distributed.cuh File Reference

#include <mpi.h>
#include <algorithm>
#include <cstdint>
#include <filesystem>
#include <fstream>
#include <limits>
#include <memory>
#include <mutex>
#include <numeric>
#include <span>
#include <string>
#include <system_error>
#include <thread>
#include <vector>
#include <cuddl/reference_database_file.cuh>
#include <cuddl/replicated_database.cuh>

Go to the source code of this file.

Classes
struct	cuddl::genome_slice
	One rank's share of a genome collection split across an MPI communicator. More...
struct	cuddl::detail::reference_file_assembly
	Builds a reference_database_file from gathered parts; the file's members are private. More...
class	cuddl::shared_tile_counter
	A tile counter shared by every rank of a communicator, for replica_search::next_tile. More...

Namespaces
namespace	cuddl
	Batch operations over contiguous device rows.
namespace	cuddl::detail

Functions
Result< void >	cuddl::detail::mpi_try (int status, char const *call)
Result< void >	cuddl::detail::agree (Result< void > local, MPI_Comm comm)
	Returns local on the rank that failed, and on every other rank an error naming the lowest failing rank, so that all ranks leave a collective step together.
Result< std::vector< std::filesystem::path > >	cuddl::detail::share_listing (std::filesystem::path const &input, int rank, MPI_Comm comm)
	Rank 0's listing of input on every rank.
size_t	cuddl::detail::slice_begin (std::span< uint64_t const > bytes, uint64_t total, int rank, int size)
	First genome of rank rank's slice: contiguous slices of about equal bytes.
Result< genome_slice >	cuddl::slice_genomes (std::filesystem::path const &input, MPI_Comm comm, unsigned workers=default_parser_workers())
	Lists a genome collection once and splits it into one contiguous slice per rank of comm, of about equal file bytes.
Result< std::vector< uint32_t > >	cuddl::detail::slice_counts (reference_database_file const &mine, genome_slice const &slice, MPI_Comm comm)
	Every rank's genome count, after checking collectively that mine holds the sketches of this rank's slice and that every rank built with rank 0's settings.
Result< MPI_Datatype >	cuddl::detail::row_type (uint32_t buckets)
	One row of buckets scores as a single MPI element, so counts of rows stay within int.
Result< reference_database_file >	cuddl::gather_sketches (reference_database_file const &mine, genome_slice const &slice, MPI_Comm comm)
	Gathers every rank's sketches of its genome_slice into one file on every rank.
template<typename Search >
Result< void >	cuddl::detail::shared_search (MPI_Comm comm, Search &&search)
	Runs search with a replica_search that shares tiles across the ranks of comm.
template<uint32_t K, size_t BucketCount, typename Layout , typename OnTile >
Result< void >	cuddl::search_all_to_all (replicated_database< K, BucketCount, Layout > &group, OnTile &&on_tile, MPI_Comm comm)
	Compares every pair of group's references, sharing the tiles among the ranks of comm; collective.
template<uint32_t K, size_t BucketCount, typename Layout , typename OnTile >
Result< void >	cuddl::search_all_to_all (replicated_database< K, BucketCount, Layout > &group, OnTile &&on_tile, search_options options, MPI_Comm comm)
	The threshold form of search_all_to_all: only pairs passing options reach on_tile.