Merge pull request #4 from dmlc/master

merge back

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8.7)
+cmake_minimum_required(VERSION 2.8.7)
 
 project(mxnet C CXX)
 
@@ -47,13 +47,13 @@ if(USE_OPENCV)
 endif()
 
 if(USE_OPENMP)
- FIND_PACKAGE( OpenMP REQUIRED)  
- if(OPENMP_FOUND)  
-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")  
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")  
-  set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")  
-  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")  
- endif()  
+ FIND_PACKAGE( OpenMP REQUIRED)
+ if(OPENMP_FOUND)
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+  set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+ endif()
 endif()
 
 # cudnn detection
@@ -86,11 +86,11 @@ if(NOT MSVC)
   # Only add c++11 flags and definitions after cuda compiling
   add_definitions(-DDMLC_USE_CXX11)
   add_definitions(-DMSHADOW_IN_CXX11)
-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c++0x")  
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x")  
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c++0x")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x")
 endif()
 
-add_library(mxnet SHARED ${SOURCE}) 
+add_library(mxnet SHARED ${SOURCE})
 target_link_libraries(mxnet ${mshadow_LINKER_LIBS})
 target_link_libraries(mxnet dmlccore)
 target_link_libraries(mxnet pslite)

R-package/R/io.R

@@ -36,11 +36,17 @@ mx.io.extract <- function(iter, field) {
 #' @param shuffle Whether shuffle the data
 #'
 #' @export
-mx.io.arrayiter <- function(data, label=NULL,
+mx.io.arrayiter <- function(data, label,
                             batch.size=128,
                             shuffle=FALSE) {
+  if (shuffle) {
+    unif.rnds <- as.array(mx.runif(c(length(label)), ctx=mx.cpu()));
+  } else {
+    unif.rnds <- mx.array(0)
+  }
   mx.io.internal.arrayiter(as.array(data),
                            as.array(label),
+                           unif.rnds,
                            batch.size,
                            shuffle)
 }

R-package/README.md

@@ -1,18 +1,23 @@
 MXNet R-Package
 ===============
-The MXNet R packages brings flexible and efficient GPU computing and deep learning to R.
+
+You have find MXNet R Package! The MXNet R packages brings flexible and efficient GPU
+computing and state-of-art deep learning to R.
 
 - It enables you to write seamless tensor/matrix computation with multiple GPUs in R.
 - It also enables you construct and customize the state-of-art deep learning models in R,
   and apply them to tasks such as image classification and data science challenges.
 
-Document
---------
+Sounds exciting? This page contains links to all the related documents on R package.
+
+Resources
+---------
 * [MXNet R Package Document](http://mxnet.readthedocs.org/en/latest/R-package/index.html)
-  - This is a online hosted documents for mxnet examples etc.
+  - Check this out for detailed documents, examples, installation guides.
+
 
 Installation
 ------------
-- First build ```../lib/libmxnet.so``` by following [Build Instruction](../doc/build.md)
-- Type ```R CMD INSTALL R-package``` in the root folder.
+Follow [Installation Guide](http://mxnet.readthedocs.org/en/latest/build.html)
+
 

R-package/demo/basic_training.R

@@ -12,23 +12,23 @@ act2 <- mx.symbol.Activation(fc2, name="relu2", act_type="relu")
 fc3 <- mx.symbol.FullyConnected(act2, name="fc3", num_hidden=10)
 softmax <- mx.symbol.Softmax(fc3, name = "sm")
 
-dtrain = mx.varg.io.MNISTIter(list(
+dtrain = mx.io.MNISTIter(
   image="data/train-images-idx3-ubyte",
   label="data/train-labels-idx1-ubyte",
   data.shape=c(784),
   batch.size=batch.size,
   flat=TRUE,
   silent=0,
-  seed=10))
+  seed=10)
 
-dtest = mx.varg.io.MNISTIter(list(
+dtest = mx.io.MNISTIter(
   image="data/t10k-images-idx3-ubyte",
   label="data/t10k-labels-idx1-ubyte",
   data.shape=c(784),
   batch.size=batch.size,
   shuffle=FALSE,
   flat=TRUE,
-  silent=0))
+  silent=0)
 # X is R's array, we load from mxnet's native iter structure, but you don't have to
 X = mx.io.extract(dtrain, "data")
 y = mx.io.extract(dtrain, "label")

R-package/src/base.h

@@ -23,8 +23,10 @@ namespace R {
 
 /*! \brief macro to be compatible with non c++11 env */
 #if DMLC_USE_CXX11 == 0
+#ifndef nullptr
 #define nullptr NULL
 #endif
+#endif
 
 /*!
  * \brief Log that enables Stop and print message to R console
@@ -90,8 +92,6 @@ void SetSeed(int seed);
  * \brief Base Movable class of MXNet Module object.
  *  This class will define several common functions.
  * \tparam Class The class name of subclass
- * \tparam HandleType The type of handle the object have.
- * \tparam finalizer The free function used to delete the handle.
  */
 template<typename Class>
 class MXNetMovable {
@@ -116,15 +116,6 @@ class MXNetMovable {
  protected:
   /*! \brief default constructor */
   MXNetMovable() : moved_(false) {}
-  /*!
-   * \brief the finalizer for Rcpp
-   * \param self the pointer to the class.
-   */
-  inline static void Finalizer(Class* self) {
-    if (!static_cast<MXNetMovable<Class>*>(self)->moved_) {
-      self->DoFinalize();
-    }
-  }
   /*!
    * \brief Default implement to Move a existing R Class object to a new one.
    * \param src The source R Object.
@@ -137,7 +128,6 @@ class MXNetMovable {
     return Rcpp::internal::make_new_object(moved);
   }
 
- private:
   /*! \brief Whether the object has been moved */
   bool moved_;
 };

R-package/src/executor.cc

@@ -220,7 +220,6 @@ Executor::RObjectType Executor::Bind(const Symbol::RObjectType& symbol,
 void Executor::InitRcppModule() {
   using namespace Rcpp;  // NOLINT(*)
   class_<Executor>("MXExecutor")
-      .finalizer(&Executor::Finalizer)
       .method("update.aux.arrays",
               &Executor::UpdateAuxArray,
               "Update auxilary states array of executor, this will mutate the executor")

R-package/src/executor.h

@@ -120,23 +120,26 @@ class Executor : public MXNetMovable<Executor> {
   static void InitRcppModule();
   // destructor
   ~Executor() {
-    // delete can handle nullptr safely
     delete out_arrays_;
     delete arg_arrays_;
     delete grad_arrays_;
     delete aux_arrays_;
+
+    if (!this->moved_) {
+      MX_CALL(MXExecutorFree(handle_));
+    }
   }
 
  private:
   // friend with symbol
   friend class Symbol;
-  friend class MXNetMovable<Executor>;
   // internal constructor, enable trivial operator=
   Executor()
       : out_arrays_(nullptr),
         arg_arrays_(nullptr),
         grad_arrays_(nullptr),
         aux_arrays_(nullptr) {}
+
   /*! \return a new Object that is moved from current one */
   inline Executor* CreateMoveObject() {
     Executor *moved = new Executor();
@@ -147,10 +150,6 @@ class Executor : public MXNetMovable<Executor> {
     aux_arrays_ = nullptr;
     return moved;
   }
-  // finalizer that invoked on non-movable object
-  inline void DoFinalize() {
-    MX_CALL(MXExecutorFree(handle_));
-  }
   /*!
    * \brief Clone src into a new space.
    * \param src source list of arrays to clone.

R-package/src/io.cc

@@ -12,10 +12,6 @@
 
 namespace mxnet {
 namespace R {
-// Rcpp random wrapper
-inline size_t RcppRandWrapper(const size_t n) {
-  return floor(unif_rand() * n);
-}
 
 void MXDataIter::Reset() {
   MX_CALL(MXDataIterBeforeFirst(handle_));
@@ -44,14 +40,22 @@ Rcpp::List MXDataIter::Value() const {
 
 ArrayDataIter::ArrayDataIter(const Rcpp::NumericVector& data,
                              const Rcpp::NumericVector& label,
+                             const Rcpp::NumericVector& unif_rnds,
                              int batch_size,
                              bool shuffle) : counter_(0) {
   std::vector<size_t> order(label.size());
   for (size_t i = 0; i < order.size(); ++i) {
     order[i] = i;
   }
+
   if (shuffle) {
-    std::random_shuffle(order.begin(), order.end(), RcppRandWrapper);
+    RCHECK(unif_rnds.size() == label.size());
+    for (size_t i = order.size() - 1; i != 0; --i) {
+      size_t idx = static_cast<size_t>(unif_rnds[i] * (i + 1));
+      if (idx < i) {
+        std::swap(order[i], order[idx]);
+      }
+    }
   }
   ArrayDataIter::Convert(data, order, batch_size, &data_);
   ArrayDataIter::Convert(label, order, batch_size, &label_);
@@ -118,9 +122,11 @@ int ArrayDataIter::NumPad() const {
 
 Rcpp::RObject ArrayDataIter::Create(const Rcpp::NumericVector& data,
                                     const Rcpp::NumericVector& label,
+                                    const Rcpp::NumericVector& unif_rnds,
                                     size_t batch_size,
                                     bool shuffle) {
-  return Rcpp::internal::make_new_object(new ArrayDataIter(data, label, batch_size, shuffle));
+  return Rcpp::internal::make_new_object(
+      new ArrayDataIter(data, label, unif_rnds, batch_size, shuffle));
 }
 
 DataIterCreateFunction::DataIterCreateFunction
@@ -185,12 +191,10 @@ void DataIter::InitRcppModule() {
       .method("num.pad", &DataIter::NumPad);
 
   class_<MXDataIter>("MXNativeDataIter")
-      .derives<DataIter>("MXDataIter")
-      .finalizer(&MXDataIter::Finalizer);
+      .derives<DataIter>("MXDataIter");
 
   class_<ArrayDataIter>("MXArrayDataIter")
-      .derives<DataIter>("MXDataIter")
-      .finalizer(&ArrayDataIter::Finalizer);
+      .derives<DataIter>("MXDataIter");
 
   function("mx.io.internal.arrayiter", &ArrayDataIter::Create);
 }

R-package/src/io.h

@@ -61,6 +61,9 @@ class MXDataIter : public DataIter {
   virtual bool Next();
   virtual int NumPad() const;
   virtual Rcpp::List Value() const;
+  virtual ~MXDataIter() {
+    MX_CALL(MXDataIterFree(handle_));
+  }
 
  private:
   friend class DataIter;
@@ -76,10 +79,6 @@ class MXDataIter : public DataIter {
   inline static Rcpp::RObject RObject(DataIterHandle handle) {
     return Rcpp::internal::make_new_object(new MXDataIter(handle));
   }
-  // finalizer that invoked on non-movable object
-  static void Finalizer(MXDataIter *iter) {
-    MX_CALL(MXDataIterFree(iter->handle_));
-  }
   /*! \brief internal data iter handle */
   DataIterHandle handle_;
 };
@@ -100,11 +99,14 @@ class ArrayDataIter : public DataIter {
    * \brief Construct a ArrayDataIter from data and label.
    * \param data The data array.
    * \param label The label array.
+   * \param unif_rnds Uniform [0,1] random number of same length as label.
+   *        Only needed when shuffle=TRUE
    * \param batch_size The size of the batch.
    * \param shuffle Whether shuffle the data.
    */
   ArrayDataIter(const Rcpp::NumericVector& data,
                 const Rcpp::NumericVector& label,
+                const Rcpp::NumericVector& unif_rnds,
                 int batch_size,
                 bool shuffle);
   virtual void Reset() {
@@ -115,6 +117,7 @@ class ArrayDataIter : public DataIter {
   virtual Rcpp::List Value() const;
   static Rcpp::RObject Create(const Rcpp::NumericVector& data,
                               const Rcpp::NumericVector& label,
+                              const Rcpp::NumericVector& unif_rnds,
                               size_t batch_size,
                               bool shuffle);
 
@@ -125,11 +128,6 @@ class ArrayDataIter : public DataIter {
                       const std::vector<size_t> &order,
                       size_t batch_size,
                       std::vector<NDArray> *out);
-  // finalizer that invoked on non-movable object
-  static void Finalizer(ArrayDataIter *iter) {
-    iter->data_.clear();
-    iter->label_.clear();
-  }
   /*! \brief The counter */
   size_t counter_;
   /*! \brief number of pad instances*/

R-package/src/kvstore.cc

@@ -152,7 +152,6 @@ Rcpp::RObject KVStore::Create(const char *type) {
 void KVStore::InitRcppModule() {
   using namespace Rcpp;  // NOLINT(*)
   class_<KVStore>("MXKVStore")
-      .finalizer(&KVStore::Finalizer)
       .method("init", &KVStore::Init)
       .method("push", &KVStore::Push)
       .method("pull", &KVStore::Pull)

R-package/src/kvstore.h

@@ -68,13 +68,14 @@ class KVStore {
   static Rcpp::RObject Create(const char *type);
   /*! \brief initialize the R cpp Module */
   static void InitRcppModule();
+  // destructor
+  ~KVStore() {
+    MX_CALL(MXKVStoreFree(handle_));
+  }
 
  private:
   explicit KVStore(KVStoreHandle handle)
       : handle_(handle), optimizer_set_(false) {}
-  static void Finalizer(KVStore *kv) {
-    MX_CALL(MXKVStoreFree(kv->handle_));
-  }
   // the internal callback to kvstore.
   NDArray CreateState(int index, const NDArray& weight) const;
   /*! \brief internal KVStore handle */

R-package/src/ndarray.h

@@ -91,6 +91,7 @@ class NDArray  {
   // operator overloading
   inline NDArray& operator=(const NDArray& other) {
     ptr_ = other.ptr_;
+    return *this;
   }
   inline NDBlob* operator->() {
     return ptr_.get();

R-package/src/symbol.cc

@@ -296,7 +296,6 @@ SEXP SymbolFunction::operator() (SEXP* args) {
 void Symbol::InitRcppModule() {
   using namespace Rcpp;  // NOLINT(*)
   class_<Symbol>("MXSymbol")
-      .finalizer(&Symbol::Finalizer)
       .method("debug.str", &Symbol::DebugStr,
               "Return the debug string of internals of symbol")
       .method("apply", &Symbol::Apply,