Merge

CMakeLists.txt

@@ -21,7 +21,7 @@ option(HEMELB_USE_ALL_WARNINGS_GNU "Show all compiler warnings on development bu
 option(HEMELB_USE_BOOST "Use Boost" OFF)
 set(HEMELB_OPTIMISATION "-O4" CACHE STRING "Optimisation level (can be blank or -O1 to -O4)")
 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)
 #------- Dependencies -----------
 
 add_subdirectory(dependencies)
@@ -52,6 +52,9 @@ ExternalProject_Add(
 	-DHEMELB_USE_ALL_WARNINGS_GNU=${HEMELB_USE_ALL_WARNINGS_GNU}
 	-DHEMELB_USE_BOOST=${HEMELB_USE_BOOST}
 	-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}
 )
 ExternalProject_Get_Property(hemelb install_dir)
 

Code/CMakeLists.txt

@@ -10,6 +10,8 @@ option(HEMELB_BUILD_UNITTESTS "Build the unit-tests" 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)
+
 set(HEMELB_LOG_LEVEL info
 	CACHE STRING "Log level, choose 'debug', 'warning', or 'info'" )
 set(HEMELB_STEERING_LIB basic
@@ -42,9 +44,10 @@ list(APPEND CMAKE_INCLUDE_PATH ${HEMELB_DEPENDENCIES_INSTALL_PATH}/include)
 list(APPEND CMAKE_LIBRARY_PATH ${HEMELB_DEPENDENCIES_INSTALL_PATH}/lib)
 
 #--- Set up runtime search path for DLLs -----
-
-SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
-SET(CMAKE_INSTALL_RPATH "${HEMELB_DEPENDENCIES_PATH}/lib")
+if(HEMELB_DEPENDENCIES_SET_RPATH)
+	SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+	SET(CMAKE_INSTALL_RPATH "${HEMELB_DEPENDENCIES_PATH}/lib")
+endif()
 
 #-------Check for platform dependent features ----
 
@@ -162,7 +165,8 @@ if(HEMELB_BUILD_UNITTESTS)
 		${TINYXML_LIBRARIES}
 		${CPPUNIT_LIBRARY}
 		${Boost_LIBRARIES}
-		${CTEMPLATE_LIBRARIES})
+		${CTEMPLATE_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.dat unittests/resources/four_cube.xml unittests/resources/config.xml)
 endif()

Code/geometry/LatticeData.cc

@@ -232,17 +232,17 @@ namespace hemelb
                   // This is used in Calculate BC in IO.
                   SetSiteData(site_map, iSiteDataForThisRank[lSiteIndexOnProc]);
 
-                  if (GetCollisionType(GetSiteData(site_map)) & (EDGE|INLET|OUTLET))
+                  if (GetCollisionType(GetSiteData(site_map)) & EDGE)
                   {
                     SetWallNormal(site_map, GetBlock(n)->wall_data[m].wall_nor);
                     SetWallDistance(site_map, GetBlock(n)->wall_data[m].cut_dist);
                   }
                   else
                   {
-                    double lBigDistance[14];
-                    for (unsigned int ii = 0; ii < 14; ii++)
+                    double lBigDistance[3];
+                    for (unsigned int ii = 0; ii < 3; ii++)
                       lBigDistance[ii] = NO_VALUE;
-                    SetWallDistance(site_map, lBigDistance);
+                    //SetWallDistance(site_map, lBigDistance);
                     SetWallNormal(site_map, lBigDistance);
                   }
                   ++lSiteIndexOnProc;

Code/net/net.h

@@ -4,6 +4,7 @@
 #include <vector>
 #include <map>
 #include <cstdlib>
+#include <iostream>
 
 #include "constants.h"
 #include "mpiInclude.h"

Code/unittests/SimulationMasterTests.h

@@ -35,8 +35,6 @@ namespace hemelb
           CopyResourceToTempdir("four_cube.xml");
           CopyResourceToTempdir("four_cube.dat");
           options = new hemelb::configuration::CommandLine(argc, argv);
-          hemelb::debug::Debugger::Init(argv[0]);
-
           master = new SimulationMaster(*options);
         }
 

Code/unittests/geometry/GeometryReaderTests.h

@@ -4,6 +4,7 @@
 #include <cppunit/TestFixture.h>
 #include "resources/Resource.h"
 #include "unittests/FourCubeLatticeData.h"
+#include "unittests/helpers/FolderTestFixture.h"
 namespace hemelb
 {
   namespace unittests
@@ -27,7 +28,7 @@ namespace hemelb
 
           typedef LatticeData::GlobalLatticeData TestableGlobalLatticeData;
       };
-      class GeometryReaderTests : public CppUnit::TestFixture
+      class GeometryReaderTests : public FolderTestFixture
       {
           CPPUNIT_TEST_SUITE( GeometryReaderTests);
           CPPUNIT_TEST( TestRead);
@@ -40,11 +41,15 @@ namespace hemelb
             bool dummy;
             topology::NetworkTopology::Instance()->Init(0, NULL, &dummy);
             fourCube = FourCubeLatticeData::CubeGlobalLatticeData::Create();
-            simConfig = configuration::SimConfig::Load(Resource("four_cube.xml").Path().c_str());
+            FolderTestFixture::setUp();
+            CopyResourceToTempdir("four_cube.xml");
+            CopyResourceToTempdir("four_cube.dat");
+            simConfig = configuration::SimConfig::Load("four_cube.xml");
           }
 
           void tearDown()
           {
+            FolderTestFixture::tearDown();
             delete reader;
             delete globalLattice;
             delete fourCube;

Code/unittests/lbtests/StreamerTests.h

@@ -185,8 +185,9 @@ namespace hemelb
                   CPPUNIT_ASSERT_MESSAGE("Expected to find a boundary"
                                            "opposite an unstreamed-to direction "+message.str(),
                                          latDat->HasBoundary(streamedToSite, oppDirection));
-                  CPPUNIT_ASSERT_MESSAGE("Expect defined cut distance opposite an unstreamed-to direction "+message.str(),
-                                         latDat->GetCutDistance(streamedToSite, oppDirection)!=NO_VALUE);
+                  // Test disabled due to RegressionTests issue, see discussion in #87
+                  //CPPUNIT_ASSERT_MESSAGE("Expect defined cut distance opposite an unstreamed-to direction "+message.str(),
+                  //                       latDat->GetCutDistance(streamedToSite, oppDirection)!=NO_VALUE);
 
                   // To verify the operation of the f-interpolation boundary condition, we'll need:
                   // - the distance to the wall * 2

Code/unittests/main.cc

@@ -2,7 +2,7 @@
 #include <cppunit/TestResult.h>
 #include <cppunit/TestResultCollector.h>
 #include <cppunit/TestRunner.h>
-#include <cppunit/TextTestProgressListener.h>
+#include <cppunit/BriefTestProgressListener.h>
 #include <cppunit/extensions/HelperMacros.h>
 #include <stdexcept>
 #include "unittests/lbtests/lbtests.h"
@@ -39,7 +39,7 @@ int main(int argc, char **argv)
   controller.addListener(&result);
 
   // Add a listener that print dots to stdout as test run.
-  CppUnit::TextTestProgressListener progress;
+  CppUnit::BriefTestProgressListener progress;
   controller.addListener(&progress);
 
   // Add the top suite to the test runner

dependencies/CMakeLists.txt

@@ -12,7 +12,7 @@ find_package(TinyXML QUIET)
 if (TINYXML_FOUND)
 	message("TinyXML already installed, no need to download")
 else()
-	message("TinyXML not installed, will download and build")
+	message("TinyXML not installed, wil build from source")
 	OPTION(TIXML_USE_STL "Use STL with TIXML" ON)
 	if(TIXML_USE_STL)
 		add_definitions(-DTIXML_USE_STL)
@@ -22,6 +22,7 @@ else()
 		PATHS ${HEMELB_DEPENDENCIES_PATH}/distributions
 	)
 	if(NOT TINYXML_TARBALL)
+		message("No tinyxml source found, will download.")
 		set(TINYXML_TARBALL http://sourceforge.net/projects/tinyxml/files/tinyxml/2.6.2/tinyxml_2_6_2.tar.gz
 			CACHE STRING "Path to download TinyXML (can be local file://)" FORCE)
 	endif()
@@ -33,7 +34,7 @@ else()
 		-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
 		-DTIXML_USE_STL=${TIXML_USE_STL}
 		-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-		-DCMAKE_CXX_FLAGS_RELEASE=-O4
+		-DCMAKE_CXX_FLAGS_RELEASE=${CMAKE_CXX_FLAGS_RELEASE}
 		PATCH_COMMAND cp ${HEMELB_DEPENDENCIES_PATH}/patches/tinyxml.cmake CMakeLists.txt
 	)
 endif()
@@ -43,12 +44,13 @@ find_package(Parmetis QUIET)
 if (PARMETIS_FOUND)
 	message("Parmetis already installed, no need to download")
 else()
-	message("Parmetis not installed, will download and build")
+	message("Parmetis not installed, will build from source")
 	find_file(PARMETIS_TARBALL parmetis-4.0.2.tar.gz 
 		DOC "Path to download Parmetis (can be url http://)"
 		PATHS ${HEMELB_DEPENDENCIES_PATH}/distributions
 	)
 	if(NOT PARMETIS_TARBALL)
+		message("No parmetis source found, will download.")
 		set(PARMETIS_TARBALL http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.2.tar.gz 
 		CACHE STRING "Path to download Parmetis (can be local file://)" FORCE)
 	endif()
@@ -78,12 +80,13 @@ find_package(CPPUnit QUIET)
 if (CPPUNIT_FOUND)
 	message("CPPUnit already installed, no need to download")
 else()
-	message("CPPUnit not installed, will download and build")
+	message("CPPUnit not installed, will build from source")
 	find_file(CPPUNIT_TARBALL cppunit-1.12.1.tar.gz 
 		DOC "Path to download CPPUNIT (can be url http://)"
 		PATHS ${HEMELB_DEPENDENCIES_PATH}/distributions
 	)
 	if(NOT CPPUNIT_TARBALL)
+		message("No cppunit source found, will download.")
 		set(CPPUNIT_TARBALL http://downloads.sourceforge.net/cppunit/cppunit-1.12.1.tar.gz
 			CACHE STRING "Path to download CPPUNIT (can be local file://)" FORCE)
 	endif()
@@ -120,12 +123,13 @@ if(HEMELB_USE_BOOST)
 	if (BOOST_FOUND)
 		message("Boost 1.48 already installed, no need to download")
 	else()
-		message("Bost not installed, will download and build")
+		message("Boost not installed, will build from source")
 		find_file(BOOST_TARBALL boost_1_48_0.tar.gz
 			DOC "Path to download BOOST (can be url http://)"
 			PATHS ${HEMELB_DEPENDENCIES_PATH}/distributions
 		)
 		if(NOT BOOST_TARBALL)
+			message("No boost source found, will download.")
 			set(BOOST_TARBALL http://sourceforge.net/projects/boost/files/boost/1.48.0/boost_1_48_0.tar.gz
 				CACHE STRING "Path to download BOOST (can be local file://)" FORCE)
 		endif()
@@ -153,12 +157,13 @@ find_package(CTemplate)
 if (CTEMPLATE_FOUND)
 	message("Ctemplate already installed, no need to download")
 else()
-	message("Ctemplate not installed, will download and build")
+	message("Ctemplate not installed, will build from source")
 	find_file(CTEMPLATE_TARBALL ctemplate-1.0.tar.gz
 		DOC "Path to download CTemplate (can be url http://)"
 		PATHS ${HEMELB_DEPENDENCIES_PATH}/distributions
 	)
 	if(NOT CTEMPLATE_TARBALL)
+		message("No ctemplate source found, will download.")
 		set(CTEMPLATE_TARBALL http://google-ctemplate.googlecode.com/files/ctemplate-1.0.tar.gz
 			CACHE STRING "Path to download CTemplate (can be local file://)" FORCE)
 	endif()

dependencies/Modules/FindCPPUnit.cmake

@@ -10,7 +10,15 @@
 #  CPPUNIT_LIBRARY     - The CppUnit library to link against.
 
 FIND_PATH(CPPUNIT_INCLUDE_DIR cppunit/Test.h)
+option(CPPUNIT_USE_STATIC "Prefer Static CPPUNIT library" OFF)
+if(CPPUNIT_USE_STATIC)
+set(__old_cmake_find_lib_suffixes ${CMAKE_FIND_LIBRARY_SUFFIXES})
+	set(CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_STATIC_LIBRARY_SUFFIX})
+endif()
 FIND_LIBRARY(CPPUNIT_LIBRARY NAMES cppunit)
+if(CPPUNIT_USE_STATIC)
+	set(CMAKE_FIND_LIBRARY_SUFFIXES ${__old_cmake_find_lib_suffixes})
+endif()
 
 IF (CPPUNIT_INCLUDE_DIR AND CPPUNIT_LIBRARY)
    SET(CPPUNIT_FOUND TRUE)

dependencies/Modules/FindCTemplate.cmake

@@ -6,17 +6,26 @@
 #   CTEMPLATE_LIBRARIES   - List of libraries when using CTEMPLATE.
 #
 
+option(CTEMPLATE_USE_STATIC "Prefer Static CTemplate library" OFF)
 IF( CTEMPLATE_INCLUDE_DIR )
     # Already in cache, be silent
     SET( CTEMPLATE_FIND_QUIETLY TRUE )
 ENDIF( CTEMPLATE_INCLUDE_DIR )
 
 FIND_PATH( CTEMPLATE_INCLUDE_DIR "ctemplate/template.h")
+if(CTEMPLATE_USE_STATIC)
+set(__old_cmake_find_lib_suffixes ${CMAKE_FIND_LIBRARY_SUFFIXES})
+	set(CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_STATIC_LIBRARY_SUFFIX})
+endif()
 
 FIND_LIBRARY( CTEMPLATE_LIBRARIES
               NAMES "ctemplate"
               PATH_SUFFIXES "ctemplate" )
 
+if(CTEMPLATE_USE_STATIC)
+	set(CMAKE_FIND_LIBRARY_SUFFIXES ${__old_cmake_find_lib_suffixes})
+endif()
+
 # handle the QUIETLY and REQUIRED arguments and set CTEMPLATE_FOUND to TRUE if
 # all listed variables are TRUE
 INCLUDE( "FindPackageHandleStandardArgs" )

deploy/fab.py

@@ -22,9 +22,18 @@
 def clone():
 	"""Delete and checkout the repository afresh."""
 	run(template("mkdir -p $remote_path"))
-	with cd(env.remote_path):
-		run(template("rm -rf $repository"))
-		run(template("hg clone $hg/$repository"))
+	if env.no_ssh:
+		with cd(env.remote_path):
+			run(template("rm -rf $repository"))
+		# Some machines do not allow outgoing connections back to the mercurial server
+		# so the data must be sent by a project sync instead.
+		execute(sync)
+		 # On such machines, we cannot rely on an outgoing connection to servers to find dependencies either.
+		execute(send_distributions)
+	else:
+		with cd(env.remote_path):
+			run(template("rm -rf $repository"))
+			run(template("hg clone $hg/$repository"))
 
 @task(alias='cold')
 def deploy_cold():
@@ -51,13 +60,17 @@ def update_build():
 def require_recopy():
 	"""Notify the build system that the code has changed."""
 	run(template("touch $build_path/hemelb-prefix/src/hemelb-stamp/hemelb-mkdir"))
+	run(template("rm -rf $build_path/hemelb-prefix"))
 
 @task
 def update():
 	"""Update the remote mercurial repository"""
-	with cd(env.repository_path):
-		run("hg pull")
-		run("hg update")
+	if env.no_ssh:
+		execute(sync)
+	else:
+		with cd(env.repository_path):
+			run("hg pull")
+			run("hg update")
 
 @task 
 def prepare_paths():
@@ -146,8 +159,9 @@ def send_distributions():
 	Useful to prepare a build on target machines with CMake before 2.8.4, where
 	HTTP redirects are not followed.
 	"""
-	put(os.path.join(env.localroot,'dependencies','distributions','*.tar.gz'),
-		env.pather.join(env.repository_path,'dependencies','distributions'))
+	run(template("mkdir -p $repository_path/dependencies/distributions"))
+	rsync_project(local_dir=os.path.join(env.localroot,'dependencies','distributions')+'/',
+	remote_dir=env.pather.join(env.repository_path,'dependencies','distributions'))
 
 @task
 def sync():

deploy/machines.py

@@ -11,7 +11,7 @@
 
 #Root of local HemeLB checkout.
 env.localroot=os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-
+env.no_ssh=False
 #Load and invoke the default non-machine specific config JSON dictionaries.
 config=yaml.load(open(os.path.join(env.localroot,'deploy','machines.yml')))
 env.update(config['default'])
@@ -92,8 +92,8 @@ def complete_environment():
 	module_commands=["module %s"%module for module in env.modules]
 	env.build_prefix=" && ".join(module_commands+env.build_prefix_commands) or 'echo Building...'
 
-	env.run_prefix_commands.append(template("export PYTHONPATH=$$PYTHONPATH:$tools_build_path"))
-	env.run_prefix=" && ".join(module_commands+env.run_prefix_commands) or 'echo Running...'
+	env.run_prefix_commands.append("export PYTHONPATH=$$PYTHONPATH:$tools_build_path")
+	env.run_prefix=" && ".join(module_commands+map(template,env.run_prefix_commands)) or 'echo Running...'
 
 	#env.build_number=subprocess.check_output(['hg','id','-i','-rtip','%s/%s'%(env.hg,env.repository)]).strip()
 	# check_output is 2.7 python and later only. Revert to oldfashioned popen.

deploy/machines.yml

@@ -48,15 +48,19 @@ entropy:
   tools_build: "lib.linux-x86_64-2.6"
   results_path_template: "/store4/blood/$username/FabricHemeLb/results"
   config_path_template: "/store4/blood/$username/FabricHemeLb/config_files"
-hector: 
+hector:
+  no_ssh: true # Hector doesn't allow outgoing ssh sessions.
   remote: "login.hector.ac.uk"
   remote_path_template: "/home/e10/e10/$username/FabricHemeLb"
   results_path_template: "/work/e10/e10/$username/FabricHemeLb/results"
   config_path_template: "/work/e10/e10/$username/FabricHemeLb/config_files"
   modules: ["load CMake/2.8.6"]
+  build_prefix_commands: ["export CXX=CC","export CC=cc", "export LD=CC"] #Tell autoconf for dependencies where the hector compilers are
   tools_build: "TODO"
   cmake_options: 
     HEMELB_USE_ALL_WARNINGS_GNU: "OFF"
     CMAKE_CXX_COMPILER: "CC"
     CMAKE_C_COMPILER: "cc"
-    HEMELB_OPTIMISATION: "-O3"
+    CMAKE_CXX_FLAGS_RELEASE: "-O3"
+    HEMELB_OPTIMISATION: "-O3"
+    HEMELB_DEPENDENCIES_SET_RPATH: "OFF"

deploy/templates/legion-unittests

@@ -34,6 +34,6 @@
 
 #load modules
 $run_prefix
-
+export TMP=$job_results
 #and run
 mpirun -machinefile $$TMPDIR/machines -np $$NSLOTS $install_path/bin/unittests_hemelb -o 'tests.xml'