LIB}_LIBRARY})
+        endforeach()
+        list( APPEND HDF5_LIBRARY_DIRS ${HDF5_${LANGUAGE}_LIBRARY_DIRS} )
+
+        # Append the libraries for this language binding to the list of all
+        # required libraries.
+        list(APPEND HDF5_LIBRARIES ${HDF5_${LANGUAGE}_LIBRARIES})
+    endforeach()
+
+    # We may have picked up some duplicates in various lists during the above
+    # process for the language bindings (both the C and C++ bindings depend on
+    # libz for example).  Remove the duplicates. It appears that the default
+    # CMake behavior is to remove duplicates from the end of a list. However,
+    # for link lines, this is incorrect since unresolved symbols are searched
+    # for down the link line. Therefore, we reverse the list, remove the
+    # duplicates, and then reverse it again to get the duplicates removed from
+    # the beginning.
+    macro( _remove_duplicates_from_beginning _list_name )
+        list( REVERSE ${_list_name} )
+        list( REMOVE_DUPLICATES ${_list_name} )
+        list( REVERSE ${_list_name} )
+    endmacro()
+
+    if( HDF5_INCLUDE_DIRS )
+        _remove_duplicates_from_beginning( HDF5_INCLUDE_DIRS )
+    endif()
+    if( HDF5_LIBRARY_DIRS )
+        _remove_duplicates_from_beginning( HDF5_LIBRARY_DIRS )
+    endif()
+
+    # If the HDF5 include directory was found, open H5pubconf.h to determine if
+    # HDF5 was compiled with parallel IO support
+    set( HDF5_IS_PARALLEL FALSE )
+    set( HDF5_VERSION "" )
+    foreach( _dir IN LISTS HDF5_INCLUDE_DIRS )
+      foreach(_hdr "${_dir}/H5pubconf.h" "${_dir}/H5pubconf-64.h" "${_dir}/H5pubconf-32.h")
+        if( EXISTS "${_hdr}" )
+            file( STRINGS "${_hdr}"
+                HDF5_HAVE_PARALLEL_DEFINE
+                REGEX "HAVE_PARALLEL 1" )
+            if( HDF5_HAVE_PARALLEL_DEFINE )
+                set( HDF5_IS_PARALLEL TRUE )
+            endif()
+            unset(HDF5_HAVE_PARALLEL_DEFINE)
+
+            file( STRINGS "${_hdr}"
+                HDF5_VERSION_DEFINE
+                REGEX "^[ \t]*#[ \t]*define[ \t]+H5_VERSION[ \t]+" )
+            if( "${HDF5_VERSION_DEFINE}" MATCHES
+                "H5_VERSION[ \t]+\"([0-9]+\\.[0-9]+\\.[0-9]+).*\"" )
+                set( HDF5_VERSION "${CMAKE_MATCH_1}" )
+            endif()
+            unset(HDF5_VERSION_DEFINE)
+        endif()
+      endforeach()
+    endforeach()
+    set( HDF5_IS_PARALLEL ${HDF5_IS_PARALLEL} CACHE BOOL
+        "HDF5 library compiled with parallel IO support" )
+    mark_as_advanced( HDF5_IS_PARALLEL )
+
+    # For backwards compatibility we set HDF5_INCLUDE_DIR to the value of
+    # HDF5_INCLUDE_DIRS
+    if( HDF5_INCLUDE_DIRS )
+        set( HDF5_INCLUDE_DIR "${HDF5_INCLUDE_DIRS}" )
+    endif()
+
+endif()
+
+find_package_handle_standard_args( HDF5
+    REQUIRED_VARS HDF5_LIBRARIES HDF5_INCLUDE_DIRS
+    VERSION_VAR   HDF5_VERSION
+)

cmake/Nektar++Config.cmake.in

@@ -103,6 +103,13 @@ IF( NEKTAR_USE_VTK )
         ${NEKTAR++_TP_INCLUDE_DIRS} ${VTK_INCLUDE_DIRS})
 ENDIF( NEKTAR_USE_VTK )
 
+SET(NEKTAR_USE_HDF5 "@NEKTAR_USE_HDF5@")
+IF( NEKTAR_USE_HDF5 )
+    SET(HDF5_INCLUDE_DIRS "@HDF5_INCLUDE_DIRS@")
+    SET(NEKTAR++_TP_INCLUDE_DIRS
+        ${NEKTAR++_TP_INCLUDE_DIRS} ${HDF5_INCLUDE_DIRS})
+ENDIF( NEKTAR_USE_HDF5 )
+
 # find and add Nektar++ libraries
 INCLUDE(${NEKTAR++_LIBRARY_DIRS}/cmake/Nektar++Libraries.cmake)
 

cmake/ThirdPartyANN.cmake

@@ -7,11 +7,14 @@
 ########################################################################
 
 IF (NOT WIN32)
-   CMAKE_DEPENDENT_OPTION(NEKTAR_USE_ANN
-       "Use ANN routines for performing Approximate Nearest Neighbour searches." ON
-       "NEKTAR_USE_MESHGEN" OFF)
+   OPTION(NEKTAR_USE_ANN
+       "Use ANN routines for performing Approximate Nearest Neighbour searches." OFF)
 ENDIF(NOT WIN32)
 
+IF( NEKTAR_USE_MESHGEN )
+    SET(NEKTAR_USE_ANN ON CACHE BOOL "" FORCE)
+ENDIF()
+
 IF (NEKTAR_USE_ANN)
     # First search for system ANN installs. Hint /opt/local for MacPorts and
     # /usr/local/opt/ann for Homebrew.

cmake/ThirdPartyCCM.cmake

@@ -2,22 +2,30 @@
 #
 # ThirdParty configuration for Nektar++
 #
-# Star CCM i/o 
+# Star CCM i/o
 #
 ########################################################################
-OPTION(NEKTAR_USE_CCM 
+OPTION(NEKTAR_USE_CCM
    "CCM star i/o library is available." OFF)
 
 IF( NEKTAR_USE_CCM )
-    FIND_LIBRARY(CCMIO_LIBRARY NAMES "ccmio" "adf" PATHS /usr/local/lib ${Nektar++_TP_LIBRARY_DIRS})
-    
+
+    set(CCMIO_LIBRARIES
+        ccmio
+        adf
+    )
+
+    FIND_LIBRARY(CCMIO_LIBRARY NAMES "ccmio" PATHS /usr/local/lib ${Nektar++_TP_LIBRARY_DIRS})
+
     IF( CCMIO_LIBRARY )
-        MESSAGE(STATUS "Found Ccmio: ${CCMIO_LIBRARY}") 
+        MESSAGE(STATUS "Found Ccmio: ${CCMIO_LIBRARY}")
         MARK_AS_ADVANCED(CCMIO_LIBRARY)
         ADD_DEFINITIONS(-DNEKTAR_USE_CCM)
         FIND_PATH (CCMIO_INCLUDE_DIR ccmio.h)
-        GET_FILENAME_COMPONENT(CCMIO_LIBRARY_PATH ${CCMIO_LIBRARY} PATH)
-        LINK_DIRECTORIES(${CCMIO_LIBRARY_PATH})
+        GET_FILENAME_COMPONENT(CCMIO_LIBRARY_DIR ${CCMIO_LIBRARY} PATH)
+        INCLUDE_DIRECTORIES(NekMesh ${CCMIO_INCLUDE_DIR})
+        LINK_DIRECTORIES(${CCMIO_LIBRARY_DIR})
+        MESSAGE(STATUS ${CCMIO_LIBRARY_DIR})
      ELSE()
         MESSAGE(FATAL_ERROR "Cound not find ccmio library")
      ENDIF()

cmake/ThirdPartyHDF5.cmake

+########################################################################
+#
+# ThirdParty configuration for Nektar++
+#
+# HDF5
+#
+########################################################################
+
+OPTION(NEKTAR_USE_HDF5
+    "Enable HDF5 I/O support." OFF)
+
+IF (NEKTAR_USE_HDF5)
+    IF (NOT NEKTAR_USE_MPI)
+        MESSAGE(FATAL_ERROR "HDF5 requires Nektar++ to be configured with "
+                "NEKTAR_USE_MPI for MPI support.")
+    ENDIF()
+
+    # Try to find parallel system HDF5 first.
+    SET(HDF5_PREFER_PARALLEL ON)
+    FIND_PACKAGE(HDF5 QUIET)
+
+    IF (HDF5_FOUND AND NOT HDF5_IS_PARALLEL)
+        MESSAGE(STATUS "Non-parallel system HDF5 detected: will build instead.")
+        SET(BUILD_HDF5 ON)
+    ELSEIF(HDF5_FOUND)
+        SET(BUILD_HDF5 OFF)
+    ELSE()
+        SET(BUILD_HDF5 ON)
+    ENDIF()
+
+    CMAKE_DEPENDENT_OPTION(THIRDPARTY_BUILD_HDF5
+        "Build HDF5 from ThirdParty" ${BUILD_HDF5}
+        "NEKTAR_USE_HDF5" OFF)
+
+    IF(THIRDPARTY_BUILD_HDF5)
+        IF (CMAKE_VERSION VERSION_LESS 3.1.0)
+            MESSAGE(FATAL_ERROR "HDF5 compilation requires CMake 3.1.0 or later.")
+        ENDIF()
+
+        INCLUDE(ExternalProject)
+        EXTERNALPROJECT_ADD(
+            hdf5-1.8.16
+            PREFIX ${TPSRC}
+            URL ${TPURL}/hdf5-1.8.16.tar.bz2
+            URL_MD5 79c1593573ebddf734eee8d43ecfe483
+            STAMP_DIR ${TPBUILD}/stamp
+            DOWNLOAD_DIR ${TPSRC}
+            SOURCE_DIR ${TPSRC}/hdf5-1.8.16
+            BINARY_DIR ${TPBUILD}/hdf5-1.8.16
+            TMP_DIR ${TPBUILD}/hdf5-1.8.16-tmp
+            INSTALL_DIR ${TPDIST}
+            CONFIGURE_COMMAND ${CMAKE_COMMAND}
+                -G ${CMAKE_GENERATOR}
+                -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
+                -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
+                -DCMAKE_INSTALL_PREFIX:PATH=${TPDIST}
+                -DHDF5_ENABLE_PARALLEL=ON
+                -DHDF5_BUILD_CPP_LIB=OFF
+                -DBUILD_TESTING=OFF