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[cudamapper] Add anchor chain output functions to chainer_utils.cuh. #590

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3588962
[cudamapper] Add anchor chain output functions to chainer_utils.cuh.
edawson Oct 19, 2020
19040dc
[cudamapper] Add anchor chain trace for RLE and add anchor chain star…
edawson Oct 19, 2020
233cfc2
[cudamapper] Clean up unnecessary functions in chainer_utils.
edawson Oct 19, 2020
1cc1c25
[cudamapper] Add tests for allocating anchor chains in chainer_utils.…
edawson Oct 20, 2020
6680ba6
Add tests for chainerutils.
edawson Oct 20, 2020
5860fb1
[cudamapper] Remove unnecessary includes.
edawson Oct 22, 2020
ef4ce77
[chainer_utils] Update docs.
edawson Oct 22, 2020
2a864de
[chainer_utils] Fix minor doc typos.
edawson Oct 22, 2020
44bf81d
Merge branch 'dev-v0.6.0' of https://github.com/clara-parabricks/geno…
edawson Oct 27, 2020
39f7232
[docs] Fix typos and doxygen docs in chainer_utils.
edawson Oct 27, 2020
8d7d1ef
Fix compile errors from missing imports
edawson Oct 27, 2020
756739f
[chainer_utils] Make arguments const / const * const where possible.
edawson Oct 27, 2020
7680371
[chainer_utils] Pass cudastream and allocation by value (not referenc…
edawson Oct 27, 2020
78da541
[chainer_utils] Address review comments.
edawson Oct 27, 2020
44f2f4d
[chainer_utils] Refactor backtrace_anchors_to_overlaps to be a grid-s…
edawson Oct 27, 2020
be3b0a4
[chainer_utils] Fix bugs in tests caused by not specifying cudastream…
edawson Oct 28, 2020
9f75411
[chainer_utils] Refactor device memory from d_* convention to *_d.
edawson Oct 28, 2020
c72e5c9
[chainerutils] Rename create_simple_overlap to create_overlap
edawson Nov 2, 2020
6df3b76
[chainerutils] Move declaration of temporary memory used by CUB.
edawson Nov 2, 2020
781c2fd
[chainerutils] Use 64bit ints for the number of anchors.
edawson Nov 2, 2020
bd07138
[chainerutils] Attempt to clean up documentation.
edawson Nov 2, 2020
178b075
Remove unnecessary assignment in chainerutils.
edawson Nov 3, 2020
6244636
[chainerutils] Refactor allocate_anchor_chains to use thrust, rather …
edawson Nov 3, 2020
d933b4c
[chainerutils] Use a gride-stride function with the block as the unit…
edawson Nov 3, 2020
b310292
[chainerutils] Convert single-block functions back to single-thread.
edawson Nov 3, 2020
9c65a4b
Update from dev-v0.6.0.
edawson Nov 5, 2020
405ec7e
[cudamapper] Fix issues from PR review.
edawson Nov 6, 2020
530adfd
[chainerutils] Address review comments.
edawson Nov 10, 2020
336d02f
Merge branch 'dev-v0.6.0' of https://github.com/clara-parabricks/geno…
edawson Nov 20, 2020
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2 changes: 1 addition & 1 deletion cudaaligner/samples/sample_cudaaligner.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -21,12 +21,12 @@
#include <claraparabricks/genomeworks/utils/genomeutils.hpp>

#include <cuda_runtime_api.h>
#include <getopt.h>
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#include <vector>
#include <string>
#include <stdexcept>
#include <iostream>
#include <random>
#include <getopt.h>

using namespace claraparabricks::genomeworks;
using namespace claraparabricks::genomeworks::genomeutils;
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1 change: 1 addition & 0 deletions cudamapper/CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@ endif()

cuda_add_library(${MODULE_NAME}
src/application_parameters.cpp
src/chainer_utils.cu
src/cudamapper.cpp
src/index_batcher.cu
src/index_descriptor.cpp
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210 changes: 210 additions & 0 deletions cudamapper/src/chainer_utils.cu
Original file line number Diff line number Diff line change
@@ -0,0 +1,210 @@
/*
* Copyright 2020 NVIDIA CORPORATION.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/

#include "chainer_utils.cuh"

#include <thrust/execution_policy.h>
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#include <thrust/transform_scan.h>
#include <thrust/reduce.h>
#include <claraparabricks/genomeworks/utils/cudautils.hpp>

namespace claraparabricks
{

namespace genomeworks
{

namespace cudamapper
{
namespace chainerutils
{

__device__ __forceinline__ Anchor empty_anchor()
{
Anchor a;
a.query_read_id_ = UINT32_MAX;
a.query_position_in_read_ = UINT32_MAX;
a.target_read_id_ = UINT32_MAX;
a.target_position_in_read_ = UINT32_MAX;
return a;
}
struct ConvertOverlapToNumResidues : public thrust::unary_function<Overlap, int32_t>
{
__host__ __device__ int32_t operator()(const Overlap& o) const
{
return o.num_residues_;
}
};

__host__ __device__ Overlap create_overlap(const Anchor& start, const Anchor& end, const int32_t num_anchors)
{
Overlap overlap;
overlap.num_residues_ = num_anchors;

overlap.query_read_id_ = start.query_read_id_;
overlap.target_read_id_ = start.target_read_id_;
assert(start.query_read_id_ == end.query_read_id_ && start.target_read_id_ == end.target_read_id_);

overlap.query_start_position_in_read_ = min(start.query_position_in_read_, end.query_position_in_read_);
overlap.query_end_position_in_read_ = max(start.query_position_in_read_, end.query_position_in_read_);
const bool is_negative_strand = end.target_position_in_read_ < start.target_position_in_read_;
if (is_negative_strand)
{
overlap.relative_strand = RelativeStrand::Reverse;
overlap.target_start_position_in_read_ = end.target_position_in_read_;
overlap.target_end_position_in_read_ = start.target_position_in_read_;
}
else
{
overlap.relative_strand = RelativeStrand::Forward;
overlap.target_start_position_in_read_ = start.target_position_in_read_;
overlap.target_end_position_in_read_ = end.target_position_in_read_;
}
return overlap;
}

__global__ void backtrace_anchors_to_overlaps(const Anchor* const anchors,
Overlap* const overlaps,
int32_t* const overlap_terminal_anchors,
const float* const scores,
bool* const max_select_mask,
const int32_t* const predecessors,
const int64_t n_anchors,
const float min_score)
{
const int64_t thread_id = blockIdx.x * blockDim.x + threadIdx.x;
const int32_t stride = blockDim.x * gridDim.x;

for (int i = thread_id; i < n_anchors; i += stride)
{
if (scores[i] >= min_score)
{
int32_t index = i;
int32_t first_index = index;
int32_t num_anchors_in_chain = 0;
Anchor final_anchor = anchors[i];

while (index != -1)
{
first_index = index;
int32_t pred = predecessors[index];
if (pred != -1)
{
max_select_mask[pred] = false;
}
num_anchors_in_chain++;
index = predecessors[index];
}
Anchor first_anchor = anchors[first_index];
overlap_terminal_anchors[i] = i;
overlaps[i] = create_overlap(first_anchor, final_anchor, num_anchors_in_chain);
}
else
{
max_select_mask[i] = false;
overlap_terminal_anchors[i] = -1;
overlaps[i] = create_overlap(empty_anchor(), empty_anchor(), 1);
}
}
}

void allocate_anchor_chains(const device_buffer<Overlap>& overlaps,
device_buffer<int32_t>& unrolled_anchor_chains,
device_buffer<int32_t>& anchor_chain_starts,
int64_t& num_total_anchors,
DefaultDeviceAllocator allocator,
cudaStream_t cuda_stream)
{
auto thrust_exec_policy = thrust::cuda::par(allocator).on(cuda_stream);
thrust::plus<int32_t> sum_op;
num_total_anchors = thrust::transform_reduce(thrust_exec_policy,
overlaps.begin(),
overlaps.end(),
ConvertOverlapToNumResidues(),
0,
sum_op);

unrolled_anchor_chains.clear_and_resize(num_total_anchors);
anchor_chain_starts.clear_and_resize(overlaps.size());

thrust::transform_exclusive_scan(thrust_exec_policy,
overlaps.begin(),
overlaps.end(),
anchor_chain_starts.data(),
ConvertOverlapToNumResidues(),
0,
sum_op);
}

__global__ void output_overlap_chains_by_backtrace(const Overlap* const overlaps,
const Anchor* const anchors,
const bool* const select_mask,
const int32_t* const predecessors,
const int32_t* const chain_terminators,
int32_t* const anchor_chains,
int32_t* const anchor_chain_starts,
const int32_t num_overlaps,
const bool check_mask)
{
const int64_t thread_id = blockIdx.x * blockDim.x + threadIdx.x;
const int32_t stride = blockDim.x * gridDim.x;

// Processes one overlap per iteration,
// "i" corresponds to an overlap
for (int i = thread_id; i < num_overlaps; i += stride)
{

if (!check_mask || (check_mask & select_mask[i]))
{
int32_t anchor_chain_index = 0;
// As chaining proceeds backwards (i.e., it's a backtrace),
// we need to fill the new anchor chain array in in reverse order.
int32_t index = chain_terminators[i];
while (index != -1)
{
anchor_chains[anchor_chain_starts[i] + (overlaps[i].num_residues_ - anchor_chain_index - 1)] = index;
index = predecessors[index];
++anchor_chain_index;
}
}
}
}

__global__ void output_overlap_chains_by_RLE(const Overlap* const overlaps,
const Anchor* const anchors,
const int32_t* const chain_starts,
const int32_t* const chain_lengths,
int32_t* const anchor_chains,
int32_t* const anchor_chain_starts,
const uint32_t num_overlaps)
{
const int32_t thread_id = blockIdx.x * blockDim.x + threadIdx.x;
const int32_t stride = blockDim.x * gridDim.x;
for (uint32_t i = thread_id; i < num_overlaps; i += stride)
{
int32_t chain_start = chain_starts[i];
int32_t chain_length = chain_lengths[i];
for (int32_t index = chain_start; index < chain_start + chain_length; ++index)
{
anchor_chains[index] = index;
}
}
}

} // namespace chainerutils
} // namespace cudamapper
} // namespace genomeworks
} // namespace claraparabricks
129 changes: 129 additions & 0 deletions cudamapper/src/chainer_utils.cuh
Original file line number Diff line number Diff line change
@@ -0,0 +1,129 @@
/*
* Copyright 2020 NVIDIA CORPORATION.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/

#pragma once

#include <claraparabricks/genomeworks/cudamapper/types.hpp>
#include <claraparabricks/genomeworks/utils/device_buffer.hpp>

namespace claraparabricks
{

namespace genomeworks
{

namespace cudamapper
{
namespace chainerutils
{

/// \brief Create an overlap from the first and last anchor in the chain and
/// the total number of anchors in the chain.
///
/// \param start The first anchor in the chain.
/// \param end The last anchor in the chain.
/// \param num_anchors The total number of anchors in the chain.
__host__ __device__ Overlap create_overlap(const Anchor& start,
const Anchor& end,
const int32_t num_anchors);

/// \brief Given an array of anchors and an array denoting the immediate
/// predecessor of each anchor, transform chains of anchors into overlaps.
///
/// \param anchors An array of anchors.
/// \param overlaps An array of overlaps to be filled.
/// \param scores An array of scores. Only chains with a score greater than min_score will be backtraced.
/// \param max_select_mask A boolean mask, used to mask out any chains which are completely contained within larger chains during the backtrace.
/// \param predecessors An array of indices into the anchors array marking the predecessor of each anchor within a chain.
/// \param n_anchors The number of anchors.
/// \param min_score The minimum score of a chain for performing backtracing.
/// Launch configuration: any number of blocks/threads, no dynamic shared memory, cuda_stream must be the same in which anchors/overlaps/scores/mask/predecessors were allocated.
/// example: backtrace_anchors_to_overlaps<<<2048, 32, 0, cuda_stream>>>(...)
__global__ void backtrace_anchors_to_overlaps(const Anchor* const anchors,
Overlap* const overlaps,
int32_t* const overlap_terminal_anchors,
const float* const scores,
bool* const max_select_mask,
const int32_t* const predecessors,
const int64_t n_anchors,
const float min_score);

/// \brief Allocate a 1-dimensional array representing an unrolled ragged array
/// of anchors within each overlap. The final array holds the indices within the anchors array used in chaining
/// of the anchors in the chain.
///
/// \param overlaps An array of Overlaps. Must have a well-formed num_residues_ field
/// \param unrolled_anchor_chains An array of int32_t. Will be resized on return.
/// \param anchor_chain_starts An array holding the index of the first anchor in an overlap within the anchors array used during chaining.
/// \param num_overlaps The number of overlaps in the overlaps array.
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Is this parameter necessary? Is the the same as overlaps.size()?

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This is not necessarily the same as overlaps.size(); I've been bitten by this multiple times at this point. Calling cub::Flagged does not create an output array guaranteed to be the exact size (only equal to or greater than the number of flagged elements). If there's a trim function for the device_buffer class I could call that.

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num_overlaps does not exist anymore

/// \param num_total_anchors The total number of anchors across all overlaps.
/// \param allocator The DefaultDeviceAllocator for this overlapper.
/// \param cuda_stream The cudastream to allocate memory within.
void allocate_anchor_chains(const device_buffer<Overlap>& overlaps,
device_buffer<int32_t>& unrolled_anchor_chains,
device_buffer<int32_t>& anchor_chain_starts,
int64_t& num_total_anchors,
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Is this necessary? I see it's used to set the size of unrolled_anchor_chains

DefaultDeviceAllocator allocator,
cudaStream_t cuda_stream = 0);

/// \brief Given an array of overlaps, fill a 1D unrolled ragged array
/// containing the anchors used to generate each overlap. Anchors must have
/// been chained with a chaining function that fills the predecessors array
/// with the immediate predecessor of each anchor.
///
/// \param overlaps An array of overlaps.
/// \param anchors The array of anchors used to generate overlaps.
/// \param select_mask An array of bools, used to mask overlaps from output.
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/// \param predecessors The predecessors array from anchor chaining.
/// \param anchor_chains An array (allocated by allocate_anchor_chains) which will hold the indices of anchors within each chain.
/// \param anchor_chain_starts An array which holds the indices of the first anchor for each overlap in the overlaps array.
/// \param num_overlaps The number of overlaps in the overlaps array
/// \param check_mask A boolean. If true, only overlaps where select_mask is true will have their anchor chains calculated.
/// Launch configuration: any number of blocks/threads, no dynamic shared memory, cuda_stream must be the same in which anchors/overlaps/scores/mask/predecessors/chains/starts were allocated.
/// example: backtrace_anchors_to_overlaps<<<2048, 32, 0, cuda_stream>>>(...)
__global__ void output_overlap_chains_by_backtrace(const Overlap* const overlaps,
const Anchor* const anchors,
const bool* const select_mask,
const int32_t* const predecessors,
const int32_t* const chain_terminators,
int32_t* const anchor_chains,
int32_t* const anchor_chain_starts,
const int32_t num_overlaps,
const bool check_mask);

/// \brief Fill a 1D unrolled ragged array with the anchors used to produce each overlap.
///
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/// \param overlaps An array of overlaps.
/// \param anchors The array of anchors used to generate overlaps.
/// \param chain_starts An array which holds the indices of the first anchor for each overlap in the overlaps array.
/// \param chain_lengths An array which holds the length of each run of anchors, corresponding to the chain_starts array.
/// \param anchor_chains An array (allocated by allocate_anchor_chains) which will hold the indices of anchors within each chain.
/// \param anchor_chain_starts An array which holds the indices of the first anchor for each overlap in the overlaps array.
/// \param num_overlaps The number of overlaps in the overlaps array.
/// Launch configuration: any number of blocks/threads, no dynamic shared memory, cuda_stream must be the same in which anchors/overlaps/scores/mask/predecessors/chains/starts were allocated.
/// example: backtrace_anchors_to_overlaps<<<2048, 32, 0, cuda_stream>>>(...)
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Further descriptions should be placed between \brief and \param

__global__ void output_overlap_chains_by_RLE(const Overlap* const overlaps,
const Anchor* const anchors,
const int32_t* const chain_starts,
const int32_t* const chain_lengths,
int32_t* const anchor_chains,
int32_t* const anchor_chain_starts,
const uint32_t num_overlaps);

} // namespace chainerutils
} // namespace cudamapper
} // namespace genomeworks
} // namespace claraparabricks
4 changes: 2 additions & 2 deletions cudamapper/src/overlapper_triggered.cu
Original file line number Diff line number Diff line change
Expand Up @@ -24,11 +24,11 @@

#include <claraparabricks/genomeworks/utils/cudautils.hpp>

#ifndef NDEBUG // only needed to check if input is sorted in assert
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#include <algorithm>

#ifndef NDEBUG
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Why is algorithm needed in release mode as well?

#include <thrust/host_vector.h>
#endif

namespace claraparabricks
{

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1 change: 1 addition & 0 deletions cudamapper/tests/CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ set(SOURCES
Test_CudamapperOverlapper.cpp
Test_CudamapperOverlapperTriggered.cu
Test_CudamapperUtilsKmerFunctions.cpp
Test_CudamapperChainerUtils.cu
)

get_property(cudamapper_data_include_dir GLOBAL PROPERTY cudamapper_data_include_dir)
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