[Performance][CUDA] Faster CSRToCOO (#5648)

Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com>

CMakeLists.txt

@@ -50,6 +50,7 @@ if(USE_CUDA)
   message(STATUS "Use external CUB/Thrust library for a consistent API and performance.")
   cuda_include_directories(BEFORE "${CMAKE_SOURCE_DIR}/third_party/thrust")
   cuda_include_directories(BEFORE "${CMAKE_SOURCE_DIR}/third_party/thrust/dependencies/cub")
+  cuda_include_directories(BEFORE "${CMAKE_SOURCE_DIR}/third_party/thrust/dependencies/libcudacxx/include")
 endif(USE_CUDA)
 
 # initial variables

src/array/cuda/csr2coo.cu

@@ -4,8 +4,12 @@
  * @brief CSR2COO
  */
 #include <dgl/array.h>
+#include <thrust/iterator/constant_iterator.h>
+#include <thrust/iterator/counting_iterator.h>
+#include <thrust/iterator/transform_iterator.h>
 
 #include "../../runtime/cuda/cuda_common.h"
+#include "./dgl_cub.cuh"
 #include "./utils.h"
 
 namespace dgl {
@@ -45,33 +49,27 @@ COOMatrix CSRToCOO<kDGLCUDA, int32_t>(CSRMatrix csr) {
       csr.num_rows, csr.num_cols, row, indices, data, true, csr.sorted);
 }
 
-/**
- * @brief Repeat elements
- * @param val Value to repeat
- * @param repeats Number of repeats for each value
- * @param pos The position of the output buffer to write the value.
- * @param out Output buffer.
- * @param length Number of values
- *
- * For example:
- * val = [3, 0, 1]
- * repeats = [1, 0, 2]
- * pos = [0, 1, 1]  # write to output buffer position 0, 1, 1
- * then,
- * out = [3, 1, 1]
- */
-template <typename DType, typename IdType>
-__global__ void _RepeatKernel(
-    const DType* val, const IdType* pos, DType* out, int64_t n_row,
-    int64_t length) {
-  IdType tx = static_cast<IdType>(blockIdx.x) * blockDim.x + threadIdx.x;
-  const int stride_x = gridDim.x * blockDim.x;
-  while (tx < length) {
-    IdType i = dgl::cuda::_UpperBound(pos, n_row, tx) - 1;
-    out[tx] = val[i];
-    tx += stride_x;
+struct RepeatIndex {
+  template <typename IdType>
+  __host__ __device__ auto operator()(IdType i) {
+    return thrust::make_constant_iterator(i);
   }
-}
+};
+
+template <typename IdType>
+struct OutputBufferIndexer {
+  const IdType* indptr;
+  IdType* buffer;
+  __host__ __device__ auto operator()(IdType i) { return buffer + indptr[i]; }
+};
+
+template <typename IdType>
+struct AdjacentDifference {
+  const IdType* indptr;
+  __host__ __device__ auto operator()(IdType i) {
+    return indptr[i + 1] - indptr[i];
+  }
+};
 
 template <>
 COOMatrix CSRToCOO<kDGLCUDA, int64_t>(CSRMatrix csr) {
@@ -80,14 +78,33 @@ COOMatrix CSRToCOO<kDGLCUDA, int64_t>(CSRMatrix csr) {
 
   const int64_t nnz = csr.indices->shape[0];
   const auto nbits = csr.indptr->dtype.bits;
-  IdArray rowids = Range(0, csr.num_rows, nbits, ctx);
   IdArray ret_row = NewIdArray(nnz, ctx, nbits);
 
-  const int nt = 256;
-  const int nb = (nnz + nt - 1) / nt;
-  CUDA_KERNEL_CALL(
-      _RepeatKernel, nb, nt, 0, stream, rowids.Ptr<int64_t>(),
-      csr.indptr.Ptr<int64_t>(), ret_row.Ptr<int64_t>(), csr.num_rows, nnz);
+  runtime::CUDAWorkspaceAllocator allocator(csr.indptr->ctx);
+  thrust::counting_iterator<int64_t> iota(0);
+
+  auto input_buffer = thrust::make_transform_iterator(iota, RepeatIndex{});
+  auto output_buffer = thrust::make_transform_iterator(
+      iota, OutputBufferIndexer<int64_t>{
+                csr.indptr.Ptr<int64_t>(), ret_row.Ptr<int64_t>()});
+  auto buffer_sizes = thrust::make_transform_iterator(
+      iota, AdjacentDifference<int64_t>{csr.indptr.Ptr<int64_t>()});
+
+  constexpr int64_t max_copy_at_once = std::numeric_limits<int32_t>::max();
+  for (int64_t i = 0; i < csr.num_rows; i += max_copy_at_once) {
+    std::size_t temp_storage_bytes = 0;
+    CUDA_CALL(cub::DeviceCopy::Batched(
+        nullptr, temp_storage_bytes, input_buffer + i, output_buffer + i,
+        buffer_sizes + i, std::min(csr.num_rows - i, max_copy_at_once),
+        stream));
+
+    auto temp = allocator.alloc_unique<char>(temp_storage_bytes);
+
+    CUDA_CALL(cub::DeviceCopy::Batched(
+        temp.get(), temp_storage_bytes, input_buffer + i, output_buffer + i,
+        buffer_sizes + i, std::min(csr.num_rows - i, max_copy_at_once),
+        stream));
+  }
 
   return COOMatrix(
       csr.num_rows, csr.num_cols, ret_row, csr.indices, csr.data, true,

thrust @ 02931a30

-Subproject commit 6a3078c64cab0e2f276340fa5dcafa0d758ed890
+Subproject commit 02931a309bee769853088b79b4e3ab1c0bd2336c