diff --git a/.gitignore b/.gitignore
index 2badc3bdaa52f2608183fa34393719be66630654..9e3a0b499f9f42856429f3a42bef313ea3df3699 100644
--- a/.gitignore
+++ b/.gitignore
@@ -25,12 +25,3 @@ third_party/
 
 # clion workspace.
 cmake-build-*
-
-# generated while compiling
-paddle/pybind/pybind.h
-CMakeFiles
-cmake_install.cmake
-paddle/.timestamp
-python/paddlepaddle.egg-info/
-paddle/fluid/pybind/pybind.h
-python/paddle/version.py
diff --git a/cmake/generic.cmake b/cmake/generic.cmake
index 3fe750f47efc149bb1af6086841bffd5dd8e85fd..e8bc285bdc95e213b9da2ee388078349a46d2798 100644
--- a/cmake/generic.cmake
+++ b/cmake/generic.cmake
@@ -251,7 +251,7 @@ function(cc_test TARGET_NAME)
     add_dependencies(${TARGET_NAME} ${cc_test_DEPS} paddle_gtest_main paddle_memory gtest gflags glog)
     add_test(NAME ${TARGET_NAME}
              COMMAND ${TARGET_NAME} ${cc_test_ARGS}
-             WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
   endif()
 endfunction(cc_test)
 
@@ -561,9 +561,9 @@ function(py_test TARGET_NAME)
     set(multiValueArgs SRCS DEPS ARGS ENVS)
     cmake_parse_arguments(py_test "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
     add_test(NAME ${TARGET_NAME}
-             COMMAND env PYTHONPATH=${PADDLE_PYTHON_BUILD_DIR}/lib-python ${py_test_ENVS}
+             COMMAND env PYTHONPATH=${PADDLE_BINARY_DIR}/python ${py_test_ENVS}
              ${PYTHON_EXECUTABLE} -u ${py_test_SRCS} ${py_test_ARGS}
-             WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
   endif()
 endfunction()
 
diff --git a/doc/fluid/CMakeLists.txt b/doc/fluid/CMakeLists.txt
index 9fe79323ef9377a459d8405cfa74c88c52ce9346..8086507bb4b7e870ad6d6091945ed07a00b5100b 100644
--- a/doc/fluid/CMakeLists.txt
+++ b/doc/fluid/CMakeLists.txt
@@ -27,7 +27,7 @@ sphinx_add_target(paddle_fluid_docs
                   ${CMAKE_CURRENT_SOURCE_DIR}
                   ${SPHINX_HTML_DIR_EN})
 
-add_dependencies(paddle_fluid_docs gen_proto_py)
+add_dependencies(paddle_fluid_docs gen_proto_py paddle_python)
 
 # configured documentation tools and intermediate build results
 set(BINARY_BUILD_DIR_CN "${CMAKE_CURRENT_BINARY_DIR}/cn/_build")
@@ -50,6 +50,6 @@ sphinx_add_target(paddle_fluid_docs_cn
                   ${CMAKE_CURRENT_SOURCE_DIR}
                   ${SPHINX_HTML_DIR_CN})
 
-add_dependencies(paddle_fluid_docs_cn gen_proto_py)
+add_dependencies(paddle_fluid_docs_cn gen_proto_py paddle_python)
 
 add_subdirectory(api)
diff --git a/doc/fluid/api/CMakeLists.txt b/doc/fluid/api/CMakeLists.txt
index ca40dfb9644cea69329be0ec231378506c138bc0..48b396f0786adad1ba6cd41f72497f853e54bc38 100644
--- a/doc/fluid/api/CMakeLists.txt
+++ b/doc/fluid/api/CMakeLists.txt
@@ -19,4 +19,4 @@ sphinx_add_target(paddle_fluid_apis
                   ${CMAKE_CURRENT_SOURCE_DIR}
                   ${SPHINX_HTML_DIR_EN})
 
-add_dependencies(paddle_fluid_apis  gen_proto_py framework_py_proto copy_paddle_pybind)
+add_dependencies(paddle_fluid_apis  gen_proto_py framework_py_proto copy_paddle_pybind paddle_python)
diff --git a/doc/templates/conf.py.cn.in b/doc/templates/conf.py.cn.in
index 260b6c9fd1b364433cae098bacea77aa7fe9e266..76b82fd97f1ed642696c4414676b694ebda9ad81 100644
--- a/doc/templates/conf.py.cn.in
+++ b/doc/templates/conf.py.cn.in
@@ -13,7 +13,7 @@
 # serve to show the default.
 import sys
 import os, subprocess
-sys.path.insert(0, os.path.abspath('@PADDLE_SOURCE_DIR@/python'))
+sys.path.insert(0, os.path.abspath('@PADDLE_BINARY_DIR@/python'))
 import shlex
 from recommonmark import parser, transform
 import paddle
diff --git a/doc/templates/conf.py.en.in b/doc/templates/conf.py.en.in
index e5757b86b43001bc6090d8edd0aaa5ff4fc476ee..5aa5c1381fa3fad4ebc181c7868da03ae0138016 100644
--- a/doc/templates/conf.py.en.in
+++ b/doc/templates/conf.py.en.in
@@ -13,7 +13,7 @@
 # serve to show the default.
 import sys
 import os, subprocess
-sys.path.insert(0, os.path.abspath('@PADDLE_SOURCE_DIR@/python'))
+sys.path.insert(0, os.path.abspath('@PADDLE_BINARY_DIR@/python'))
 import shlex
 from recommonmark import parser, transform
 import paddle
diff --git a/doc/v2/CMakeLists.txt b/doc/v2/CMakeLists.txt
index 82de7a3a3e1ca7724e1eda877d53454a4fa4129a..be957d37b14c618e9346251b3bd3dbaf1541773f 100644
--- a/doc/v2/CMakeLists.txt
+++ b/doc/v2/CMakeLists.txt
@@ -27,7 +27,7 @@ sphinx_add_target(paddle_v2_docs
                   ${CMAKE_CURRENT_SOURCE_DIR}
                   ${SPHINX_HTML_DIR_EN})
 
-add_dependencies(paddle_v2_docs gen_proto_py)
+add_dependencies(paddle_v2_docs gen_proto_py paddle_python)
 
 # configured documentation tools and intermediate build results
 set(BINARY_BUILD_DIR_CN "${CMAKE_CURRENT_BINARY_DIR}/cn/_build")
@@ -50,6 +50,6 @@ sphinx_add_target(paddle_v2_docs_cn
                   ${CMAKE_CURRENT_SOURCE_DIR}
                   ${SPHINX_HTML_DIR_CN})
 
-add_dependencies(paddle_v2_docs_cn gen_proto_py)
+add_dependencies(paddle_v2_docs_cn gen_proto_py paddle_python)
 
 add_subdirectory(api)
diff --git a/doc/v2/api/CMakeLists.txt b/doc/v2/api/CMakeLists.txt
index da1eafc02ed8cd155d4f0f1fbadcb7b237b6fcc1..2670a21a227546ffcee4f10f395feef3c58df9b4 100644
--- a/doc/v2/api/CMakeLists.txt
+++ b/doc/v2/api/CMakeLists.txt
@@ -19,4 +19,4 @@ sphinx_add_target(paddle_v2_apis
                   ${CMAKE_CURRENT_SOURCE_DIR}
                   ${SPHINX_HTML_DIR_EN})
 
-add_dependencies(paddle_v2_apis  gen_proto_py framework_py_proto copy_paddle_pybind)
+add_dependencies(paddle_v2_apis  gen_proto_py framework_py_proto copy_paddle_pybind paddle_python)
diff --git a/paddle/api/CMakeLists.txt b/paddle/api/CMakeLists.txt
index cf84568ecdf1227b0d0ed3606a4a9a6e5186af72..06e1f5d5f0884efabfcdf917ca5c35d94ad5dce9 100644
--- a/paddle/api/CMakeLists.txt
+++ b/paddle/api/CMakeLists.txt
@@ -89,16 +89,17 @@ SWIG_LINK_LIBRARIES(swig_paddle
     ${START_END}
 )
 
-add_custom_command(OUTPUT ${PADDLE_SOURCE_DIR}/paddle/py_paddle/_swig_paddle.so
-    COMMAND cp ${CMAKE_CURRENT_BINARY_DIR}/swig_paddle.py ${PADDLE_SOURCE_DIR}/paddle/py_paddle
-    COMMAND cp ${CMAKE_CURRENT_BINARY_DIR}/_swig_paddle.so ${PADDLE_SOURCE_DIR}/paddle/py_paddle
-    COMMAND ${CMAKE_COMMAND} -E touch .timestamp
+add_custom_command(OUTPUT ${PADDLE_BINARY_DIR}/python/py_paddle/_swig_paddle.so
+    COMMAND ${CMAKE_COMMAND} -E make_directory ${PADDLE_BINARY_DIR}/python/py_paddle
+    COMMAND cp ${CMAKE_CURRENT_BINARY_DIR}/swig_paddle.py ${PADDLE_BINARY_DIR}/python/py_paddle
+    COMMAND cp ${CMAKE_CURRENT_BINARY_DIR}/_swig_paddle.so ${PADDLE_BINARY_DIR}/python/py_paddle
+    COMMAND ${CMAKE_COMMAND} -E touch ${PADDLE_BINARY_DIR}/.timestamp
     WORKING_DIRECTORY ${PADDLE_SOURCE_DIR}/paddle
     DEPENDS _swig_paddle
 )
 
 # TODO(yuyang18) : make wheel name calculated by cmake
-add_custom_target(python_api_wheel ALL DEPENDS ${PADDLE_SOURCE_DIR}/paddle/py_paddle/_swig_paddle.so)
+add_custom_target(python_api_wheel ALL DEPENDS ${PADDLE_BINARY_DIR}/python/py_paddle/_swig_paddle.so)
 
 if(WITH_TESTING)
     IF(NOT PY_PIP_FOUND)
diff --git a/paddle/api/test/CMakeLists.txt b/paddle/api/test/CMakeLists.txt
index 761aeb5b174105edece8880a9f5012c13a63fd11..13cb79129cc2272d215cdb475fb146b37266699e 100644
--- a/paddle/api/test/CMakeLists.txt
+++ b/paddle/api/test/CMakeLists.txt
@@ -1,3 +1,8 @@
+add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/testTrain.py
+    COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/*.py ${CMAKE_CURRENT_BINARY_DIR}
+)
+add_custom_target(copy_api_test ALL DEPENDS testTrain.py)
+
 py_test(testTrain SRCS testTrain.py)
 py_test(testMatrix SRCS testMatrix.py)
 py_test(testVector SRCS testVector.py)
diff --git a/paddle/fluid/framework/CMakeLists.txt b/paddle/fluid/framework/CMakeLists.txt
index c425c71160a8fa3830a5fbdae1baaed850710877..a473ed7400012b7d0cbc5ab9bed263b3cca8c6ec 100644
--- a/paddle/fluid/framework/CMakeLists.txt
+++ b/paddle/fluid/framework/CMakeLists.txt
@@ -74,8 +74,8 @@ py_proto_compile(framework_py_proto SRCS framework.proto)
 add_custom_target(framework_py_proto_init ALL COMMAND ${CMAKE_COMMAND} -E touch __init__.py)
 add_dependencies(framework_py_proto framework_py_proto_init)
 add_custom_command(TARGET framework_py_proto POST_BUILD
-    COMMAND ${CMAKE_COMMAND} -E make_directory ${PADDLE_SOURCE_DIR}/python/paddle/fluid/proto
-    COMMAND cp *.py ${PADDLE_SOURCE_DIR}/python/paddle/fluid/proto/
+    COMMAND ${CMAKE_COMMAND} -E make_directory ${PADDLE_BINARY_DIR}/python/paddle/fluid/proto
+    COMMAND cp *.py ${PADDLE_BINARY_DIR}/python/paddle/fluid/proto/
     COMMENT "Copy generated python proto into directory paddle/fluid/proto."
     WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
 
diff --git a/paddle/fluid/inference/tests/book/CMakeLists.txt b/paddle/fluid/inference/tests/book/CMakeLists.txt
index e7ffb00ec8d8926193fe510ebdb7185f75c90906..6ed77adb9d891c75e7de358d0d7a0c06c9af96dd 100644
--- a/paddle/fluid/inference/tests/book/CMakeLists.txt
+++ b/paddle/fluid/inference/tests/book/CMakeLists.txt
@@ -4,7 +4,7 @@ function(inference_test TARGET_NAME)
   set(multiValueArgs ARGS)
   cmake_parse_arguments(inference_test "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
 
-  set(PYTHON_TESTS_DIR ${PADDLE_SOURCE_DIR}/python/paddle/fluid/tests)
+  set(PYTHON_TESTS_DIR ${PADDLE_BINARY_DIR}/python/paddle/fluid/tests)
   set(arg_list "")
   if(inference_test_ARGS)
     foreach(arg ${inference_test_ARGS})
diff --git a/paddle/fluid/operators/CMakeLists.txt b/paddle/fluid/operators/CMakeLists.txt
index 952ac8b1dcf9221d0e5718cc073f1e390176e5a2..84eabab563e3404ad2a28bf76116c592db04742e 100644
--- a/paddle/fluid/operators/CMakeLists.txt
+++ b/paddle/fluid/operators/CMakeLists.txt
@@ -3,8 +3,8 @@ string(REPLACE "_mkldnn" "" GENERAL_OPS "${GENERAL_OPS}")
 string(REPLACE ".cc" "" GENERAL_OPS "${GENERAL_OPS}")
 list(REMOVE_DUPLICATES GENERAL_OPS)
 set(DEPS_OPS "")
-set(pybind_file ${PADDLE_SOURCE_DIR}/paddle/fluid/pybind/pybind.h)
-file(WRITE ${pybind_file} "// Generated by the paddle/operator/CMakeLists.txt.  DO NOT EDIT!\n\n")
+set(pybind_file ${PADDLE_BINARY_DIR}/paddle/fluid/pybind/pybind.h)
+file(WRITE ${pybind_file} "// Generated by the paddle/fluid/operator/CMakeLists.txt.  DO NOT EDIT!\n\n")
 function(op_library TARGET)
     # op_library is a function to create op library. The interface is same as
     # cc_library. But it handle split GPU/CPU code and link some common library
diff --git a/paddle/fluid/platform/CMakeLists.txt b/paddle/fluid/platform/CMakeLists.txt
index 686c0889140f0050b37192542ca98e2f3e5f23df..6780b8cc6deca64e9eaefa0b40d309449e730c8c 100644
--- a/paddle/fluid/platform/CMakeLists.txt
+++ b/paddle/fluid/platform/CMakeLists.txt
@@ -6,8 +6,8 @@ add_custom_target(profiler_py_proto_init ALL COMMAND ${CMAKE_COMMAND} -E touch _
 add_dependencies(profiler_py_proto profiler_py_proto_init)
 
 add_custom_command(TARGET profiler_py_proto POST_BUILD
-        COMMAND ${CMAKE_COMMAND} -E make_directory ${PADDLE_SOURCE_DIR}/python/paddle/fluid/proto/profiler
-        COMMAND cp *.py ${PADDLE_SOURCE_DIR}/python/paddle/fluid/proto/profiler
+        COMMAND ${CMAKE_COMMAND} -E make_directory ${PADDLE_BINARY_DIR}/python/paddle/fluid/proto/profiler
+        COMMAND cp *.py ${PADDLE_BINARY_DIR}/python/paddle/fluid/proto/profiler
         COMMENT "Copy generated python proto into directory paddle/fluid/proto/profiler."
         WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
 
diff --git a/paddle/gserver/tests/CMakeLists.txt b/paddle/gserver/tests/CMakeLists.txt
index 9839375c22e2c64e002255752c22224fc6bbb24e..9d7cad7584d1defefe38bdd4d041b98bd9e45bf0 100644
--- a/paddle/gserver/tests/CMakeLists.txt
+++ b/paddle/gserver/tests/CMakeLists.txt
@@ -14,6 +14,11 @@ function(gserver_test TARGET)
       COMMAND ${TARGET})
 endfunction()
 
+add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/concat_dotmul_a.conf
+    COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/* ${CMAKE_CURRENT_BINARY_DIR}
+)
+add_custom_target(copy_gserver_conf ALL DEPENDS concat_dotmul_a.conf)
+
 gserver_test(test_LayerGrad)
 gserver_test(test_CRFLayerGrad)
 gserver_test(test_CrossEntropyOverBeamGrad)
@@ -31,12 +36,12 @@ gserver_test(test_Upsample)
 
 set(PYTHON_PATH 
    ${PADDLE_SOURCE_DIR}/paddle/.set_python_path.sh -d 
-   ${PADDLE_SOURCE_DIR}/python/:${PADDLE_SOURCE_DIR}/paddle/gserver/tests)
+   ${PADDLE_BINARY_DIR}/python/:${PADDLE_BINARY_DIR}/paddle/gserver/tests)
 function(gserver_test_with_python TARGET)
   add_unittest_without_exec(${TARGET} ${TARGET}.cpp)
   add_test(NAME ${TARGET}
     COMMAND ${PYTHON_PATH} ${CMAKE_CURRENT_BINARY_DIR}/${TARGET}
-      WORKING_DIRECTORY ${PADDLE_SOURCE_DIR}/paddle/)
+      WORKING_DIRECTORY ${PADDLE_BINARY_DIR}/paddle/)
 endfunction()
 
 gserver_test_with_python(test_PyDataProvider2)
@@ -57,7 +62,7 @@ if(WITH_MKLDNN)
         LayerGradUtil.cpp)
     add_test(NAME test_MKLDNN
         COMMAND ${PYTHON_PATH} ${CMAKE_CURRENT_BINARY_DIR}/test_MKLDNN
-            WORKING_DIRECTORY ${PADDLE_SOURCE_DIR}/paddle)
+            WORKING_DIRECTORY ${PADDLE_BINARY_DIR}/paddle)
 endif()
 
 ############### test_WarpCTCLayer #######################
@@ -66,7 +71,7 @@ if(NOT WITH_DOUBLE AND NOT MOBILE_INFERENCE)
         test_WarpCTCLayer.cpp)
     add_test(NAME test_WarpCTCLayer
         COMMAND ${CMAKE_CURRENT_BINARY_DIR}/test_WarpCTCLayer --warpctc_dir=${WARPCTC_LIB_DIR}
-        WORKING_DIRECTORY ${PADDLE_SOURCE_DIR}/paddle)
+        WORKING_DIRECTORY ${PADDLE_BINARY_DIR}/paddle)
 endif()
 
 if(NOT MOBILE_INFERENCE)
@@ -84,15 +89,15 @@ if(NOT MOBILE_INFERENCE)
     endif()
     add_test(NAME test_NetworkCompare
         COMMAND ${PYTHON_PATH} ${CMAKE_CURRENT_BINARY_DIR}/test_NetworkCompare --use_gpu=${use_gpu}
-        WORKING_DIRECTORY ${PADDLE_SOURCE_DIR}/paddle)
+        WORKING_DIRECTORY ${PADDLE_BINARY_DIR}/paddle)
 
     ############ test_CompareSparse ################
     add_unittest_without_exec(test_CompareSparse
         test_CompareSparse.cpp)
     if(NOT ON_TRAVIS)
       add_test(NAME test_CompareSparse
-        COMMAND ${PYTHON_PATH} ./.set_port.sh -p port -n 6
+        COMMAND ${PYTHON_PATH} ${PADDLE_SOURCE_DIR}/paddle/.set_port.sh -p port -n 6
                 ${CMAKE_CURRENT_BINARY_DIR}/test_CompareSparse
-        WORKING_DIRECTORY ${PADDLE_SOURCE_DIR}/paddle/)
+        WORKING_DIRECTORY ${PADDLE_BINARY_DIR}/paddle/)
     endif()
 endif()
diff --git a/paddle/trainer/tests/CMakeLists.txt b/paddle/trainer/tests/CMakeLists.txt
index bd518d8598f5aa7c32298ed2110a96a2743536b3..12c9ea8cef79a6bdbd6e26c35612d0abbe00257b 100644
--- a/paddle/trainer/tests/CMakeLists.txt
+++ b/paddle/trainer/tests/CMakeLists.txt
@@ -1,11 +1,16 @@
+add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/sample_trainer_config.conf
+    COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/* ${CMAKE_CURRENT_BINARY_DIR}
+)
+add_custom_target(copy_trainer_conf ALL DEPENDS sample_trainer_config.conf)
+
 set(PYTHON_PATH 
    ${PADDLE_SOURCE_DIR}/paddle/.set_python_path.sh -d 
-   ${PADDLE_SOURCE_DIR}/python/:${PADDLE_SOURCE_DIR}/paddle/trainer/tests)
+   ${PADDLE_BINARY_DIR}/python/:${PADDLE_BINARY_DIR}/paddle/trainer/tests)
 function(trainer_test TARGET)
   add_unittest_without_exec(${TARGET} ${TARGET}.cpp)
   add_test(NAME ${TARGET}
     COMMAND ${PYTHON_PATH} ${CMAKE_CURRENT_BINARY_DIR}/${TARGET}
-      WORKING_DIRECTORY ${PADDLE_SOURCE_DIR}/paddle/)
+      WORKING_DIRECTORY ${PADDLE_BINARY_DIR}/paddle/)
 endfunction()
 
 trainer_test(test_Compare)
@@ -22,11 +27,11 @@ if(WITH_PYTHON)
   add_test(NAME test_TrainerOnePass
     COMMAND ${PYTHON_PATH} ${PADDLE_SOURCE_DIR}/paddle/.set_port.sh -p port 
           ${CMAKE_CURRENT_BINARY_DIR}/test_TrainerOnePass
-      WORKING_DIRECTORY ${PADDLE_SOURCE_DIR}/paddle/)
+      WORKING_DIRECTORY ${PADDLE_BINARY_DIR}/paddle/)
 endif()
 
 #################### test_config_parser #########################
 add_test(NAME test_config_parser
   COMMAND ${PYTHON_PATH} ${PYTHON_EXECUTABLE} 
         ${PADDLE_SOURCE_DIR}/paddle/trainer/tests/config_parser_test.py
-    WORKING_DIRECTORY ${PADDLE_SOURCE_DIR}/paddle/)
+    WORKING_DIRECTORY ${PADDLE_BINARY_DIR}/paddle/)
diff --git a/paddle/utils/CMakeLists.txt b/paddle/utils/CMakeLists.txt
index 7a4977935ede4878c07f4fb6ba0dd76bf50acd42..6292e7fa52cd86c71724d9fe84ea622e98ff1e08 100644
--- a/paddle/utils/CMakeLists.txt
+++ b/paddle/utils/CMakeLists.txt
@@ -2,8 +2,8 @@
 file(GLOB UTIL_HEADERS . *.h)
 file(GLOB UTIL_SOURCES . *.cpp)
 create_resources(${CMAKE_CURRENT_SOURCE_DIR}/enable_virtualenv.py
-  ${CMAKE_CURRENT_SOURCE_DIR}/enable_virtualenv.c)
-set(UTIL_RES ${CMAKE_CURRENT_SOURCE_DIR}/enable_virtualenv.c)
+  ${CMAKE_CURRENT_BINARY_DIR}/enable_virtualenv.c)
+set(UTIL_RES ${CMAKE_CURRENT_BINARY_DIR}/enable_virtualenv.c)
 
 if(APPLE)
     file(GLOB UTIL_ARCH_SOURCES . arch/osx/*.cpp)
diff --git a/proto/CMakeLists.txt b/proto/CMakeLists.txt
index 556bcd1d7e60c27fece43de666e9531ab4203414..a075eeb83bda64133920f9ab0275eb6c0e0fb8c4 100644
--- a/proto/CMakeLists.txt
+++ b/proto/CMakeLists.txt
@@ -15,13 +15,14 @@ foreach(filename ${proto_filenames})
     get_filename_component(ABS_FIL ${filename} ABSOLUTE)
     get_filename_component(FIL_WE ${filename} NAME_WE)
     set(CUR_PROTO_GEN_PY
-            ${PADDLE_SOURCE_DIR}/paddle/python/paddle/proto/${FIL_WE}_pb2.py)
+            ${PADDLE_BINARY_DIR}/paddle/python/paddle/proto/${FIL_WE}_pb2.py)
     set(PROTO_GEN_PY
             ${CUR_PROTO_GEN_PY}
             ${PROTO_GEN_PY})
     add_custom_command(OUTPUT ${CUR_PROTO_GEN_PY}
+            COMMAND ${CMAKE_COMMAND} -E make_directory ${PADDLE_BINARY_DIR}/python/paddle/proto
             COMMAND ${PROTOBUF_PROTOC_EXECUTABLE}
-            ARGS "--python_out=${PADDLE_SOURCE_DIR}/python/paddle/proto"
+            ARGS "--python_out=${PADDLE_BINARY_DIR}/python/paddle/proto"
             "-I" ${CMAKE_CURRENT_SOURCE_DIR} ${ABS_FIL}
             DEPENDS ${ABS_FIL} protoc)
 endforeach()
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
index d074b0136d77fa5a1ce5c29cd52347d04475b029..7cbd7f22bf2968b29dc0665e893101b892808b5e 100644
--- a/python/CMakeLists.txt
+++ b/python/CMakeLists.txt
@@ -47,14 +47,16 @@ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup.py.in
     ${CMAKE_CURRENT_BINARY_DIR}/setup.py)
 
 
-add_custom_command(OUTPUT ${PADDLE_SOURCE_DIR}/python/paddle/fluid/core.so
-        COMMAND cmake -E copy $<TARGET_FILE:paddle_pybind> ${PADDLE_SOURCE_DIR}/python/paddle/fluid/core.so
+add_custom_command(OUTPUT ${PADDLE_BINARY_DIR}/python/paddle/fluid/core.so
+        COMMAND cmake -E copy $<TARGET_FILE:paddle_pybind> ${PADDLE_BINARY_DIR}/python/paddle/fluid/core.so
         DEPENDS paddle_pybind)
-add_custom_target(copy_paddle_pybind ALL DEPENDS ${PADDLE_SOURCE_DIR}/python/paddle/fluid/core.so)
+add_custom_target(copy_paddle_pybind ALL DEPENDS ${PADDLE_BINARY_DIR}/python/paddle/fluid/core.so)
 
 
 add_custom_command(OUTPUT ${PADDLE_PYTHON_BUILD_DIR}/.timestamp
     COMMAND touch stub.cc
+    COMMAND ${CMAKE_COMMAND} -E copy_directory ${PADDLE_SOURCE_DIR}/python/paddle ${PADDLE_BINARY_DIR}/python/paddle
+    COMMAND cp -r ${PADDLE_SOURCE_DIR}/paddle/py_paddle ${PADDLE_BINARY_DIR}/python/
     COMMAND env ${py_env} ${PYTHON_EXECUTABLE} setup.py bdist_wheel
     COMMAND ${CMAKE_COMMAND} -E touch ${PADDLE_PYTHON_BUILD_DIR}/.timestamp
     COMMAND ${CMAKE_COMMAND} -E remove_directory ${PADDLE_PYTHON_BUILD_DIR}/lib-python
diff --git a/python/paddle/fluid/tests/unittests/CMakeLists.txt b/python/paddle/fluid/tests/unittests/CMakeLists.txt
index 1b2d29a47fd050e40f83443432f8194984c71214..f10ef9b63412ecf74471f4fb94eb91ac72d5f8f9 100644
--- a/python/paddle/fluid/tests/unittests/CMakeLists.txt
+++ b/python/paddle/fluid/tests/unittests/CMakeLists.txt
@@ -22,9 +22,9 @@ function(py_test_modules TARGET_NAME)
     set(multiValueArgs MODULES DEPS ARGS ENVS)
     cmake_parse_arguments(py_test_modules "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
     add_test(NAME ${TARGET_NAME}
-             COMMAND env PYTHONPATH=${PADDLE_PYTHON_BUILD_DIR}/lib-python ${py_test_modules_ENVS}
+             COMMAND env PYTHONPATH=${PADDLE_BINARY_DIR}/python ${py_test_modules_ENVS}
              ${PYTHON_EXECUTABLE} -u -m unittest --verbose ${py_test_modules_MODULES} ${py_test_modules_ARGS}
-             WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
   endif()
 endfunction()
 
diff --git a/python/paddle/trainer_config_helpers/tests/CMakeLists.txt b/python/paddle/trainer_config_helpers/tests/CMakeLists.txt
index 580aef935b5cec385a88fb0b4f5b9a5ddeddb40c..30e0b9906c406d846d4b086a1a1c89587394afea 100644
--- a/python/paddle/trainer_config_helpers/tests/CMakeLists.txt
+++ b/python/paddle/trainer_config_helpers/tests/CMakeLists.txt
@@ -1,17 +1,17 @@
 #################### test_config_parser #########################
 add_test(NAME layers_test
-  COMMAND ${PADDLE_SOURCE_DIR}/paddle/.set_python_path.sh -d ${PADDLE_SOURCE_DIR}/python/
+  COMMAND ${PADDLE_SOURCE_DIR}/paddle/.set_python_path.sh -d ${PADDLE_BINARY_DIR}/python/
         ${PYTHON_EXECUTABLE} ${PADDLE_SOURCE_DIR}/python/paddle/trainer_config_helpers/tests/layers_test.py
     WORKING_DIRECTORY ${PADDLE_SOURCE_DIR}/python/paddle)
 
 add_test(NAME test_reset_hook
-  COMMAND ${PADDLE_SOURCE_DIR}/paddle/.set_python_path.sh -d ${PADDLE_SOURCE_DIR}/python/
+  COMMAND ${PADDLE_SOURCE_DIR}/paddle/.set_python_path.sh -d ${PADDLE_BINARY_DIR}/python/
         ${PYTHON_EXECUTABLE} ${PADDLE_SOURCE_DIR}/python/paddle/trainer_config_helpers/tests/test_reset_hook.py
     WORKING_DIRECTORY ${PADDLE_SOURCE_DIR}/python/paddle)
 
 add_paddle_exe(protobuf_equal ProtobufEqualMain.cpp)
 add_test(NAME test_layerHelpers
-  COMMAND
-  ${PADDLE_SOURCE_DIR}/python/paddle/trainer_config_helpers/tests/configs/run_tests.sh ${PYTHON_EXECUTABLE}
+  COMMAND ${PADDLE_SOURCE_DIR}/paddle/.set_python_path.sh -d ${PADDLE_BINARY_DIR}/python/
+  ${PADDLE_BINARY_DIR}/python/paddle/trainer_config_helpers/tests/configs/run_tests.sh ${PYTHON_EXECUTABLE}
   ${CMAKE_CURRENT_BINARY_DIR}/protobuf_equal
 )
diff --git a/python/paddle/trainer_config_helpers/tests/configs/generate_protostr.sh b/python/paddle/trainer_config_helpers/tests/configs/generate_protostr.sh
index 8a318879630cd491573afcaf798dda2ca75e335d..44a75a60cc78e85f85d111a911999b7812db0f49 100755
--- a/python/paddle/trainer_config_helpers/tests/configs/generate_protostr.sh
+++ b/python/paddle/trainer_config_helpers/tests/configs/generate_protostr.sh
@@ -2,7 +2,6 @@
 
 set -e
 cd `dirname $0`
-export PYTHONPATH=$PWD/../../../../
 
 protostr=$PWD/protostr
 . file_list.sh
diff --git a/python/setup.py.in b/python/setup.py.in
index 08a448934d3248b46618acdef9e1894f94a93893..2707d34a2ab327ab4282aa7473d78a3f5c08e890 100644
--- a/python/setup.py.in
+++ b/python/setup.py.in
@@ -58,7 +58,7 @@ def mkl():
             'istaged': ISTAGED,
             'with_mkl': '@WITH_MKL@'})
 
-write_version_py(filename='@PADDLE_SOURCE_DIR@/python/paddle/version.py')
+write_version_py(filename='@PADDLE_BINARY_DIR@/python/paddle/version.py')
 
 
 packages=['paddle',
@@ -109,7 +109,7 @@ package_dir={
     'paddle.fluid.proto': '${PADDLE_BINARY_DIR}/paddle/fluid/framework',
 }
 if '${WITH_FLUID_ONLY}'== 'OFF':
-    package_dir['py_paddle']='${PADDLE_SOURCE_DIR}/paddle/py_paddle'
+    package_dir['py_paddle']='${PADDLE_BINARY_DIR}/python/py_paddle'
     
 
 paddle_rt_lib_dir = 'lib'