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Safe-guard offsets_builder.set with mutex #83

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Merged
jermp merged 5 commits into from
Oct 7, 2025
Merged

Safe-guard offsets_builder.set with mutex #83

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9dc43a4
Try safe-guarding offsets_builder.set with mutex
adamant-pwn Oct 6, 2025
a01f0f8
fix kmer_t processing for uint_kmer_bits > 64
adamant-pwn Oct 6, 2025
6578ddd
Single-threaded build_sparse_index
adamant-pwn Oct 7, 2025
b47bec1
fixes per review
adamant-pwn Oct 7, 2025
96cecad
return newline after pragma once
adamant-pwn Oct 7, 2025
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82 changes: 18 additions & 64 deletions include/builder/build_sparse_index.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -28,17 +28,12 @@ struct bucket_size_iterator {

template <class kmer_t>
buckets_statistics build_sparse_index(parse_data<kmer_t>& data, buckets<kmer_t>& m_buckets,
build_configuration const& build_config) //
build_configuration const& /*build_config*/) //
{
const uint64_t num_kmers = data.num_kmers;
const uint64_t num_minimizer_positions = data.minimizers.num_minimizer_positions();
const uint64_t num_super_kmers = data.minimizers.num_super_kmers();
const uint64_t num_buckets = data.minimizers.num_minimizers();
const uint64_t num_threads = build_config.num_threads;

bits::compact_vector::builder offsets_builder;
offsets_builder.resize(num_minimizer_positions,
std::ceil(std::log2(data.strings.num_bits() / kmer_t::bits_per_char)));

std::cout << "bits_per_offset = ceil(log2(" << data.strings.num_bits() / kmer_t::bits_per_char
<< ")) = " << std::ceil(std::log2(data.strings.num_bits() / kmer_t::bits_per_char))
Expand Down Expand Up @@ -66,66 +61,25 @@ buckets_statistics build_sparse_index(parse_data<kmer_t>& data, buckets<kmer_t>&
buckets_statistics buckets_stats(num_buckets, num_kmers, num_minimizer_positions);

timer.start();
const uint64_t block_size = (num_super_kmers + num_threads - 1) / num_threads;
std::vector<uint64_t> offsets;
offsets.reserve(num_threads + 1);
for (uint64_t offset = -1; offset != num_super_kmers;) {
offsets.push_back(offset + 1);
offset = std::min<uint64_t>((offset + 1) + block_size, num_super_kmers);
minimizer_tuple const* b = begin + offset;
uint64_t curr_minimizer = (*b).minimizer;
while (b + 1 < end) { // adjust offset
uint64_t next_minimizer = (*(b + 1)).minimizer;
if (curr_minimizer != next_minimizer) break;
b += 1;
offset += 1;

bits::compact_vector::builder offsets_builder;
offsets_builder.resize(num_minimizer_positions,
std::ceil(std::log2(data.strings.num_bits() / kmer_t::bits_per_char)));
uint64_t prev_minimizer = constants::invalid_uint64, prev_pos_in_seq = constants::invalid_uint64, bucket_size = 0;
for (auto mt : input) {
if (mt.minimizer != prev_minimizer) {
auto [bucket_begin, bucket_end] = m_buckets.locate_bucket(mt.minimizer);
bucket_size = bucket_end - bucket_begin;
buckets_stats.add_bucket_size(bucket_size);
prev_minimizer = mt.minimizer;
prev_pos_in_seq = constants::invalid_uint64;
}
}
offsets.push_back(num_super_kmers);

std::vector<buckets_statistics> threads_buckets_stats;
threads_buckets_stats.reserve(num_threads);

auto exe = [&](const uint64_t thread_id) {
assert(thread_id + 1 < offsets.size());
const uint64_t offset_begin = offsets[thread_id];
const uint64_t offset_end = offsets[thread_id + 1];
auto& tbs = threads_buckets_stats[thread_id];
for (minimizers_tuples_iterator it(begin + offset_begin, begin + offset_end); //
it.has_next(); //
it.next()) //
{
const uint64_t bucket_id = it.minimizer();
const auto [begin, end] = m_buckets.locate_bucket(bucket_id);
assert(end > begin);
const uint64_t bucket_size = end - begin;
assert(bucket_size == it.bucket().size());
tbs.add_bucket_size(bucket_size);
uint64_t pos = 0;
auto bucket = it.bucket();
uint64_t prev_pos_in_seq = constants::invalid_uint64;
for (auto mt : bucket) {
if (mt.pos_in_seq != prev_pos_in_seq) {
offsets_builder.set(begin + pos++, mt.pos_in_seq);
prev_pos_in_seq = mt.pos_in_seq;
}
tbs.add_num_kmers_in_super_kmer(bucket_size, mt.num_kmers_in_super_kmer);
}
assert(pos == bucket_size);
buckets_stats.add_num_kmers_in_super_kmer(bucket_size, mt.num_kmers_in_super_kmer);
if (mt.pos_in_seq != prev_pos_in_seq) {
offsets_builder.push_back(mt.pos_in_seq);
prev_pos_in_seq = mt.pos_in_seq;
}
};

std::vector<std::thread> threads;
threads.reserve(num_threads);
assert(offsets.size() <= num_threads + 1);
for (uint64_t thread_id = 0; thread_id + 1 < size(offsets); ++thread_id) {
threads_buckets_stats.emplace_back(num_buckets, num_kmers, num_minimizer_positions);
threads.emplace_back(exe, thread_id);
}
for (auto& t : threads) {
if (t.joinable()) t.join();
}
for (auto const& tbs : threads_buckets_stats) buckets_stats += tbs;

input.close();
timer.stop();
Expand All @@ -145,4 +99,4 @@ buckets_statistics build_sparse_index(parse_data<kmer_t>& data, buckets<kmer_t>&
return buckets_stats;
}

} // namespace sshash
} // namespace sshash
5 changes: 4 additions & 1 deletion include/builder/parse_file.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -173,7 +173,10 @@ void parse_file(std::istream& is, parse_data<kmer_t>& data,

/* Push a final sentinel (dummy) value to avoid bounds' checking in
kmer_iterator::fill_buff(). */
bvb_strings.append_bits(0, kmer_t::uint_kmer_bits);
static_assert(kmer_t::uint_kmer_bits % 64 == 0);
for (int dummy_bits = kmer_t::uint_kmer_bits; dummy_bits; dummy_bits -= 64) {
bvb_strings.append_bits(0, 64);
}

bvb_strings.build(data.strings);

Expand Down
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