Makefile: fix boost::thread linking, drop pthread, sort

Makefile

@@ -159,9 +159,9 @@ ifneq ($(CPU_ONLY), 1)
 	LIBRARIES := cudart cublas curand
 endif
 LIBRARIES += \
-	glog gflags pthread protobuf leveldb snappy \
+	glog gflags protobuf leveldb snappy \
 	lmdb \
-	boost_system boost_thread \
+	boost_system \
 	hdf5_hl hdf5 \
 	opencv_core opencv_highgui opencv_imgproc
 PYTHON_LIBRARIES := boost_python python2.7
@@ -205,16 +205,8 @@ ifeq ($(LINUX), 1)
 	ifeq ($(shell echo $(GCCVERSION) \< 4.6 | bc), 1)
 		WARNINGS += -Wno-uninitialized
 	endif
-endif
-
-# CPU-only configuration
-ifeq ($(CPU_ONLY), 1)
-	OBJS := $(PROTO_OBJS) $(CXX_OBJS)
-	TEST_OBJS := $(TEST_CXX_OBJS)
-	TEST_BINS := $(TEST_CXX_BINS)
-	ALL_WARNS := $(ALL_CXX_WARNS)
-	TEST_FILTER := --gtest_filter="-*GPU*"
-	COMMON_FLAGS += -DCPU_ONLY
+	# boost::thread is reasonably called boost_thread (compare OS X)
+	LIBRARIES += boost_thread
 endif
 
 # OS X:
@@ -228,6 +220,8 @@ ifeq ($(OSX), 1)
 		CXXFLAGS += -stdlib=libstdc++
 		LINKFLAGS += -stdlib=libstdc++
 	endif
+	# boost::thread is called boost_thread-mt to mark multithreading on OS X
+	LIBRARIES += boost_thread-mt
 endif
 
 # Custom compiler
@@ -242,6 +236,16 @@ else
 	COMMON_FLAGS += -DNDEBUG -O2
 endif
 
+# CPU-only configuration
+ifeq ($(CPU_ONLY), 1)
+	OBJS := $(PROTO_OBJS) $(CXX_OBJS)
+	TEST_OBJS := $(TEST_CXX_OBJS)
+	TEST_BINS := $(TEST_CXX_BINS)
+	ALL_WARNS := $(ALL_CXX_WARNS)
+	TEST_FILTER := --gtest_filter="-*GPU*"
+	COMMON_FLAGS += -DCPU_ONLY
+endif
+
 # BLAS configuration (default = ATLAS)
 BLAS ?= atlas
 ifeq ($(BLAS), mkl)
@@ -273,7 +277,7 @@ LIBRARY_DIRS += $(BLAS_LIB)
 
 # Complete build flags.
 COMMON_FLAGS += $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir))
-CXXFLAGS += -pthread -fPIC $(COMMON_FLAGS) $(WARNINGS)
+CXXFLAGS += -fPIC $(COMMON_FLAGS) $(WARNINGS)
 NVCCFLAGS := -ccbin=$(CXX) -Xcompiler -fPIC $(COMMON_FLAGS)
 # mex may invoke an older gcc that is too liberal with -Wuninitalized
 MATLAB_CXXFLAGS := $(CXXFLAGS) -Wno-uninitialized