Merge pull request #55 from Intel-HLS/dev

Version 0.4.0

Author: stavrospapadopoulos

Makefile

@@ -11,18 +11,21 @@ endif
 
 # --- Configuration flags --- #
 CPPFLAGS = -std=gnu++11 -fPIC -fvisibility=hidden \
-      -D_FILE_OFFSET_BITS=64 
+      -D_FILE_OFFSET_BITS=64
 
 # For the Travis integration
 ifdef TRAVIS
   CPPFLAGS += --coverage
 endif
 
 # --- Support for OpenMP --- #
+OPENMP =
 OPENMP_FLAG =
-ifeq ($(COMPILER), gcc)
-  CPPFLAGS += -DOPENMP
-  OPENMP_FLAG = -fopenmp
+ifeq ($(COMPILER), gcc) 
+  ifeq ($(OPENMP), 1)
+    CPPFLAGS += -DHAVE_OPENMP
+    OPENMP_FLAG = -fopenmp
+  endif
 endif
 
 # --- Debug/Release mode handler --- #
@@ -42,12 +45,27 @@ endif
 # --- Verbose mode handler --- #
 VERBOSE =
 ifeq ($(VERBOSE),1)
-  CPPFLAGS += -DNVERBOSE
+  CPPFLAGS += -DVERBOSE
+endif
+
+# --- Use parallel sort --- #
+USE_PARALLEL_SORT =
+ifeq ($(USE_PARALLEL_SORT),1)
+  CPPFLAGS += -DUSE_PARALLEL_SORT 
+endif
+
+# --- Support for MPI --- #
+MPI =
+ifeq ($(MPI),1)
+  CPPFLAGS += -DHAVE_MPI
 endif
 
 # --- Compilers --- #
 CXX = g++   
 
+# --- GTest Filters --- #
+GTEST_FILTER='*'
+
 # --- Directories --- #
 CORE_INCLUDE_DIR = core/include
 CORE_INCLUDE_SUBDIRS = $(wildcard core/include/*)
@@ -87,10 +105,22 @@ ifeq ($(BUILD),release)
   EXAMPLES_OBJ_DIR = $(EXAMPLES_OBJ_REL_DIR)
   EXAMPLES_BIN_DIR = $(EXAMPLES_BIN_REL_DIR)
 endif
-TEST_SRC_SUBDIRS = $(wildcard test/src/*)
+TEST_INCLUDE_DIR = test/include
+TEST_INCLUDE_SUBDIRS = $(wildcard test/include/*)
 TEST_SRC_DIR = test/src
-TEST_OBJ_DIR = test/obj
-TEST_BIN_DIR = test/bin
+TEST_SRC_SUBDIRS = $(wildcard test/src/*)
+TEST_OBJ_DEB_DIR = test/obj/debug
+TEST_BIN_DEB_DIR = test/bin/debug
+ifeq ($(BUILD),debug)
+  TEST_OBJ_DIR = $(TEST_OBJ_DEB_DIR)
+  TEST_BIN_DIR = $(TEST_BIN_DEB_DIR)
+endif
+TEST_OBJ_REL_DIR = test/obj/release
+TEST_BIN_REL_DIR = test/bin/release
+ifeq ($(BUILD),release)
+  TEST_OBJ_DIR = $(TEST_OBJ_REL_DIR)
+  TEST_BIN_DIR = $(TEST_BIN_REL_DIR)
+endif
 DOXYGEN_DIR = doxygen
 DOXYGEN_MAINPAGE = $(DOXYGEN_DIR)/mainpage.dox
 
@@ -99,7 +129,8 @@ INCLUDE_PATHS =
 CORE_INCLUDE_PATHS = $(addprefix -I, $(CORE_INCLUDE_SUBDIRS))
 EXAMPLES_INCLUDE_PATHS = -I$(EXAMPLES_INCLUDE_DIR)
 TEST_INCLUDE_PATHS = $(addprefix -I, $(CORE_INCLUDE_SUBDIRS))
-LIBRARY_PATHS =
+TEST_INCLUDE_PATHS += $(addprefix -I, $(TEST_INCLUDE_SUBDIRS)) 
+LIBRARY_PATHS = 
 
 ifdef TRAVIS
   LIBRARY_PATHS += --coverage
@@ -110,6 +141,7 @@ ZLIB = -lz
 OPENSSLLIB = -lcrypto
 GTESTLIB = -lgtest -lgtest_main
 MPILIB =
+PTHREADLIB = -pthread
 
 # --- For the TileDB dynamic library --- #
 ifeq ($(OS), Darwin)
@@ -128,6 +160,7 @@ EXAMPLES_OBJ := $(patsubst $(EXAMPLES_SRC_DIR)/%.cc,\
                              $(EXAMPLES_OBJ_DIR)/%.o, $(EXAMPLES_SRC))
 EXAMPLES_BIN := $(patsubst $(EXAMPLES_SRC_DIR)/%.cc,\
                              $(EXAMPLES_BIN_DIR)/%, $(EXAMPLES_SRC)) 
+TEST_INCLUDE := $(foreach D,$(TEST_INCLUDE_SUBDIRS),$D/*.h)                    
 TEST_SRC := $(wildcard $(foreach D,$(TEST_SRC_SUBDIRS),$D/*.cc))
 TEST_OBJ := $(patsubst $(TEST_SRC_DIR)/%.cc, $(TEST_OBJ_DIR)/%.o, $(TEST_SRC))
 
@@ -151,7 +184,7 @@ doc: doxyfile.inc
 
 test: libtiledb $(TEST_BIN_DIR)/tiledb_test
 	@echo "Running TileDB tests"
-	@$(TEST_BIN_DIR)/tiledb_test
+	@$(TEST_BIN_DIR)/tiledb_test --gtest_filter=$(GTEST_FILTER)
 
 clean: clean_core clean_libtiledb \
        clean_test clean_doc clean_examples 
@@ -204,7 +237,7 @@ $(CORE_LIB_DIR)/libtiledb.$(SHLIB_EXT): $(CORE_OBJ)
 	@mkdir -p $(CORE_LIB_DIR)
 	@echo "Creating dynamic library libtiledb.$(SHLIB_EXT)"
 	@$(CXX) $(SHLIB_FLAGS) $(SONAME) -o $@ $^ $(LIBRARY_PATHS) $(MPILIB) \
-		$(ZLIB) $(OPENSSLLIB) $(OPENMP_FLAG)
+		$(PTHREADLIB) $(ZLIB) $(OPENSSLLIB) $(OPENMP_FLAG)
 
 $(CORE_LIB_DIR)/libtiledb.a: $(CORE_OBJ)
 	@mkdir -p $(CORE_LIB_DIR)
@@ -243,7 +276,7 @@ $(EXAMPLES_BIN_DIR)/%: $(EXAMPLES_OBJ_DIR)/%.o $(CORE_LIB_DIR)/libtiledb.a
 	@mkdir -p $(EXAMPLES_BIN_DIR)
 	@echo "Creating $@"
 	@$(CXX) -std=gnu++11 -o $@ $^ $(LIBRARY_PATHS) $(MPILIB) $(ZLIB) \
-		 $(OPENSSLLIB) $(OPENMP_FLAG) 
+		 $(PTHREADLIB) $(OPENSSLLIB) $(OPENMP_FLAG) 
 
 # --- Cleaning --- #
 
@@ -264,8 +297,8 @@ $(TEST_OBJ_DIR)/%.o: $(TEST_SRC_DIR)/%.cc
 	@mkdir -p $(dir $@) 
 	@echo "Compiling $<"
 	@$(CXX) $(CPPFLAGS) $(OPENMP_FLAG) $(TEST_INCLUDE_PATHS) \
-		$(INCLUDE_PATHS) -c $< -o $@
-	@$(CXX) -MM $(TEST_INCLUDE_PATHS) \
+		$(INCLUDE_PATHS) $(PTHREADLIB) -c $< -o $@
+	@$(CXX) -MM $(TEST_INCLUDE_PATHS) $(PTHREADLIB) \
                 $(CORE_INCLUDE_PATHS) $(INCLUDE_PATHS) $< > $(@:.o=.d)
 	@mv -f $(@:.o=.d) $(@:.o=.d.tmp)
 	@sed 's|.*:|$@:|' < $(@:.o=.d.tmp) > $(@:.o=.d)
@@ -276,8 +309,8 @@ $(TEST_OBJ_DIR)/%.o: $(TEST_SRC_DIR)/%.cc
 $(TEST_BIN_DIR)/tiledb_test: $(TEST_OBJ) $(CORE_LIB_DIR)/libtiledb.a
 	@mkdir -p $(TEST_BIN_DIR)
 	@echo "Creating test_cmd"
-	@$(CXX) -std=gnu++11 -o $@ $^ $(LIBRARY_PATHS) $(MPILIB) $(ZLIB) \
-		$(OPENSSLLIB) $(GTESTLIB) $(OPENMP_FLAG) 
+	@$(CXX) -o $@ $^ $(LIBRARY_PATHS) $(MPILIB) $(ZLIB) \
+		$(PTHREADLIB) $(OPENSSLLIB) $(GTESTLIB) $(OPENMP_FLAG) 
 
 # --- Cleaning --- #
 

core/include/array/aio_request.h

@@ -61,6 +61,15 @@ struct AIO_Request {
   void* completion_data_;
   /** A unique request id. */
   size_t id_;
+  /** 
+   * It can be one of the following:
+   *    - TILEDB_ARRAY_READ 
+   *    - TILEDB_ARRAY_READ_SORTED_COL
+   *    - TILEDB_ARRAY_READ_SORTED_ROW
+   *    - TILEDB_ARRAY_WRITE
+   *    - TILEDB_ARRAY_WRITE_UNSORTED
+   */
+  int mode_;
   /** 
    * Applicable only to read requests.
    * Indicates whether a buffer has overflowed during a read request.