finish refactor, need debug

Makefile

@@ -1,19 +1,19 @@
 export CC  = gcc
 export CXX = g++
 export LDFLAGS= -pthread -lm 
-# note for R module
-# add include path to Rinternals.h here
+
+export CFLAGS = -Wall -O3 -msse2  -Wno-unknown-pragmas -fPIC
 
 ifeq ($(no_omp),1)
-	export CFLAGS = -Wall -O3 -msse2  -Wno-unknown-pragmas -DDISABLE_OPENMP -funroll-loops 
-else
-	export CFLAGS = -Wall -O3 -msse2 -Wno-unknown-pragmas -fopenmp  -funroll-loops 
+	CFLAGS += -DDISABLE_OPENMP 
+else 
+	CFLAGS += -fopenmp
 endif
 
 # specify tensor path
-BIN =
-OBJ = updater.o gbm.o xgboost_main.o
-#SLIB = wrapper/libxgboostwrapper.so 
+BIN = xgboost
+OBJ = updater.o gbm.o io.o
+SLIB = wrapper/libxgboostwrapper.so 
 #RLIB = wrapper/libxgboostR.so 
 .PHONY: clean all R python
 
@@ -22,10 +22,11 @@ all: $(BIN) $(OBJ)
 #xgboost: src/xgboost_main.cpp src/io/io.cpp src/data.h src/tree/*.h src/tree/*.hpp src/gbm/*.h src/gbm/*.hpp src/utils/*.h src/learner/*.h src/learner/*.hpp 
 
 # now the wrapper takes in two files. io and wrapper part
-#wrapper/libxgboostwrapper.so: wrapper/xgboost_wrapper.cpp src/io/io.cpp src/*.h src/*/*.hpp src/*/*.h
+wrapper/libxgboostwrapper.so: wrapper/xgboost_wrapper.cpp $(OBJ)
 updater.o: src/tree/updater.cpp 
 gbm.o: src/gbm/gbm.cpp 
-xgboost_main.o: src/xgboost_main.cpp
+io.o: src/io/io.cpp
+xgboost: src/xgboost_main.cpp $(OBJ)
 
 $(BIN) : 
 	$(CXX) $(CFLAGS) $(LDFLAGS) -o $@ $(filter %.cpp %.o %.c, $^)

src/data.h

@@ -78,7 +78,7 @@ struct SparseBatch {
     /*! \brief pointer to the elements*/
     const Entry *data;
     /*! \brief length of the instance */
-    const bst_uint length;
+    bst_uint length;
     /*! \brief constructor */
     Inst(const Entry *data, bst_uint length) : data(data), length(length) {}
     /*! \brief get i-th pair in the sparse vector*/
@@ -147,7 +147,7 @@ class IFMatrix {
   /*! \return number of columns in the FMatrix */
   virtual size_t NumCol(void) const = 0;
   /*! \brief get number of non-missing entries in column */
-  virtual float GetColSize(size_t cidx) const = 0;
+  virtual size_t GetColSize(size_t cidx) const = 0;
   /*! \brief get column density */  
   virtual float GetColDensity(size_t cidx) const = 0;  
   /*! \brief reference of buffered rowset */

src/io/simple_dmatrix-inl.hpp

@@ -16,6 +16,7 @@
 #include "../utils/utils.h"
 #include "../learner/dmatrix.h"
 #include "./io.h"
+#include "./simple_fmatrix-inl.hpp"
 
 namespace xgboost {
 namespace io {
@@ -24,11 +25,16 @@ class DMatrixSimple : public DataMatrix {
  public:
   // constructor
   DMatrixSimple(void) : DataMatrix(kMagic) {
-    this->fmat.set_iter(new OneBatchIter(this));
+    fmat_ = new FMatrixS(new OneBatchIter(this));
     this->Clear();
   }
   // virtual destructor
-  virtual ~DMatrixSimple(void) {}
+  virtual ~DMatrixSimple(void) {
+    delete fmat_;
+  }
+  virtual IFMatrix *fmat(void) const {
+    return fmat_;
+  }
   /*! \brief clear the storage */
   inline void Clear(void) {
     row_ptr_.clear();
@@ -41,7 +47,7 @@ class DMatrixSimple : public DataMatrix {
     this->info = src.info;
     this->Clear();
     // clone data content in thos matrix
-    utils::IIterator<RowBatch> *iter = src.fmat.RowIterator();
+    utils::IIterator<RowBatch> *iter = src.fmat()->RowIterator();
     iter->BeforeFirst();
     while (iter->Next()) {
       const RowBatch &batch = iter->Value();
@@ -145,7 +151,7 @@ class DMatrixSimple : public DataMatrix {
 
     info.LoadBinary(fs);
     FMatrixS::LoadBinary(fs, &row_ptr_, &row_data_);
-    fmat.LoadColAccess(fs);
+    fmat_->LoadColAccess(fs);
 
     if (!silent) {
       printf("%lux%lu matrix with %lu entries is loaded",
@@ -172,7 +178,7 @@ class DMatrixSimple : public DataMatrix {
 
     info.SaveBinary(fs);
     FMatrixS::SaveBinary(fs, row_ptr_, row_data_);
-    fmat.SaveColAccess(fs);
+    fmat_->SaveColAccess(fs);
     fs.Close();
 
     if (!silent) {
@@ -212,6 +218,8 @@ class DMatrixSimple : public DataMatrix {
   std::vector<size_t> row_ptr_;
   /*! \brief data in the row */
   std::vector<RowBatch::Entry> row_data_;
+  /*! \brief the real fmatrix */
+  FMatrixS *fmat_;
   /*! \brief magic number used to identify DMatrix */
   static const int kMagic = 0xffffab01;
 
@@ -244,7 +252,7 @@ class DMatrixSimple : public DataMatrix {
     DMatrixSimple *parent_;
     // temporal space for batch
     RowBatch batch_;
-  };
+  }; 
 };
 }  // namespace io
 }  // namespace xgboost

src/learner/dmatrix.h

@@ -7,6 +7,7 @@
  * \author Tianqi Chen
  */
 #include <vector>
+#include <cstring>
 #include "../data.h"
 #include "../utils/io.h"
 namespace xgboost {
@@ -150,8 +151,6 @@ struct DMatrix {
   const int magic;
   /*! \brief meta information about the dataset */
   MetaInfo info;
-  /*! \brief feature matrix about data content */
-  IFMatrix *fmat;
   /*! 
    * \brief cache pointer to verify if the data structure is cached in some learner
    *  used to verify if DMatrix is cached
@@ -159,10 +158,10 @@ struct DMatrix {
   void *cache_learner_ptr_;
   /*! \brief default constructor */
   explicit DMatrix(int magic) : magic(magic), cache_learner_ptr_(NULL) {}
+  /*! \brief get feature matrix about data content */
+  virtual IFMatrix *fmat(void) const = 0;
   // virtual destructor
-  virtual ~DMatrix(void){
-    delete fmat;
-  }
+  virtual ~DMatrix(void){}
 };
 
 }  // namespace learner

src/learner/learner-inl.hpp

@@ -158,7 +158,7 @@ class BoostLearner {
    * \param p_train pointer to the matrix used by training
    */
   inline void CheckInit(DMatrix *p_train) {
-    p_train->fmat->InitColAccess(prob_buffer_row);
+    p_train->fmat()->InitColAccess(prob_buffer_row);
   }
   /*!
    * \brief update the model for one iteration
@@ -168,7 +168,7 @@ class BoostLearner {
   inline void UpdateOneIter(int iter, const DMatrix &train) {
     this->PredictRaw(train, &preds_);
     obj_->GetGradient(preds_, train.info, iter, &gpair_);
-    gbm_->DoBoost(train.fmat, train.info.info, &gpair_);
+    gbm_->DoBoost(train.fmat(), train.info.info, &gpair_);
   }
   /*!
    * \brief evaluate the model for specific iteration
@@ -248,7 +248,7 @@ class BoostLearner {
    */
   inline void PredictRaw(const DMatrix &data,
                          std::vector<float> *out_preds) const {
-    gbm_->Predict(data.fmat, this->FindBufferOffset(data),
+    gbm_->Predict(data.fmat(), this->FindBufferOffset(data),
                   data.info.info, out_preds);
     // add base margin
     std::vector<float> &preds = *out_preds;