Commit 2970121f authored by Chris Cantwell's avatar Chris Cantwell

Merge branch 'master' into feature/ExpFromFile

parents 446dd271 d199ea62
......@@ -13,5 +13,4 @@ AllowShortLoopsOnASingleLine: false
IndentCaseLabels: true
Standard: Cpp03
AccessModifierOffset: -4
BinPackParameters: false
BinPackArguments: false
BinPackParameters: true
......@@ -3,25 +3,86 @@ Changelog
v4.4.0
------
**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
(!656)
- Sped up interpolataion from pts files and fixed parallel pts import (!584)
- Increased required boost version to 1.56.0 (!584)
- 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)
**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)
- Output Sourceterm (!664)
**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
------
**Library**:
- Auto-detect a shared filesystem and removed --shared-filesystem option (!654)
- Fix filters when using adaptive driver to avoid output being overwritten after
each adaptive update (!588)
- Minor fix to suppress Xxt output unless `--verbose` is specified (!642)
- Fix of DirectFull solver in case where only Neumann boundary conditions
are imposed. (!655)
**FieldConvert**:
- Fix to avoid repeated import of field file (!649)
- Fix issue with C^0 projection (!644)
- Fix verbose output when using --procid (!648)
**NekMesh:**
- Fix namespace issue in Star-CCM+ input header in NekMesh (!661)
**CompressibleFlowSolver**:
- Fix issue with residual output (!647)
- Issues with 1D Euler solver fixed (!565)
- Fix deadlocking issue with boundary conditions (!657)
**Packaging**:
- Fix NekMesh dependencies for DEB package (!650)
- Fix PETSc build on newer linux distributions (!646)
v4.3.2
------
......@@ -34,6 +95,7 @@ v4.3.2
output is produced in physical space (!621).
- Fix minor performance issue with time integration schemes (!632)
- Fix FilterCheckpoint filter to be consistent with `IO_CheckSteps` (!633)
- Fix CMake configuration for building on Windows 10 with VS 2015 (!641)
- Fix `IO_CheckSteps` to avoid missing first checkpoint (!639)
- Fix bug in iterative solver where only root process would ASSERT when
exceeding the maximum number of iterations (!636)
......@@ -103,7 +165,7 @@ v4.3.0
(!537)
- Fix bug with initial conditions of CG simulations using variable P (!543)
- Fix bug in 3DH2D with non-zero Dirichlet boundary conditions (!545)
- Added in a method to convert equispaced interpolated points back to
- Added in a method to convert equispaced interpolated points back to
coefficients which requires the introduction of a new StdRegions matrix.(!561)
- Empty XML tags which would override non-empty XML tags are now ignored (!581)
- Add contribution guide (!551)
......
......@@ -97,7 +97,9 @@ MARK_AS_ADVANCED(NEKTAR_BUILD_PACKAGES)
OPTION(NEKTAR_TEST_ALL "Include full set of regression tests to this build." OFF)
# Meshing utilities and library
OPTION(NEKTAR_USE_MESHGEN "Build mesh generation utilities." OFF)
IF (NOT WIN32)
OPTION(NEKTAR_USE_MESHGEN "Build mesh generation utilities." OFF)
ENDIF()
# Build options
OPTION(NEKTAR_FULL_DEBUG "Enable Full Debugging." OFF)
......@@ -176,19 +178,20 @@ ENDIF ()
INCLUDE (ThirdPartyTinyxml)
INCLUDE (ThirdPartyLoki)
INCLUDE (ThirdPartyMetis)
INCLUDE (ThirdPartyHDF5)
INCLUDE (ThirdPartyScotch)
INCLUDE (ThirdPartyZlib)
INCLUDE (ThirdPartyBoost)
INCLUDE (ThirdPartyFFTW)
INCLUDE (ThirdPartyOCC)
INCLUDE (ThirdPartyArpack)
INCLUDE (ThirdPartyMPI)
INCLUDE (ThirdPartyPETSc)
INCLUDE (ThirdPartyVTK)
INCLUDE (ThirdPartyQT4)
INCLUDE (ThirdPartySMV)
INCLUDE (ThirdPartyTriangle)
INCLUDE (ThirdPartyOCC)
INCLUDE (ThirdPartyTetGen)
INCLUDE (ThirdPartyANN)
INCLUDE (ThirdPartyCCM)
INCLUDE (Doxygen)
......@@ -283,7 +286,7 @@ INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR})
# Build active components
IF (NEKTAR_BUILD_LIBRARY)
SET(NEKTAR++_LIBRARIES SolverUtils LibUtilities StdRegions SpatialDomains LocalRegions
MultiRegions Collections GlobalMapping NekMeshUtils)
MultiRegions Collections GlobalMapping FieldUtils NekMeshUtils)
INCLUDE_DIRECTORIES(library)
ADD_SUBDIRECTORY(library)
INSTALL(EXPORT Nektar++Libraries DESTINATION ${LIB_DIR}/cmake COMPONENT dev)
......
......@@ -51,6 +51,7 @@ project. It's a pretty simple process:
new features?
- Have you run your branch through buildbot and do all the tests pass?
- Is there documentation in the user guide and/or developer guide?
- Have you added a CHANGELOG entry, including the MR number?
- Are there any massive files you might have added in the commit history? We try
to keep test files as small as possible. If so you'll need to rebase or
filter-branch to remove those from the commit history.
......
#.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} )