primitives.h

Go to the documentation of this file.

/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *    * Redistributions of source code must retain the above copyright
 *      notice, this list of conditions and the following disclaimer.
 *    * Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in the
 *      documentation and/or other materials provided with the distribution.
 *    * Neither the name of the NVIDIA CORPORATION nor the
 *      names of its contributors may be used to endorse or promote products
 *      derived from this software without specific prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY
 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

#include <nvbio/basic/types.h>
#include <nvbio/basic/console.h>
#include <nvbio/basic/thrust_view.h>
#include <thrust/device_vector.h>
#include <cub/cub.cuh>


namespace nvbio {
namespace cuda {




template <typename VectorType>
void alloc_temp_storage(VectorType& vec, const uint64 size);

template <typename PredicateIterator>
bool any(
    const uint32            n,
    const PredicateIterator pred);

template <typename PredicateIterator>
bool all(
    const uint32            n,
    const PredicateIterator pred);

template <typename Iterator>
bool is_sorted(
    const uint32            n,
    const Iterator          values);

template <typename Iterator, typename Headflags>
bool is_segment_sorted(
    const uint32            n,
    const Iterator          values,
    const Headflags         flags);

template <typename InputIterator, typename BinaryOp>
typename std::iterator_traits<InputIterator>::value_type reduce(
    const uint32                  n,
    InputIterator                 d_in,
    BinaryOp                      op,
    thrust::device_vector<uint8>& d_temp_storage);

template <typename InputIterator, typename OutputIterator, typename BinaryOp>
void inclusive_scan(
    const uint32                  n,
    InputIterator                 d_in,
    OutputIterator                d_out,
    BinaryOp                      op,
    thrust::device_vector<uint8>& d_temp_storage);

template <typename InputIterator, typename OutputIterator, typename BinaryOp, typename Identity>
void exclusive_scan(
    const uint32                  n,
    InputIterator                 d_in,
    OutputIterator                d_out,
    BinaryOp                      op,
    Identity                      identity,
    thrust::device_vector<uint8>& d_temp_storage);

template <typename InputIterator, typename FlagsIterator, typename OutputIterator>
uint32 copy_flagged(
    const uint32                  n,
    InputIterator                 d_in,
    FlagsIterator                 d_flags,
    OutputIterator                d_out,
    thrust::device_vector<uint8>& d_temp_storage);

template <typename InputIterator, typename OutputIterator, typename Predicate>
uint32 copy_if(
    const uint32                  n,
    InputIterator                 d_in,
    OutputIterator                d_out,
    const Predicate               pred,
    thrust::device_vector<uint8>& d_temp_storage);

template <typename InputIterator, typename OutputIterator, typename CountIterator>
uint32 runlength_encode(
    const uint32                  n,
    InputIterator                 d_in,
    OutputIterator                d_out,
    CountIterator                 d_counts,
    thrust::device_vector<uint8>& d_temp_storage);

template <typename KeyIterator, typename ValueIterator, typename OutputKeyIterator, typename OutputValueIterator, typename ReductionOp>
uint32 reduce_by_key(
    const uint32                  n,
    KeyIterator                   d_keys_in,
    ValueIterator                 d_values_in,
    OutputKeyIterator             d_keys_out,
    OutputValueIterator           d_values_out,
    ReductionOp                   reduction_op,
    thrust::device_vector<uint8>& d_temp_storage);


} // namespace cuda
} // namespace nvbio

#include <nvbio/basic/cuda/primitives_inl.h>