diff --git a/Dockerfile b/Dockerfile
index fc5069a6c080ed23317695e6822c4c46b5b5c7f9..48c750358cfcb227667c429f19befcaa2f51ebbd 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -23,7 +23,7 @@ ENV HOME /root
 COPY ./paddle/scripts/docker/root/ /root/
 
 RUN apt-get update && \
-    apt-get install -y --allow-downgrades \
+    apt-get install -y --allow-downgrades patchelf \
     git python-pip python-dev python-opencv openssh-server bison \
     libnccl2=2.1.2-1+cuda8.0 libnccl-dev=2.1.2-1+cuda8.0 \
     wget unzip unrar tar xz-utils bzip2 gzip coreutils ntp \
diff --git a/doc/fluid/api/transpiler.rst b/doc/fluid/api/transpiler.rst
index 943d39331d26c05764c90cb24f6774997c976bfe..d2ac04f1449c32cb414cea1b76d7469bbe9ccb85 100644
--- a/doc/fluid/api/transpiler.rst
+++ b/doc/fluid/api/transpiler.rst
@@ -14,6 +14,15 @@ DistributeTranspiler
     :members:
     :noindex:
 
+.. _api_fluid_transpiler_InferenceTranspiler:
+
+InferenceTranspiler
+-------------------
+
+..  autoclass:: paddle.fluid.transpiler.InferenceTranspiler
+    :members:
+    :noindex:
+
 .. _api_fluid_transpiler_memory_optimize:
 
 memory_optimize
diff --git a/paddle/scripts/paddle_build.sh b/paddle/scripts/paddle_build.sh
index 09bbe4185e1709d379a819a94a712820ac1e9d89..d173b41e86f61954954b6a5ea9957d2e172deca0 100755
--- a/paddle/scripts/paddle_build.sh
+++ b/paddle/scripts/paddle_build.sh
@@ -318,7 +318,7 @@ function assert_api_not_changed() {
     virtualenv .env
     source .env/bin/activate
     pip install ${PADDLE_ROOT}/build/python/dist/*whl
-    curl ${PADDLE_API_SPEC_URL:-https://raw.githubusercontent.com/reyoung/FluidAPISpec/master/API.spec} \
+    curl ${PADDLE_API_SPEC_URL:-https://raw.githubusercontent.com/PaddlePaddle/FluidAPISpec/master/API.spec} \
         > origin.spec
     python ${PADDLE_ROOT}/tools/print_signatures.py paddle.fluid > new.spec
     python ${PADDLE_ROOT}/tools/diff_api.py origin.spec new.spec
diff --git a/python/paddle/fluid/transpiler/inference_transpiler.py b/python/paddle/fluid/transpiler/inference_transpiler.py
index d32c69d148dfa1633ce344611ca3fe7879a234e9..b8afeae5ebd6ef7948a7c0c2775f419af461da04 100644
--- a/python/paddle/fluid/transpiler/inference_transpiler.py
+++ b/python/paddle/fluid/transpiler/inference_transpiler.py
@@ -19,7 +19,7 @@ from ..framework import Program
 from ..executor import global_scope
 
 
-class InferenceTranspiler:
+class InferenceTranspiler(object):
     '''
     Convert the fluid program to optimized inference program.
 
diff --git a/python/paddle/libs/__init__.py b/python/paddle/libs/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..34d4f4d07ed0d452c1965c5f1f198230571931aa
--- /dev/null
+++ b/python/paddle/libs/__init__.py
@@ -0,0 +1,15 @@
+# Copyright (c) 2018 PaddlePaddle Authors. All Rights Reserved
+#
+# 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.
+
+# used for setup.py.in to store the thirdparty shared libraries
diff --git a/python/setup.py.in b/python/setup.py.in
index a0917e3eafb6d08127c6390b78b5ea0f08d7e5aa..2b052574c0716e0606e362200b1cb70cd214e2b0 100644
--- a/python/setup.py.in
+++ b/python/setup.py.in
@@ -1,6 +1,8 @@
 from setuptools import setup, Distribution, Extension
 import subprocess
+import os
 import re
+import shutil
 class BinaryDistribution(Distribution):
     def has_ext_modules(foo):
         return True
@@ -103,6 +105,7 @@ write_version_py(filename='@PADDLE_BINARY_DIR@/python/paddle/version.py')
 
 
 packages=['paddle',
+          'paddle.libs',
           'paddle.utils',
           'paddle.dataset',
           'paddle.reader',
@@ -155,11 +158,32 @@ package_dir={
 if '${WITH_FLUID_ONLY}'== 'OFF':
     package_dir['py_paddle']='${PADDLE_BINARY_DIR}/python/py_paddle'
 
-
-paddle_rt_lib_dir = 'lib'
-paddle_rt_libs = ['${WARPCTC_LIBRARIES}']
-if '${MKL_SHARED_LIBS}'!= '':
-  paddle_rt_libs += '${MKL_SHARED_LIBS}'.split(';')
+# put all thirdparty libraries in paddle.libs
+package_data['paddle.libs']=['libwarpctc.so']
+libs_path='${PADDLE_BINARY_DIR}/python/paddle/libs'
+shutil.copy('${WARPCTC_LIBRARIES}', libs_path)
+if '${WITH_MKL}' == 'ON':
+    shutil.copy('${MKLML_LIB}', libs_path)
+    shutil.copy('${MKLML_IOMP_LIB}', libs_path)
+    package_data['paddle.libs']+=['libmklml_intel.so','libiomp5.so']
+if '${WITH_MKLDNN}' == 'ON':
+    # change rpath of libmkldnn.so.0, add $ORIGIN/ to it.
+    # The reason is that all thirdparty libraries in the same directory,
+    # thus, libmkldnn.so.0 will find libmklml_intel.so and libiomp5.so.
+    command = "patchelf --set-rpath '$ORIGIN/' ${MKLDNN_SHARED_LIB}"
+    os.system(command)
+    package_data['paddle.libs']+=['libmkldnn.so.0']
+    shutil.copy('${MKLDNN_SHARED_LIB}', libs_path)
+# remove unused paddle/libs/__init__.py
+os.remove(libs_path+'/__init__.py')
+package_dir['paddle.libs']=libs_path
+
+# change rpath of core.so, add $ORIGIN/../libs/ to it.
+# The reason is that libwarpctc.so, libiomp5.so etc are in paddle.libs, and
+# core.so is in paddle.fluid, thus paddle/fluid/../libs will pointer to above libraries.
+# This operation will fix https://github.com/PaddlePaddle/Paddle/issues/3213
+command = "patchelf --set-rpath '$ORIGIN/../libs/' ${PADDLE_BINARY_DIR}/python/paddle/fluid/core.so"
+os.system(command)
 
 setup(name='${PACKAGE_NAME}',
       version='${PADDLE_VERSION}',
@@ -169,6 +193,5 @@ setup(name='${PACKAGE_NAME}',
       ext_modules=[Extension('_foo', ['stub.cc'])],
       package_data=package_data,
       package_dir=package_dir,
-      scripts=paddle_bins,
-      data_files=[(paddle_rt_lib_dir, paddle_rt_libs)]
+      scripts=paddle_bins
 )