Merge branch 'main' into red_blood_cells/merge - a difficult merge!

Notable things:
- Adopted CMake from main branch

- Adopted main's dependency handling, including addubg for VTK and HDF

- Made use of the RBC controlled by a top-level CMake var
  (HEMELB_BUILD_RBC default OFF)

- Isolated all RBC code and libraries within that library as far as
  possible

- Added basic error handling for VTK code

- Got most unit tests passing and all executing without crash (some
  are failing)

- Removed HEMELB_LATTICE type aliases from Distribution output/input
  to deal with new LB Traits class

.gitignore

@@ -47,6 +47,7 @@ Tools/hemeTools/parsers/geometry/BaseSite.h
 Tools/hemeTools/parsers/geometry/BaseSite.so
 Tools/hemeTools/utils/xdr.c
 Tools/hemeTools/utils/xdr.so
+revision_info.txt
 hemelb-prefix/src/hemelb-stamp/hemelb-urlinfo.txt
 .*.sw[p, o, n]
 tags

AUTHORS

@@ -0,0 +1,29 @@
+This file lists the contributors to HemeLB. If their contributions are
+owned by their institution(s), this is listed in parentheses after
+their name. The details of authorship can be viewed in the git log.
+
+UCL = University College London, UK
+UoE = The University of Edinburgh, UK
+BUL = Brunel University London, UK
+
+James Hetherington (UCL)
+Hywel Carver (UCL)
+Rupert Nash (UCL, UoE)
+Miguel O. Bernabeu (UCL, UoE)
+Marco Mazzeo (UCL)
+Steven Manos (UCL)
+Derek Groen (UCL, BUL)
+David Scott (UoE)
+Nick Westlake (UCL)
+Daniel Holmes (UoE)
+Stefan Zasada (UCL)
+Jens H. Nielsen (UCL)
+Mayeul d'Avezac (UCL)
+Wojciech Kozlowski (UCL)
+Robert Haines (University of Manchester)
+Jiri Jaros (UCL)
+Gary Doctors (UCL)
+Robin Richardson (UCL)
+Mohamed Itani (UCL)
+Sebastian Schmieschek (UCL)
+David Abou Chacra

CMakeLists.txt

@@ -1,113 +1,39 @@
-cmake_minimum_required (VERSION 3.1)
+# This file is part of HemeLB and is Copyright (C)
+# the HemeLB team and/or their institutions, as detailed in the
+# file AUTHORS. This software is provided under the terms of the
+# license in the file LICENSE.
+
+cmake_minimum_required (VERSION 3.10)
+
 Project(HemeLBMaster)
-include(ExternalProject)
 
-#------- Conditional compile options ----------
+include(ExternalProject)
 
-OPTION(TIXML_USE_STL "Use STL with TIXML" ON)
-if(TIXML_USE_STL)
-	add_definitions(-DTIXML_USE_STL)
-endif(TIXML_USE_STL)
+set(HEMELB_ROOT_DIR ${CMAKE_CURRENT_SOURCE_DIR})
 
-option(HEMELB_USE_DEBUGGER "Use built in hemelb debugger" OFF)
-option(HEMELB_VALIDATE_GEOMETRY "Validate geometry" OFF)
-set(HEMELB_READING_GROUP_SIZE 5
-  CACHE INTEGER "Number of cores to use to read geometry file.")
-set(HEMELB_LOG_LEVEL Info
-	CACHE STRING "Log level, choose 'Critical', 'Error', 'Warning', 'Info', 'Debug' or 'Trace'" )
-set_property(CACHE HEMELB_LOG_LEVEL PROPERTY STRINGS Critical Error Warning Info Debug Trace)
-set(HEMELB_STEERING_LIB basic
-	CACHE STRING "Steering library, choose 'basic' or 'none'" )
-set_property(CACHE HEMELB_STEERING_LIB PROPERTY STRINGS basic none)
-option(HEMELB_USE_MULTIMACHINE "Use multi-level parallelism support" OFF)
-option(HEMELB_BUILD_UNITTESTS "Build the unit-tests" ON)
-option(HEMELB_USE_STREAKLINES "Calculate streakline images" OFF)
-option(HEMELB_USE_ALL_WARNINGS_GNU "Show all compiler warnings on development builds (gnu-style-compilers)" ON)
-option(HEMELB_STATIC_ASSERT "Use simple compile-time assertions" ON)
-set(HEMELB_OPTIMISATION "-O4" CACHE STRING "Optimisation level (can be blank or -O1 to -O4)")
-option(HEMELB_BUILD_MULTISCALE "Build HemeLB Multiscale functionality" OFF)
-set(HEMELB_LATTICE "D3Q15"
-  CACHE STRING "Select the lattice type to use (D3Q15,D3Q19,D3Q27)")
-set(HEMELB_KERNEL "LBGK"
-  CACHE STRING
-  "Select the kernel to use
-  (LBGK,EntropicAnsumali,EntropicChik,MRT,NNCY,NNCYMOUSE,NNC,NNTPL,GuoForcingLBGK)")
-set_property(CACHE HEMELB_KERNEL PROPERTY STRINGS
-  LBGK EntropicAnsumali EntropicChik MRT NNCY NNCYMOUSE NNC NNTPL GuoForcingLBGK)
-set(HEMELB_WALL_BOUNDARY "SIMPLEBOUNCEBACK"
-  CACHE STRING "Select the boundary conditions to be used at the walls (BFL,GZS,SIMPLEBOUNCEBACK,JUNKYANG)")
-set(HEMELB_INLET_BOUNDARY "NASHZEROTHORDERPRESSUREIOLET"
-  CACHE STRING "Select the boundary conditions to be used at the inlet (NASHZEROTHORDERPRESSUREIOLET,LADDIOLET)")
-set(HEMELB_OUTLET_BOUNDARY "NASHZEROTHORDERPRESSUREIOLET"
-  CACHE STRING "Select the boundary conditions to be used at the outlets (NASHZEROTHORDERPRESSUREIOLET,LADDIOLET)")
-set(HEMELB_WALL_INLET_BOUNDARY "NASHZEROTHORDERPRESSURESBB"
-  CACHE STRING "Select the boundary conditions to be used at corners between walls and inlets (NASHZEROTHORDERPRESSURESBB,NASHZEROTHORDERPRESSUREBFL,LADDIOLETSBB,LADDIOLETBFL)")
-set(HEMELB_WALL_OUTLET_BOUNDARY "NASHZEROTHORDERPRESSURESBB"
-  CACHE STRING "Select the boundary conditions to be used at corners between walls and outlets (NASHZEROTHORDERPRESSURESBB,NASHZEROTHORDERPRESSUREBFL,LADDIOLETSBB,LADDIOLETBFL)")
-set(HEMELB_STEERING_HOST "CCS" CACHE STRING "Use a default host suffix for steering? (CCS, NGS2Leeds, NGS2Manchester, LONI, NCSA or blank)")
-option(HEMELB_DEPENDENCIES_SET_RPATH "Set runtime RPATH" ON)
-set(HEMELB_SUBPROJECT_MAKE_JOBS 1 CACHE INTEGER "Number of jobs to use for subproject build steps")
-option(HEMELB_WAIT_ON_CONNECT "Wait for steering client" OFF)
-option(HEMELB_IMAGES_TO_NULL "Write images to null" OFF) 
-option(HEMELB_USE_SSE3 "Use SSE3 intrinsics" OFF)
-set(HEMELB_COMPUTE_ARCHITECTURE "AMDBULLDOZER"
-  CACHE STRING "Select the architecture of the machine being used (INTELSANDYBRIDGE,AMDBULLDOZER,NEUTRAL,ISBFILEVELOCITYINLET)")
-option(HEMELB_USE_VELOCITY_WEIGHTS_FILE "Use Velocity weights file" OFF)
+# Include the options for the main code
+include("Code/cmake/options.cmake")
+# and create a list of them to pass to the main configure step
+hemelb_pass_cmake_defines(HEMELB_CODE_CMAKE_DEFINES)
 
 #------- Dependencies -----------
 
 add_subdirectory(dependencies)
-	
+
 # ------ HemeLB ------------------
 message("${PROJECT_SOURCE_DIR}/Code")
+
 ExternalProject_Add(
-   hemelb
-   DOWNLOAD_COMMAND ""
-    SOURCE_DIR "${PROJECT_SOURCE_DIR}/Code"
-    CMAKE_ARGS
-	-DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} 
-	-DHEMELB_DEPENDENCIES_PATH=${CMAKE_CURRENT_SOURCE_DIR}/dependencies
-	-DHEMELB_DEPENDENCIES_INSTALL_PATH=${HEMELB_DEPENDENCIES_INSTALL_PATH}
-	-DTIXML_USE_STL=${TIXML_USE_STL}
-	-DHEMELB_USE_DEBUGGER=${HEMELB_USE_DEBUGGER}
-        -DHEMELB_VALIDATE_GEOMETRY=${HEMELB_VALIDATE_GEOMETRY}
-	-DHEMELB_LOG_LEVEL=${HEMELB_LOG_LEVEL}
-	-DHEMELB_STEERING_LIB=${HEMELB_STEERING_LIB}
-	-DHEMELB_USE_MULTIMACHINE=${HEMELB_USE_MULTIMACHINE}
-	-DHEMELB_BUILD_UNITTESTS=${HEMELB_BUILD_UNITTESTS}
-	-DHEMELB_USE_STREAKLINES=${HEMELB_USE_STREAKLINES}
-	-DHEMELB_OPTIMISATION=${HEMELB_OPTIMISATION}
-	-DHEMELB_READING_GROUP_SIZE=${HEMELB_READING_GROUP_SIZE}
-	-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-	-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-	-DMPI_C_COMPILER=${MPI_C_COMPILER}
-	-DMPI_CXX_COMPILER=${MPI_CXX_COMPILER}
-	-DMPI_C_NO_INTERROGATE=${MPI_C_NO_INTERROGATE}
-	-DMPI_CXX_NO_INTERROGATE=${MPI_CXX_NO_INTERROGATE}
-	-DHEMELB_USE_ALL_WARNINGS_GNU=${HEMELB_USE_ALL_WARNINGS_GNU}
-	-DHEMELB_STEERING_HOST=${HEMELB_STEERING_HOST}
-	-DCTEMPLATE_USE_STATIC=${CTEMPLATE_USE_STATIC}
-	-DCPPUNIT_USE_STATIC=${CPPUNIT_USE_STATIC}
-	-DHEMELB_DEPENDENCIES_SET_RPATH=${HEMELB_DEPENDENCIES_SET_RPATH}
-	-DHEMELB_STATIC_ASSERT=${HEMELB_STATIC_ASSERT}
-        -DHEMELB_LATTICE=${HEMELB_LATTICE}
-        -DHEMELB_KERNEL=${HEMELB_KERNEL}
-        -DHEMELB_WALL_BOUNDARY=${HEMELB_WALL_BOUNDARY}
-	-DHEMELB_INLET_BOUNDARY=${HEMELB_INLET_BOUNDARY}
-	-DHEMELB_OUTLET_BOUNDARY=${HEMELB_OUTLET_BOUNDARY}
-	-DHEMELB_WALL_INLET_BOUNDARY=${HEMELB_WALL_INLET_BOUNDARY}
-	-DHEMELB_WALL_OUTLET_BOUNDARY=${HEMELB_WALL_OUTLET_BOUNDARY}
-	-DHEMELB_WAIT_ON_CONNECT=${HEMELB_WAIT_ON_CONNECT}
-	-DHEMELB_BUILD_MULTISCALE=${HEMELB_BUILD_MULTISCALE}
-	-DHEMELB_IMAGES_TO_NULL=${HEMELB_IMAGES_TO_NULL}
-        -DHEMELB_USE_SSE3=${HEMELB_USE_SSE3}
-    -DHEMELB_COMPUTE_ARCHITECTURE=${HEMELB_COMPUTE_ARCHITECTURE}
-    -DHEMELB_USE_VELOCITY_WEIGHTS_FILE=${HEMELB_USE_VELOCITY_WEIGHTS_FILE}
-	BUILD_COMMAND make -j${HEMELB_SUBPROJECT_MAKE_JOBS}
-)
+  hemelb
+  SOURCE_DIR ${PROJECT_SOURCE_DIR}/Code
+  CONFIGURE_COMMAND "${CMAKE_COMMAND};${PROJECT_SOURCE_DIR}/Code;${HEMELB_CODE_CMAKE_DEFINES}"
+  BUILD_COMMAND make -j${HEMELB_SUBPROJECT_MAKE_JOBS}
+  )
+
+# These are handled in dependencies/CMakeLists.txt and needed here
+# to ensure they are build in correct order.
 
-foreach(dep cppunit parmetis tinyxml boost ctemplate zlib mpwide cookoff hdf5 vtk)
-  if(TARGET ${dep})
-    add_dependencies(hemelb ${dep})
-  endif()
-endforeach()
+add_dependencies(hemelb parmetis tinyxml boost catch2 ctemplate zlib)
+if(HEMELB_BUILD_MULTISCALE)
+  add_dependencies(hemelb MPWide)
+endif()