From 654d8114ed5f7526e2c1755e54cbff224341170c Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sat, 29 Mar 2014 17:46:39 -0700
Subject: [PATCH 01/18] put TEST_GPUID in Makefile.config

---
 Makefile                | 1 -
 Makefile.config.example | 3 +++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index acef07d6837..a432c871b89 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,5 @@
 # The makefile for caffe. Extremely hacky.
 PROJECT := caffe
-TEST_GPUID := 0
 
 include Makefile.config
 
diff --git a/Makefile.config.example b/Makefile.config.example
index e747d2a76ad..09aea6f94eb 100644
--- a/Makefile.config.example
+++ b/Makefile.config.example
@@ -48,3 +48,6 @@ DISTRIBUTE_DIR := distribute
 
 # uncomment for debugging
 #DEBUG := 1
+
+# The ID of the GPU that 'make runtest' will use to run unit tests.
+TEST_GPUID := 0

From 3abb10e9107226e2e9353913abef691b37e84377 Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sat, 29 Mar 2014 17:47:58 -0700
Subject: [PATCH 02/18] create superclean Makefile target to delete all files
 with generated extensions

---
 Makefile | 37 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 36 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index a432c871b89..ac91df729d5 100644
--- a/Makefile
+++ b/Makefile
@@ -124,7 +124,8 @@ PYTHON_LDFLAGS := $(LDFLAGS) $(foreach library,$(PYTHON_LIBRARIES),-l$(library))
 # Define build targets
 ##############################
 .PHONY: all init test clean linecount lint tools examples py mat distribute \
-        py$(PROJECT) mat$(PROJECT) proto runtest
+        py$(PROJECT) mat$(PROJECT) proto runtest \
+	superclean supercleanlist supercleanfiles
 
 all: init $(NAME) $(STATIC_NAME) tools examples
 	@echo $(CXX_OBJS)
@@ -260,6 +261,40 @@ clean:
 	@- $(RM) -rf $(BUILD_DIR)
 	@- $(RM) -rf $(DISTRIBUTE_DIR)
 
+# make superclean recursively* deletes all files ending with an extension
+# suggesting that Caffe built them.  This may be useful if you've built older
+# versions of Caffe that do not place all generated files in a location known
+# to make clean.
+#
+# make supercleanlist will list the files to be deleted by make superclean.
+#
+# * Recursive with the exception that symbolic links are never followed, per the
+# default behavior of 'find'.
+SUPERCLEAN_EXTS := .so .a .o .bin .testbin .pb.cc .pb.h _pb2.py .cuo
+
+supercleanfiles:
+	$(eval SUPERCLEAN_FILES := \
+		$(strip $(foreach ext,$(SUPERCLEAN_EXTS), \
+		$(shell find . -name '*$(ext)'))))
+
+supercleanlist: supercleanfiles
+	@ \
+	if [ -z "$(SUPERCLEAN_FILES)" ]; then \
+	  echo "No generated files found."; \
+	else \
+	  echo $(SUPERCLEAN_FILES); \
+	fi
+
+superclean: clean supercleanfiles
+	@ \
+	if [ -z "$(SUPERCLEAN_FILES)" ]; then \
+	  echo "No generated files found."; \
+	else \
+	  echo "Deleting the following generated files:"; \
+	  echo $(SUPERCLEAN_FILES); \
+	  $(RM) $(SUPERCLEAN_FILES); \
+	fi
+
 distribute: all
 	mkdir $(DISTRIBUTE_DIR)
 	# add include

From a750a31c5eef6d6e31b9607156036e735478a7e0 Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sat, 29 Mar 2014 18:29:15 -0700
Subject: [PATCH 03/18] create softlink to test directory at build/test

---
 Makefile | 31 +++++++++++++++++++++++--------
 1 file changed, 23 insertions(+), 8 deletions(-)

diff --git a/Makefile b/Makefile
index ac91df729d5..e9f48d826c1 100644
--- a/Makefile
+++ b/Makefile
@@ -75,7 +75,11 @@ GTEST_OBJ := $(addprefix $(BUILD_DIR)/, ${GTEST_SRC:.cpp=.o})
 TOOL_BINS := ${TOOL_OBJS:.o=.bin}
 EXAMPLE_BINS := ${EXAMPLE_OBJS:.o=.bin}
 TEST_BINS := ${TEST_OBJS:.o=.testbin}
-TEST_ALL_BIN := $(BUILD_DIR)/src/$(PROJECT)/test/test_all.testbin
+TEST_BUILD_SUB_DIR := src/$(PROJECT)/test
+TEST_DIR = $(BUILD_DIR)/$(TEST_BUILD_SUB_DIR)
+TEST_ALL_BIN := $(TEST_DIR)/test_all.testbin
+# A shortcut to the directory of test binaries for convenience.
+TEST_DIR_LINK := $(BUILD_DIR)/test
 
 ##############################
 # Derive include and lib directories
@@ -123,9 +127,10 @@ PYTHON_LDFLAGS := $(LDFLAGS) $(foreach library,$(PYTHON_LIBRARIES),-l$(library))
 ##############################
 # Define build targets
 ##############################
-.PHONY: all init test clean linecount lint tools examples py mat distribute \
-        py$(PROJECT) mat$(PROJECT) proto runtest \
-	superclean supercleanlist supercleanfiles
+.PHONY: all init test clean linecount lint tools examples distribute \
+	py mat py$(PROJECT) mat$(PROJECT) proto runtest \
+	superclean supercleanlist supercleanfiles \
+	testshortcut
 
 all: init $(NAME) $(STATIC_NAME) tools examples
 	@echo $(CXX_OBJS)
@@ -184,11 +189,21 @@ $(STATIC_NAME): init $(PROTO_OBJS) $(OBJS)
 runtest: $(TEST_ALL_BIN)
 	$(TEST_ALL_BIN) $(TEST_GPUID)
 
-$(TEST_BINS): %.testbin : %.o $(GTEST_OBJ) $(STATIC_NAME) $(TEST_HDRS)
-	$(CXX) $(TEST_MAIN_SRC) $< $(GTEST_OBJ) $(STATIC_NAME) -o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+$(TEST_BINS): %.testbin : %.o $(GTEST_OBJ) $(STATIC_NAME) $(TEST_HDRS) testshortcut
+	$(CXX) $(TEST_MAIN_SRC) $< $(GTEST_OBJ) $(STATIC_NAME) \
+		-o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
 
-$(TEST_ALL_BIN): $(GTEST_OBJ) $(STATIC_NAME) $(TEST_OBJS)
-	$(CXX) $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME) -o $(TEST_ALL_BIN) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+$(TEST_ALL_BIN): $(GTEST_OBJ) $(STATIC_NAME) $(TEST_OBJS) testshortcut
+	$(CXX) $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME) \
+		-o $(TEST_ALL_BIN) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+
+testshortcut: $(TEST_DIR_LINK)
+
+$(TEST_DIR_LINK): $(TEST_DIR)
+	@ln -s $(TEST_BUILD_SUB_DIR) $(TEST_DIR_LINK)
+
+$(TEST_DIR):
+	@mkdir -p $(TEST_DIR)
 
 $(TOOL_BINS): %.bin : %.o $(STATIC_NAME)
 	$(CXX) $< $(STATIC_NAME) -o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)

From e29838ddf14fcbc01e4d4925750eef7d75c09575 Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sat, 29 Mar 2014 19:36:05 -0700
Subject: [PATCH 04/18] put proto-generated .cc and .h files in build directory

---
 Makefile | 35 ++++++++++++++++++++++++-----------
 1 file changed, 24 insertions(+), 11 deletions(-)

diff --git a/Makefile b/Makefile
index e9f48d826c1..23d7b6fe324 100644
--- a/Makefile
+++ b/Makefile
@@ -31,8 +31,15 @@ TEST_HDRS := $(shell find src/$(PROJECT) -name "test_*.hpp")
 TOOL_SRCS := $(shell find tools -name "*.cpp")
 # EXAMPLE_SRCS are the source files for the example binaries
 EXAMPLE_SRCS := $(shell find examples -name "*.cpp")
+# BUILD_INCLUDE_DIR contains any generated header files we want to include.
+BUILD_INCLUDE_DIR := $(BUILD_DIR)/include
 # PROTO_SRCS are the protocol buffer definitions
-PROTO_SRCS := $(wildcard src/$(PROJECT)/proto/*.proto)
+PROTO_SRC_DIR := src/$(PROJECT)/proto
+PROTO_SRCS := $(wildcard $(PROTO_SRC_DIR)/*.proto)
+# PROTO_BUILD_DIR will contain the .cc and obj files generated from
+# PROTO_SRCS; PROTO_BUILD_INCLUDE_DIR will contain the .h header files
+PROTO_BUILD_DIR := $(BUILD_DIR)/$(PROTO_SRC_DIR)
+PROTO_BUILD_INCLUDE_DIR := $(BUILD_INCLUDE_DIR)/$(PROJECT)/proto
 # NONGEN_CXX_SRCS includes all source/header files except those generated
 # automatically (e.g., by proto).
 NONGEN_CXX_SRCS := $(shell find \
@@ -56,15 +63,15 @@ MAT$(PROJECT)_SO := matlab/$(PROJECT)/$(PROJECT)
 # Derive generated files
 ##############################
 # The generated files for protocol buffers
-PROTO_GEN_HEADER := ${PROTO_SRCS:.proto=.pb.h}
-PROTO_GEN_CC := ${PROTO_SRCS:.proto=.pb.cc}
+PROTO_GEN_HEADER := $(addprefix $(BUILD_DIR)/, ${PROTO_SRCS:.proto=.pb.h})
+PROTO_GEN_CC := $(addprefix $(BUILD_DIR)/, ${PROTO_SRCS:.proto=.pb.cc})
 PROTO_GEN_PY := ${PROTO_SRCS:.proto=_pb2.py}
 # The objects corresponding to the source files
 # These objects will be linked into the final shared library, so we
 # exclude the tool, example, and test objects.
 CXX_OBJS := $(addprefix $(BUILD_DIR)/, ${CXX_SRCS:.cpp=.o})
 CU_OBJS := $(addprefix $(BUILD_DIR)/, ${CU_SRCS:.cu=.cuo})
-PROTO_OBJS := $(addprefix $(BUILD_DIR)/, ${PROTO_GEN_CC:.cc=.o})
+PROTO_OBJS := ${PROTO_GEN_CC:.cc=.o}
 OBJS := $(PROTO_OBJS) $(CXX_OBJS) $(CU_OBJS)
 # tool, example, and test objects
 TOOL_OBJS := $(addprefix $(BUILD_DIR)/, ${TOOL_SRCS:.cpp=.o})
@@ -90,6 +97,7 @@ MKL_INCLUDE_DIR := $(MKL_DIR)/include
 MKL_LIB_DIR := $(MKL_DIR)/lib $(MKL_DIR)/lib/intel64
 
 INCLUDE_DIRS += ./src ./include $(CUDA_INCLUDE_DIR)
+INCLUDE_DIRS += $(BUILD_INCLUDE_DIR)
 LIBRARY_DIRS += $(CUDA_LIB_DIR)
 LIBRARIES := cudart cublas curand \
 	pthread \
@@ -200,10 +208,10 @@ $(TEST_ALL_BIN): $(GTEST_OBJ) $(STATIC_NAME) $(TEST_OBJS) testshortcut
 testshortcut: $(TEST_DIR_LINK)
 
 $(TEST_DIR_LINK): $(TEST_DIR)
-	@ln -s $(TEST_BUILD_SUB_DIR) $(TEST_DIR_LINK)
+	ln -s $(TEST_BUILD_SUB_DIR) $(TEST_DIR_LINK)
 
 $(TEST_DIR):
-	@mkdir -p $(TEST_DIR)
+	mkdir -p $(TEST_DIR)
 
 $(TOOL_BINS): %.bin : %.o $(STATIC_NAME)
 	$(CXX) $< $(STATIC_NAME) -o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
@@ -259,14 +267,19 @@ $(PROTO_GEN_PY): $(PROTO_SRCS)
 	protoc --proto_path=src --python_out=python $(PROTO_SRCS)
 	@echo
 
-proto: $(PROTO_GEN_CC)
+proto: init $(PROTO_GEN_CC)
 
-$(PROTO_GEN_CC): $(PROTO_SRCS)
-	protoc --proto_path=src --cpp_out=src $(PROTO_SRCS)
-	mkdir -p include/$(PROJECT)/proto
-	cp $(PROTO_GEN_HEADER) include/$(PROJECT)/proto/
+$(PROTO_GEN_CC): $(PROTO_SRCS) $(PROTO_BUILD_DIR) $(PROTO_BUILD_INCLUDE_DIR)
+	protoc --proto_path=src --cpp_out=build/src $(PROTO_SRCS)
+	cp $(PROTO_GEN_HEADER) $(PROTO_BUILD_INCLUDE_DIR)
 	@echo
 
+$(PROTO_BUILD_DIR):
+	mkdir -p $(PROTO_BUILD_DIR)
+
+$(PROTO_BUILD_INCLUDE_DIR):
+	mkdir -p $(PROTO_BUILD_INCLUDE_DIR)
+
 clean:
 	@- $(RM) $(NAME) $(STATIC_NAME)
 	@- $(RM) $(PROTO_GEN_HEADER) $(PROTO_GEN_CC) $(PROTO_GEN_PY)

From 5d9040a3d8cc039eebed29b43a2d90c6e6f54844 Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sat, 29 Mar 2014 20:12:24 -0700
Subject: [PATCH 05/18] cleanup superclean output

---
 Makefile | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/Makefile b/Makefile
index 23d7b6fe324..b413df67a80 100644
--- a/Makefile
+++ b/Makefile
@@ -301,16 +301,15 @@ clean:
 SUPERCLEAN_EXTS := .so .a .o .bin .testbin .pb.cc .pb.h _pb2.py .cuo
 
 supercleanfiles:
-	$(eval SUPERCLEAN_FILES := \
-		$(strip $(foreach ext,$(SUPERCLEAN_EXTS), \
-		$(shell find . -name '*$(ext)'))))
+	$(eval SUPERCLEAN_FILES := $(strip \
+		$(foreach ext,$(SUPERCLEAN_EXTS), $(shell find . -name '*$(ext)'))))
 
 supercleanlist: supercleanfiles
 	@ \
 	if [ -z "$(SUPERCLEAN_FILES)" ]; then \
 	  echo "No generated files found."; \
 	else \
-	  echo $(SUPERCLEAN_FILES); \
+	  echo $(SUPERCLEAN_FILES) | tr ' ' '\n'; \
 	fi
 
 superclean: clean supercleanfiles
@@ -319,7 +318,7 @@ superclean: clean supercleanfiles
 	  echo "No generated files found."; \
 	else \
 	  echo "Deleting the following generated files:"; \
-	  echo $(SUPERCLEAN_FILES); \
+	  echo $(SUPERCLEAN_FILES) | tr ' ' '\n'; \
 	  $(RM) $(SUPERCLEAN_FILES); \
 	fi
 

From 060c5f1ad6852b132cc42c3837dd845fe43ef233 Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sat, 29 Mar 2014 22:26:46 -0700
Subject: [PATCH 06/18] messed around with Makefile - currently in very messy
 state

---
 Makefile | 50 ++++++++++++++++++++++++++++++++------------------
 1 file changed, 32 insertions(+), 18 deletions(-)

diff --git a/Makefile b/Makefile
index b413df67a80..ad74fb870a2 100644
--- a/Makefile
+++ b/Makefile
@@ -63,7 +63,9 @@ MAT$(PROJECT)_SO := matlab/$(PROJECT)/$(PROJECT)
 # Derive generated files
 ##############################
 # The generated files for protocol buffers
-PROTO_GEN_HEADER := $(addprefix $(BUILD_DIR)/, ${PROTO_SRCS:.proto=.pb.h})
+PROTO_GEN_HEADER := $(addprefix $(PROTO_BUILD_INCLUDE_DIR)/, \
+	$(notdir ${PROTO_SRCS:.proto=.pb.h}))
+HXX_SRCS += $(PROTO_GEN_HEADER)
 PROTO_GEN_CC := $(addprefix $(BUILD_DIR)/, ${PROTO_SRCS:.proto=.pb.cc})
 PROTO_GEN_PY := ${PROTO_SRCS:.proto=_pb2.py}
 # The objects corresponding to the source files
@@ -166,7 +168,7 @@ $(LINT_REPORT): $(NONGEN_CXX_SRCS)
 
 test: init $(TEST_BINS) $(TEST_ALL_BIN)
 
-tools: init $(TOOL_BINS)
+tools: init proto $(TOOL_BINS)
 
 examples: init $(EXAMPLE_BINS)
 
@@ -197,7 +199,9 @@ $(STATIC_NAME): init $(PROTO_OBJS) $(OBJS)
 runtest: $(TEST_ALL_BIN)
 	$(TEST_ALL_BIN) $(TEST_GPUID)
 
-$(TEST_BINS): %.testbin : %.o $(GTEST_OBJ) $(STATIC_NAME) $(TEST_HDRS) testshortcut
+$(BUILD_DIR)/src/$(PROJECT)/test/%.testbin: \
+		$(BUILD_DIR)/src/$(PROJECT)/test/%.o \
+		$(GTEST_OBJ) $(STATIC_NAME) testshortcut
 	$(CXX) $(TEST_MAIN_SRC) $< $(GTEST_OBJ) $(STATIC_NAME) \
 		-o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
 
@@ -205,9 +209,9 @@ $(TEST_ALL_BIN): $(GTEST_OBJ) $(STATIC_NAME) $(TEST_OBJS) testshortcut
 	$(CXX) $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME) \
 		-o $(TEST_ALL_BIN) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
 
-testshortcut: $(TEST_DIR_LINK)
+testshortcut: | $(TEST_DIR_LINK)
 
-$(TEST_DIR_LINK): $(TEST_DIR)
+$(TEST_DIR_LINK): | $(TEST_DIR)
 	ln -s $(TEST_BUILD_SUB_DIR) $(TEST_DIR_LINK)
 
 $(TEST_DIR):
@@ -221,23 +225,29 @@ $(EXAMPLE_BINS): %.bin : %.o $(STATIC_NAME)
 	$(CXX) $< $(STATIC_NAME) -o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
 	@echo
 
-$(OBJS): $(PROTO_GEN_CC) $(HXX_SRCS)
-
 $(BUILD_DIR)/src/$(PROJECT)/%.o: src/$(PROJECT)/%.cpp
 	$(CXX) $< $(CXXFLAGS) -c -o $@
 	@echo
 
-$(BUILD_DIR)/src/$(PROJECT)/layers/%.o: src/$(PROJECT)/layers/%.cpp
+$(OBJS): $(PROTO_GEN_HEADER) $(HXX_SRCS)
+	@echo matched the first objs!!
+
+
+LAYERS_DIR := $(BUILD_DIR)/src/$(PROJECT)/layers
+$(LAYERS_DIR):
+	@ mkdir -p $(LAYERS_DIR)
+
+$(BUILD_DIR)/src/$(PROJECT)/layers/%.o: \
+		src/$(PROJECT)/layers/%.cpp $(HXX_SRCS) | $(LAYERS_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
 	@echo
 
-$(BUILD_DIR)/src/$(PROJECT)/proto/%.o: src/$(PROJECT)/proto/%.cc
+$(BUILD_DIR)/src/$(PROJECT)/proto/%.o: src/$(PROJECT)/proto/%.cc src/$(PROJECT)/proto/%.h
 	$(CXX) $< $(CXXFLAGS) -c -o $@
 	@echo
 
-$(BUILD_DIR)/src/$(PROJECT)/test/%.o: src/test/%.cpp
+$(BUILD_DIR)/src/$(PROJECT)/test/%.o: $(PROTO_GEN_HEADER) src/$(PROJECT)/test/%.cpp
 	$(CXX) $< $(CXXFLAGS) -c -o $@
-	@echo
 
 $(BUILD_DIR)/src/$(PROJECT)/util/%.o: src/$(PROJECT)/util/%.cpp
 	$(CXX) $< $(CXXFLAGS) -c -o $@
@@ -255,11 +265,11 @@ $(BUILD_DIR)/src/$(PROJECT)/util/%.cuo: src/$(PROJECT)/util/%.cu
 	$(CUDA_DIR)/bin/nvcc $(NVCCFLAGS) $(CUDA_ARCH) -c $< -o $@
 	@echo
 
-$(BUILD_DIR)/tools/%.o: tools/%.cpp
+$(BUILD_DIR)/tools/%.o: tools/%.cpp $(PROTO_GEN_HEADER)
 	$(CXX) $< $(CXXFLAGS) -c -o $@ $(LDFLAGS)
 	@echo
 
-$(BUILD_DIR)/examples/%.o: examples/%.cpp
+$(BUILD_DIR)/examples/%.o: examples/%.cpp $(PROTO_GEN_HEADER)
 	$(CXX) $< $(CXXFLAGS) -c -o $@ $(LDFLAGS)
 	@echo
 
@@ -267,12 +277,16 @@ $(PROTO_GEN_PY): $(PROTO_SRCS)
 	protoc --proto_path=src --python_out=python $(PROTO_SRCS)
 	@echo
 
-proto: init $(PROTO_GEN_CC)
+proto: init $(PROTO_GEN_CC) $(PROTO_GEN_HEADER)
+	@echo PROTO_GEN_CC: $(PROTO_GEN_CC)
+	@echo PROTO_GEN_HEADER: $(PROTO_GEN_HEADER)
+	@echo PROTO_OBJS: $(PROTO_OBJS)
 
-$(PROTO_GEN_CC): $(PROTO_SRCS) $(PROTO_BUILD_DIR) $(PROTO_BUILD_INCLUDE_DIR)
-	protoc --proto_path=src --cpp_out=build/src $(PROTO_SRCS)
-	cp $(PROTO_GEN_HEADER) $(PROTO_BUILD_INCLUDE_DIR)
-	@echo
+$(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_BUILD_DIR)/%.pb.h \
+		$(PROTO_BUILD_INCLUDE_DIR)/%.pb.h: \
+		$(PROTO_SRC_DIR)/%.proto | $(PROTO_BUILD_DIR) $(PROTO_BUILD_INCLUDE_DIR)
+	protoc --proto_path=src --cpp_out=build/src $<
+	cp $(PROTO_BUILD_DIR)/$(*F).pb.h $(PROTO_BUILD_INCLUDE_DIR)/$(*F).pb.h
 
 $(PROTO_BUILD_DIR):
 	mkdir -p $(PROTO_BUILD_DIR)

From fd09cb3641fbc132ba590e0ec8e2d58c921596a7 Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sun, 30 Mar 2014 04:14:48 -0700
Subject: [PATCH 07/18] lots of corrections to dependencies etc., things seem
 to mostly build coherently now

---
 Makefile | 230 +++++++++++++++++++++++++++++--------------------------
 1 file changed, 120 insertions(+), 110 deletions(-)

diff --git a/Makefile b/Makefile
index ad74fb870a2..26c9517e821 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-# The makefile for caffe. Extremely hacky.
+# The makefile for caffe. Pretty hacky.
 PROJECT := caffe
 
 include Makefile.config
@@ -33,7 +33,7 @@ TOOL_SRCS := $(shell find tools -name "*.cpp")
 EXAMPLE_SRCS := $(shell find examples -name "*.cpp")
 # BUILD_INCLUDE_DIR contains any generated header files we want to include.
 BUILD_INCLUDE_DIR := $(BUILD_DIR)/include
-# PROTO_SRCS are the protocol buffer definitions
+# PROTO_SRCS are the protocol buffer defions
 PROTO_SRC_DIR := src/$(PROJECT)/proto
 PROTO_SRCS := $(wildcard $(PROTO_SRC_DIR)/*.proto)
 # PROTO_BUILD_DIR will contain the .cc and obj files generated from
@@ -63,32 +63,45 @@ MAT$(PROJECT)_SO := matlab/$(PROJECT)/$(PROJECT)
 # Derive generated files
 ##############################
 # The generated files for protocol buffers
+PROTO_GEN_HEADER_SRCS := $(addprefix $(PROTO_BUILD_DIR)/, \
+	$(notdir ${PROTO_SRCS:.proto=.pb.h}))
 PROTO_GEN_HEADER := $(addprefix $(PROTO_BUILD_INCLUDE_DIR)/, \
 	$(notdir ${PROTO_SRCS:.proto=.pb.h}))
 HXX_SRCS += $(PROTO_GEN_HEADER)
 PROTO_GEN_CC := $(addprefix $(BUILD_DIR)/, ${PROTO_SRCS:.proto=.pb.cc})
-PROTO_GEN_PY := ${PROTO_SRCS:.proto=_pb2.py}
+PROTO_GEN_PY := $(foreach file,${PROTO_SRCS:.proto=_pb2.py},python/$(PROJECT)/proto/$(notdir $(file)))
 # The objects corresponding to the source files
 # These objects will be linked into the final shared library, so we
 # exclude the tool, example, and test objects.
 CXX_OBJS := $(addprefix $(BUILD_DIR)/, ${CXX_SRCS:.cpp=.o})
 CU_OBJS := $(addprefix $(BUILD_DIR)/, ${CU_SRCS:.cu=.cuo})
 PROTO_OBJS := ${PROTO_GEN_CC:.cc=.o}
+OBJ_BUILD_DIR := $(BUILD_DIR)/src/$(PROJECT)
+LAYER_BUILD_DIR := $(OBJ_BUILD_DIR)/layers
+UTIL_BUILD_DIR := $(OBJ_BUILD_DIR)/util
 OBJS := $(PROTO_OBJS) $(CXX_OBJS) $(CU_OBJS)
 # tool, example, and test objects
 TOOL_OBJS := $(addprefix $(BUILD_DIR)/, ${TOOL_SRCS:.cpp=.o})
-EXAMPLE_OBJS := $(addprefix $(BUILD_DIR)/, ${EXAMPLE_SRCS:.cpp=.o})
+TOOL_BUILD_DIR := $(BUILD_DIR)/tools
+TOOL_BUILD_DIRS := $(sort $(foreach obj,$(TOOL_OBJS),$(dir $(obj))))
+TEST_BUILD_DIR := $(BUILD_DIR)/src/$(PROJECT)/test
 TEST_OBJS := $(addprefix $(BUILD_DIR)/, ${TEST_SRCS:.cpp=.o})
 GTEST_OBJ := $(addprefix $(BUILD_DIR)/, ${GTEST_SRC:.cpp=.o})
+GTEST_BUILD_DIR := $(dir $(GTEST_OBJ))
+EXAMPLE_OBJS := $(addprefix $(BUILD_DIR)/, ${EXAMPLE_SRCS:.cpp=.o})
+EXAMPLE_BUILD_DIR := $(BUILD_DIR)/examples
+EXAMPLE_BUILD_DIRS := $(EXAMPLE_BUILD_DIR)
+EXAMPLE_BUILD_DIRS += $(foreach obj,$(EXAMPLE_OBJS),$(dir $(obj)))
 # tool, example, and test bins
 TOOL_BINS := ${TOOL_OBJS:.o=.bin}
 EXAMPLE_BINS := ${EXAMPLE_OBJS:.o=.bin}
 TEST_BINS := ${TEST_OBJS:.o=.testbin}
-TEST_BUILD_SUB_DIR := src/$(PROJECT)/test
-TEST_DIR = $(BUILD_DIR)/$(TEST_BUILD_SUB_DIR)
-TEST_ALL_BIN := $(TEST_DIR)/test_all.testbin
+TEST_ALL_BIN := $(TEST_BUILD_DIR)/test_all.testbin
+TEST_ALL_BINS := $(TEST_ALL_BIN) $(TEST_BINS)
 # A shortcut to the directory of test binaries for convenience.
-TEST_DIR_LINK := $(BUILD_DIR)/test
+TEST_LINK_DIR := $(BUILD_DIR)/test
+TEST_ALL_BIN_LINKS := $(foreach \
+		bin,$(TEST_ALL_BINS),$(TEST_LINK_DIR)/$(notdir $(bin)))
 
 ##############################
 # Derive include and lib directories
@@ -110,7 +123,27 @@ LIBRARIES := cudart cublas curand \
 PYTHON_LIBRARIES := boost_python python2.7
 WARNINGS := -Wall
 
-ifdef DEBUG
+##############################
+# Set build directories
+##############################
+
+DISTRIBUTE_SUBDIRS := $(DISTRIBUTE_DIR)/bin $(DISTRIBUTE_DIR)/lib
+DIST_ALIASES := dist
+ifneq ($(strip $(DISTRIBUTE_DIR)),distribute)
+		DIST_ALIASES += distribute
+endif
+
+ALL_BUILD_DIRS := $(BUILD_DIR) $(OBJ_BUILD_DIR) \
+		$(LAYER_BUILD_DIR) $(UTIL_BUILD_DIR) $(TOOL_BUILD_DIRS) \
+		$(TEST_BUILD_DIR) $(TEST_LINK_DIR) $(GTEST_BUILD_DIR) \
+		$(EXAMPLE_BUILD_DIRS) \
+		$(PROTO_BUILD_DIR) $(PROTO_BUILD_INCLUDE_DIR) \
+		$(DISTRIBUTE_SUBDIRS)
+
+ALL_BUILD_DIRS := $(sort $(ALL_BUILD_DIRS))
+
+DEBUG ?= 0
+ifeq ($(DEBUG), 1)
 	COMMON_FLAGS := -DDEBUG -g -O0
 else
 	COMMON_FLAGS := -DNDEBUG -O2
@@ -134,31 +167,34 @@ LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) \
 		$(foreach library,$(LIBRARIES),-l$(library))
 PYTHON_LDFLAGS := $(LDFLAGS) $(foreach library,$(PYTHON_LIBRARIES),-l$(library))
 
+# 'superclean' target recursively* deletes all files ending with an extension
+# suggesting that Caffe built them.  This may be useful if you've built older
+# versions of Caffe that do not place all generated files in a location known
+# to make clean.
+#
+# 'supercleanlist' will list the files to be deleted by make superclean.
+#
+# * Recursive with the exception that symbolic links are never followed, per the
+# default behavior of 'find'.
+SUPERCLEAN_EXTS := .so .a .o .bin .testbin .pb.cc .pb.h _pb2.py .cuo
+
 ##############################
 # Define build targets
 ##############################
-.PHONY: all init test clean linecount lint tools examples distribute \
+.PHONY: all test clean linecount lint tools examples dist \
 	py mat py$(PROJECT) mat$(PROJECT) proto runtest \
-	superclean supercleanlist supercleanfiles \
-	testshortcut
+	superclean supercleanlist supercleanfiles
 
-all: init $(NAME) $(STATIC_NAME) tools examples
-	@echo $(CXX_OBJS)
+.SECONDARY: $(PROTO_GEN_HEADER_SRCS) $(TEST_BINS)
 
-init:
-	@ mkdir -p $(foreach obj,$(OBJS),$(dir $(obj)))
-	@ mkdir -p $(foreach obj,$(TOOL_OBJS),$(dir $(obj)))
-	@ mkdir -p $(foreach obj,$(EXAMPLE_OBJS),$(dir $(obj)))
-	@ mkdir -p $(foreach obj,$(TEST_OBJS),$(dir $(obj)))
-	@ mkdir -p $(foreach obj,$(GTEST_OBJ),$(dir $(obj)))
+all: $(NAME) $(STATIC_NAME) tools examples
 
 linecount: clean
 	cloc --read-lang-def=$(PROJECT).cloc src/$(PROJECT)/
 
 lint: $(LINT_REPORT)
 
-$(LINT_REPORT): $(NONGEN_CXX_SRCS)
-	@ mkdir -p $(BUILD_DIR)
+$(LINT_REPORT): $(NONGEN_CXX_SRCS) | $(BUILD_DIR)
 	@ (python ./scripts/cpp_lint.py $(NONGEN_CXX_SRCS) > $(LINT_REPORT) 2>&1 \
 		&& (rm -f $(FAILED_LINT_REPORT); echo "No lint errors!")) || ( \
 			mv $(LINT_REPORT) $(FAILED_LINT_REPORT); \
@@ -166,133 +202,119 @@ $(LINT_REPORT): $(NONGEN_CXX_SRCS)
 			echo "Found 1 or more lint errors; see log at $(FAILED_LINT_REPORT)"; \
 			exit 1)
 
-test: init $(TEST_BINS) $(TEST_ALL_BIN)
+test: $(TEST_ALL_BIN_LINKS)
 
-tools: init proto $(TOOL_BINS)
+tools: $(TOOL_BINS)
 
-examples: init $(EXAMPLE_BINS)
+examples: $(EXAMPLE_BINS)
 
 py$(PROJECT): py
 
-py: init $(STATIC_NAME) $(PY$(PROJECT)_SRC) $(PROTO_GEN_PY)
-	$(CXX) -shared -o $(PY$(PROJECT)_SO) $(PY$(PROJECT)_SRC) \
+py: $(PY$(PROJECT)_SO) $(PROTO_GEN_PY)
+
+$(PY$(PROJECT)_SO): $(STATIC_NAME) $(PY$(PROJECT)_SRC)
+	$(CXX) -shared -o $@ $(PY$(PROJECT)_SRC) \
 		$(STATIC_NAME) $(CXXFLAGS) $(PYTHON_LDFLAGS)
-	@echo
 
 mat$(PROJECT): mat
 
-mat: init $(STATIC_NAME) $(MAT$(PROJECT)_SRC)
+mat: $(STATIC_NAME) $(MAT$(PROJECT)_SRC)
 	$(MATLAB_DIR)/bin/mex $(MAT$(PROJECT)_SRC) $(STATIC_NAME) \
 		CXXFLAGS="\$$CXXFLAGS $(CXXFLAGS) $(WARNINGS)" \
 		CXXLIBS="\$$CXXLIBS $(LDFLAGS)" \
 		-o $(MAT$(PROJECT)_SO)
-	@echo
+	@ echo
+
+runtest: $(TEST_ALL_BIN)
+	$(TEST_ALL_BIN) $(TEST_GPUID)
+
+$(ALL_BUILD_DIRS):
+	@ mkdir -p $@
 
-$(NAME): init $(PROTO_OBJS) $(OBJS)
+$(NAME): $(PROTO_OBJS) $(OBJS)
 	$(CXX) -shared -o $(NAME) $(OBJS) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
-	@echo
 
-$(STATIC_NAME): init $(PROTO_OBJS) $(OBJS)
+$(STATIC_NAME): $(PROTO_OBJS) $(OBJS)
 	ar rcs $(STATIC_NAME) $(PROTO_OBJS) $(OBJS)
-	@echo
 
-runtest: $(TEST_ALL_BIN)
-	$(TEST_ALL_BIN) $(TEST_GPUID)
-
-$(BUILD_DIR)/src/$(PROJECT)/test/%.testbin: \
-		$(BUILD_DIR)/src/$(PROJECT)/test/%.o \
-		$(GTEST_OBJ) $(STATIC_NAME) testshortcut
+$(TEST_BUILD_DIR)/%.testbin: $(TEST_BUILD_DIR)/%.o $(GTEST_OBJ) $(STATIC_NAME) \
+		| $(TEST_BUILD_DIR)
 	$(CXX) $(TEST_MAIN_SRC) $< $(GTEST_OBJ) $(STATIC_NAME) \
 		-o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
 
-$(TEST_ALL_BIN): $(GTEST_OBJ) $(STATIC_NAME) $(TEST_OBJS) testshortcut
+$(TEST_ALL_BIN): $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME)
 	$(CXX) $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME) \
 		-o $(TEST_ALL_BIN) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
 
-testshortcut: | $(TEST_DIR_LINK)
-
-$(TEST_DIR_LINK): | $(TEST_DIR)
-	ln -s $(TEST_BUILD_SUB_DIR) $(TEST_DIR_LINK)
-
-$(TEST_DIR):
-	mkdir -p $(TEST_DIR)
+$(TEST_LINK_DIR)/%.testbin: $(TEST_BUILD_DIR)/%.testbin | $(TEST_LINK_DIR)
+	@ $(RM) $@
+	@ ln -s ../../$(TEST_BUILD_DIR)/$(@F) $@
 
 $(TOOL_BINS): %.bin : %.o $(STATIC_NAME)
 	$(CXX) $< $(STATIC_NAME) -o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
-	@echo
+	@ echo
 
 $(EXAMPLE_BINS): %.bin : %.o $(STATIC_NAME)
 	$(CXX) $< $(STATIC_NAME) -o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
-	@echo
-
-$(BUILD_DIR)/src/$(PROJECT)/%.o: src/$(PROJECT)/%.cpp
-	$(CXX) $< $(CXXFLAGS) -c -o $@
-	@echo
-
-$(OBJS): $(PROTO_GEN_HEADER) $(HXX_SRCS)
-	@echo matched the first objs!!
-
+	@ echo
 
-LAYERS_DIR := $(BUILD_DIR)/src/$(PROJECT)/layers
-$(LAYERS_DIR):
-	@ mkdir -p $(LAYERS_DIR)
-
-$(BUILD_DIR)/src/$(PROJECT)/layers/%.o: \
-		src/$(PROJECT)/layers/%.cpp $(HXX_SRCS) | $(LAYERS_DIR)
+$(LAYER_BUILD_DIR)/%.o: \
+		src/$(PROJECT)/layers/%.cpp $(HXX_SRCS) | $(LAYER_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
-	@echo
 
-$(BUILD_DIR)/src/$(PROJECT)/proto/%.o: src/$(PROJECT)/proto/%.cc src/$(PROJECT)/proto/%.h
+$(PROTO_BUILD_DIR)/%.pb.o: $(PROTO_BUILD_DIR)/%.pb.cc \
+		$(PROTO_GEN_HEADER) | $(PROTO_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
-	@echo
+	@ echo
 
-$(BUILD_DIR)/src/$(PROJECT)/test/%.o: $(PROTO_GEN_HEADER) src/$(PROJECT)/test/%.cpp
+$(TEST_BUILD_DIR)/%.o: src/$(PROJECT)/test/%.cpp $(HXX_SRCS) | $(TEST_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
 
-$(BUILD_DIR)/src/$(PROJECT)/util/%.o: src/$(PROJECT)/util/%.cpp
+$(UTIL_BUILD_DIR)/%.o: src/$(PROJECT)/util/%.cpp $(HXX_SRCS) | $(UTIL_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
-	@echo
+	@ echo
 
-$(BUILD_DIR)/src/gtest/%.o: src/gtest/%.cpp
+$(GTEST_OBJ): $(GTEST_SRC) | $(GTEST_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
-	@echo
+	@ echo
 
-$(BUILD_DIR)/src/$(PROJECT)/layers/%.cuo: src/$(PROJECT)/layers/%.cu
+$(LAYER_BUILD_DIR)/%.cuo: \
+		src/$(PROJECT)/layers/%.cu $(HXX_SRCS) | $(LAYER_BUILD_DIR)
 	$(CUDA_DIR)/bin/nvcc $(NVCCFLAGS) $(CUDA_ARCH) -c $< -o $@
-	@echo
+	@ echo
 
-$(BUILD_DIR)/src/$(PROJECT)/util/%.cuo: src/$(PROJECT)/util/%.cu
+$(UTIL_BUILD_DIR)/%.cuo: src/$(PROJECT)/util/%.cu | $(UTIL_BUILD_DIR)
 	$(CUDA_DIR)/bin/nvcc $(NVCCFLAGS) $(CUDA_ARCH) -c $< -o $@
-	@echo
+	@ echo
 
-$(BUILD_DIR)/tools/%.o: tools/%.cpp $(PROTO_GEN_HEADER)
+$(TOOL_BUILD_DIR)/%.o: tools/%.cpp $(PROTO_GEN_HEADER) | $(TOOL_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@ $(LDFLAGS)
-	@echo
+	@ echo
 
-$(BUILD_DIR)/examples/%.o: examples/%.cpp $(PROTO_GEN_HEADER)
+$(EXAMPLE_BUILD_DIR)/%.o: examples/%.cpp $(PROTO_GEN_HEADER) \
+		| $(EXAMPLE_BUILD_DIRS)
 	$(CXX) $< $(CXXFLAGS) -c -o $@ $(LDFLAGS)
-	@echo
+	@ echo
+
+$(BUILD_DIR)/src/$(PROJECT)/%.o: src/$(PROJECT)/%.cpp $(HXX_SRCS)
+	$(CXX) $< $(CXXFLAGS) -c -o $@
+	@ echo
 
 $(PROTO_GEN_PY): $(PROTO_SRCS)
 	protoc --proto_path=src --python_out=python $(PROTO_SRCS)
-	@echo
+	@ echo
 
-proto: init $(PROTO_GEN_CC) $(PROTO_GEN_HEADER)
-	@echo PROTO_GEN_CC: $(PROTO_GEN_CC)
-	@echo PROTO_GEN_HEADER: $(PROTO_GEN_HEADER)
-	@echo PROTO_OBJS: $(PROTO_OBJS)
+proto: $(PROTO_GEN_CC) $(PROTO_GEN_HEADER)
 
-$(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_BUILD_DIR)/%.pb.h \
-		$(PROTO_BUILD_INCLUDE_DIR)/%.pb.h: \
-		$(PROTO_SRC_DIR)/%.proto | $(PROTO_BUILD_DIR) $(PROTO_BUILD_INCLUDE_DIR)
+$(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_BUILD_DIR)/%.pb.h : \
+		$(PROTO_SRC_DIR)/%.proto | $(PROTO_BUILD_DIR)
 	protoc --proto_path=src --cpp_out=build/src $<
-	cp $(PROTO_BUILD_DIR)/$(*F).pb.h $(PROTO_BUILD_INCLUDE_DIR)/$(*F).pb.h
 
-$(PROTO_BUILD_DIR):
-	mkdir -p $(PROTO_BUILD_DIR)
-
-$(PROTO_BUILD_INCLUDE_DIR):
-	mkdir -p $(PROTO_BUILD_INCLUDE_DIR)
+$(PROTO_BUILD_INCLUDE_DIR)/%.pb.h: $(PROTO_BUILD_DIR)/%.pb.h \
+		| $(PROTO_BUILD_INCLUDE_DIR)
+	@ $(RM) $(PROTO_BUILD_INCLUDE_DIR)/$(*F).pb.h
+	@ ln -s ../../../../$(PROTO_BUILD_DIR)/$(*F).pb.h \
+			$(PROTO_BUILD_INCLUDE_DIR)/$(*F).pb.h
 
 clean:
 	@- $(RM) $(NAME) $(STATIC_NAME)
@@ -303,20 +325,9 @@ clean:
 	@- $(RM) -rf $(BUILD_DIR)
 	@- $(RM) -rf $(DISTRIBUTE_DIR)
 
-# make superclean recursively* deletes all files ending with an extension
-# suggesting that Caffe built them.  This may be useful if you've built older
-# versions of Caffe that do not place all generated files in a location known
-# to make clean.
-#
-# make supercleanlist will list the files to be deleted by make superclean.
-#
-# * Recursive with the exception that symbolic links are never followed, per the
-# default behavior of 'find'.
-SUPERCLEAN_EXTS := .so .a .o .bin .testbin .pb.cc .pb.h _pb2.py .cuo
-
 supercleanfiles:
 	$(eval SUPERCLEAN_FILES := $(strip \
-		$(foreach ext,$(SUPERCLEAN_EXTS), $(shell find . -name '*$(ext)'))))
+			$(foreach ext,$(SUPERCLEAN_EXTS), $(shell find . -name '*$(ext)'))))
 
 supercleanlist: supercleanfiles
 	@ \
@@ -336,16 +347,15 @@ superclean: clean supercleanfiles
 	  $(RM) $(SUPERCLEAN_FILES); \
 	fi
 
-distribute: all
-	mkdir $(DISTRIBUTE_DIR)
+$(DIST_ALIASES): $(DISTRIBUTE_DIR)
+
+$(DISTRIBUTE_DIR): all py $(HXX_SRCS) | $(DISTRIBUTE_SUBDIRS)
 	# add include
 	cp -r include $(DISTRIBUTE_DIR)/
 	# add tool and example binaries
-	mkdir $(DISTRIBUTE_DIR)/bin
 	cp $(TOOL_BINS) $(DISTRIBUTE_DIR)/bin
 	cp $(EXAMPLE_BINS) $(DISTRIBUTE_DIR)/bin
 	# add libraries
-	mkdir $(DISTRIBUTE_DIR)/lib
 	cp $(NAME) $(DISTRIBUTE_DIR)/lib
 	cp $(STATIC_NAME) $(DISTRIBUTE_DIR)/lib
 	# add python - it's not the standard way, indeed...

From 195ba81b8836846da69b9ec192dec457ba82f959 Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sun, 30 Mar 2014 04:36:22 -0700
Subject: [PATCH 08/18] everything prints a blank line after compiling

---
 Makefile | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/Makefile b/Makefile
index 26c9517e821..9ba87f31d76 100644
--- a/Makefile
+++ b/Makefile
@@ -215,6 +215,7 @@ py: $(PY$(PROJECT)_SO) $(PROTO_GEN_PY)
 $(PY$(PROJECT)_SO): $(STATIC_NAME) $(PY$(PROJECT)_SRC)
 	$(CXX) -shared -o $@ $(PY$(PROJECT)_SRC) \
 		$(STATIC_NAME) $(CXXFLAGS) $(PYTHON_LDFLAGS)
+	@ echo
 
 mat$(PROJECT): mat
 
@@ -233,18 +234,22 @@ $(ALL_BUILD_DIRS):
 
 $(NAME): $(PROTO_OBJS) $(OBJS)
 	$(CXX) -shared -o $(NAME) $(OBJS) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+	@ echo
 
 $(STATIC_NAME): $(PROTO_OBJS) $(OBJS)
 	ar rcs $(STATIC_NAME) $(PROTO_OBJS) $(OBJS)
+	@ echo
 
 $(TEST_BUILD_DIR)/%.testbin: $(TEST_BUILD_DIR)/%.o $(GTEST_OBJ) $(STATIC_NAME) \
 		| $(TEST_BUILD_DIR)
 	$(CXX) $(TEST_MAIN_SRC) $< $(GTEST_OBJ) $(STATIC_NAME) \
 		-o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+	@ echo
 
 $(TEST_ALL_BIN): $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME)
 	$(CXX) $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME) \
 		-o $(TEST_ALL_BIN) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+	@ echo
 
 $(TEST_LINK_DIR)/%.testbin: $(TEST_BUILD_DIR)/%.testbin | $(TEST_LINK_DIR)
 	@ $(RM) $@
@@ -261,6 +266,7 @@ $(EXAMPLE_BINS): %.bin : %.o $(STATIC_NAME)
 $(LAYER_BUILD_DIR)/%.o: \
 		src/$(PROJECT)/layers/%.cpp $(HXX_SRCS) | $(LAYER_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
+	@ echo
 
 $(PROTO_BUILD_DIR)/%.pb.o: $(PROTO_BUILD_DIR)/%.pb.cc \
 		$(PROTO_GEN_HEADER) | $(PROTO_BUILD_DIR)
@@ -269,6 +275,7 @@ $(PROTO_BUILD_DIR)/%.pb.o: $(PROTO_BUILD_DIR)/%.pb.cc \
 
 $(TEST_BUILD_DIR)/%.o: src/$(PROJECT)/test/%.cpp $(HXX_SRCS) | $(TEST_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
+	@ echo
 
 $(UTIL_BUILD_DIR)/%.o: src/$(PROJECT)/util/%.cpp $(HXX_SRCS) | $(UTIL_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
@@ -309,6 +316,7 @@ proto: $(PROTO_GEN_CC) $(PROTO_GEN_HEADER)
 $(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_BUILD_DIR)/%.pb.h : \
 		$(PROTO_SRC_DIR)/%.proto | $(PROTO_BUILD_DIR)
 	protoc --proto_path=src --cpp_out=build/src $<
+	@ echo
 
 $(PROTO_BUILD_INCLUDE_DIR)/%.pb.h: $(PROTO_BUILD_DIR)/%.pb.h \
 		| $(PROTO_BUILD_INCLUDE_DIR)

From 9f14265cfd05762a404bd033a73df4f125bd0194 Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sun, 30 Mar 2014 04:42:43 -0700
Subject: [PATCH 09/18] libcaffe.* in build/lib/

---
 Makefile | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/Makefile b/Makefile
index 9ba87f31d76..6e3610a0a48 100644
--- a/Makefile
+++ b/Makefile
@@ -8,8 +8,9 @@ include Makefile.config
 ##############################################################################
 
 # The target static library and shared library name
-NAME := lib$(PROJECT).so
-STATIC_NAME := lib$(PROJECT).a
+LIB_BUILD_DIR := $(BUILD_DIR)/lib
+NAME := $(LIB_BUILD_DIR)/lib$(PROJECT).so
+STATIC_NAME := $(LIB_BUILD_DIR)/lib$(PROJECT).a
 
 ##############################
 # Get all source files
@@ -133,7 +134,7 @@ ifneq ($(strip $(DISTRIBUTE_DIR)),distribute)
 		DIST_ALIASES += distribute
 endif
 
-ALL_BUILD_DIRS := $(BUILD_DIR) $(OBJ_BUILD_DIR) \
+ALL_BUILD_DIRS := $(BUILD_DIR) $(LIB_BUILD_DIR) $(OBJ_BUILD_DIR) \
 		$(LAYER_BUILD_DIR) $(UTIL_BUILD_DIR) $(TOOL_BUILD_DIRS) \
 		$(TEST_BUILD_DIR) $(TEST_LINK_DIR) $(GTEST_BUILD_DIR) \
 		$(EXAMPLE_BUILD_DIRS) \
@@ -232,11 +233,11 @@ runtest: $(TEST_ALL_BIN)
 $(ALL_BUILD_DIRS):
 	@ mkdir -p $@
 
-$(NAME): $(PROTO_OBJS) $(OBJS)
+$(NAME): $(PROTO_OBJS) $(OBJS) | $(LIB_BUILD_DIR)
 	$(CXX) -shared -o $(NAME) $(OBJS) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
 	@ echo
 
-$(STATIC_NAME): $(PROTO_OBJS) $(OBJS)
+$(STATIC_NAME): $(PROTO_OBJS) $(OBJS) | $(LIB_BUILD_DIR)
 	ar rcs $(STATIC_NAME) $(PROTO_OBJS) $(OBJS)
 	@ echo
 

From a034d629588f4717476f3427c793dc7f32200669 Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sun, 30 Mar 2014 04:44:17 -0700
Subject: [PATCH 10/18] minor cleanup

---
 Makefile | 20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

diff --git a/Makefile b/Makefile
index 6e3610a0a48..783cc6042b2 100644
--- a/Makefile
+++ b/Makefile
@@ -84,7 +84,6 @@ OBJS := $(PROTO_OBJS) $(CXX_OBJS) $(CU_OBJS)
 # tool, example, and test objects
 TOOL_OBJS := $(addprefix $(BUILD_DIR)/, ${TOOL_SRCS:.cpp=.o})
 TOOL_BUILD_DIR := $(BUILD_DIR)/tools
-TOOL_BUILD_DIRS := $(sort $(foreach obj,$(TOOL_OBJS),$(dir $(obj))))
 TEST_BUILD_DIR := $(BUILD_DIR)/src/$(PROJECT)/test
 TEST_OBJS := $(addprefix $(BUILD_DIR)/, ${TEST_SRCS:.cpp=.o})
 GTEST_OBJ := $(addprefix $(BUILD_DIR)/, ${GTEST_SRC:.cpp=.o})
@@ -134,14 +133,13 @@ ifneq ($(strip $(DISTRIBUTE_DIR)),distribute)
 		DIST_ALIASES += distribute
 endif
 
-ALL_BUILD_DIRS := $(BUILD_DIR) $(LIB_BUILD_DIR) $(OBJ_BUILD_DIR) \
-		$(LAYER_BUILD_DIR) $(UTIL_BUILD_DIR) $(TOOL_BUILD_DIRS) \
+ALL_BUILD_DIRS := $(sort \
+		$(BUILD_DIR) $(LIB_BUILD_DIR) $(OBJ_BUILD_DIR) \
+		$(LAYER_BUILD_DIR) $(UTIL_BUILD_DIR) $(TOOL_BUILD_DIR) \
 		$(TEST_BUILD_DIR) $(TEST_LINK_DIR) $(GTEST_BUILD_DIR) \
 		$(EXAMPLE_BUILD_DIRS) \
 		$(PROTO_BUILD_DIR) $(PROTO_BUILD_INCLUDE_DIR) \
-		$(DISTRIBUTE_SUBDIRS)
-
-ALL_BUILD_DIRS := $(sort $(ALL_BUILD_DIRS))
+		$(DISTRIBUTE_SUBDIRS))
 
 DEBUG ?= 0
 ifeq ($(DEBUG), 1)
@@ -197,7 +195,7 @@ lint: $(LINT_REPORT)
 
 $(LINT_REPORT): $(NONGEN_CXX_SRCS) | $(BUILD_DIR)
 	@ (python ./scripts/cpp_lint.py $(NONGEN_CXX_SRCS) > $(LINT_REPORT) 2>&1 \
-		&& (rm -f $(FAILED_LINT_REPORT); echo "No lint errors!")) || ( \
+		&& ($(RM) $(FAILED_LINT_REPORT); echo "No lint errors!")) || ( \
 			mv $(LINT_REPORT) $(FAILED_LINT_REPORT); \
 			grep -v "^Done processing " $(FAILED_LINT_REPORT); \
 			echo "Found 1 or more lint errors; see log at $(FAILED_LINT_REPORT)"; \
@@ -264,13 +262,13 @@ $(EXAMPLE_BINS): %.bin : %.o $(STATIC_NAME)
 	$(CXX) $< $(STATIC_NAME) -o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
 	@ echo
 
-$(LAYER_BUILD_DIR)/%.o: \
-		src/$(PROJECT)/layers/%.cpp $(HXX_SRCS) | $(LAYER_BUILD_DIR)
+$(LAYER_BUILD_DIR)/%.o: src/$(PROJECT)/layers/%.cpp $(HXX_SRCS) \
+		| $(LAYER_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
 	@ echo
 
-$(PROTO_BUILD_DIR)/%.pb.o: $(PROTO_BUILD_DIR)/%.pb.cc \
-		$(PROTO_GEN_HEADER) | $(PROTO_BUILD_DIR)
+$(PROTO_BUILD_DIR)/%.pb.o: $(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_GEN_HEADER) \
+		| $(PROTO_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
 	@ echo
 

From 209b4c82eeb6f936936e0843184d2b39ec0623d0 Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sun, 30 Mar 2014 05:22:52 -0700
Subject: [PATCH 11/18] add test header dependency and fix mat targets

---
 Makefile | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/Makefile b/Makefile
index 783cc6042b2..040a34ff1da 100644
--- a/Makefile
+++ b/Makefile
@@ -218,11 +218,12 @@ $(PY$(PROJECT)_SO): $(STATIC_NAME) $(PY$(PROJECT)_SRC)
 
 mat$(PROJECT): mat
 
-mat: $(STATIC_NAME) $(MAT$(PROJECT)_SRC)
+mat: $(MAT$(PROJECT)_SO)
+
+$(MAT$(PROJECT)_SO): $(MAT$(PROJECT)_SRC) $(STATIC_NAME)
 	$(MATLAB_DIR)/bin/mex $(MAT$(PROJECT)_SRC) $(STATIC_NAME) \
-		CXXFLAGS="\$$CXXFLAGS $(CXXFLAGS) $(WARNINGS)" \
-		CXXLIBS="\$$CXXLIBS $(LDFLAGS)" \
-		-o $(MAT$(PROJECT)_SO)
+			CXXFLAGS="\$$CXXFLAGS $(CXXFLAGS) $(WARNINGS)" \
+			CXXLIBS="\$$CXXLIBS $(LDFLAGS)" -o $@
 	@ echo
 
 runtest: $(TEST_ALL_BIN)
@@ -232,7 +233,7 @@ $(ALL_BUILD_DIRS):
 	@ mkdir -p $@
 
 $(NAME): $(PROTO_OBJS) $(OBJS) | $(LIB_BUILD_DIR)
-	$(CXX) -shared -o $(NAME) $(OBJS) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+	$(CXX) -shared -o $@ $(OBJS) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
 	@ echo
 
 $(STATIC_NAME): $(PROTO_OBJS) $(OBJS) | $(LIB_BUILD_DIR)
@@ -247,7 +248,7 @@ $(TEST_BUILD_DIR)/%.testbin: $(TEST_BUILD_DIR)/%.o $(GTEST_OBJ) $(STATIC_NAME) \
 
 $(TEST_ALL_BIN): $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME)
 	$(CXX) $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME) \
-		-o $(TEST_ALL_BIN) $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+		-o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
 	@ echo
 
 $(TEST_LINK_DIR)/%.testbin: $(TEST_BUILD_DIR)/%.testbin | $(TEST_LINK_DIR)
@@ -272,7 +273,8 @@ $(PROTO_BUILD_DIR)/%.pb.o: $(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_GEN_HEADER) \
 	$(CXX) $< $(CXXFLAGS) -c -o $@
 	@ echo
 
-$(TEST_BUILD_DIR)/%.o: src/$(PROJECT)/test/%.cpp $(HXX_SRCS) | $(TEST_BUILD_DIR)
+$(TEST_BUILD_DIR)/%.o: src/$(PROJECT)/test/%.cpp $(HXX_SRCS) $(TEST_HDRS) \
+		| $(TEST_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
 	@ echo
 
@@ -306,10 +308,6 @@ $(BUILD_DIR)/src/$(PROJECT)/%.o: src/$(PROJECT)/%.cpp $(HXX_SRCS)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
 	@ echo
 
-$(PROTO_GEN_PY): $(PROTO_SRCS)
-	protoc --proto_path=src --python_out=python $(PROTO_SRCS)
-	@ echo
-
 proto: $(PROTO_GEN_CC) $(PROTO_GEN_HEADER)
 
 $(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_BUILD_DIR)/%.pb.h : \
@@ -323,6 +321,10 @@ $(PROTO_BUILD_INCLUDE_DIR)/%.pb.h: $(PROTO_BUILD_DIR)/%.pb.h \
 	@ ln -s ../../../../$(PROTO_BUILD_DIR)/$(*F).pb.h \
 			$(PROTO_BUILD_INCLUDE_DIR)/$(*F).pb.h
 
+$(PROTO_GEN_PY): $(PROTO_SRCS)
+	protoc --proto_path=src --python_out=python $(PROTO_SRCS)
+	@ echo
+
 clean:
 	@- $(RM) $(NAME) $(STATIC_NAME)
 	@- $(RM) $(PROTO_GEN_HEADER) $(PROTO_GEN_CC) $(PROTO_GEN_PY)

From db26e5a8f3f294782d5b5adefc441452f57b8cdd Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sun, 30 Mar 2014 06:21:38 -0700
Subject: [PATCH 12/18] compile test bins directly into build/test

---
 Makefile | 47 +++++++++++++++++++----------------------------
 1 file changed, 19 insertions(+), 28 deletions(-)

diff --git a/Makefile b/Makefile
index 040a34ff1da..7c35c60199e 100644
--- a/Makefile
+++ b/Makefile
@@ -65,12 +65,13 @@ MAT$(PROJECT)_SO := matlab/$(PROJECT)/$(PROJECT)
 ##############################
 # The generated files for protocol buffers
 PROTO_GEN_HEADER_SRCS := $(addprefix $(PROTO_BUILD_DIR)/, \
-	$(notdir ${PROTO_SRCS:.proto=.pb.h}))
+		$(notdir ${PROTO_SRCS:.proto=.pb.h}))
 PROTO_GEN_HEADER := $(addprefix $(PROTO_BUILD_INCLUDE_DIR)/, \
-	$(notdir ${PROTO_SRCS:.proto=.pb.h}))
+		$(notdir ${PROTO_SRCS:.proto=.pb.h}))
 HXX_SRCS += $(PROTO_GEN_HEADER)
 PROTO_GEN_CC := $(addprefix $(BUILD_DIR)/, ${PROTO_SRCS:.proto=.pb.cc})
-PROTO_GEN_PY := $(foreach file,${PROTO_SRCS:.proto=_pb2.py},python/$(PROJECT)/proto/$(notdir $(file)))
+PROTO_GEN_PY := $(foreach file,${PROTO_SRCS:.proto=_pb2.py}, \
+		python/$(PROJECT)/proto/$(notdir $(file)))
 # The objects corresponding to the source files
 # These objects will be linked into the final shared library, so we
 # exclude the tool, example, and test objects.
@@ -95,13 +96,11 @@ EXAMPLE_BUILD_DIRS += $(foreach obj,$(EXAMPLE_OBJS),$(dir $(obj)))
 # tool, example, and test bins
 TOOL_BINS := ${TOOL_OBJS:.o=.bin}
 EXAMPLE_BINS := ${EXAMPLE_OBJS:.o=.bin}
-TEST_BINS := ${TEST_OBJS:.o=.testbin}
-TEST_ALL_BIN := $(TEST_BUILD_DIR)/test_all.testbin
-TEST_ALL_BINS := $(TEST_ALL_BIN) $(TEST_BINS)
 # A shortcut to the directory of test binaries for convenience.
-TEST_LINK_DIR := $(BUILD_DIR)/test
-TEST_ALL_BIN_LINKS := $(foreach \
-		bin,$(TEST_ALL_BINS),$(TEST_LINK_DIR)/$(notdir $(bin)))
+TEST_BIN_DIR := $(BUILD_DIR)/test
+TEST_BINS := $(addprefix $(TEST_BIN_DIR)/, \
+		$(foreach obj,$(TEST_OBJS),$(notdir $(obj))))
+TEST_ALL_BIN := $(TEST_BIN_DIR)/test_all.testbin
 
 ##############################
 # Derive include and lib directories
@@ -136,7 +135,7 @@ endif
 ALL_BUILD_DIRS := $(sort \
 		$(BUILD_DIR) $(LIB_BUILD_DIR) $(OBJ_BUILD_DIR) \
 		$(LAYER_BUILD_DIR) $(UTIL_BUILD_DIR) $(TOOL_BUILD_DIR) \
-		$(TEST_BUILD_DIR) $(TEST_LINK_DIR) $(GTEST_BUILD_DIR) \
+		$(TEST_BUILD_DIR) $(TEST_BIN_DIR) $(GTEST_BUILD_DIR) \
 		$(EXAMPLE_BUILD_DIRS) \
 		$(PROTO_BUILD_DIR) $(PROTO_BUILD_INCLUDE_DIR) \
 		$(DISTRIBUTE_SUBDIRS))
@@ -184,8 +183,6 @@ SUPERCLEAN_EXTS := .so .a .o .bin .testbin .pb.cc .pb.h _pb2.py .cuo
 	py mat py$(PROJECT) mat$(PROJECT) proto runtest \
 	superclean supercleanlist supercleanfiles
 
-.SECONDARY: $(PROTO_GEN_HEADER_SRCS) $(TEST_BINS)
-
 all: $(NAME) $(STATIC_NAME) tools examples
 
 linecount: clean
@@ -201,7 +198,7 @@ $(LINT_REPORT): $(NONGEN_CXX_SRCS) | $(BUILD_DIR)
 			echo "Found 1 or more lint errors; see log at $(FAILED_LINT_REPORT)"; \
 			exit 1)
 
-test: $(TEST_ALL_BIN_LINKS)
+test: $(TEST_ALL_BIN) $(TEST_BINS)
 
 tools: $(TOOL_BINS)
 
@@ -237,13 +234,12 @@ $(NAME): $(PROTO_OBJS) $(OBJS) | $(LIB_BUILD_DIR)
 	@ echo
 
 $(STATIC_NAME): $(PROTO_OBJS) $(OBJS) | $(LIB_BUILD_DIR)
-	ar rcs $(STATIC_NAME) $(PROTO_OBJS) $(OBJS)
+	ar rcs $@ $(PROTO_OBJS) $(OBJS)
 	@ echo
 
-$(TEST_BUILD_DIR)/%.testbin: $(TEST_BUILD_DIR)/%.o $(GTEST_OBJ) $(STATIC_NAME) \
+$(TEST_BUILD_DIR)/%.o: src/$(PROJECT)/test/%.cpp $(HXX_SRCS) $(TEST_HDRS) \
 		| $(TEST_BUILD_DIR)
-	$(CXX) $(TEST_MAIN_SRC) $< $(GTEST_OBJ) $(STATIC_NAME) \
-		-o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+	$(CXX) $< $(CXXFLAGS) -c -o $@
 	@ echo
 
 $(TEST_ALL_BIN): $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME)
@@ -251,9 +247,11 @@ $(TEST_ALL_BIN): $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME)
 		-o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
 	@ echo
 
-$(TEST_LINK_DIR)/%.testbin: $(TEST_BUILD_DIR)/%.testbin | $(TEST_LINK_DIR)
-	@ $(RM) $@
-	@ ln -s ../../$(TEST_BUILD_DIR)/$(@F) $@
+$(TEST_BIN_DIR)/%.testbin: $(TEST_BUILD_DIR)/%.o $(GTEST_OBJ) $(STATIC_NAME) \
+		| $(TEST_BIN_DIR)
+	$(CXX) $(TEST_MAIN_SRC) $< $(GTEST_OBJ) $(STATIC_NAME) \
+		-o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
+	@ echo
 
 $(TOOL_BINS): %.bin : %.o $(STATIC_NAME)
 	$(CXX) $< $(STATIC_NAME) -o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
@@ -273,11 +271,6 @@ $(PROTO_BUILD_DIR)/%.pb.o: $(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_GEN_HEADER) \
 	$(CXX) $< $(CXXFLAGS) -c -o $@
 	@ echo
 
-$(TEST_BUILD_DIR)/%.o: src/$(PROJECT)/test/%.cpp $(HXX_SRCS) $(TEST_HDRS) \
-		| $(TEST_BUILD_DIR)
-	$(CXX) $< $(CXXFLAGS) -c -o $@
-	@ echo
-
 $(UTIL_BUILD_DIR)/%.o: src/$(PROJECT)/util/%.cpp $(HXX_SRCS) | $(UTIL_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
 	@ echo
@@ -317,9 +310,7 @@ $(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_BUILD_DIR)/%.pb.h : \
 
 $(PROTO_BUILD_INCLUDE_DIR)/%.pb.h: $(PROTO_BUILD_DIR)/%.pb.h \
 		| $(PROTO_BUILD_INCLUDE_DIR)
-	@ $(RM) $(PROTO_BUILD_INCLUDE_DIR)/$(*F).pb.h
-	@ ln -s ../../../../$(PROTO_BUILD_DIR)/$(*F).pb.h \
-			$(PROTO_BUILD_INCLUDE_DIR)/$(*F).pb.h
+	@ cp $(PROTO_BUILD_DIR)/$(*F).pb.h $(PROTO_BUILD_INCLUDE_DIR)/$(*F).pb.h
 
 $(PROTO_GEN_PY): $(PROTO_SRCS)
 	protoc --proto_path=src --python_out=python $(PROTO_SRCS)

From 39ca2def3528610e38233bb2b97c810e126a32e9 Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sun, 30 Mar 2014 06:58:17 -0700
Subject: [PATCH 13/18] cleanup python build and clean

---
 Makefile                       | 27 +++++++++++++++------------
 python/caffe/proto/__init__.py |  0
 2 files changed, 15 insertions(+), 12 deletions(-)
 delete mode 100644 python/caffe/proto/__init__.py

diff --git a/Makefile b/Makefile
index 7c35c60199e..8cbb278ce5d 100644
--- a/Makefile
+++ b/Makefile
@@ -70,8 +70,10 @@ PROTO_GEN_HEADER := $(addprefix $(PROTO_BUILD_INCLUDE_DIR)/, \
 		$(notdir ${PROTO_SRCS:.proto=.pb.h}))
 HXX_SRCS += $(PROTO_GEN_HEADER)
 PROTO_GEN_CC := $(addprefix $(BUILD_DIR)/, ${PROTO_SRCS:.proto=.pb.cc})
+PY_PROTO_BUILD_DIR := python/$(PROJECT)/proto
+PY_PROTO_INIT := python/$(PROJECT)/proto/__init__.py
 PROTO_GEN_PY := $(foreach file,${PROTO_SRCS:.proto=_pb2.py}, \
-		python/$(PROJECT)/proto/$(notdir $(file)))
+		$(PY_PROTO_BUILD_DIR)/$(notdir $(file)))
 # The objects corresponding to the source files
 # These objects will be linked into the final shared library, so we
 # exclude the tool, example, and test objects.
@@ -137,7 +139,7 @@ ALL_BUILD_DIRS := $(sort \
 		$(LAYER_BUILD_DIR) $(UTIL_BUILD_DIR) $(TOOL_BUILD_DIR) \
 		$(TEST_BUILD_DIR) $(TEST_BIN_DIR) $(GTEST_BUILD_DIR) \
 		$(EXAMPLE_BUILD_DIRS) \
-		$(PROTO_BUILD_DIR) $(PROTO_BUILD_INCLUDE_DIR) \
+		$(PROTO_BUILD_DIR) $(PROTO_BUILD_INCLUDE_DIR) $(PY_PROTO_BUILD_DIR) \
 		$(DISTRIBUTE_SUBDIRS))
 
 DEBUG ?= 0
@@ -279,8 +281,8 @@ $(GTEST_OBJ): $(GTEST_SRC) | $(GTEST_BUILD_DIR)
 	$(CXX) $< $(CXXFLAGS) -c -o $@
 	@ echo
 
-$(LAYER_BUILD_DIR)/%.cuo: \
-		src/$(PROJECT)/layers/%.cu $(HXX_SRCS) | $(LAYER_BUILD_DIR)
+$(LAYER_BUILD_DIR)/%.cuo: src/$(PROJECT)/layers/%.cu $(HXX_SRCS) \
+		| $(LAYER_BUILD_DIR)
 	$(CUDA_DIR)/bin/nvcc $(NVCCFLAGS) $(CUDA_ARCH) -c $< -o $@
 	@ echo
 
@@ -312,18 +314,19 @@ $(PROTO_BUILD_INCLUDE_DIR)/%.pb.h: $(PROTO_BUILD_DIR)/%.pb.h \
 		| $(PROTO_BUILD_INCLUDE_DIR)
 	@ cp $(PROTO_BUILD_DIR)/$(*F).pb.h $(PROTO_BUILD_INCLUDE_DIR)/$(*F).pb.h
 
-$(PROTO_GEN_PY): $(PROTO_SRCS)
-	protoc --proto_path=src --python_out=python $(PROTO_SRCS)
+$(PY_PROTO_BUILD_DIR)/%_pb2.py : $(PROTO_SRC_DIR)/%.proto \
+		$(PY_PROTO_INIT) | $(PY_PROTO_BUILD_DIR)
+	protoc --proto_path=src --python_out=python $<
 	@ echo
 
+$(PY_PROTO_INIT): | $(PY_PROTO_BUILD_DIR)
+	touch $(PY_PROTO_INIT)
+
 clean:
-	@- $(RM) $(NAME) $(STATIC_NAME)
-	@- $(RM) $(PROTO_GEN_HEADER) $(PROTO_GEN_CC) $(PROTO_GEN_PY)
-	@- $(RM) include/$(PROJECT)/proto/$(PROJECT).pb.h
-	@- $(RM) python/$(PROJECT)/proto/$(PROJECT)_pb2.py
-	@- $(RM) python/$(PROJECT)/*.so
-	@- $(RM) -rf $(BUILD_DIR)
+	@- $(RM) -rf $(ALL_BUILD_DIRS)
 	@- $(RM) -rf $(DISTRIBUTE_DIR)
+	@- $(RM) $(PY$(PROJECT)_SO)
+	@- $(RM) $(MAT$(PROJECT)_SO)
 
 supercleanfiles:
 	$(eval SUPERCLEAN_FILES := $(strip \
diff --git a/python/caffe/proto/__init__.py b/python/caffe/proto/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000

From 48994cf0ddcaac0ca875c166dd3a1d0a3d1f4c8b Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Sun, 30 Mar 2014 07:21:00 -0700
Subject: [PATCH 14/18] fix test bugs and minor cleanup

---
 Makefile | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/Makefile b/Makefile
index 8cbb278ce5d..7172b3c7574 100644
--- a/Makefile
+++ b/Makefile
@@ -34,7 +34,7 @@ TOOL_SRCS := $(shell find tools -name "*.cpp")
 EXAMPLE_SRCS := $(shell find examples -name "*.cpp")
 # BUILD_INCLUDE_DIR contains any generated header files we want to include.
 BUILD_INCLUDE_DIR := $(BUILD_DIR)/include
-# PROTO_SRCS are the protocol buffer defions
+# PROTO_SRCS are the protocol buffer definitions
 PROTO_SRC_DIR := src/$(PROJECT)/proto
 PROTO_SRCS := $(wildcard $(PROTO_SRC_DIR)/*.proto)
 # PROTO_BUILD_DIR will contain the .cc and obj files generated from
@@ -98,10 +98,10 @@ EXAMPLE_BUILD_DIRS += $(foreach obj,$(EXAMPLE_OBJS),$(dir $(obj)))
 # tool, example, and test bins
 TOOL_BINS := ${TOOL_OBJS:.o=.bin}
 EXAMPLE_BINS := ${EXAMPLE_OBJS:.o=.bin}
-# A shortcut to the directory of test binaries for convenience.
+# Put the test binaries in build/test for convenience.
 TEST_BIN_DIR := $(BUILD_DIR)/test
-TEST_BINS := $(addprefix $(TEST_BIN_DIR)/, \
-		$(foreach obj,$(TEST_OBJS),$(notdir $(obj))))
+TEST_BINS := $(addsuffix .testbin,$(addprefix $(TEST_BIN_DIR)/, \
+		$(foreach obj,$(TEST_OBJS),$(basename $(notdir $(obj))))))
 TEST_ALL_BIN := $(TEST_BIN_DIR)/test_all.testbin
 
 ##############################
@@ -168,9 +168,9 @@ LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) \
 PYTHON_LDFLAGS := $(LDFLAGS) $(foreach library,$(PYTHON_LIBRARIES),-l$(library))
 
 # 'superclean' target recursively* deletes all files ending with an extension
-# suggesting that Caffe built them.  This may be useful if you've built older
+# in $(SUPERCLEAN_EXTS) below.  This may be useful if you've built older
 # versions of Caffe that do not place all generated files in a location known
-# to make clean.
+# to the 'clean' target.
 #
 # 'supercleanlist' will list the files to be deleted by make superclean.
 #
@@ -181,7 +181,7 @@ SUPERCLEAN_EXTS := .so .a .o .bin .testbin .pb.cc .pb.h _pb2.py .cuo
 ##############################
 # Define build targets
 ##############################
-.PHONY: all test clean linecount lint tools examples dist \
+.PHONY: all test clean linecount lint tools examples $(DIST_ALIASES) \
 	py mat py$(PROJECT) mat$(PROJECT) proto runtest \
 	superclean supercleanlist supercleanfiles
 
@@ -244,7 +244,8 @@ $(TEST_BUILD_DIR)/%.o: src/$(PROJECT)/test/%.cpp $(HXX_SRCS) $(TEST_HDRS) \
 	$(CXX) $< $(CXXFLAGS) -c -o $@
 	@ echo
 
-$(TEST_ALL_BIN): $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME)
+$(TEST_ALL_BIN): $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME) \
+		| $(TEST_BIN_DIR)
 	$(CXX) $(TEST_MAIN_SRC) $(TEST_OBJS) $(GTEST_OBJ) $(STATIC_NAME) \
 		-o $@ $(CXXFLAGS) $(LDFLAGS) $(WARNINGS)
 	@ echo

From abf44a6174df4cfd69849c91cc237bb33a4e6e3e Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Mon, 31 Mar 2014 14:16:11 -0700
Subject: [PATCH 15/18] matcaffe fixes

---
 Makefile | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/Makefile b/Makefile
index 7172b3c7574..a84d3b0d008 100644
--- a/Makefile
+++ b/Makefile
@@ -1,11 +1,8 @@
 # The makefile for caffe. Pretty hacky.
 PROJECT := caffe
 
-include Makefile.config
-
-##############################################################################
-# After this line, things should happen automatically.
-##############################################################################
+CONFIG_FILE := Makefile.config
+include $(CONFIG_FILE)
 
 # The target static library and shared library name
 LIB_BUILD_DIR := $(BUILD_DIR)/lib
@@ -58,7 +55,10 @@ PY$(PROJECT)_SRC := python/$(PROJECT)/_$(PROJECT).cpp
 PY$(PROJECT)_SO := python/$(PROJECT)/_$(PROJECT).so
 # MAT$(PROJECT)_SRC is the matlab wrapper for $(PROJECT)
 MAT$(PROJECT)_SRC := matlab/$(PROJECT)/mat$(PROJECT).cpp
-MAT$(PROJECT)_SO := matlab/$(PROJECT)/$(PROJECT)
+ifneq ($(MATLAB_DIR),)
+	MAT_SO_EXT := $(shell $(MATLAB_DIR)/bin/mexext)
+endif
+MAT$(PROJECT)_SO := matlab/$(PROJECT)/$(PROJECT).$(MAT_SO_EXT)
 
 ##############################
 # Derive generated files
@@ -220,6 +220,11 @@ mat$(PROJECT): mat
 mat: $(MAT$(PROJECT)_SO)
 
 $(MAT$(PROJECT)_SO): $(MAT$(PROJECT)_SRC) $(STATIC_NAME)
+	@ if [ -z "$(MATLAB_DIR)" ]; then \
+		echo "MATLAB_DIR must be specified in $(CONFIG_FILE)" \
+			"to build mat$(PROJECT)."; \
+		exit 1; \
+	fi
 	$(MATLAB_DIR)/bin/mex $(MAT$(PROJECT)_SRC) $(STATIC_NAME) \
 			CXXFLAGS="\$$CXXFLAGS $(CXXFLAGS) $(WARNINGS)" \
 			CXXLIBS="\$$CXXLIBS $(LDFLAGS)" -o $@

From 74a3788298226e9e6552651efc3dc8a97ff29307 Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Mon, 31 Mar 2014 14:25:42 -0700
Subject: [PATCH 16/18] remove silly thing where I copied proto headers to a
 separate build/include dir

---
 Makefile | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/Makefile b/Makefile
index a84d3b0d008..b9688d7f66f 100644
--- a/Makefile
+++ b/Makefile
@@ -30,7 +30,7 @@ TOOL_SRCS := $(shell find tools -name "*.cpp")
 # EXAMPLE_SRCS are the source files for the example binaries
 EXAMPLE_SRCS := $(shell find examples -name "*.cpp")
 # BUILD_INCLUDE_DIR contains any generated header files we want to include.
-BUILD_INCLUDE_DIR := $(BUILD_DIR)/include
+BUILD_INCLUDE_DIR := $(BUILD_DIR)/src
 # PROTO_SRCS are the protocol buffer definitions
 PROTO_SRC_DIR := src/$(PROJECT)/proto
 PROTO_SRCS := $(wildcard $(PROTO_SRC_DIR)/*.proto)
@@ -316,10 +316,6 @@ $(PROTO_BUILD_DIR)/%.pb.cc $(PROTO_BUILD_DIR)/%.pb.h : \
 	protoc --proto_path=src --cpp_out=build/src $<
 	@ echo
 
-$(PROTO_BUILD_INCLUDE_DIR)/%.pb.h: $(PROTO_BUILD_DIR)/%.pb.h \
-		| $(PROTO_BUILD_INCLUDE_DIR)
-	@ cp $(PROTO_BUILD_DIR)/$(*F).pb.h $(PROTO_BUILD_INCLUDE_DIR)/$(*F).pb.h
-
 $(PY_PROTO_BUILD_DIR)/%_pb2.py : $(PROTO_SRC_DIR)/%.proto \
 		$(PY_PROTO_INIT) | $(PY_PROTO_BUILD_DIR)
 	protoc --proto_path=src --python_out=python $<

From 6b3d257eea7680c96332e6359c12eba93a784c75 Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Wed, 2 Apr 2014 11:29:01 -0700
Subject: [PATCH 17/18] include build/ before other dirs so old proto built
 files in src/ and include/ don't interfere

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index b9688d7f66f..094719685ec 100644
--- a/Makefile
+++ b/Makefile
@@ -112,8 +112,8 @@ CUDA_LIB_DIR := $(CUDA_DIR)/lib64 $(CUDA_DIR)/lib
 MKL_INCLUDE_DIR := $(MKL_DIR)/include
 MKL_LIB_DIR := $(MKL_DIR)/lib $(MKL_DIR)/lib/intel64
 
-INCLUDE_DIRS += ./src ./include $(CUDA_INCLUDE_DIR)
 INCLUDE_DIRS += $(BUILD_INCLUDE_DIR)
+INCLUDE_DIRS += ./src ./include $(CUDA_INCLUDE_DIR)
 LIBRARY_DIRS += $(CUDA_LIB_DIR)
 LIBRARIES := cudart cublas curand \
 	pthread \

From 76caca3a5a5027e1cbe43123a6db9e9d89ac347d Mon Sep 17 00:00:00 2001
From: Jeff Donahue <jeff.donahue@gmail.com>
Date: Fri, 4 Apr 2014 13:44:34 -0700
Subject: [PATCH 18/18] gitignore python/caffe/proto/; superclean ignore data
 dir

---
 .gitignore | 1 +
 Makefile   | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 3997e463cdb..5aeb3dc24e2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -34,6 +34,7 @@ build/*
 distribute/*
 *.testbin
 *.bin
+python/caffe/proto/
 
 # Editor temporaries
 *.swp
diff --git a/Makefile b/Makefile
index 094719685ec..83117e3ae41 100644
--- a/Makefile
+++ b/Makefile
@@ -332,7 +332,8 @@ clean:
 
 supercleanfiles:
 	$(eval SUPERCLEAN_FILES := $(strip \
-			$(foreach ext,$(SUPERCLEAN_EXTS), $(shell find . -name '*$(ext)'))))
+			$(foreach ext,$(SUPERCLEAN_EXTS), $(shell find . -name '*$(ext)' \
+			-not -path './data/*'))))
 
 supercleanlist: supercleanfiles
 	@ \