diff --git a/CMakeLists.txt b/CMakeLists.txt
index 784876f0899c6c280b057bf75570a7366bd094bb..9ed757bd1bfbd23ca24445c15e7cf8e13860d26f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,18 @@
-cmake_minimum_required(VERSION 2.8)
+# Copyright (c) 2016 PaddlePaddle Authors. All Rights Reserve.
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License
+
+cmake_minimum_required(VERSION 3.0)
 
 project(paddle CXX C)
 
@@ -6,11 +20,11 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake")
 set(PROJ_ROOT ${CMAKE_SOURCE_DIR})
 
 find_package(Sphinx)
-find_package(Doxygen)
 find_package(CUDA QUIET)
 find_package(Git REQUIRED)
 find_package(Threads REQUIRED)
 
+include(system)
 include(simd)
 
 ###################### Configurations ############################
@@ -35,9 +49,8 @@ include(external/gflags)    # download, build, install gflags
 include(external/glog)      # download, build, install glog
 include(external/gtest)     # download, build, install gtest
 include(external/protobuf)  # download, build, install protobuf
-include(external/openblas)  # download, build, install openblas
 include(external/python)    # download, build, install python
-include(external/numpy)     # download, build, install numpy
+include(external/openblas)  # download, build, install openblas
 include(external/swig)      # download, build, install swig
 include(external/warpctc)   # download, build, install warpctc
 
@@ -52,8 +65,7 @@ include(version)            # set PADDLE_VERSION
 include(coveralls)          # set code coverage
 include(python_module)      # set python module
 
-include(check_packages)     # check configuration
-include(definitions)        # add paddle definitions
+include(configure)          # add paddle env configuration
 
 include_directories("${PROJ_ROOT}")
 include_directories("${PROJ_ROOT}/paddle/cuda/include")
@@ -64,7 +76,7 @@ set(EXTERNAL_LIBS
     ${GFLAGS_LIBRARIES}
     ${GLOG_LIBRARIES}
     ${CBLAS_LIBRARIES}
-    ${PROTOBUF_LIBRARIES}
+    ${PROTOBUF_LIBRARY}
     ${ZLIB_LIBRARIES}
 )
 
diff --git a/cmake/cblas.cmake b/cmake/cblas.cmake
index 685334c6585060c0344e552c6f3fda2c7324de03..4e1ae7dc81231943c4bf3db4d4ac6f073f4fd1c4 100644
--- a/cmake/cblas.cmake
+++ b/cmake/cblas.cmake
@@ -13,6 +13,7 @@
 # system paths.
 #
 
+set(CBLAS_FOUND OFF)
 
 ## Find MKL First.
 set(MKL_ROOT $ENV{MKL_ROOT} CACHE PATH "Folder contains MKL")
@@ -35,11 +36,12 @@ find_library(MKL_INTEL_LP64 NAMES mkl_intel_lp64 PATHS
 if(MKL_INCLUDE_DIR AND MKL_CORE_LIB AND MKL_SEQUENTIAL_LIB AND MKL_INTEL_LP64)
   set(CBLAS_PROVIDER MKL)
   set(CBLAS_INC_DIR ${MKL_INCLUDE_DIR})
-  set(CBLAS_LIBS ${MKL_INTEL_LP64}
+  set(CBLAS_LIBRARIES ${MKL_INTEL_LP64}
           ${MKL_SEQUENTIAL_LIB}
           ${MKL_CORE_LIB})
   add_definitions(-DPADDLE_USE_MKL)
-  message(STATUS "Found MKL (include: ${CBLAS_INC_DIR}, library: ${CBLAS_LIBS})")
+  message(STATUS "Found MKL (include: ${CBLAS_INC_DIR}, library: ${CBLAS_LIBRARIES})")
+  set(CBLAS_FOUND ON)
   return() # return file.
 endif()
 
@@ -68,9 +70,10 @@ find_library(ATLAS_LIB NAMES lapack_atlas liblapack_atlas.so.3
 if(ATLAS_INC_DIR AND ATLAS_CBLAS_LIB AND ATLAS_LIB)
   set(CBLAS_PROVIDER ATLAS)
   set(CBLAS_INC_DIR ${ATLAS_INC_DIR} ${ATLAS_CLAPACK_INC_DIR})
-  set(CBLAS_LIBS ${ATLAS_LIB} ${ATLAS_CBLAS_LIB})
+  set(CBLAS_LIBRARIES ${ATLAS_LIB} ${ATLAS_CBLAS_LIB})
   add_definitions(-DPADDLE_USE_ATLAS)  
-  message(STATUS "Found Atlas (include: ${CBLAS_INC_DIR}, library: ${CBLAS_LIBS})")
+  message(STATUS "Found Atlas (include: ${CBLAS_INC_DIR}, library: ${CBLAS_LIBRARIES})")
+  set(CBLAS_FOUND ON)
   return()
 endif()
 
@@ -98,8 +101,9 @@ find_library(OPENBLAS_LIB NAMES openblas
 if(OPENBLAS_INC_DIR AND OPENBLAS_LIB)
   set(CBLAS_PROVIDER OPENBLAS)
   set(CBLAS_INC_DIR ${OPENBLAS_INC_DIR})
-  set(CBLAS_LIBS ${OPENBLAS_LIB})
-  message(STATUS "Found OpenBlas (include: ${CBLAS_INC_DIR}, library: ${CBLAS_LIBS})")
+  set(CBLAS_LIBRARIES ${OPENBLAS_LIB})
+  message(STATUS "Found OpenBlas (include: ${CBLAS_INC_DIR}, library: ${CBLAS_LIBRARIES})")
+  set(CBLAS_FOUND ON)
   return()
 endif()
 
@@ -130,9 +134,7 @@ find_library(REFERENCE_CBLAS_LIBRARY NAMES cblas PATHS
 if (REFERENCE_CBLAS_INCLUDE_DIR AND REFERENCE_CBLAS_LIBRARY)
   set(CBLAS_PROVIDER REFERENCE)
   set(CBLAS_INC_DIR ${REFERENCE_CBLAS_INCLUDE_DIR})
-  set(CBLAS_LIBS ${REFERENCE_CBLAS_LIBRARY})
-  return()
+  set(CBLAS_LIBRARIES ${REFERENCE_CBLAS_LIBRARY})
+  message(STATUS "Found reference-cblas (include: ${CBLAS_INC_DIR}, library: ${CBLAS_LIBS})")
+  set(CBLAS_FOUND ON)
 endif()
-
-message(FATAL_ERROR "CBlas must be set. Paddle support MKL, ATLAS, OpenBlas, reference-cblas."
-  " Try set MKL_ROOT, ATLAS_ROOT, OPENBLAS_ROOT or REFERENCE_CBLAS_ROOT.")
diff --git a/cmake/check_packages.cmake b/cmake/check_packages.cmake
deleted file mode 100644
index 8f0ed26256650cdc608690bc249f055fa44487aa..0000000000000000000000000000000000000000
--- a/cmake/check_packages.cmake
+++ /dev/null
@@ -1,14 +0,0 @@
-# Check package for each cmake option
-
-if(WITH_GPU)
-  find_package(CUDA REQUIRED)  # CUDA is required when use gpu
-endif(WITH_GPU)
-
-if(WITH_DOC)
-  find_package(Sphinx REQUIRED)
-  find_python_module(recommonmark REQUIRED)
-endif(WITH_DOC)
-
-if(WITH_SWIG_PY)
-  find_python_module(wheel REQUIRED)  # package wheel
-endif(WITH_SWIG_PY)
diff --git a/cmake/cpplint.cmake b/cmake/cpplint.cmake
index 241af9a0835b2f100c8fb8b246426e631e42aef3..38c636b30edc0af1c07255814e8bc2b1ad9514da 100644
--- a/cmake/cpplint.cmake
+++ b/cmake/cpplint.cmake
@@ -53,7 +53,7 @@ macro(add_style_check_target TARGET_NAME)
             if(LINT MATCHES ON)
                 add_custom_command(TARGET ${TARGET_NAME}
                     PRE_BUILD
-                    COMMAND "${PYTHON_EXECUTABLE}" "${PROJ_ROOT}/paddle/scripts/cpplint.py"
+                    COMMAND env ${py_env} "${PYTHON_EXECUTABLE}" "${PROJ_ROOT}/paddle/scripts/cpplint.py"
                                 "--filter=${STYLE_FILTER}" ${filename}
                     WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR})
             endif()
diff --git a/cmake/definitions.cmake b/cmake/definitions.cmake
deleted file mode 100644
index 99a52ad764b902f7ffbf87ea00b84a7e804919d0..0000000000000000000000000000000000000000
--- a/cmake/definitions.cmake
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright (c) 2016 PaddlePaddle Authors. All Rights Reserve.
-# 
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-# 
-# http://www.apache.org/licenses/LICENSE-2.0
-# 
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-if(WITH_DSO)
-    add_definitions(-DPADDLE_USE_DSO)
-endif(WITH_DSO)
-
-if(WITH_DOUBLE)
-    add_definitions(-DPADDLE_TYPE_DOUBLE)
-endif(WITH_DOUBLE)
-
-if(NOT WITH_TIMER)
-    add_definitions(-DPADDLE_DISABLE_TIMER)
-endif(NOT WITH_TIMER)
-
-if(NOT WITH_PROFILER)
-    add_definitions(-DPADDLE_DISABLE_PROFILER)
-endif(NOT WITH_PROFILER)
-
-if(NOT WITH_GPU)
-    add_definitions(-DPADDLE_ONLY_CPU)
-    add_definitions(-DHPPL_STUB_FUNC)
-
-    list(APPEND CMAKE_CXX_SOURCE_FILE_EXTENSIONS cu)
-else()
-    if(${CUDA_VERSION_MAJOR} VERSION_LESS 7)
-        message(FATAL_ERROR "Paddle need CUDA >= 7.0 to compile")
-    endif()
-
-    if(NOT CUDNN_FOUND)
-        message(FATAL_ERROR "Paddle need cudnn to compile")
-    endif()
-
-    if(WITH_AVX)
-        set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} "-Xcompiler ${AVX_FLAG}")
-    else(WITH_AVX)
-        set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} "-Xcompiler ${SSE3_FLAG}")
-    endif(WITH_AVX)
-
-    # Include cuda and cudnn
-    include_directories(${CUDNN_INCLUDE_DIR})
-    include_directories(${CUDA_TOOLKIT_INCLUDE})
-endif(NOT WITH_GPU)
-
-if(WITH_AVX)
-    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${AVX_FLAG}")
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${AVX_FLAG}")
-else(WITH_AVX)
-    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${SSE3_FLAG}")
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SSE3_FLAG}")
-endif(WITH_AVX)
diff --git a/cmake/util.cmake b/cmake/util.cmake
index b8d20266f4bcfdfd1c3ffeb959a9305d55c9190c..c9b48e5f8fc3bcb2160b9f999cb36886ae479f94 100644
--- a/cmake/util.cmake
+++ b/cmake/util.cmake
@@ -24,7 +24,7 @@ function(target_circle_link_libraries TARGET_NAME)
                 list(APPEND libsInArgn ${arg})
             endif()
         endforeach()
-        if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+        if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang" OR "${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang")
             list(APPEND LIBS "-undefined dynamic_lookup")
         endif()
         list(REVERSE libsInArgn)
@@ -105,7 +105,7 @@ function(link_paddle_exe TARGET_NAME)
 
     if(WITH_PYTHON)
         target_link_libraries(${TARGET_NAME}
-            ${PYTHON_LIBRARIES})
+            ${PYTHON_LIBRARIES} util)
     endif()
 
     if(WITH_GPU)
diff --git a/paddle/cuda/CMakeLists.txt b/paddle/cuda/CMakeLists.txt
index 0a058978540a4549652b8afb7e9cec9e0ca08f14..57fb89608f4bcf3e6829fe850a61c2a626adfbdc 100755
--- a/paddle/cuda/CMakeLists.txt
+++ b/paddle/cuda/CMakeLists.txt
@@ -88,7 +88,7 @@ else()
                 ${CUDA_CXX_SOURCES})
 endif()
 
-add_dependencies(paddle_cuda warpctc)
+add_dependencies(paddle_cuda ${external_project_dependencies})
 
 add_style_check_target(paddle_cuda
                        ${CUDA_SOURCES}