Wrapper for the library GraphOne

cwida · Dec 5, 2019 · 1a93f90 · 1a93f90
1 parent e77edcf
commit 1a93f90
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Showing 109 changed files with 2,747 additions and 373 deletions.
diff --git a/Makefile.in b/Makefile.in
@@ -91,6 +91,9 @@ ifneq (,$(findstring -DHAVE_LLAMA,${ALL_CPPFLAGS}))
 	sources += $(addprefix library/llama/, llama_bfs.cpp llama_class.cpp llama_cdlp.cpp llama_internal.cpp llama_lcc.cpp llama_pagerank.cpp llama_sssp.cpp llama_wcc.cpp)
 	sources += $(addprefix library/llama-dv/, llama-dv.cpp)
 endif
+ifneq (,$(findstring -DHAVE_GRAPHONE,${ALL_CPPFLAGS}))
+	sources += $(addprefix library/graphone/, graphone.cpp)
+endif
 
 
 #############################################################################
@@ -111,7 +114,7 @@ all: ${builddir}/gfe_driver
 #############################################################################
 # Artifacts to build
 ${builddir}/gfe_driver: ${objectdir}/main_driver.o ${dependencies} | ${builddir}
-	${CXX} ${LDFLAGS} $^ -o $@
+	${CXX} $^ ${LDFLAGS} -o $@
 
 #############################################################################
 # Compiling the objects
@@ -170,7 +173,7 @@ check: ${testartifacts}
 
 ${testartifacts}: ${dependencies} | ${gtestlibs}
 ${testartifacts}: % : %.cpp | ${testbindir} ${testgraphs}
-	${CXX} -I ${srcdir}/third-party/googletest/googletest/include $(ALL_CXXFLAGS) ${LDFLAGS} $< -o $@ ${dependencies} ${gtestlibs}
+	${CXX} $(ALL_CXXFLAGS) -I ${srcdir}/third-party/googletest/googletest/include $< ${dependencies} ${gtestlibs} ${LDFLAGS} -o $@
 
 ${gtestlibs}: ${gtestdir}
 ${gtestdir}:

diff --git a/configuration.cpp b/configuration.cpp
@@ -38,7 +38,9 @@ using namespace common;
 using namespace std;
 
 #undef CURRENT_ERROR_TYPE
-#define CURRENT_ERROR_TYPE ConfigurationError
+#define CURRENT_ERROR_TYPE ::gfe::ConfigurationError
+
+namespace gfe {
 
 /*****************************************************************************
  *                                                                           *
@@ -239,7 +241,7 @@ bool Configuration::has_database() const {
     return !m_database_path.empty();
 }
 
-common::Database* Configuration::db(){
+::common::Database* Configuration::db(){
     if(m_database == nullptr && has_database()){
         m_database = new Database{m_database_path};
         auto params = m_database->create_execution();
@@ -366,3 +368,5 @@ void Configuration::save_parameters() {
     sort(begin(params), end(params));
     db()->store_parameters(params);
 }
+
+} // namespace
diff --git a/configuration.hpp b/configuration.hpp
@@ -27,9 +27,11 @@
 
 #include "common/error.hpp"
 
-class Configuration; // forward declaration
 namespace common { class Database; } // forward declaration
-namespace library { class Interface; } // forward declaration
+namespace gfe { class Configuration; } // forward declaration
+namespace gfe::library { class Interface; } // forward declaration
+
+namespace gfe {
 
 // Singleton interface
 Configuration& configuration(); // retrieve the current singleton (client, server or standalone)
@@ -155,7 +157,7 @@ class Configuration {
     bool has_database() const;
 
     // Retrieve the handle to the database connection, where the final results of the experiments are stored
-    common::Database* db();
+    ::common::Database* db();
 
     // Save the configuration properties into the database
     void save_parameters();
@@ -170,3 +172,5 @@ class Configuration {
     const std::string& get_database_path() const { return m_database_path; }
 };
 
+} // namespace
+
diff --git a/configure.ac b/configure.ac
@@ -52,11 +52,29 @@ if test x"${have_openmp}" == x"yes"; then
 	CPPFLAGS="${CPPFLAGS} -DHAVE_OPENMP"
 fi
 
+#############################################################################
+# Intel TBB
+have_tbb="unknown"; # Perform the check only once when invoking MY_INTEL_TBB()
+AC_DEFUN([MY_INTEL_TBB], [
+	if test x"${have_tbb}" == x"unknown"; then
+		have_tbb="yes" # assume so
+		AC_CHECK_HEADER([tbb/tbb.h], [
+			AC_SEARCH_LIBS([TBB_runtime_interface_version], [tbb], 
+			[CPPFLAGS="${CPPFLAGS} -DHAVE_TBB"], 
+			[have_tbb="no"])
+		], [have_tbb="no"], [ [/* avoid default includes */] ])
+	fi
+	
+	if test x"${have_tbb}" == x"no"; then
+		AC_MSG_ERROR(["The dependency library Intel TBB is not available in this machine"]);
+	fi
+])
+
 #############################################################################
 # pthreads
 AC_SEARCH_LIBS([pthread_create], [pthread], [],
     [ AC_MSG_ERROR([missing prerequisite: this program requires pthreads to work (dependency for sqlite3)]) ])
-
+    
 #############################################################################
 # libnuma
 have_libnuma="yes"
@@ -331,25 +349,13 @@ elif ( test x"${with_llama}" != x"yes" && test x"${with_llama}" != x"auto" ); th
 fi
 
 dnl check whether we can compile & link a program that makes usage of omp.h
-if ( test x"${with_llama}" != x"no" ); then
-    AC_MSG_CHECKING([whether the llama library can include <omp.h>, the OpenMP runtime library])
-    AC_LINK_IFELSE([
-        AC_LANG_PROGRAM([[
-            @%:@include <omp.h>
-        ]], [[
-            /* nop */
-        ]])
-    ], [
-        AC_MSG_RESULT([yes])
-    ], [
-        AC_MSG_RESULT([no])
-        if ( test x"${with_llama}" = x"auto" ); then
-            AC_MSG_NOTICE([llama support disabled: the OpenMP header omp.h is missing.])
-            with_llama="no";
-        else
-            AC_MSG_FAILURE([llama: missing prerequisite header omp.h (OpenMP runtime library)])
-        fi
-    ])
+if ( test "${have_openmp}" == "no" ); then
+    if ( test x"${with_llama}" = x"auto" ); then
+        AC_MSG_NOTICE([llama support disabled: the OpenMP header omp.h is missing.])
+        with_llama="no";
+    else
+        AC_MSG_FAILURE([llama: missing prerequisite header omp.h (OpenMP runtime library)])
+    fi
 fi
 
 dnl check whether we can compile & link a simple program invoking functions from the llama library
@@ -379,12 +385,81 @@ if ( test x"${with_llama}" != x"no" ); then
     ])
 fi
 
-dnl add the definition HAVE_STINGER into the list of preprocessor variables $CPPFLAGS
+dnl add the definition HAVE_LLAMA into the list of preprocessor variables $CPPFLAGS
 if( test x"${with_llama}" != x"no" ); then
     AC_MSG_NOTICE([llama support enabled])
     AS_VAR_APPEND([CPPFLAGS], [" -DHAVE_LLAMA"])
 fi
 
+#############################################################################
+# Support for the GraphOne framework
+# Usage:
+# --with-graphone=/path/to/graphone/build
+#
+AC_ARG_WITH([graphone], [AS_HELP_STRING([--with-graphone@<:@=ARG@:>@], [
+    Link to the GraphOne library. The argument needs to be the path where the library has been built.
+])], [])
+
+if ( test x"${with_graphone}" != x"" && test x"${with_graphone}" != "no" ); then
+	dnl check whether we can compile & link a program that makes usage of omp.h
+	if ( test "${have_openmp}" == "no" ); then
+        AC_MSG_FAILURE([GraphOne: missing prerequisite header omp.h (OpenMP runtime library)])
+	fi
+
+	AC_MSG_NOTICE([GraphOne: checking whether Intel TBB is present in the machine...])
+	MY_INTEL_TBB()
+
+	if( test x"${with_graphone}" == x"yes" ); then
+		AC_MSG_ERROR(["the full path to the GraphOne build needs to be specified, e.g. --with-graphone=/path/to/graphone/build"]);
+	fi
+
+	path_onedata=$(realpath "${with_graphone}/onedata/libonedata64.a")
+		AC_CHECK_FILE([${path_onedata}], 
+		[ LIBS="${path_onedata} ${LIBS}" ], 
+		[ AC_MSG_ERROR(["file not found: ${path_onedata}"]) ]
+	)
+
+	path_graphone_library=$(realpath "${with_graphone}/src/libsrc64.a")
+	AC_CHECK_FILE([${path_graphone_library}], 
+		[ LIBS="${path_graphone_library} ${LIBS}" ], 
+		[ AC_MSG_ERROR(["file not found: ${path_graphone_library}"]) ]
+	)
+
+	path_graphone_cmakecache=$(realpath "${with_graphone}/CMakeCache.txt")
+	AC_CHECK_FILE([${path_graphone_cmakecache}], [], [AC_MSG_ERROR(["file not found: ${path_graphone_cmakecache}. This file is used to infer the path to the source directory of GraphOne"])])
+	path_graphone_srcdir=$(awk -F= '$1 ~ /CMAKE_HOME_DIRECTORY/ {print $2}' ${path_graphone_cmakecache})
+	AC_MSG_NOTICE([GraphOne source directory: ${path_graphone_srcdir}])
+    AS_VAR_APPEND([CPPFLAGS], [" -I${path_graphone_srcdir}/src -I${path_graphone_srcdir}/include -I${path_graphone_srcdir}/include -I${path_graphone_srcdir}/gview -I${path_graphone_srcdir}/gview -I${path_graphone_srcdir}/analytics -I${path_graphone_srcdir}/onedata"])
+
+	dnl check whether we can compile & link a simple program invoking functions from the graphone library
+    AC_MSG_CHECKING([whether we can compile and link against the GraphOne library])
+    AC_LINK_IFELSE([
+        AC_LANG_PROGRAM([[
+            #define OVER_COMMIT 
+            #define TBB
+           	#define PLAIN_GRAPH
+           	#define B64
+           	#define DEL
+        	@%:@include <omp.h>
+            @%:@include "graph.h"
+			
+            /* required globals */
+            graph* g = new graph; 
+			int THD_COUNT = omp_get_max_threads() -1;
+        ]], [[
+            /* empty main, it uses the global variable g as a global */
+        ]])
+    ], [
+        AC_MSG_RESULT([yes])
+    ], [
+        AC_MSG_RESULT([no])
+        AC_MSG_FAILURE([unable to compile and link an executable with GraphOne])
+    ])
+
+    AC_MSG_NOTICE([GraphOne support enabled])
+    AS_VAR_APPEND([CPPFLAGS], [" -DHAVE_GRAPHONE"])
+fi
+
 #############################################################################
 # Remove extra blanks from our variables
 EXTRA_CPPFLAGS=$(echo ${EXTRA_CPPFLAGS} | xargs)

diff --git a/experiment/aging.cpp b/experiment/aging.cpp
@@ -44,7 +44,7 @@
 #include "configuration.hpp"
 
 using namespace common;
-using namespace experiment::details;
+using namespace gfe::experiment::details;
 using namespace std;
 
 /*****************************************************************************
@@ -66,7 +66,7 @@ extern mutex _log_mutex [[maybe_unused]];
  * Aging                                                                     *
  *                                                                           *
  *****************************************************************************/
-namespace experiment {
+namespace gfe::experiment {
 
 Aging::Aging(std::shared_ptr<library::UpdateInterface> interface, std::shared_ptr<graph::WeightedEdgeStream> stream, double mult_num_operations, int64_t num_threads) :
         Aging(interface,stream, stream->num_edges() * mult_num_operations, num_threads, interface->is_directed(), stream->max_weight()) { }
@@ -366,5 +366,4 @@ void Aging::save() {
     }
 }
 
-
-} // namespace experiment
+} // namespace
diff --git a/experiment/aging.hpp b/experiment/aging.hpp
@@ -32,21 +32,21 @@
 #include "third-party/libcuckoo/cuckoohash_map.hh"
 
 // forward declarations
-namespace graph { class WeightedEdgeStream; }
-namespace experiment::details { class AgingThread; }
-namespace experiment::details { class AsyncBatch; }
-namespace library { class UpdateInterface; }
+namespace gfe::graph { class WeightedEdgeStream; }
+namespace gfe::experiment::details { class AgingThread; }
+namespace gfe::experiment::details { class AsyncBatch; }
+namespace gfe::library { class UpdateInterface; }
 
-namespace experiment {
+namespace gfe::experiment {
 
 class Aging {
     friend class details::AgingThread;
 
     Aging(const Aging&) = delete;
     Aging& operator=(const Aging&) = delete;
 
-    std::shared_ptr<library::UpdateInterface> m_interface; // the library where vertices and edges will be inserted
-    std::shared_ptr<graph::WeightedEdgeStream> m_stream; // the final graph to insert
+    std::shared_ptr<gfe::library::UpdateInterface> m_interface; // the library where vertices and edges will be inserted
+    std::shared_ptr<gfe::graph::WeightedEdgeStream> m_stream; // the final graph to insert
 
     cuckoohash_map<uint64_t, bool> m_vertices_present; // current list of vertices present
     const cuckoohash_map<uint64_t, uint64_t> m_vertices_final; // list of vertices in the final graph
@@ -106,10 +106,10 @@ class Aging {
      * @param mult_num_operations coefficient for the total number of operations to perform, the final amount is given by mult_num_operations * stream->num_edges()
      * @param num_threads number of threads to use
      */
-    Aging(std::shared_ptr<library::UpdateInterface> interface, std::shared_ptr<graph::WeightedEdgeStream> stream, double mult_num_operations, int64_t num_threads);
+    Aging(std::shared_ptr<library::UpdateInterface> interface, std::shared_ptr<gfe::graph::WeightedEdgeStream> stream, double mult_num_operations, int64_t num_threads);
 
 
-    Aging(std::shared_ptr<library::UpdateInterface> interface, std::shared_ptr<graph::WeightedEdgeStream> stream, uint64_t num_operations, int64_t num_threads, bool is_directed, double max_weight);
+    Aging(std::shared_ptr<library::UpdateInterface> interface, std::shared_ptr<gfe::graph::WeightedEdgeStream> stream, uint64_t num_operations, int64_t num_threads, bool is_directed, double max_weight);
 
     // destructor
     ~Aging();

diff --git a/experiment/aging2_experiment.cpp b/experiment/aging2_experiment.cpp
@@ -49,7 +49,7 @@ extern mutex _log_mutex [[maybe_unused]];
  *                                                                           *
  *****************************************************************************/
 
-namespace experiment {
+namespace gfe::experiment {
 
 Aging2Experiment::Aging2Experiment(){ }
 

diff --git a/experiment/aging2_experiment.hpp b/experiment/aging2_experiment.hpp
@@ -24,13 +24,13 @@
 #include "aging2_result.hpp"
 
 // forward declarations
-namespace graph { class WeightedEdgeStream; }
-namespace experiment { class Aging2Experiment; }
-namespace experiment::details { class Aging2Master; }
-namespace experiment::details { class Aging2Worker; }
-namespace library { class UpdateInterface; }
+namespace gfe::graph { class WeightedEdgeStream; }
+namespace gfe::experiment { class Aging2Experiment; }
+namespace gfe::experiment::details { class Aging2Master; }
+namespace gfe::experiment::details { class Aging2Worker; }
+namespace gfe::library { class UpdateInterface; }
 
-namespace experiment {
+namespace gfe::experiment {
 
 /**
  * Builder/factory class to create & execute instances of the Aging experiment.
@@ -42,7 +42,7 @@ class Aging2Experiment {
     friend class details::Aging2Master;
     friend class details::Aging2Worker;
 
-    std::shared_ptr<library::UpdateInterface> m_library; // the library to evaluate
+    std::shared_ptr<gfe::library::UpdateInterface> m_library; // the library to evaluate
     std::string m_path_log; // the path to the log file [graphlog] with the sequence of updates to perform
     uint64_t m_num_threads = 1; // set the number of threads to use
     uint64_t m_worker_granularity = 1024; // the granularity of a task for a worker, that is the number of contiguous operations (inserts/deletes) performed inside the threads between each invocation to the scheduler.
@@ -56,7 +56,7 @@ class Aging2Experiment {
     Aging2Experiment();
 
     // Set the library to evaluate
-    void set_library(std::shared_ptr<library::UpdateInterface> library);
+    void set_library(std::shared_ptr<gfe::library::UpdateInterface> library);
 
     // Set the path to the log file with all updates
     void set_log(const std::string& path_log);

diff --git a/experiment/aging2_result.cpp b/experiment/aging2_result.cpp
@@ -27,7 +27,7 @@
 using namespace common;
 using namespace std;
 
-namespace experiment {
+namespace gfe::experiment {
 
 Aging2Result::Aging2Result(const Aging2Experiment& parameters) : m_num_threads(parameters.m_num_threads), m_worker_granularity(parameters.m_worker_granularity){
 

diff --git a/experiment/aging2_result.hpp b/experiment/aging2_result.hpp
@@ -22,13 +22,16 @@
 
 // forward declarations
 namespace common { class Database; }
-namespace experiment { class Aging2Experiment; }
-namespace experiment::details { class Aging2Master; }
-namespace experiment::details { class Aging2Worker; }
-namespace experiment::details { class LatencyStatistics; }
+namespace gfe::experiment { class Aging2Experiment; }
+namespace gfe::experiment::details { class Aging2Master; }
+namespace gfe::experiment::details { class Aging2Worker; }
+namespace gfe::experiment::details { class LatencyStatistics; }
 
-namespace experiment {
+namespace gfe::experiment {
 
+/**
+ * This is a container for the parameters and the measured results of a single execution of the Aging2 experiment
+ */
 class Aging2Result {
     friend class details::Aging2Master;
     friend class details::Aging2Worker;

diff --git a/experiment/details/aging2_master.cpp b/experiment/details/aging2_master.cpp
@@ -61,7 +61,7 @@ extern mutex _log_mutex [[maybe_unused]];
  * Init                                                                      *
  *                                                                           *
  *****************************************************************************/
-namespace experiment::details {
+namespace gfe::experiment::details {
 
 Aging2Master::Aging2Master(const Aging2Experiment& parameters) :
     m_parameters(parameters),