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

cmake/external/swig.cmake

@@ -38,14 +38,6 @@ IF(NOT SWIG_FOUND)
         SET(SWIG_DIR ${SWIG_SOURCES_DIR} CACHE FILEPATH "SWIG Directory" FORCE)
         SET(SWIG_EXECUTABLE ${SWIG_SOURCES_DIR}/swig.exe  CACHE FILEPATH "SWIG Executable" FORCE)
     ELSE(WIN32)
-        # From PCRE configure
-        ExternalProject_Add(pcre
-            ${EXTERNAL_PROJECT_LOG_ARGS}
-            GIT_REPOSITORY https://github.com/svn2github/pcre.git
-            PREFIX ${SWIG_SOURCES_DIR}/pcre
-            CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${SWIG_INSTALL_DIR}/pcre
-        )
-
         # swig uses bison find it by cmake and pass it down
         FIND_PACKAGE(BISON)
 
@@ -54,16 +46,11 @@ IF(NOT SWIG_FOUND)
             GIT_REPOSITORY      https://github.com/swig/swig.git
             GIT_TAG             rel-3.0.10
             PREFIX              ${SWIG_SOURCES_DIR}
-            CONFIGURE_COMMAND   cd ${SWIG_SOURCES_DIR}/src/swig && ./autogen.sh
-            CONFIGURE_COMMAND   cd ${SWIG_SOURCES_DIR}/src/swig &&
-            env "PCRE_LIBS=${SWIG_INSTALL_DIR}/pcre/lib/libpcre.a ${SWIG_INSTALL_DIR}/pcre/lib/libpcrecpp.a ${SWIG_INSTALL_DIR}/pcre/lib/libpcreposix.a"
-            ./configure
-                --prefix=${SWIG_INSTALL_DIR}
-                --with-pcre-prefix=${SWIG_INSTALL_DIR}/pcre
-            BUILD_COMMAND   cd ${SWIG_SOURCES_DIR}/src/swig && make
-            INSTALL_COMMAND cd ${SWIG_SOURCES_DIR}/src/swig && make install
+            CONFIGURE_COMMAND   cd <SOURCE_DIR> && ./autogen.sh && ./configure
+                                --prefix=${SWIG_INSTALL_DIR} --without-pcre
+            BUILD_COMMAND       cd <SOURCE_DIR> && make
+            INSTALL_COMMAND     cd <SOURCE_DIR> && make install
             UPDATE_COMMAND      ""
-            DEPENDS pcre
         )
 
         SET(SWIG_DIR ${SWIG_INSTALL_DIR}/share/swig/${SWIG_TARGET_VERSION})

demo/traffic_prediction/predict.sh

@@ -25,6 +25,6 @@ paddle train \
     --config_args=is_predict=1 \
     --predict_output_dir=. 
 
-python gen_result.py > result.txt
+python gen_result.py > result.csv
 
 rm -rf rank-00000

doc/getstarted/build_and_install/build_from_source_en.md

@@ -18,9 +18,10 @@ cd paddle
 
 To compile the source code, your computer must be equipped with the following dependencies.
 
-- **Compiler**: GCC >= 4.8 or Clang >= 3.3 (AppleClang >= 5.1)
-- **CMake**: version >= 3.0 (at least CMake 3.4 on Mac OS X)
+- **Compiler**: GCC >= 4.8 or Clang >= 3.3 (AppleClang >= 5.1) and gfortran compiler
+- **CMake**: CMake >= 3.0 (at least CMake 3.4 on Mac OS X)
 - **BLAS**: MKL, OpenBlas or ATLAS
+- **Python**: only support Python 2.7
 
 **Note:** For CUDA 7.0 and CUDA 7.5, GCC 5.0 and up are not supported!
 For CUDA 8.0, GCC versions later than 5.3 are not supported!
@@ -97,14 +98,19 @@ As a simple example, consider the following:
 
 ### Install Dependencies
 
-- **CPU Dependencies**
+- **Paddle Dependencies**
 
     ```bash
     # necessary
     sudo apt-get update
-    sudo apt-get install -y g++ make cmake build-essential python python-pip libpython-dev git
-    sudo pip install wheel numpy
-    sudo pip install 'protobuf>=3.0.0'
+    sudo apt-get install -y git curl gcc g++ gfortran make build-essential automake
+    sudo apt-get install -y python python-pip python-numpy libpython-dev bison
+    sudo pip install 'protobuf==3.1.0.post1'
+
+    # install cmake 3.4
+    curl -sSL https://cmake.org/files/v3.4/cmake-3.4.1.tar.gz | tar -xz && \
+        cd cmake-3.4.1 && ./bootstrap && make -j4 && sudo make install && \
+        cd .. && rm -rf cmake-3.4.1
     ```
 
 - **GPU Dependencies (optional)**

paddle/math/RowBuffer.h

+/* Copyright (c) 2016 PaddlePaddle Authors. 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. */
+
+#pragma once
+#include <vector>
+#include "MemoryHandle.h"
+#include "paddle/utils/Util.h"
+
+namespace paddle {
+
+/**
+ * @brief The RowBuffer class
+ * Represent the SparseRow Matrix Data.
+ *
+ * If not set memory handler, then the data could be auto growth.
+ */
+class RowBuffer {
+public:
+  /**
+   * @brief RowBuffer create a auto-growth row buffer. The row length is width.
+   * @param width the length of each row, a.k.a matrix width.
+   */
+  explicit RowBuffer(size_t width) : width_(width) {}
+
+  /**
+   * @brief RowBuffer create a row buffer, which cannot be auto-growth.
+   * @param mem the pre-allocated memory.
+   * @param width the length of each row, a.k.a matrix width.
+   */
+  RowBuffer(const CpuMemHandlePtr& mem, size_t width)
+      : preallocatedBuf_(mem), width_(width) {}
+
+  /**
+   * @brief resize resize the buffer with rowCount
+   * @param rowCnt number of row. matrix height.
+   */
+  inline void resize(int rowCnt) {
+    if (preallocatedBuf_) {
+      CHECK(preallocatedBuf_->getSize() >= rowCnt * width_ * sizeof(real));
+    } else {
+      rowStore_.resize(rowCnt * width_);
+    }
+  }
+
+  /**
+   * @brief get a row buffer with row index.
+   * @param row the index of row.
+   * @return row buffer.
+   */
+  inline real* get(int row) const {
+    if (preallocatedBuf_) {
+      CHECK_LE((row + 1) * width_ * sizeof(real), preallocatedBuf_->getSize());
+      return reinterpret_cast<real*>(preallocatedBuf_->getBuf()) + row * width_;
+    } else {
+      CHECK_LE((row + 1) * width_, rowStore_.size());
+      return const_cast<real*>(rowStore_.data() + row * width_);
+    }
+  }
+
+  /**
+   * @brief get a row buffer with row index. If row index is larger than local
+   *        buffer, the size of local buffer will grow.
+   * @param row the index of row.
+   * @return row buffer.
+   */
+  inline real* getWithAutoGrowth(int row) {
+    if (preallocatedBuf_) {
+      return get(row);
+    } else {
+      if ((rowStore_.size() <= row * width_)) {
+        rowStore_.resize((row + 1) * width_);
+      }
+      return rowStore_.data() + row * width_;
+    }
+  }
+
+  /**
+   * @return raw data buffer.
+   */
+  inline real* data() {
+    if (preallocatedBuf_) {
+      return reinterpret_cast<real*>(preallocatedBuf_->getBuf());
+    } else {
+      return rowStore_.data();
+    }
+  }
+
+  /**
+   * @brief clear local buffer. It only affect auto-growth buffer.
+   */
+  inline void clear() { rowStore_.clear(); }
+
+  /**
+   * @brief get current number of rows.
+   * @return number of rows.
+   */
+  inline size_t getRowCount() const {
+    if (preallocatedBuf_) {
+      return preallocatedBuf_->getSize() / sizeof(real) / width_;
+    } else {
+      return rowStore_.size() / width_;
+    }
+  }
+
+  /**
+   * @brief get is this buffer can automatically grow or not.
+   * @return ture if can automacitally grow.
+   */
+  inline bool isAutoGrowth() const { return !preallocatedBuf_; }
+
+  /**
+   * @brief return the width of matrix. a.k.a length of row.
+   * @return width of matrix
+   */
+  inline size_t getWidth() const { return width_; }
+
+private:
+  //! TODO(yuyang18): Add resize method to CpuMemHandlePtr, then we can get rid
+  //! of std::vector here.
+  CpuMemHandlePtr preallocatedBuf_;
+  std::vector<real, AlignedAllocator<real, 32>> rowStore_;
+  size_t width_;
+};
+}  // namespace paddle

paddle/math/SparseRowMatrix.h

@@ -18,6 +18,7 @@ limitations under the License. */
 #include <string.h>
 #include <algorithm>
 #include "Matrix.h"
+#include "RowBuffer.h"
 #include "paddle/utils/Util.h"
 
 DECLARE_bool(allow_inefficient_sparse_update);
@@ -45,12 +46,9 @@ public:
                      IndexDictPtr indexDictHandle = nullptr,
                      bool trans = false)
       : CpuMatrix(nullptr, height, width, trans),
-        storeMat_(dataHandle,
-                  dataHandle ? dataHandle->getSize() / sizeof(real) / width : 0,
-                  width,
-                  trans),
         indexDictHandle_(indexDictHandle) {
     init(height, width);
+    buf_.reset(new RowBuffer(dataHandle, width));
   }
 
   virtual ~SparseRowCpuMatrix() {}
@@ -71,25 +69,16 @@ public:
    *
    *  @param row row id in local storage
    */
-  real* getLocalRow(size_t row) {
-    if (storeMat_.getData()) return storeMat_.rowBuf(row);
-    if (rowStore_.size() <= row * width_) {
-      rowStore_.resize((row + 1) * width_);
-    }
-    return rowStore_.data() + row * width_;
-  }
+  real* getLocalRow(size_t row) { return buf_->getWithAutoGrowth(row); }
 
   /**
-   *  reserve the storage for rows according to current size of indexDictHandle.
+   *  reserve the storage for rows according to current size of
+   * indexDictHandle.
    *
    *  This is only used when SparseRowCpuMatrix is constructed with
    *  indexDictHandle.
    */
-  void reserveStore() {
-    if (!storeMat_.getData() && !localIndices_->empty()) {
-      rowStore_.resize(localIndices_->size() * width_);
-    }
-  }
+  void reserveStore() { buf_->resize(localIndices_->size()); }
 
   // row is the row id in the original matrix
   virtual real* getRowBuf(size_t row) { return getRow(row); }
@@ -117,7 +106,8 @@ public:
    *
    * If L1 decay set use L1, else if L2 set use L2, otherwise no decay atall.
    *
-   * t0 is a int vector used by L1/L2 decay, size = height of parameter matrix,
+   * t0 is a int vector used by L1/L2 decay, size = height of parameter
+   * matrix,
    * store the time that each weight row last updated.
    *
    * Time is batchId, currentTime is current batchId.
@@ -176,8 +166,7 @@ public:
 protected:
   template <typename Func>
   void apply(Func f) {
-    real* data = storeMat_.getData() ? storeMat_.getData() : rowStore_.data();
-    f(data, localIndices_->size() * width_);
+    f(buf_->data(), localIndices_->size() * width_);
   }
 
   void init(size_t height, size_t width);
@@ -188,25 +177,24 @@ protected:
       globalIndices_[id] = kUnusedId_;
     }
     localIndices_->clear();
-    rowStore_.clear();
+    buf_->clear();
   }
 
   inline void checkStoreSize() {
-    if (storeMat_.getData()) {
-      CHECK_LE(localIndices_->size(), storeMat_.getHeight());
-    } else if (!FLAGS_allow_inefficient_sparse_update) {
-      if (localIndices_->size() > 0.5 * height_) {
+    if (buf_->isAutoGrowth()) {
+      if (buf_->getRowCount() > 0.5 * height_) {
         LOG(WARNING)
             << "There are more than 0.5*height (" << localIndices_->size()
             << ") rows are used for sparse "
             << "update, which is not efficient. Considering not use "
             << "sparse_update or set --allow_inefficient_sparse_update=true";
       }
+    } else {
+      CHECK_LE(localIndices_->size(), buf_->getRowCount());
     }
   }
 
-  CpuMatrix storeMat_;
-  std::vector<real, AlignedAllocator<real, 32>> rowStore_;
+  std::unique_ptr<RowBuffer> buf_;
   IndexDictPtr indexDictHandle_;
   std::vector<unsigned int>* localIndices_;  // =&indexDictHandle_->localIndices
   unsigned int* globalIndices_;  // =indexDictHandle_->globalIndices.data();

paddle/math/tests/CMakeLists.txt

@@ -4,6 +4,7 @@ add_simple_unittest(test_ExecViaCpu)
 add_simple_unittest(test_SIMDFunctions)
 add_simple_unittest(test_TrainingAlgorithm)
 add_simple_unittest(test_SparseMatrix)
+add_simple_unittest(test_RowBuffer)
 
 # TODO(yuyang18): Refactor TestUtil.cpp. Remove this cross module reference.
 add_unittest(test_matrixCompare

paddle/math/tests/test_RowBuffer.cpp

+/* Copyright (c) 2016 PaddlePaddle Authors. 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 <gtest/gtest.h>
+#include "paddle/math/RowBuffer.h"
+
+TEST(RowBuffer, testAutoGrow) {
+  paddle::RowBuffer buf(128);
+  ASSERT_EQ(128, buf.getWidth());
+  ASSERT_TRUE(buf.isAutoGrowth());
+  buf.resize(2);
+  ASSERT_EQ(2, buf.getRowCount());
+  for (size_t i = 0; i < buf.getWidth() * 2; ++i) {
+    buf.data()[i] = i;
+  }
+  for (size_t i = 0; i < buf.getRowCount(); ++i) {
+    for (size_t j = 0; j < buf.getWidth(); ++j) {
+      ASSERT_NEAR(i * buf.getWidth() + j, buf.get(i)[j], 1e-5);
+    }
+  }
+
+  auto data = buf.getWithAutoGrowth(2);
+  for (size_t i = 0; i < buf.getWidth(); ++i) {
+    data[i] = i;
+  }
+
+  ASSERT_EQ(3, buf.getRowCount());
+  for (size_t i = 0; i < buf.getRowCount() - 1; ++i) {
+    for (size_t j = 0; j < buf.getWidth(); ++j) {
+      ASSERT_NEAR(i * buf.getWidth() + j, buf.get(i)[j], 1e-5);
+    }
+  }
+  for (size_t i = 0; i < buf.getWidth(); ++i) {
+    ASSERT_NEAR(i, buf.get(2)[i], 1e-5);
+  }
+}
+
+TEST(RowBuffer, testWithMemBuf) {
+  paddle::CpuMemHandlePtr mem =
+      std::make_shared<paddle::CpuMemoryHandle>(128 * 2 * sizeof(real));
+  paddle::RowBuffer buf(mem, 128);
+  ASSERT_TRUE(!buf.isAutoGrowth());
+  ASSERT_EQ(2, buf.getRowCount());
+  for (size_t i = 0; i < buf.getWidth() * 2; ++i) {
+    buf.data()[i] = i;
+  }
+  for (size_t i = 0; i < buf.getRowCount(); ++i) {
+    for (size_t j = 0; j < buf.getWidth(); ++j) {
+      ASSERT_NEAR(i * buf.getWidth() + j, buf.getWithAutoGrowth(i)[j], 1e-5);
+    }
+  }
+
+  ASSERT_DEATH_IF_SUPPORTED(buf.getWithAutoGrowth(3), ".*");
+}

paddle/scripts/docker/Dockerfile

@@ -4,28 +4,32 @@ MAINTAINER PaddlePaddle Authors <paddle-dev@baidu.com>
 ARG DEBIAN_FRONTEND=noninteractive
 ARG UBUNTU_MIRROR
 RUN /bin/bash -c 'if [[ -n ${UBUNTU_MIRROR} ]]; then sed -i 's#http://archive.ubuntu.com#${UBUNTU_MIRROR}#g' /etc/apt/sources.list; fi'
-RUN apt-get update \
-    && apt-get install -y cmake libprotobuf-dev protobuf-compiler git \
-    libgoogle-glog-dev libgflags-dev libgtest-dev \
-    libatlas-dev libatlas3-base g++ m4 python-pip \
-    python-protobuf python-numpy python-dev swig openssh-server \
-    wget unzip python-matplotlib tar xz-utils bzip2 gzip coreutils \
-    sed grep graphviz libjpeg-dev zlib1g-dev doxygen \
-    clang-3.8 llvm-3.8 libclang-3.8-dev \
-    && apt-get clean -y
-RUN cd /usr/src/gtest && cmake . && make && cp *.a /usr/lib
-RUN pip install -U BeautifulSoup docopt PyYAML pillow \
-    sphinx sphinx_rtd_theme recommonmark jupyter
+
+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 automake clang-3.8 llvm-3.8 libclang-3.8-dev && \
+    apt-get clean -y
+
+RUN pip install --upgrade pip && \ 
+    pip install 'protobuf==3.1.0.post1' && \
+    pip install -U wheel pillow BeautifulSoup && \
+    pip install -U docopt PyYAML sphinx && \
+    pip install -U sphinx_rtd_theme recommonmark jupyter
+
+RUN curl -sSL https://cmake.org/files/v3.4/cmake-3.4.1.tar.gz | tar -xz && \
+    cd cmake-3.4.1 && ./bootstrap && make -j4 && make install && \
+    cd .. && rm -rf cmake-3.4.1
 
 ARG WITH_AVX
 ARG WITH_DOC
-ARG WITH_SWIG_PY
 ARG WITH_STYLE_CHECK
 
 ENV WITH_GPU=OFF
 ENV WITH_AVX=${WITH_AVX:-ON}
 ENV WITH_DOC=${WITH_DOC:-ON}
-ENV WITH_SWIG_PY=${WITH_SWIG_PY:-ON}
 ENV WITH_STYLE_CHECK=${WITH_STYLE_CHECK:-OFF}
 
 RUN mkdir /paddle

paddle/scripts/docker/Dockerfile.gpu

@@ -4,28 +4,32 @@ MAINTAINER PaddlePaddle Authors <paddle-dev@baidu.com>
 ARG DEBIAN_FRONTEND=noninteractive
 ARG UBUNTU_MIRROR
 RUN /bin/bash -c 'if [[ -n ${UBUNTU_MIRROR} ]]; then sed -i 's#http://archive.ubuntu.com#${UBUNTU_MIRROR}#g' /etc/apt/sources.list; fi'
-RUN apt-get update \
-    && apt-get install -y cmake libprotobuf-dev protobuf-compiler git \
-    libgoogle-glog-dev libgflags-dev libgtest-dev \
-    libatlas-dev libatlas3-base g++ m4 python-pip \
-    python-protobuf python-numpy python-dev swig openssh-server \
-    wget unzip python-matplotlib tar xz-utils bzip2 gzip coreutils \
-    sed grep graphviz libjpeg-dev zlib1g-dev doxygen \
-    clang-3.8 llvm-3.8 libclang-3.8-dev \
-    && apt-get clean -y
-RUN cd /usr/src/gtest && cmake . && make && cp *.a /usr/lib
-RUN pip install -U BeautifulSoup docopt PyYAML pillow \
-    sphinx sphinx_rtd_theme recommonmark jupyter
+
+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 automake clang-3.8 llvm-3.8 libclang-3.8-dev && \
+    apt-get clean -y
+
+RUN pip install --upgrade pip && \ 
+    pip install 'protobuf==3.1.0.post1' && \
+    pip install -U wheel pillow BeautifulSoup && \
+    pip install -U docopt PyYAML sphinx && \
+    pip install -U sphinx_rtd_theme recommonmark jupyter
+
+RUN curl -sSL https://cmake.org/files/v3.4/cmake-3.4.1.tar.gz | tar -xz && \
+    cd cmake-3.4.1 && ./bootstrap && make -j4 && make install && \
+    cd .. && rm -rf cmake-3.4.1
 
 ARG WITH_AVX
 ARG WITH_DOC
-ARG WITH_SWIG_PY
 ARG WITH_STYLE_CHECK
 
 ENV WITH_GPU=ON
 ENV WITH_AVX=${WITH_AVX:-ON}
 ENV WITH_DOC=${WITH_DOC:-ON}
-ENV WITH_SWIG_PY=${WITH_SWIG_PY:-ON}
 ENV WITH_STYLE_CHECK=${WITH_STYLE_CHECK:-OFF}
 
 RUN mkdir /paddle