diff --git a/python/paddle/trainer_config_helpers/tests/CMakeLists.txt b/python/paddle/trainer_config_helpers/tests/CMakeLists.txt
index cf52b06bfea06d6a88b5f11558627936a74bd0b9..78505c85e1b9c8b87612a3f17c294035e221774f 100644
--- a/python/paddle/trainer_config_helpers/tests/CMakeLists.txt
+++ b/python/paddle/trainer_config_helpers/tests/CMakeLists.txt
@@ -4,7 +4,11 @@ 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
 )
diff --git a/python/paddle/trainer_config_helpers/tests/ProtobufEqualMain.cpp b/python/paddle/trainer_config_helpers/tests/ProtobufEqualMain.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..06f7de9306307e2f92958ef211ec137d54c99d1c
--- /dev/null
+++ b/python/paddle/trainer_config_helpers/tests/ProtobufEqualMain.cpp
@@ -0,0 +1,59 @@
+/* Copyright (c) 2016 Baidu, Inc. 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. */
+
+#include <google/protobuf/text_format.h>
+#include <google/protobuf/util/message_differencer.h>
+#include <fstream>
+#include <iostream>
+#include "TrainerConfig.pb.h"
+
+bool loadPb(google::protobuf::Message* conf, const std::string& filename) {
+  std::ifstream fin;
+  fin.open(filename.c_str());
+  if (fin.is_open()) {
+    std::string str((std::istreambuf_iterator<char>(fin)),
+                    std::istreambuf_iterator<char>());
+    bool ok = google::protobuf::TextFormat::ParseFromString(str, conf);
+    fin.close();
+    return ok;
+  } else {
+    return false;
+  }
+}
+
+int main(int argc, char** argv) {
+  std::unique_ptr<google::protobuf::Message> config1;
+  std::unique_ptr<google::protobuf::Message> config2;
+  if (argc == 3) {
+    config1.reset(new paddle::ModelConfig());
+    config2.reset(new paddle::ModelConfig());
+  } else if (argc == 4) {
+    config1.reset(new paddle::TrainerConfig());
+    config2.reset(new paddle::TrainerConfig());
+  }
+  if (!config1 || !config2) {
+    return 1;
+  } else if (!loadPb(config1.get(), argv[1])) {
+    return 2;
+  } else if (!loadPb(config2.get(), argv[2])) {
+    return 3;
+  } else {
+    if (google::protobuf::util::MessageDifferencer::ApproximatelyEquals(
+            *config1, *config2)) {
+      return 0;
+    } else {
+      return 4;
+    }
+  }
+}
diff --git a/python/paddle/trainer_config_helpers/tests/configs/.gitignore b/python/paddle/trainer_config_helpers/tests/configs/.gitignore
index eb646b4a71ec1ac0e7992aabf2992fef7a9264a0..c654bd41b0b4dd0cb510943540b660b4e4a147d9 100644
--- a/python/paddle/trainer_config_helpers/tests/configs/.gitignore
+++ b/python/paddle/trainer_config_helpers/tests/configs/.gitignore
@@ -1 +1 @@
-protostr/*.unitest
+protostr/*.unittest
diff --git a/python/paddle/trainer_config_helpers/tests/configs/file_list.sh b/python/paddle/trainer_config_helpers/tests/configs/file_list.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3f1d99701afe5425553feb129c7619b5e3e689fa
--- /dev/null
+++ b/python/paddle/trainer_config_helpers/tests/configs/file_list.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+export configs=(test_fc layer_activations projections test_print_layer
+test_sequence_pooling test_lstmemory_layer test_grumemory_layer
+last_first_seq test_expand_layer test_ntm_layers test_hsigmoid
+img_layers img_trans_layers util_layers simple_rnn_layers unused_layers test_cost_layers
+test_rnn_group shared_fc shared_lstm test_cost_layers_with_weight
+test_spp_layer test_bilinear_interp test_maxout test_bi_grumemory math_ops)
+
+export whole_configs=(test_split_datasource)
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 bb594ac2c245d8882569ba2c3cf00623a8fa8e2c..e55f9bd3884a907dcc17a882e3c1dfd71fef79bb 100755
--- a/python/paddle/trainer_config_helpers/tests/configs/generate_protostr.sh
+++ b/python/paddle/trainer_config_helpers/tests/configs/generate_protostr.sh
@@ -5,24 +5,16 @@ cd `dirname $0`
 export PYTHONPATH=$PWD/../../../../
 
 protostr=$PWD/protostr
-
-configs=(test_fc layer_activations projections test_print_layer
-test_sequence_pooling test_lstmemory_layer test_grumemory_layer
-last_first_seq test_expand_layer test_ntm_layers test_hsigmoid
-img_layers img_trans_layers util_layers simple_rnn_layers unused_layers test_cost_layers
-test_rnn_group shared_fc shared_lstm test_cost_layers_with_weight
-test_spp_layer test_bilinear_interp test_maxout test_bi_grumemory math_ops)
-
-whole_configs=(test_split_datasource)
+. file_list.sh
 
 for conf in ${configs[*]}
 do
     echo "Generating " $conf
-    python -m paddle.utils.dump_config $conf.py > $protostr/$conf.protostr.unitest
+    python -m paddle.utils.dump_config $conf.py > $protostr/$conf.protostr.unittest
 done
 
 for conf in ${whole_configs[*]}
 do
     echo "Generating " $conf
-    python -m paddle.utils.dump_config $conf.py "" --whole > $protostr/$conf.protostr.unitest
+    python -m paddle.utils.dump_config $conf.py "" --whole > $protostr/$conf.protostr.unittest
 done
diff --git a/python/paddle/trainer_config_helpers/tests/configs/run_tests.sh b/python/paddle/trainer_config_helpers/tests/configs/run_tests.sh
index 968328835842667470467830c7ca59e4b9fa723d..5f6ed91030bc54481495f42539e3581eefc64b1a 100755
--- a/python/paddle/trainer_config_helpers/tests/configs/run_tests.sh
+++ b/python/paddle/trainer_config_helpers/tests/configs/run_tests.sh
@@ -9,9 +9,27 @@ files=`ls $protostr | grep -v "unitest"`
 
 ./generate_protostr.sh
 
-for file in $files
-do
-    base_protostr=$protostr/$file
-    new_protostr=$protostr/$file.unitest
-    diff $base_protostr $new_protostr -u
-done
+. ./file_list.sh
+
+if [ -z $1 ]; then
+  for file in $files
+  do
+      base_protostr=$protostr/$file
+      new_protostr=$protostr/$file.unittest
+      diff $base_protostr $new_protostr -u
+  done
+else
+  for file in ${configs[*]}
+  do
+    if ! $1 $protostr/$file.protostr $protostr/$file.protostr.unittest; then
+      diff $protostr/$file.protostr $protostr/$file.protostr.unittest -u
+    fi
+  done
+
+  for file in ${whole_configs[*]}
+  do
+    if ! $1 $protostr/$file.protostr $protostr/$file.protostr.unittest --whole; then
+      diff $protostr/$file.protostr $protostr/$file.protostr.unittest -u
+    fi
+  done
+fi