diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7d685587a7a7f388167f79cc8874003ab445f433..7ef9368ef5aca23363c2b9d74479ffe487570512 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -12,6 +12,17 @@ include(package)
 find_package(SWIG 2.0)
 find_package(CUDA QUIET)
 find_package(Protobuf REQUIRED)
+
+# Check protobuf library version.
+execute_process(COMMAND ${PROTOBUF_PROTOC_EXECUTABLE} --version
+	OUTPUT_VARIABLE PROTOBUF_VERSION)
+string(REPLACE "libprotoc " "" PROTOBUF_VERSION ${PROTOBUF_VERSION})
+
+set(PROTOBUF_3 OFF)
+if (${PROTOBUF_VERSION} VERSION_GREATER "3.0.0" OR ${PROTOBUF_VERSION} VERSION_EQUAL "3.0.0")
+    set(PROTOBUF_3 ON)
+endif()
+
 find_package(PythonLibs 2.7 REQUIRED)
 find_package(PythonInterp 2.7 REQUIRED)
 find_package(ZLIB REQUIRED)
diff --git a/proto/CMakeLists.txt b/proto/CMakeLists.txt
index ec68b53d440185f869566e2975a65d0c3fec5bc5..d7f523bc8d9bce00ba72c41284d2b3eb3cde6529 100644
--- a/proto/CMakeLists.txt
+++ b/proto/CMakeLists.txt
@@ -1,12 +1,3 @@
-execute_process(COMMAND ${PROTOBUF_PROTOC_EXECUTABLE} --version
-	OUTPUT_VARIABLE PROTOBUF_VERSION)
-string(REPLACE "libprotoc " "" PROTOBUF_VERSION ${PROTOBUF_VERSION})
-
-set(PROTOBUF_3 OFF)
-if (${PROTOBUF_VERSION} VERSION_GREATER "3.0.0" OR ${PROTOBUF_VERSION} VERSION_EQUAL "3.0.0")
-    set(PROTOBUF_3 ON)
-endif()
-
 set(proto_filenames
     DataConfig.proto
     DataFormat.proto
diff --git a/python/paddle/trainer_config_helpers/tests/CMakeLists.txt b/python/paddle/trainer_config_helpers/tests/CMakeLists.txt
index 78505c85e1b9c8b87612a3f17c294035e221774f..6180b2efbcad87e511a4b981d533f204f45fb5dc 100644
--- a/python/paddle/trainer_config_helpers/tests/CMakeLists.txt
+++ b/python/paddle/trainer_config_helpers/tests/CMakeLists.txt
@@ -4,11 +4,17 @@ add_test(NAME layers_test
         python ${PROJ_ROOT}/python/paddle/trainer_config_helpers/tests/layers_test.py
     WORKING_DIRECTORY ${PROJ_ROOT}/python/paddle)
 
-add_paddle_exe(protobuf_equal
-  ProtobufEqualMain.cpp)
-
-add_test(NAME test_layerHelpers
-  COMMAND
-  ${PROJ_ROOT}/python/paddle/trainer_config_helpers/tests/configs/run_tests.sh
-  ${CMAKE_CURRENT_BINARY_DIR}/protobuf_equal
-)
+if (PROTOBUF_3)
+  add_paddle_exe(protobuf_equal
+    ProtobufEqualMain.cpp)
+  add_test(NAME test_layerHelpers
+    COMMAND
+    ${PROJ_ROOT}/python/paddle/trainer_config_helpers/tests/configs/run_tests.sh
+    ${CMAKE_CURRENT_BINARY_DIR}/protobuf_equal
+  )
+else()
+  add_test(NAME test_layerHelpers
+    COMMAND
+    ${PROJ_ROOT}/python/paddle/trainer_config_helpers/tests/configs/run_tests.sh
+  )
+endif()