Merge pull request #4645 from ClimbsRocks/patch-1
updates tense in docs

updates tense in docs
Merge pull request #4646 from ClimbsRocks/patch-2
fixes typo- duplicate "a a"
BVLC · jeffdonahue · jeffdonahue · jeffdonahue · intelfx · intelfx
Unified Split

Showing 351 changed files with 13,565 additions and 26,584 deletions.
diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
@@ -0,0 +1,19 @@
+Please use the [caffe-users list](https://groups.google.com/forum/#!forum/caffe-users) for usage, installation, or modeling questions, or other requests for help.
+_Do not post such requests to Issues._ Doing so interferes with the development of Caffe.
+
+Please read the [guidelines for contributing](https://github.com/BVLC/caffe/blob/master/CONTRIBUTING.md) before submitting this issue.
+
+### Issue summary
+
+
+### Steps to reproduce
+
+If you are having difficulty building Caffe or training a model, please ask the caffe-users mailing list. If you are reporting a build error that seems to be due to a bug in Caffe, please attach your build configuration (either Makefile.config or CMakeCache.txt) and the output of the make (or cmake) command.
+
+### Your system configuration
+Operating system:
+Compiler:
+CUDA version (if applicable):
+CUDNN version (if applicable):
+BLAS:
+Python or MATLAB version (for pycaffe and matcaffe respectively):
diff --git a/.gitignore b/.gitignore
@@ -47,6 +47,9 @@
 # PyCharm files
 .idea
 
+# Visual Studio Code files
+.vscode
+
 # OSX dir files
 .DS_Store
 
@@ -81,6 +84,7 @@ cmake_build
 
 # Generated documentation
 docs/_site
+docs/_includes
 docs/gathered
 _site
 doxygen
diff --git a/.travis.yml b/.travis.yml
@@ -1,40 +1,52 @@
-# Use a build matrix to do two builds in parallel:
-# one using CMake, and one using make.
+dist: trusty
+sudo: required
+
+language: cpp
+compiler: gcc
+
 env:
+  global:
+    - NUM_THREADS=4
   matrix:
-    - WITH_CUDA=false WITH_CMAKE=false WITH_IO=true
-    - WITH_CUDA=false WITH_CMAKE=true WITH_IO=true PYTHON_VERSION=3
-    - WITH_CUDA=true WITH_CMAKE=false WITH_IO=true
-    - WITH_CUDA=true WITH_CMAKE=true WITH_IO=true
-    - WITH_CUDA=false WITH_CMAKE=false WITH_IO=false
-    - WITH_CUDA=false WITH_CMAKE=true WITH_IO=false PYTHON_VERSION=3
+    # Use a build matrix to test many builds in parallel
+    # envvar defaults:
+    #   WITH_CMAKE: false
+    #   WITH_PYTHON3: false
+    #   WITH_IO: true
+    #   WITH_CUDA: false
+    #   WITH_CUDNN: false
+    - BUILD_NAME="default-make"
+#   - BUILD_NAME="python3-make" WITH_PYTHON3=true
+    - BUILD_NAME="no-io-make" WITH_IO=false
+    - BUILD_NAME="cuda-make" WITH_CUDA=true
+    - BUILD_NAME="cudnn-make" WITH_CUDA=true WITH_CUDNN=true
 
-language: cpp
+    - BUILD_NAME="default-cmake" WITH_CMAKE=true
+    - BUILD_NAME="python3-cmake" WITH_CMAKE=true WITH_PYTHON3=true
+    - BUILD_NAME="no-io-cmake" WITH_CMAKE=true WITH_IO=false
+    - BUILD_NAME="cuda-cmake" WITH_CMAKE=true WITH_CUDA=true
+    - BUILD_NAME="cudnn-cmake" WITH_CMAKE=true WITH_CUDA=true WITH_CUDNN=true
 
-# Cache Ubuntu apt packages.
 cache:
   apt: true
   directories:
-  - /home/travis/miniconda
-  - /home/travis/miniconda2
-  - /home/travis/miniconda3
-
-compiler: gcc
+    - ~/protobuf3
 
 before_install:
-  - export NUM_THREADS=4
-  - export SCRIPTS=./scripts/travis
-  - export CONDA_DIR="/home/travis/miniconda$PYTHON_VERSION"
+  - source ./scripts/travis/defaults.sh
 
 install:
-  - sudo -E $SCRIPTS/travis_install.sh
+  - sudo -E ./scripts/travis/install-deps.sh
+  - ./scripts/travis/setup-venv.sh ~/venv
+  - source ~/venv/bin/activate
+  - ./scripts/travis/install-python-deps.sh
 
 before_script:
-  - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib:/usr/local/cuda/lib64:$CONDA_DIR/lib
-  - export PATH=$CONDA_DIR/bin:$PATH
-  - if ! $WITH_CMAKE; then $SCRIPTS/travis_setup_makefile_config.sh; fi
+  - ./scripts/travis/configure.sh
 
-script: $SCRIPTS/travis_build_and_test.sh
+script:
+  - ./scripts/travis/build.sh
+  - ./scripts/travis/test.sh
 
 notifications:
 # Emails are sent to the committer's git-configured email address by default,
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -10,14 +10,15 @@ endif()
 project(Caffe C CXX)
 
 # ---[ Caffe version
-set(CAFFE_TARGET_VERSION "1.0.0-rc3")
-set(CAFFE_TARGET_SOVERSION "1.0.0-rc3")
+set(CAFFE_TARGET_VERSION "1.0.0" CACHE STRING "Caffe logical version")
+set(CAFFE_TARGET_SOVERSION "1.0.0" CACHE STRING "Caffe soname version")
 add_definitions(-DCAFFE_VERSION=${CAFFE_TARGET_VERSION})
 
 # ---[ Using cmake scripts and modules
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/Modules)
 
 include(ExternalProject)
+include(GNUInstallDirs)
 
 include(cmake/Utils.cmake)
 include(cmake/Targets.cmake)
@@ -28,6 +29,7 @@ include(cmake/ConfigGen.cmake)
 # ---[ Options
 caffe_option(CPU_ONLY  "Build Caffe without CUDA support" OFF) # TODO: rename to USE_CUDA
 caffe_option(USE_CUDNN "Build Caffe with cuDNN library support" ON IF NOT CPU_ONLY)
+caffe_option(USE_NCCL "Build Caffe with NCCL library support" OFF)
 caffe_option(BUILD_SHARED_LIBS "Build shared libraries" ON)
 caffe_option(BUILD_python "Build Python wrapper" ON)
 set(python_version "2" CACHE STRING "Specify which Python version to use")
@@ -38,6 +40,7 @@ caffe_option(USE_OPENCV "Build with OpenCV support" ON)
 caffe_option(USE_LEVELDB "Build with levelDB" ON)
 caffe_option(USE_LMDB "Build with lmdb" ON)
 caffe_option(ALLOW_LMDB_NOLOCK "Allow MDB_NOLOCK when reading LMDB files (only if necessary)" OFF)
+caffe_option(USE_OPENMP "Link with OpenMP (when your BLAS wants OpenMP and you get linker errors)" OFF)
 
 # ---[ Dependencies
 include(cmake/Dependencies.cmake)
@@ -47,13 +50,13 @@ if(UNIX OR APPLE)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -Wall")
 endif()
 
+caffe_set_caffe_link()
+
 if(USE_libstdcpp)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libstdc++")
   message("-- Warning: forcing libstdc++ (controlled by USE_libstdcpp option in cmake)")
 endif()
 
-add_definitions(-DGTEST_USE_OWN_TR1_TUPLE)
-
 # ---[ Warnings
 caffe_warnings_disable(CMAKE_CXX_FLAGS -Wno-sign-compare -Wno-uninitialized)
 
@@ -62,8 +65,26 @@ configure_file(cmake/Templates/caffe_config.h.in "${PROJECT_BINARY_DIR}/caffe_co
 
 # ---[ Includes
 set(Caffe_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/include)
-include_directories(${Caffe_INCLUDE_DIR} ${PROJECT_BINARY_DIR})
-include_directories(BEFORE src) # This is needed for gtest.
+set(Caffe_SRC_DIR ${PROJECT_SOURCE_DIR}/src)
+include_directories(${PROJECT_BINARY_DIR})
+
+# ---[ Includes & defines for CUDA
+
+# cuda_compile() does not have per-call dependencies or include pathes
+# (cuda_compile() has per-call flags, but we set them here too for clarity)
+#
+# list(REMOVE_ITEM ...) invocations remove PRIVATE and PUBLIC keywords from collected definitions and include pathes
+if(HAVE_CUDA)
+  # pass include pathes to cuda_include_directories()
+  set(Caffe_ALL_INCLUDE_DIRS ${Caffe_INCLUDE_DIRS})
+  list(REMOVE_ITEM Caffe_ALL_INCLUDE_DIRS PRIVATE PUBLIC)
+  cuda_include_directories(${Caffe_INCLUDE_DIR} ${Caffe_SRC_DIR} ${Caffe_ALL_INCLUDE_DIRS})
+
+  # add definitions to nvcc flags directly
+  set(Caffe_ALL_DEFINITIONS ${Caffe_DEFINITIONS})
+  list(REMOVE_ITEM Caffe_ALL_DEFINITIONS PRIVATE PUBLIC)
+  list(APPEND CUDA_NVCC_FLAGS ${Caffe_ALL_DEFINITIONS})
+endif()
 
 # ---[ Subdirectories
 add_subdirectory(src/gtest)
@@ -83,8 +104,19 @@ if(BUILD_python)
   add_dependencies(pytest pycaffe)
 endif()
 
+# ---[ uninstall target
+configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Uninstall.cmake.in
+    ${CMAKE_CURRENT_BINARY_DIR}/cmake/Uninstall.cmake
+    IMMEDIATE @ONLY)
+
+add_custom_target(uninstall
+    COMMAND ${CMAKE_COMMAND} -P
+    ${CMAKE_CURRENT_BINARY_DIR}/cmake/Uninstall.cmake)
+
 # ---[ Configuration summary
 caffe_print_configuration_summary()
 
 # ---[ Export configs generation
 caffe_generate_export_configs()
+
diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
@@ -1,6 +1,6 @@
 # Contributors
 
-Caffe is developed by a core set of BVLC members and the open-source community.
+Caffe is developed by a core set of BAIR members and the open-source community.
 
 We thank all of our [contributors](https://github.com/BVLC/caffe/graphs/contributors)!
 
diff --git a/LICENSE b/LICENSE
@@ -1,11 +1,11 @@
 COPYRIGHT
 
 All contributions by the University of California:
-Copyright (c) 2014, 2015, The Regents of the University of California (Regents)
+Copyright (c) 2014-2017 The Regents of the University of California (Regents)
 All rights reserved.
 
 All other contributions:
-Copyright (c) 2014, 2015, the respective contributors
+Copyright (c) 2014-2017, the respective contributors
 All rights reserved.
 
 Caffe uses a shared copyright model: each contributor holds copyright over
diff --git a/Makefile b/Makefile
@@ -34,7 +34,7 @@ LIB_BUILD_DIR := $(BUILD_DIR)/lib
 STATIC_NAME := $(LIB_BUILD_DIR)/lib$(LIBRARY_NAME).a
 DYNAMIC_VERSION_MAJOR 		:= 1
 DYNAMIC_VERSION_MINOR 		:= 0
-DYNAMIC_VERSION_REVISION 	:= 0-rc3
+DYNAMIC_VERSION_REVISION 	:= 0
 DYNAMIC_NAME_SHORT := lib$(LIBRARY_NAME).so
 #DYNAMIC_SONAME_SHORT := $(DYNAMIC_NAME_SHORT).$(DYNAMIC_VERSION_MAJOR)
 DYNAMIC_VERSIONED_NAME_SHORT := $(DYNAMIC_NAME_SHORT).$(DYNAMIC_VERSION_MAJOR).$(DYNAMIC_VERSION_MINOR).$(DYNAMIC_VERSION_REVISION)
@@ -192,12 +192,12 @@ ifeq ($(USE_LMDB), 1)
 	LIBRARIES += lmdb
 endif
 ifeq ($(USE_OPENCV), 1)
-	LIBRARIES += opencv_core opencv_highgui opencv_imgproc 
+	LIBRARIES += opencv_core opencv_highgui opencv_imgproc
 
 	ifeq ($(OPENCV_VERSION), 3)
 		LIBRARIES += opencv_imgcodecs
 	endif
-		
+
 endif
 PYTHON_LIBRARIES ?= boost_python python2.7
 WARNINGS := -Wall -Wno-sign-compare
@@ -248,6 +248,8 @@ ifeq ($(UNAME), Linux)
 	LINUX := 1
 else ifeq ($(UNAME), Darwin)
 	OSX := 1
+	OSX_MAJOR_VERSION := $(shell sw_vers -productVersion | cut -f 1 -d .)
+	OSX_MINOR_VERSION := $(shell sw_vers -productVersion | cut -f 2 -d .)
 endif
 
 # Linux
@@ -270,22 +272,29 @@ endif
 ifeq ($(OSX), 1)
 	CXX := /usr/bin/clang++
 	ifneq ($(CPU_ONLY), 1)
-		CUDA_VERSION := $(shell $(CUDA_DIR)/bin/nvcc -V | grep -o 'release \d' | grep -o '\d')
+		CUDA_VERSION := $(shell $(CUDA_DIR)/bin/nvcc -V | grep -o 'release [0-9.]*' | tr -d '[a-z ]')
 		ifeq ($(shell echo | awk '{exit $(CUDA_VERSION) < 7.0;}'), 1)
 			CXXFLAGS += -stdlib=libstdc++
 			LINKFLAGS += -stdlib=libstdc++
 		endif
 		# clang throws this warning for cuda headers
 		WARNINGS += -Wno-unneeded-internal-declaration
+		# 10.11 strips DYLD_* env vars so link CUDA (rpath is available on 10.5+)
+		OSX_10_OR_LATER   := $(shell [ $(OSX_MAJOR_VERSION) -ge 10 ] && echo true)
+		OSX_10_5_OR_LATER := $(shell [ $(OSX_MINOR_VERSION) -ge 5 ] && echo true)
+		ifeq ($(OSX_10_OR_LATER),true)
+			ifeq ($(OSX_10_5_OR_LATER),true)
+				LDFLAGS += -Wl,-rpath,$(CUDA_LIB_DIR)
+			endif
+		endif
 	endif
 	# gtest needs to use its own tuple to not conflict with clang
 	COMMON_FLAGS += -DGTEST_USE_OWN_TR1_TUPLE=1
 	# boost::thread is called boost_thread-mt to mark multithreading on OS X
 	LIBRARIES += boost_thread-mt
 	# we need to explicitly ask for the rpath to be obeyed
-	DYNAMIC_FLAGS := -install_name @rpath/libcaffe.so
 	ORIGIN := @loader_path
-	VERSIONFLAGS += -Wl,-install_name,$(DYNAMIC_VERSIONED_NAME_SHORT) -Wl,-rpath,$(ORIGIN)/../../build/lib
+	VERSIONFLAGS += -Wl,-install_name,@rpath/$(DYNAMIC_VERSIONED_NAME_SHORT) -Wl,-rpath,$(ORIGIN)/../../build/lib
 else
 	ORIGIN := \$$ORIGIN
 endif
@@ -319,6 +328,12 @@ ifeq ($(USE_CUDNN), 1)
 	COMMON_FLAGS += -DUSE_CUDNN
 endif
 
+# NCCL acceleration configuration
+ifeq ($(USE_NCCL), 1)
+	LIBRARIES += nccl
+	COMMON_FLAGS += -DUSE_NCCL
+endif
+
 # configure IO libraries
 ifeq ($(USE_OPENCV), 1)
 	COMMON_FLAGS += -DUSE_OPENCV
@@ -355,9 +370,9 @@ ifeq ($(BLAS), mkl)
 	# MKL
 	LIBRARIES += mkl_rt
 	COMMON_FLAGS += -DUSE_MKL
-	MKL_DIR ?= /opt/intel/mkl
-	BLAS_INCLUDE ?= $(MKL_DIR)/include
-	BLAS_LIB ?= $(MKL_DIR)/lib $(MKL_DIR)/lib/intel64
+	MKLROOT ?= /opt/intel/mkl
+	BLAS_INCLUDE ?= $(MKLROOT)/include
+	BLAS_LIB ?= $(MKLROOT)/lib $(MKLROOT)/lib/intel64
 else ifeq ($(BLAS), open)
 	# OpenBLAS
 	LIBRARIES += openblas
@@ -373,8 +388,11 @@ else
 		LIBRARIES += cblas
 		# 10.10 has accelerate while 10.9 has veclib
 		XCODE_CLT_VER := $(shell pkgutil --pkg-info=com.apple.pkg.CLTools_Executables | grep 'version' | sed 's/[^0-9]*\([0-9]\).*/\1/')
+		XCODE_CLT_GEQ_7 := $(shell [ $(XCODE_CLT_VER) -gt 6 ] && echo 1)
 		XCODE_CLT_GEQ_6 := $(shell [ $(XCODE_CLT_VER) -gt 5 ] && echo 1)
-		ifeq ($(XCODE_CLT_GEQ_6), 1)
+		ifeq ($(XCODE_CLT_GEQ_7), 1)
+			BLAS_INCLUDE ?= /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/$(shell ls /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/ | sort | tail -1)/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/Headers
+		else ifeq ($(XCODE_CLT_GEQ_6), 1)
 			BLAS_INCLUDE ?= /System/Library/Frameworks/Accelerate.framework/Versions/Current/Frameworks/vecLib.framework/Headers/
 			LDFLAGS += -framework Accelerate
 		else
@@ -552,7 +570,7 @@ $(ALL_BUILD_DIRS): | $(BUILD_DIR_LINK)
 
 $(DYNAMIC_NAME): $(OBJS) | $(LIB_BUILD_DIR)
 	@ echo LD -o $@
-	$(Q)$(CXX) -shared -o $@ $(OBJS) $(VERSIONFLAGS) $(LINKFLAGS) $(LDFLAGS) $(DYNAMIC_FLAGS)
+	$(Q)$(CXX) -shared -o $@ $(OBJS) $(VERSIONFLAGS) $(LINKFLAGS) $(LDFLAGS)
 	@ cd $(BUILD_DIR)/lib; rm -f $(DYNAMIC_NAME_SHORT);   ln -s $(DYNAMIC_VERSIONED_NAME_SHORT) $(DYNAMIC_NAME_SHORT)
 
 $(STATIC_NAME): $(OBJS) | $(LIB_BUILD_DIR)
diff --git a/Makefile.config.example b/Makefile.config.example
@@ -31,13 +31,17 @@ CUDA_DIR := /usr/local/cuda
 # CUDA_DIR := /usr
 
 # CUDA architecture setting: going with all of them.
-# For CUDA < 6.0, comment the *_50 lines for compatibility.
+# For CUDA < 6.0, comment the *_50 through *_61 lines for compatibility.
+# For CUDA < 8.0, comment the *_60 and *_61 lines for compatibility.
 CUDA_ARCH := -gencode arch=compute_20,code=sm_20 \
 		-gencode arch=compute_20,code=sm_21 \
 		-gencode arch=compute_30,code=sm_30 \
 		-gencode arch=compute_35,code=sm_35 \
 		-gencode arch=compute_50,code=sm_50 \
-		-gencode arch=compute_50,code=compute_50
+		-gencode arch=compute_52,code=sm_52 \
+		-gencode arch=compute_60,code=sm_60 \
+		-gencode arch=compute_61,code=sm_61 \
+		-gencode arch=compute_61,code=compute_61
 
 # BLAS choice:
 # atlas for ATLAS (default)
@@ -68,7 +72,7 @@ PYTHON_INCLUDE := /usr/include/python2.7 \
 # ANACONDA_HOME := $(HOME)/anaconda
 # PYTHON_INCLUDE := $(ANACONDA_HOME)/include \
 		# $(ANACONDA_HOME)/include/python2.7 \
-		# $(ANACONDA_HOME)/lib/python2.7/site-packages/numpy/core/include \
+		# $(ANACONDA_HOME)/lib/python2.7/site-packages/numpy/core/include
 
 # Uncomment to use Python 3 (default is Python 2)
 # PYTHON_LIBRARIES := boost_python3 python3.5m
@@ -94,10 +98,15 @@ LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib
 # INCLUDE_DIRS += $(shell brew --prefix)/include
 # LIBRARY_DIRS += $(shell brew --prefix)/lib
 
+# NCCL acceleration switch (uncomment to build with NCCL)
+# https://github.com/NVIDIA/nccl (last tested version: v1.2.3-1+cuda8.0)
+# USE_NCCL := 1
+
 # Uncomment to use `pkg-config` to specify OpenCV library paths.
 # (Usually not necessary -- OpenCV libraries are normally installed in one of the above $LIBRARY_DIRS.)
 # USE_PKG_CONFIG := 1
 
+# N.B. both build and distribute dirs are cleared on `make clean`
 BUILD_DIR := build
 DISTRIBUTE_DIR := distribute