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NCBI C++ ToolKit: include/util/bitset/bmsparsevec_parallel.h Source File

<

SVect,

Lock>

bvector_type::optmode

opt_mode = bvector_type::opt_compress,

sparse_vector_type::statistics*

= 0)

rsize = sv.get_bmatrix().rows();

(

k = 0; k < rsize; ++k)

bvector_type::statistics stbv;

bv->optimize(tb, opt_mode, &stbv);

<

BV>

.build_nb_digest_and_xor_matrix(sim_model.

,

bvector_type::size_type nb_count = sim_model.

.count();

tv.reserve(nb_count);

bvector_type::enumerator en(sim_model.

);

(

col = 0; en.valid(); ++en, ++col)

[nb, col, &xs_params, &sm_matr, &

] (

*

) {

xor_scan.sync_nb_vect();

xor_scan.compute_sim_model(sm_matr, nb, col, xs_params);

batch.

(task, 0);

<

SV>

planes = sv.stored_slices();

tv.reserve(planes + 1);

(

= 0;

< planes; ++

)

SV::bvector_type_const_ptr bv = sv.get_slice(

);

[bv_idx, &sv_layout] (

*

) {

tdescr.

(task, (

*)&tdescr);

[&sv_layout] (

*

) {

tdescr.

(task_final, (

*)&tdescr);

#define BM_DECLARE_TEMP_BLOCK(x)

Serialization for sparse_vector<>

List of reference bit-vectors with their true index associations.

static size_type not_found() noexcept

not-found value for find methods

size_type find_bv(const bvector_type *bv) const noexcept

Find vector index by the pointer.

Parallel plan builder for the XOR filter scanner.

bvector_type::allocator_type allocator_type

bm::bv_ref_vector< BV > bv_ref_vector_type

void build_plan(task_batch &batch, bm::xor_sim_model< BV > &sim_model, const bv_ref_vector_type &ref_vect, const bm::xor_sim_params &xs_params)

Construct task batch for parallel execution.

Simple scoped lock guard.

Builder class to prepare a batch of tasks for parallel optimization of a sparse vector.

bvector_type::allocator_type allocator_type

sparse_vector_type::statistics sv_statistics_type

sparse_vector_type::bvector_type bvector_type

bvector_type::optmode optmode_type

static void build_plan(task_batch &batch, sparse_vector_type &sv, typename bvector_type::optmode opt_mode=bvector_type::opt_compress, typename sparse_vector_type::statistics *st=0)

Build paralell optimization batch (of tasks) for sparse vector.

Parallel plan builder for succinct sparse vector serialization.

sv_serialization_plan_builder()

static void * task_run(void *argp)

Task execution Entry Point.

bm::xor_sim_model< bvector_type > xor_sim_model_type

static void * task_run_final(void *argp)

void build_plan(task_batch &batch, sparse_vector_serial_layout< SV > &sv_layout, const sparse_vector_type &sv)

void set_sim_model(const xor_sim_model_type *sim_model) noexcept

bm::bv_ref_vector< bvector_type > bv_ref_vector_type

bvector_type::allocator_type allocator_type

SV::bvector_type bvector_type

serialization_params s_params_

void set_xor_ref(const bv_ref_vector_type *bv_ref_ptr) noexcept

void set_bookmarks(bool enable, unsigned bm_interval=256) noexcept

Basic implementation for collection of tasks for parallel execution.

task_vector_type & get_task_vector() noexcept

Get access to internal task vector.

void add(task_function_t f, void *argptr)

std::vector< bm::task_descr > task_vector_type

XOR scanner to search for complement-similarities in collections of bit-vectors.

void set_ref_vector(const bv_ref_vector_type *ref_vect) noexcept

std::function< int(void *)> task_function_t

Typedef for a call-back functional for lambda capture.

const unsigned set_compression_default

Default compression level.

static SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static SLJIT_INLINE sljit_ins lg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

std::vector< bm::id64_t > ref_vect

parent_type::task_vector_type task_vector_type

bm::task_batch< allocator_type > parent_type

bm::task_batch< allocator_type > parent_type

parent_type::task_vector_type task_vector_type

layout class for serialization buffer structure

void set_plane(unsigned i, unsigned char *ptr, size_t buf_size) noexcept

Set plane output pointer and size.

unsigned compression_level_

const xor_sim_model_type * sim_model_ptr_

unsigned sb_range_

Desired bookmarks interval.

const bv_ref_vector_type * bv_ref_ptr_

bool sb_bookmarks_

Bookmarks flag.

bm::task_batch< allocator_type > parent_type

serialization_params s_params

parent_type::task_vector_type task_vector_type

BitMagic task with a captured function.

@ barrier_ok

barrier waits all prev.tasks done without error

void init(task_function_t f, void *argptr) noexcept

matrix_chain_type matr

model matrix

bvector_type bv_blocks

blocks digest

Parameters for XOR similarity search.

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