Update release branch to 0.2.6

--HG--
branch : release

.hgignore

@@ -8,6 +8,7 @@ build/*
 Tools/visclients/dependencies/jogamp
 Code/build/*
 Code/build_clang/*
+install/*
 results/*
 dependencies/build/*
 deploy/.jobscripts
@@ -34,7 +35,13 @@ dependencies/cppunit-prefix
 dependencies/tinyxml-prefix
 Tools/visim/visim
 Tools/setuptool/*.gdb
+Tools/steering/javagui/dependencies
 Tools/setuptool/HemeLbSetupTool/Model/_Generation.so
 Tools/setuptool/HemeLbSetupTool/Model/Generation.py 
 Tools/setuptool/HemeLbSetupTool/Model/Generation/Wrap.cpp
+Tools/steering/javagui/dependencies/jogamp/
 Tools/visclients/hs_err*.log
+Tools/analysis/config.yml
+Tools/analysis/plot.sh
+Tools/derek
+hemelb-prefix/src/hemelb-stamp/hemelb-urlinfo.txt

.hgtags

@@ -8,3 +8,4 @@ cf69e9e672eb2366c422909f4a7c8c61beef7e46 C++ Vis-client removed - Java one, whic
 5b8334f7529800dff017ad588034ff26441d86ea 0.1.0
 a6b66311e3c4712559ff6852157263d8e46f1eed 0.2.0
 85a80e60d1452e3d440752034db94be3feeae12d 0.2.1
+b7694be48d4ec46562ad386822a01ea7de9e0619 0.2.2

CMakeLists.txt

@@ -10,6 +10,7 @@ if(TIXML_USE_STL)
 endif(TIXML_USE_STL)
 
 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
@@ -23,6 +24,7 @@ option(HEMELB_USE_ALL_WARNINGS_GNU "Show all compiler warnings on development bu
 option(HEMELB_USE_BOOST "Use Boost" OFF)
 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"
@@ -32,6 +34,7 @@ set(HEMELB_WALL_BOUNDARY "SIMPLEBOUNCEBACK"
 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)
 #------- Dependencies -----------
 
 add_subdirectory(dependencies)
@@ -47,6 +50,7 @@ ExternalProject_Add(
 	-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=${HEMELB_USE_MULTIMACHINE}
@@ -70,7 +74,8 @@ ExternalProject_Add(
         -DHEMELB_LATTICE=${HEMELB_LATTICE}
         -DHEMELB_KERNEL=${HEMELB_KERNEL}
         -DHEMELB_WALL_BOUNDARY=${HEMELB_WALL_BOUNDARY}
-
+	-DHEMELB_WAIT_ON_CONNECT=${HEMELB_WAIT_ON_CONNECT}
+	-DHEMELB_BUILD_MULTISCALE=${HEMELB_BUILD_MULTISCALE}
 	BUILD_COMMAND make -j${HEMELB_SUBPROJECT_MAKE_JOBS}
 )
 

Code/.project

@@ -5,9 +5,13 @@
 	<projects>
 	</projects>
 	<buildSpec>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 		<buildCommand>
 			<name>org.eclipse.cdt.managedbuilder.core.genmakebuilder</name>
-			<triggers>clean,full,incremental,</triggers>
 			<arguments>
 				<dictionary>
 					<key>?name?</key>
@@ -19,27 +23,31 @@
 				</dictionary>
 				<dictionary>
 					<key>org.eclipse.cdt.make.core.autoBuildTarget</key>
-					<value>all</value>
+					<value></value>
 				</dictionary>
 				<dictionary>
 					<key>org.eclipse.cdt.make.core.buildArguments</key>
-					<value></value>
+					<value>-j4</value>
 				</dictionary>
 				<dictionary>
 					<key>org.eclipse.cdt.make.core.buildCommand</key>
 					<value>make</value>
 				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.buildLocation</key>
+					<value>${workspace_loc:/Code/build}</value>
+				</dictionary>
 				<dictionary>
 					<key>org.eclipse.cdt.make.core.cleanBuildTarget</key>
-					<value>clean_all</value>
+					<value>clean</value>
 				</dictionary>
 				<dictionary>
 					<key>org.eclipse.cdt.make.core.contents</key>
 					<value>org.eclipse.cdt.make.core.activeConfigSettings</value>
 				</dictionary>
 				<dictionary>
 					<key>org.eclipse.cdt.make.core.enableAutoBuild</key>
-					<value>false</value>
+					<value>true</value>
 				</dictionary>
 				<dictionary>
 					<key>org.eclipse.cdt.make.core.enableCleanBuild</key>
@@ -75,5 +83,6 @@
 		<nature>org.eclipse.cdt.core.ccnature</nature>
 		<nature>org.eclipse.cdt.managedbuilder.core.managedBuildNature</nature>
 		<nature>org.eclipse.cdt.managedbuilder.core.ScannerConfigNature</nature>
+		<nature>org.python.pydev.pythonNature</nature>
 	</natures>
 </projectDescription>

Code/.settings/org.eclipse.cdt.core.prefs

@@ -1,6 +1,8 @@
-#Thu Jan 12 10:43:36 GMT 2012
+#Mon May 21 17:33:11 BST 2012
 eclipse.preferences.version=1
 environment/project/cdt.managedbuild.toolchain.gnu.base.825880950.1300491428=
+environment/project/cdt.managedbuild.toolchain.gnu.base.825880950.1300491428.770148502/append=true
+environment/project/cdt.managedbuild.toolchain.gnu.base.825880950.1300491428.770148502/appendContributed=true
 environment/project/cdt.managedbuild.toolchain.gnu.base.825880950.1300491428/HEMELB_MACHINE/delimiter=\:
 environment/project/cdt.managedbuild.toolchain.gnu.base.825880950.1300491428/HEMELB_MACHINE/operation=append
 environment/project/cdt.managedbuild.toolchain.gnu.base.825880950.1300491428/HEMELB_MACHINE/value=CCS

Code/CMakeLists.txt

@@ -5,13 +5,18 @@ project(HemeLB)
 #---- OPTION switches accepted by the build -------
 
 option(HEMELB_USE_DEBUGGER "Use built in hemelb debugger" OFF)
+option(HEMELB_VALIDATE_GEOMETRY "Validate geometry" OFF)
 option(HEMELB_USE_MULTIMACHINE "Use multi-level parallelism support" OFF)
-option(HEMELB_BUILD_UNITTESTS "Build the unit-tests" ON)
+option(HEMELB_BUILD_TESTS_ALL "Build all the tests" ON)
+option(HEMELB_BUILD_TESTS_UNIT "Build the unit-tests (HEMELB_BUILD_TESTS_ALL takes precedence)" ON)
+option(HEMELB_BUILD_TESTS_FUNCTIONAL "Build the functional tests (HEMELB_BUILD_TESTS_ALL takes precedence)" ON)
 option(HEMELB_USE_ALL_WARNINGS_GNU "Show all compiler warnings on development builds (gnu-style-compilers)" ON)
 option(HEMELB_USE_STREAKLINES "Calculate streakline images" ON)
 option(HEMELB_USE_BOOST "Use Boost" OFF)
 option(HEMELB_DEPENDENCIES_SET_RPATH "Set runtime RPATH" ON)
 option(HEMELB_STATIC_ASSERT "Use simple compile-time assertions" ON)
+option(HEMELB_WAIT_ON_CONNECT "Wait for steering client" OFF)
+option(HEMELB_BUILD_MULTISCALE "Build HemeLB Multiscale functionality" OFF)
 
 set(HEMELB_READING_GROUP_SIZE 5
   CACHE INTEGER "Number of cores to use to read geometry file.")
@@ -46,10 +51,18 @@ add_definitions(-DHEMELB_LATTICE=${HEMELB_LATTICE})
 add_definitions(-DHEMELB_KERNEL=${HEMELB_KERNEL})
 add_definitions(-DHEMELB_WALL_BOUNDARY=${HEMELB_WALL_BOUNDARY})
 
+if(HEMELB_VALIDATE_GEOMETRY)
+  add_definitions(-DHEMELB_VALIDATE_GEOMETRY)
+endif()
+
 if (NOT HEMELB_USE_STREAKLINES)
 	add_definitions(-DNO_STREAKLINES)
 endif()
 
+if (HEMELB_WAIT_ON_CONNECT)
+	add_definitions(-DHEMELB_WAIT_ON_CONNECT)
+endif()
+
 if (NOT HEMELB_STATIC_ASSERT)
 	add_definitions(-DHEMELB_NO_STATIC_ASSERT)
 endif()
@@ -72,21 +85,26 @@ list(APPEND CMAKE_LIBRARY_PATH ${HEMELB_DEPENDENCIES_INSTALL_PATH}/lib)
 #--- Set up runtime search path for DLLs -----
 if(HEMELB_DEPENDENCIES_SET_RPATH)
 	SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
-	SET(CMAKE_INSTALL_RPATH "${HEMELB_DEPENDENCIES_PATH}/lib")
+	SET(CMAKE_INSTALL_RPATH "${HEMELB_DEPENDENCIES_INSTALL_PATH}/lib")
 endif()
 
 #-------Check for platform dependent features ----
 
 include(CheckCXXSourceCompiles)
 CHECK_CXX_SOURCE_COMPILES("#include <cmath>\n int main(int c,char** v){ return isnan(1.0); }" HAVE_ISNAN)
 CHECK_CXX_SOURCE_COMPILES("#include <cmath>\n int main(int c,char** v){ return std::isnan(1.0); }" HAVE_STD_ISNAN)
+CHECK_CXX_SOURCE_COMPILES("#include <sys/time.h>\n#include <sys/resource.h>\nint main(int c,char** v){ rusage usage;\ngetrusage(RUSAGE_SELF, &usage);\nreturn usage.ru_maxrss; }" HAVE_RUSAGE)
 
 if(HAVE_ISNAN)
   add_definitions(-DHAVE_ISNAN)
 endif()
 
-if( HAVE_STD_ISNAN)
-  add_definitions(-D HAVE_STD_ISNAN)
+if(HAVE_STD_ISNAN)
+  add_definitions(-DHAVE_STD_ISNAN)
+endif()
+
+if(HAVE_RUSAGE)
+  add_definitions(-DHAVE_RUSAGE)
 endif()
 
 # ------MPI------------------
@@ -118,6 +136,12 @@ endif()
 #------CTemplate ----------------
 find_package(CTemplate REQUIRED)
 include_directories(${CTEMPLATE_INCLUDE_DIR})
+if(HEMELB_BUILD_MULTISCALE)
+  #------MPWide ----------------
+  find_package(MPWide REQUIRED)
+  include_directories(${MPWide_INCLUDE_DIR})
+  add_definitions(-DHEMELB_BUILD_MULTISCALE)
+endif()
 
 #------zlib ----------------
 find_package(ZLIB REQUIRED)
@@ -138,7 +162,7 @@ configure_file (
 # so that we will find TutorialConfig.h
 include_directories("${PROJECT_BINARY_DIR}")
 
-# ----------- HemeLB ------------------s
+# ----------- HemeLB ------------------
 if (APPLE)
 	add_definitions(-DHEMELB_CFG_ON_BSD -DHEMELB_CFG_ON_OSX)
 endif()
@@ -149,6 +173,7 @@ endif()
 
 set(root_sources SimulationMaster.cc mpiInclude.cc)
 add_executable(hemelb main.cc ${root_sources})
+
 include_directories(${PROJECT_SOURCE_DIR})
 set(package_subdirs
 	configuration
@@ -180,14 +205,65 @@ target_link_libraries(hemelb
 	${Boost_LIBRARIES}
 	${CTEMPLATE_LIBRARIES}
 	${ZLIB_LIBRARIES}
+  ${MPWide_LIBRARIES}
 	)
 INSTALL(TARGETS hemelb RUNTIME DESTINATION bin)
 list(APPEND RESOURCES resources/report.txt.ctp resources/report.xml.ctp)
+
+# ----------- HemeLB Multiscale ------------------
+if (HEMELB_BUILD_MULTISCALE)
+	if (APPLE)
+		add_definitions(-DHEMELB_CFG_ON_BSD -DHEMELB_CFG_ON_OSX)
+	endif()
+	if (HEMELB_USE_DEBUGGER)
+		# Force a debug build, because the debugger makes no sense without debug symbols
+		set(CMAKE_BUILD_TYPE DEBUG)
+	endif()
+
+	set(root_sources SimulationMaster.cc mpiInclude.cc multiscale/MultiscaleSimulationMaster.h)
+	add_executable(ms_hemelb mainMultiscale.cc ${root_sources})
+	include_directories(${PROJECT_SOURCE_DIR})
+	set(package_subdirs
+		configuration
+		extraction
+		reporting
+		steering
+		vis
+		geometry
+		lb
+		net
+		debug
+		topology
+		util
+		io
+		log
+	    colloids
+		)
+	foreach(subdir ${package_subdirs})
+		set(lib "hemelb_${subdir}")
+		list(APPEND heme_libraries ${lib})
+#		add_subdirectory(${subdir})
+	endforeach()
+#	add_subdirectory(resources)
+	target_link_libraries(ms_hemelb 
+		${heme_libraries}
+		${MPI_LIBRARIES}
+		${PARMETIS_LIBRARIES}
+		${TINYXML_LIBRARIES}
+		${Boost_LIBRARIES}
+		${CTEMPLATE_LIBRARIES}
+		${ZLIB_LIBRARIES}
+	    ${MPWide_LIBRARIES}
+		)
+	INSTALL(TARGETS ms_hemelb RUNTIME DESTINATION bin)
+	list(APPEND RESOURCES resources/report.txt.ctp resources/report.xml.ctp)
+endif()
+
 # ----------- HEMELB unittests ---------------
-if(HEMELB_BUILD_UNITTESTS)
+if(HEMELB_BUILD_TESTS_ALL OR HEMELB_BUILD_TESTS_UNIT)
 	#------CPPUnit ---------------
-		find_package(CPPUnit REQUIRED)
-		include_directories(${CPPUNIT_INCLUDE_DIR})
+	find_package(CPPUnit REQUIRED)
+	include_directories(${CPPUNIT_INCLUDE_DIR})
 	add_executable(unittests_hemelb ${root_sources})
 	add_subdirectory(unittests)
 	target_link_libraries(unittests_hemelb 
@@ -200,6 +276,7 @@ if(HEMELB_BUILD_UNITTESTS)
 		${Boost_LIBRARIES}
 		${CTEMPLATE_LIBRARIES}
 		${ZLIB_LIBRARIES}
+		${MPWide_LIBRARIES}
 		${CMAKE_DL_LIBS}) #Because on some systems CPPUNIT needs to be linked to libdl
 	INSTALL(TARGETS unittests_hemelb RUNTIME DESTINATION bin)
 	list(APPEND RESOURCES unittests/resources/four_cube.gmy unittests/resources/four_cube.xml unittests/resources/four_cube_multiscale.xml
@@ -208,6 +285,28 @@ if(HEMELB_BUILD_UNITTESTS)
 		)
 endif()
 
+# ----------- HEMELB functionaltests ---------------
+if(HEMELB_BUILD_TESTS_ALL OR HEMELB_BUILD_TESTS_FUNCTIONAL)
+	#------CPPUnit ---------------
+	find_package(CPPUnit REQUIRED)
+	include_directories(${CPPUNIT_INCLUDE_DIR})
+	add_executable(functionaltests_hemelb ${root_sources})
+	add_subdirectory(functionaltests/cpptests)
+	target_link_libraries(functionaltests_hemelb 
+		hemelb_functionaltests 
+		${heme_libraries}
+		${MPI_LIBRARIES}
+		${PARMETIS_LIBRARIES}
+		${TINYXML_LIBRARIES}
+		${CPPUNIT_LIBRARY}
+		${Boost_LIBRARIES}
+		${CTEMPLATE_LIBRARIES}
+		${MPWide_LIBRARIES}
+		${ZLIB_LIBRARIES}
+		${CMAKE_DL_LIBS}) #Because on some systems CPPUNIT needs to be linked to libdl
+	INSTALL(TARGETS functionaltests_hemelb RUNTIME DESTINATION bin)
+endif()
+
 #-------- Copy and install resources --------------
 
 foreach(resource ${RESOURCES})