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Merge branch 'develop' of https://github.com/PaddlePaddle/Paddle into gfortran

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feature/design_of_v2_layer_converter
liaogang 8 years ago
parent e5b10732b2 5b41fe4217
commit 9aa4190541
30 changed files with 190 additions and 1126 deletions
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2
Dockerfile
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@ -26,7 +26,7 @@ RUN apt-get update && \
apt-get install -y git python-pip python-dev openssh-server bison && \
apt-get install -y wget unzip tar xz-utils bzip2 gzip coreutils && \
apt-get install -y curl sed grep graphviz libjpeg-dev zlib1g-dev && \
apt-get install -y python-numpy python-matplotlib gcc g++ gfortran && \
apt-get install -y python-numpy python-matplotlib gcc g++ liblapack-dev liblapacke-dev && \
apt-get install -y automake locales clang-format-3.8 swig doxygen && \
apt-get clean -y

2
cmake/external/python.cmake vendored
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@ -19,7 +19,7 @@ FIND_PACKAGE(PythonInterp 2.7)
FIND_PACKAGE(PythonLibs 2.7)
SET(py_env "")
SET(USE_VIRTUALENV_FOR_TEST 1)
IF(PYTHONLIBS_FOUND AND PYTHONINTERP_FOUND)
find_python_module(pip REQUIRED)
find_python_module(numpy REQUIRED)

11
cmake/make_resource.py
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@ -0,0 +1,11 @@
import os
import re
import sys
res = sys.argv[1]
out = sys.argv[2]
var = re.sub(r'[ .-]', '_', os.path.basename(res))
open(out, "w").write("const unsigned char " + var + "[] = {" + ",".join([
"0x%02x" % ord(c) for c in open(res).read()
]) + ",0};\n" + "const unsigned " + var + "_size = sizeof(" + var + ");\n")

29
cmake/util.cmake
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@ -138,17 +138,20 @@ macro(add_simple_unittest TARGET_NAME)
endmacro()
# Creates C resources file from files in given resource file
function(create_resources res_file output)
# Create empty output file
file(WRITE ${output} "")
# Get short filename
string(REGEX MATCH "([^/]+)$" filename ${res_file})
# Replace filename spaces & extension separator for C compatibility
string(REGEX REPLACE "\\.| |-" "_" filename ${filename})
# Read hex data from file
file(READ ${res_file} filedata HEX)
# Convert hex data for C compatibility
string(REGEX REPLACE "([0-9a-f][0-9a-f])" "0x\\1," filedata ${filedata})
# Append data to output file
file(APPEND ${output} "const unsigned char ${filename}[] = {${filedata}0};\nconst unsigned ${filename}_size = sizeof(${filename});\n")
function(create_resources res_file output_file)
add_custom_command(
OUTPUT ${output_file}
COMMAND python ARGS ${PROJ_ROOT}/cmake/make_resource.py ${res_file} ${output_file}
DEPENDS ${res_file} ${PROJ_ROOT}/cmake/make_resource.py)
endfunction()
# Create a python unittest using run_python_tests.sh,
# which takes care of making correct running environment
function(add_python_test TEST_NAME)
message("PYTHON: ${PYTHON_EXECUTABLE}")
add_test(NAME ${TEST_NAME}
COMMAND bash ${PROJ_ROOT}/paddle/scripts/run_python_tests.sh
${USE_VIRTUALENV_FOR_TEST} ${PYTHON_EXECUTABLE} ${ARGN}
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
endfunction()

108
doc/api/v1/trainer_config_helpers/activations.rst
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@ -1,108 +0,0 @@
===========
Activations
===========
BaseActivation
==============
.. automodule:: paddle.trainer_config_helpers.activations
:members: BaseActivation
:noindex:
AbsActivation
===============
.. automodule:: paddle.trainer_config_helpers.activations
:members: AbsActivation
:noindex:
ExpActivation
===============
.. automodule:: paddle.trainer_config_helpers.activations
:members: ExpActivation
:noindex:
IdentityActivation
==================
.. automodule:: paddle.trainer_config_helpers.activations
:members: IdentityActivation
:noindex:
LinearActivation
==================
.. automodule:: paddle.trainer_config_helpers.activations
:members: LinearActivation
:noindex:
LogActivation
==================
.. automodule:: paddle.trainer_config_helpers.activations
:members: LogActivation
:noindex:
SquareActivation
================
.. automodule:: paddle.trainer_config_helpers.activations
:members: SquareActivation
:noindex:
SigmoidActivation
=================
.. automodule:: paddle.trainer_config_helpers.activations
:members: SigmoidActivation
:noindex:
SoftmaxActivation
=================
.. automodule:: paddle.trainer_config_helpers.activations
:members: SoftmaxActivation
:noindex:
SequenceSoftmaxActivation
=========================
.. automodule:: paddle.trainer_config_helpers.activations
:members: SequenceSoftmaxActivation
:noindex:
ReluActivation
==============
.. automodule:: paddle.trainer_config_helpers.activations
:members: ReluActivation
:noindex:
BReluActivation
===============
.. automodule:: paddle.trainer_config_helpers.activations
:members: BReluActivation
:noindex:
SoftReluActivation
==================
.. automodule:: paddle.trainer_config_helpers.activations
:members: SoftReluActivation
:noindex:
TanhActivation
==============
.. automodule:: paddle.trainer_config_helpers.activations
:members: TanhActivation
:noindex:
STanhActivation
===============
.. automodule:: paddle.trainer_config_helpers.activations
:members: STanhActivation
:noindex:

5
doc/api/v1/trainer_config_helpers/attrs.rst
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@ -1,5 +0,0 @@
Parameter Attributes
=======================
.. automodule:: paddle.trainer_config_helpers.attrs
:members:

7
doc/api/v1/trainer_config_helpers/data_sources.rst
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@ -1,7 +0,0 @@
.. _api_trainer_config_helpers_data_sources:
DataSources
===========
.. automodule:: paddle.trainer_config_helpers.data_sources
:members:

108
doc/api/v1/trainer_config_helpers/evaluators.rst
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@ -1,108 +0,0 @@
.. _api_trainer_config_helpers_evaluators:
==========
Evaluators
==========
Base
====
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: evaluator_base
:noindex:
Classification
==============
classification_error_evaluator
------------------------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: classification_error_evaluator
:noindex:
auc_evaluator
-------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: auc_evaluator
:noindex:
ctc_error_evaluator
-------------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: ctc_error_evaluator
:noindex:
chunk_evaluator
---------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: chunk_evaluator
:noindex:
precision_recall_evaluator
--------------------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: precision_recall_evaluator
:noindex:
Rank
====
pnpair_evaluator
----------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: pnpair_evaluator
:noindex:
Utils
=====
sum_evaluator
-------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: sum_evaluator
:noindex:
column_sum_evaluator
--------------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: column_sum_evaluator
:noindex:
Print
=====
classification_error_printer_evaluator
--------------------------------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: classification_error_printer_evaluator
:noindex:
gradient_printer_evaluator
--------------------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: gradient_printer_evaluator
:noindex:
maxid_printer_evaluator
-----------------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: maxid_printer_evaluator
:noindex:
maxframe_printer_evaluator
---------------------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: maxframe_printer_evaluator
:noindex:
seqtext_printer_evaluator
-------------------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: seqtext_printer_evaluator
:noindex:
value_printer_evaluator
-----------------------
.. automodule:: paddle.trainer_config_helpers.evaluators
:members: value_printer_evaluator
:noindex:

514
doc/api/v1/trainer_config_helpers/layers.rst
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123
doc/api/v1/trainer_config_helpers/networks.rst
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@ -1,123 +0,0 @@
========
Networks
========
The networks module contains pieces of neural network that combine multiple layers.
NLP
===
sequence_conv_pool
------------------
.. automodule:: paddle.trainer_config_helpers.networks
:members: sequence_conv_pool
:noindex:
.. _api_trainer_config_helpers_network_text_conv_pool:
text_conv_pool
--------------
.. automodule:: paddle.trainer_config_helpers.networks
:members: text_conv_pool
:noindex:
Images
======
img_conv_bn_pool
----------------
.. automodule:: paddle.trainer_config_helpers.networks
:members: img_conv_bn_pool
:noindex:
img_conv_group
--------------
.. automodule:: paddle.trainer_config_helpers.networks
:members: img_conv_group
:noindex:
.. _api_trainer_config_helpers_network_simple_img_conv_pool:
simple_img_conv_pool
--------------------
.. automodule:: paddle.trainer_config_helpers.networks
:members: simple_img_conv_pool
:noindex:
vgg_16_network
---------------
.. automodule:: paddle.trainer_config_helpers.networks
:members: vgg_16_network
:noindex:
Recurrent
=========
LSTM
----
lstmemory_unit
``````````````
.. automodule:: paddle.trainer_config_helpers.networks
:members: lstmemory_unit
:noindex:
lstmemory_group
```````````````
.. automodule:: paddle.trainer_config_helpers.networks
:members: lstmemory_group
:noindex:
simple_lstm
```````````
.. automodule:: paddle.trainer_config_helpers.networks
:members: simple_lstm
:noindex:
bidirectional_lstm
``````````````````
.. automodule:: paddle.trainer_config_helpers.networks
:members: bidirectional_lstm
:noindex:
GRU
---
gru_unit
````````
.. automodule:: paddle.trainer_config_helpers.networks
:members: gru_unit
:noindex:
gru_group
`````````
.. automodule:: paddle.trainer_config_helpers.networks
:members: gru_group
:noindex:
simple_gru
``````````
.. automodule:: paddle.trainer_config_helpers.networks
:members: simple_gru
:noindex:
simple_attention
----------------
.. automodule:: paddle.trainer_config_helpers.networks
:members: simple_attention
:noindex:
Miscs
=====
dropout_layer
--------------
.. automodule:: paddle.trainer_config_helpers.networks
:members: dropout_layer
:noindex:
outputs
-------
.. automodule:: paddle.trainer_config_helpers.networks
:members: outputs
:noindex:

61
doc/api/v1/trainer_config_helpers/optimizers.rst
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@ -1,61 +0,0 @@
.. _api_trainer_config_helpers_optimizers:
==========
Optimizers
==========
BaseSGDOptimizer
================
.. automodule:: paddle.trainer_config_helpers.optimizers
:members: BaseSGDOptimizer
:noindex:
MomentumOptimizer
=================
.. automodule:: paddle.trainer_config_helpers.optimizers
:members: MomentumOptimizer
:noindex:
AdamOptimizer
=============
.. automodule:: paddle.trainer_config_helpers.optimizers
:members: AdamOptimizer
:noindex:
AdamaxOptimizer
================
.. automodule:: paddle.trainer_config_helpers.optimizers
:members: AdamaxOptimizer
:noindex:
AdaGradOptimizer
================
.. automodule:: paddle.trainer_config_helpers.optimizers
:members: AdaGradOptimizer
:noindex:
DecayedAdaGradOptimizer
=======================
.. automodule:: paddle.trainer_config_helpers.optimizers
:members: DecayedAdaGradOptimizer
:noindex:
AdaDeltaOptimizer
=================
.. automodule:: paddle.trainer_config_helpers.optimizers
:members: AdaDeltaOptimizer
:noindex:
RMSPropOptimizer
================
.. automodule:: paddle.trainer_config_helpers.optimizers
:members: RMSPropOptimizer
:noindex:
.. _api_trainer_config_helpers_optimizers_settings:
settings
========
.. automodule:: paddle.trainer_config_helpers.optimizers
:members: settings
:noindex:

33
doc/api/v1/trainer_config_helpers/poolings.rst
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@ -1,33 +0,0 @@
========
Poolings
========
BasePoolingType
===============
.. automodule:: paddle.trainer_config_helpers.poolings
:members: BasePoolingType
:noindex:
AvgPooling
==========
.. automodule:: paddle.trainer_config_helpers.poolings
:members: AvgPooling
:noindex:
MaxPooling
==========
.. automodule:: paddle.trainer_config_helpers.poolings
:members: MaxPooling
:noindex:
SumPooling
==========
.. automodule:: paddle.trainer_config_helpers.poolings
:members: SumPooling
:noindex:
SquareRootNPooling
==================
.. automodule:: paddle.trainer_config_helpers.poolings
:members: SquareRootNPooling
:noindex:

101
doc/api/v2/config/evaluators.rst
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@ -0,0 +1,101 @@
.. _api_v2:
==========
Evaluators
==========
Classification
==============
classification_error
--------------------
.. automodule:: paddle.v2.evaluator
:members: classification_error
:noindex:
auc
---
.. automodule:: paddle.v2.evaluator
:members: auc
:noindex:
ctc_error
---------
.. automodule:: paddle.v2.evaluator
:members: ctc_error
:noindex:
chunk
-----
.. automodule:: paddle.v2.evaluator
:members: chunk
:noindex:
precision_recall
----------------
.. automodule:: paddle.v2.evaluator
:members: precision_recall
:noindex:
Rank
====
pnpair
------
.. automodule:: paddle.v2.evaluator
:members: pnpair
:noindex:
Utils
=====
sum
---
.. automodule:: paddle.v2.evaluator
:members: sum
:noindex:
column_sum
----------
.. automodule:: paddle.v2.evaluator
:members: column_sum
:noindex:
Print
=====
classification_error_printer
----------------------------
.. automodule:: paddle.v2.evaluator
:members: classification_error_printer
:noindex:
gradient_printer
----------------
.. automodule:: paddle.v2.evaluator
:members: gradient_printer
:noindex:
maxid_printer
-------------
.. automodule:: paddle.v2.evaluator
:members: maxid_printer
:noindex:
maxframe_printer
----------------
.. automodule:: paddle.v2.evaluator
:members: maxframe_printer
:noindex:
seqtext_printer
---------------
.. automodule:: paddle.v2.evaluator
:members: seqtext_printer
:noindex:
value_printer
-------------
.. automodule:: paddle.v2.evaluator
:members: value_printer
:noindex:

18
doc/api/v2/config/networks.rst
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@ -44,6 +44,12 @@ simple_img_conv_pool
:members: simple_img_conv_pool
:noindex:
small_vgg
---------
.. automodule:: paddle.v2.networks
:members: small_vgg
:noindex:
vgg_16_network
---------------
.. automodule:: paddle.v2.networks
@ -101,6 +107,18 @@ simple_gru
:members: simple_gru
:noindex:
simple_gru2
```````````
.. automodule:: paddle.v2.networks
:members: simple_gru2
:noindex:
bidirectional_gru
``````````````````
.. automodule:: paddle.v2.networks
:members: bidirectional_gru
:noindex:
simple_attention
----------------
.. automodule:: paddle.v2.networks

1
doc/api/v2/model_configs.rst
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@ -6,6 +6,7 @@ Model Configuration
config/activation.rst
config/layer.rst
config/evaluators.rst
config/optimizer.rst
config/pooling.rst
config/networks.rst

4
paddle/api/test/CMakeLists.txt
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@ -1,2 +1,2 @@
add_test(NAME test_swig_api
COMMAND bash ${PROJ_ROOT}/paddle/api/test/run_tests.sh ${PYTHON_EXECUTABLE})
add_python_test(test_swig_api
testArguments.py testGradientMachine.py testMatrix.py testVector.py testTrain.py testTrainer.py)

1
paddle/capi/Main.cpp
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@ -25,7 +25,6 @@ limitations under the License. */
static void initPaddle(int argc, char** argv) {
paddle::initMain(argc, argv);
paddle::initPython(argc, argv);
feenableexcept(FE_INVALID | FE_DIVBYZERO | FE_OVERFLOW);
}
extern "C" {

3
paddle/gserver/tests/test_NetworkCompare.cpp
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@ -261,9 +261,12 @@ TEST(Compare, img_conv2) {
std::string config_file_a = "./gserver/tests/img_conv_a.conf";
std::string config_file_b = "./gserver/tests/img_conv_c.conf";
bool useGpu = FLAGS_use_gpu;
double eps = FLAGS_checkgrad_eps;
FLAGS_use_gpu = true;
FLAGS_checkgrad_eps = 1e-3;
compareNetwork(config_file_a, config_file_b);
FLAGS_use_gpu = useGpu;
FLAGS_checkgrad_eps = eps;
}
#endif

7
paddle/scripts/docker/build.sh
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@ -1,6 +1,6 @@
#!/bin/bash
set -e
set -xe
# Set BASE_IMAGE according to env variables
if [ ${WITH_GPU} == "ON" ]; then
@ -34,7 +34,8 @@ cmake .. \
-DCMAKE_EXPORT_COMPILE_COMMANDS=ON
make -j `nproc`
if [ ${WITH_TESTING:-OFF} == "ON" ] && [ ${RUN_TEST:-OFF} == "ON" ] ; then
make test
pip uninstall -y py-paddle paddle || true
ctest -V
fi
make install
pip install /usr/local/opt/paddle/share/wheels/*.whl
@ -71,7 +72,7 @@ if [[ ${WOBOQ:-OFF} == 'ON' ]]; then
cmake -DLLVM_CONFIG_EXECUTABLE=/usr/bin/llvm-config-3.8 \
-DCMAKE_BUILD_TYPE=Release \
.
make
make -j `nproc`
export WOBOQ_OUT=/woboq_out/paddle
export BUILD_DIR=/paddle/build

24
paddle/api/test/run_tests.sh → paddle/scripts/run_python_tests.sh
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@ -18,19 +18,29 @@ pushd `dirname $0` > /dev/null
SCRIPTPATH=$PWD
popd > /dev/null
cd $SCRIPTPATH
USE_VIRTUALENV_FOR_TEST=$1; shift
PYTHON=$1; shift
$1 -m pip install ../../dist/*.whl
if [ $USE_VIRTUALENV_FOR_TEST -ne 0 ]; then
rm -rf .test_env
virtualenv .test_env
source .test_env/bin/activate
PYTHON=python
fi
test_list="testArguments.py testGradientMachine.py testMatrix.py testVector.py testTrain.py testTrainer.py"
export PYTHONPATH=$SCRIPTPATH/../../python/
$PYTHON -m pip install $SCRIPTPATH/../dist/*.whl requests matplotlib ipython==5.3
export PYTHONPATH=$PWD/../../../python/
for fn in $test_list
for fn in "$@"
do
echo "test $fn"
$1 $fn
$PYTHON $fn
if [ $? -ne 0 ]; then
exit 1
fi
done
if [ $USE_VIRTUALENV_FOR_TEST -ne 0 ]; then
deactivate
rm -rf .test_env
fi

2
paddle/scripts/submit_local.sh.in
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@ -95,7 +95,7 @@ if [ $? -eq 1 ]; then # Older version installed, or not installed at all
echo "First time run paddle, need to install some python dependencies."
# setuptools normalizes package version, so we need to use normalized
# package version for paddle python package
PYTHON_PADDLE_VERSION=$(python -c 'import packaging
PYTHON_PADDLE_VERSION=$(python -c 'import packaging.version
import setuptools
print str(packaging.version.Version("@PADDLE_VERSION@"))
' 2>/dev/null)

5
paddle/utils/CMakeLists.txt
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@ -1,8 +1,9 @@
# The utilities for paddle
file(GLOB UTIL_HEADERS . *.h)
file(GLOB UTIL_SOURCES . *.cpp)
create_resources(enable_virtualenv.py enable_virtualenv.c)
set(UTIL_RES enable_virtualenv.c)
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)
if(APPLE)
file(GLOB UTIL_ARCH_SOURCES . arch/osx/*.cpp)

5
python/paddle/v2/inference.py
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@ -79,8 +79,9 @@ def infer(output_layer, parameters, input, feeding=None, field='value'):
.. code-block:: python
result = paddle.infer(prediction, parameters, input=SomeData,
batch_size=32)
result = paddle.infer(outptut_layer=prediction,
parameters=parameters,
input=SomeData)
print result
:param output_layer: output of the neural network that would be inferred

2
python/paddle/v2/parameters.py
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@ -249,7 +249,7 @@ class Parameters(object):
size = reduce(lambda a, b: a * b, param.shape)
f.write(struct.pack("IIQ", 0, 4, size))
param = param.astype(np.float32)
f.write(param.tobytes())
f.write(param.tostring())
def deserialize(self, name, f):
"""

4
python/paddle/v2/plot/tests/CMakeLists.txt
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@ -1,3 +1 @@
add_test(NAME test_ploter
COMMAND bash ${PROJ_ROOT}/python/paddle/v2/plot/tests/run_tests.sh
${PYTHON_EXECUTABLE})
add_python_test(test_ploter test_ploter.py)

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