use -rpath to fix libmklml_intel.so not found

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 \

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

python/setup.py.in

@@ -1,5 +1,7 @@
 from setuptools import setup, Distribution, Extension
 import subprocess
+import shutil
+import os
 class BinaryDistribution(Distribution):
     def has_ext_modules(foo):
         return True
@@ -62,6 +64,7 @@ write_version_py(filename='@PADDLE_BINARY_DIR@/python/paddle/version.py')
 
 
 packages=['paddle',
+          'paddle.libs',
           'paddle.utils',
           'paddle.dataset',
           'paddle.reader',
@@ -113,12 +116,30 @@ 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 '${WITH_MKLDNN}'== 'ON':
+    package_data['paddle.libs']+=['libmkldnn.so.0']
+    shutil.copy('${MKLDNN_SHARED_LIB}', libs_path)
+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
+os.environ['core_rpath']=str(os.popen("patchelf --print-rpath \
+    ${PADDLE_BINARY_DIR}/python/paddle/fluid/core.so").read().strip('\n'))
+os.environ['core_rpath']=os.environ['core_rpath']+":'$ORIGIN/../libs/'"
+command = "patchelf --set-rpath " + os.environ['core_rpath'] +\
+    " ${PADDLE_BINARY_DIR}/python/paddle/fluid/core.so"
+os.system(command)
 
 setup(name='${PACKAGE_NAME}',
       version='${PADDLE_VERSION}',
@@ -128,6 +149,5 @@ 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
 )