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Loop over copy_if (#6201)

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* Loop over copy_if

* Catch OOM.

Co-authored-by: fis <jm.yuan@outlook.com>
This commit is contained in:
Rory Mitchell
2020-10-14 10:23:16 +13:00
committed by GitHub
parent 0fc263ead5
commit 734a911a26
3 changed files with 64 additions and 18 deletions
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41
src/data/simple_dmatrix.cu
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@@ -35,24 +35,38 @@ void CountRowOffsets(const AdapterBatchT& batch, common::Span<bst_row_t> offset,
thrust::device_pointer_cast(offset.data()));
}
template <typename AdapterBatchT>
struct COOToEntryOp {
AdapterBatchT batch;
__device__ Entry operator()(size_t idx) {
const auto& e = batch.GetElement(idx);
return Entry(e.column_idx, e.value);
}
};
// Here the data is already correctly ordered and simply needs to be compacted
// to remove missing data
template <typename AdapterT>
void CopyDataToDMatrix(AdapterT* adapter, common::Span<Entry> data,
int device_idx, float missing,
common::Span<size_t> row_ptr) {
auto& batch = adapter->Value();
auto transform_f = [=] __device__(size_t idx) {
const auto& e = batch.GetElement(idx);
return Entry(e.column_idx, e.value);
}; // NOLINT
float missing) {
auto batch = adapter->Value();
auto counting = thrust::make_counting_iterator(0llu);
thrust::transform_iterator<decltype(transform_f), decltype(counting), Entry>
transform_iter(counting, transform_f);
dh::XGBCachingDeviceAllocator<char> alloc;
thrust::copy_if(
thrust::cuda::par(alloc), transform_iter, transform_iter + batch.Size(),
thrust::device_pointer_cast(data.data()), IsValidFunctor(missing));
COOToEntryOp<decltype(batch)> transform_op{batch};
thrust::transform_iterator<decltype(transform_op), decltype(counting)>
transform_iter(counting, transform_op);
// We loop over batches because thrust::copy_if cant deal with sizes > 2^31
// See thrust issue #1302
size_t max_copy_size = std::numeric_limits<int>::max() / 2;
auto begin_output = thrust::device_pointer_cast(data.data());
for (size_t offset = 0; offset < batch.Size(); offset += max_copy_size) {
auto begin_input = transform_iter + offset;
auto end_input =
transform_iter + std::min(offset + max_copy_size, batch.Size());
begin_output =
thrust::copy_if(thrust::cuda::par(alloc), begin_input, end_input,
begin_output, IsValidFunctor(missing));
}
}
// Does not currently support metainfo as no on-device data source contains this
@@ -77,8 +91,7 @@ SimpleDMatrix::SimpleDMatrix(AdapterT* adapter, float missing, int nthread) {
CountRowOffsets(batch, s_offset, adapter->DeviceIdx(), missing);
info_.num_nonzero_ = sparse_page_.offset.HostVector().back();
sparse_page_.data.Resize(info_.num_nonzero_);
CopyDataToDMatrix(adapter, sparse_page_.data.DeviceSpan(),
adapter->DeviceIdx(), missing, s_offset);
CopyDataToDMatrix(adapter, sparse_page_.data.DeviceSpan(), missing);
info_.num_col_ = adapter->NumColumns();
info_.num_row_ = adapter->NumRows();