Device dmatrix (#5420)

src/common/compressed_iterator.h

@@ -32,8 +32,8 @@ static const int kPadding = 4;  // Assign padding so we can read slightly off
                                // the beginning of the array
 
 // The number of bits required to represent a given unsigned range
-static size_t SymbolBits(size_t num_symbols) {
-  auto bits = std::ceil(std::log2(num_symbols));
+inline XGBOOST_DEVICE size_t SymbolBits(size_t num_symbols) {
+  auto bits = std::ceil(log2(static_cast<double>(num_symbols)));
   return std::max(static_cast<size_t>(bits), size_t(1));
 }
 }  // namespace detail
@@ -50,14 +50,11 @@ static size_t SymbolBits(size_t num_symbols) {
  */
 
 class CompressedBufferWriter {
- private:
   size_t symbol_bits_;
-  size_t offset_;
 
  public:
-  explicit CompressedBufferWriter(size_t num_symbols) : offset_(0) {
-    symbol_bits_ = detail::SymbolBits(num_symbols);
-  }
+  XGBOOST_DEVICE explicit CompressedBufferWriter(size_t num_symbols)
+      : symbol_bits_(detail::SymbolBits(num_symbols)) {}
 
   /**
    * \fn  static size_t CompressedBufferWriter::CalculateBufferSize(int
@@ -164,18 +161,15 @@ class CompressedBufferWriter {
   }
 };
 
-template <typename T>
-
 /**
- * \class CompressedIterator
- *
- * \brief Read symbols from a bit compressed memory buffer. Usable on device and
- * host.
+ * \brief Read symbols from a bit compressed memory buffer. Usable on device and host.
  *
  * \author  Rory
  * \date  7/9/2017
+ *
+ * \tparam  T Generic type parameter.
  */
-
+template <typename T>
 class CompressedIterator {
  public:
   // Type definitions for thrust

src/common/device_helpers.cuh

@@ -1540,4 +1540,12 @@ DEV_INLINE void AtomicAddGpair(OutputGradientT* dest,
             static_cast<typename OutputGradientT::ValueT>(gpair.GetHess()));
 }
 
+
+// Thrust version of this function causes error on Windows
+template <typename ReturnT, typename IterT, typename FuncT>
+thrust::transform_iterator<FuncT, IterT, ReturnT> MakeTransformIterator(
+  IterT iter, FuncT func) {
+  return thrust::transform_iterator<FuncT, IterT, ReturnT>(iter, func);
+}
+
 }  // namespace dh

src/common/hist_util.cu

@@ -338,31 +338,6 @@ HistogramCuts DeviceSketch(int device, DMatrix* dmat, int max_bins,
   return cuts;
 }
 
-struct IsValidFunctor : public thrust::unary_function<Entry, bool> {
-  explicit IsValidFunctor(float missing) : missing(missing) {}
-
-  float missing;
-  __device__ bool operator()(const data::COOTuple& e) const {
-    if (common::CheckNAN(e.value) || e.value == missing) {
-      return false;
-    }
-    return true;
-  }
-  __device__ bool operator()(const Entry& e) const {
-    if (common::CheckNAN(e.fvalue) || e.fvalue == missing) {
-      return false;
-    }
-    return true;
-  }
-};
-
-// Thrust version of this function causes error on Windows
-template <typename ReturnT, typename IterT, typename FuncT>
-thrust::transform_iterator<FuncT, IterT, ReturnT> MakeTransformIterator(
-  IterT iter, FuncT func) {
-  return thrust::transform_iterator<FuncT, IterT, ReturnT>(iter, func);
-}
-
 template <typename AdapterT>
 void ProcessBatch(AdapterT* adapter, size_t begin, size_t end, float missing,
                   SketchContainer* sketch_container, int num_cuts) {
@@ -372,10 +347,10 @@ void ProcessBatch(AdapterT* adapter, size_t begin, size_t end, float missing,
   auto &batch = adapter->Value();
   // Enforce single batch
   CHECK(!adapter->Next());
-  auto batch_iter = MakeTransformIterator<data::COOTuple>(
+  auto batch_iter = dh::MakeTransformIterator<data::COOTuple>(
     thrust::make_counting_iterator(0llu),
     [=] __device__(size_t idx) { return batch.GetElement(idx); });
-  auto entry_iter = MakeTransformIterator<Entry>(
+  auto entry_iter = dh::MakeTransformIterator<Entry>(
       thrust::make_counting_iterator(0llu), [=] __device__(size_t idx) {
         return Entry(batch.GetElement(idx).column_idx,
                      batch.GetElement(idx).value);
@@ -385,7 +360,7 @@ void ProcessBatch(AdapterT* adapter, size_t begin, size_t end, float missing,
                                                       0);
 
   auto d_column_sizes_scan = column_sizes_scan.data().get();
-  IsValidFunctor is_valid(missing);
+  data::IsValidFunctor is_valid(missing);
   dh::LaunchN(adapter->DeviceIdx(), end - begin, [=] __device__(size_t idx) {
     auto e = batch_iter[begin + idx];
     if (is_valid(e)) {

src/common/hist_util.h

@@ -105,10 +105,10 @@ class HistogramCuts {
     auto end = cut_ptrs_.ConstHostVector().at(column_id + 1);
     const auto &values = cut_values_.ConstHostVector();
     auto it = std::upper_bound(values.cbegin() + beg, values.cbegin() + end, value);
-    if (it == values.cend()) {
-      it = values.cend() - 1;
-    }
     BinIdx idx = it - values.cbegin();
+    if (idx == end) {
+      idx -= 1;
+    }
     return idx;
   }