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patch, test: improvements to vectors with rank support unit tests
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@SGSSGene
SGSSGene committed Aug 9, 2024
1 parent a65df28 commit a2186bd
Showing 1 changed file with 144 additions and 3 deletions.
147 changes: 144 additions & 3 deletions src/test_fmindex-collection/rankvector/checkRankVector.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ static auto getName() {
}
#endif

TEMPLATE_TEST_CASE("check if rank on the symbol vectors is working", "[RankVector]", ALLRANKVECTORS(256)) {
TEMPLATE_TEST_CASE("check if rank on the symbol vectors is working", "[RankVector][256]", ALLRANKVECTORS(256)) {
using Vector = TestType;
auto vector_name = getName<Vector>();
INFO(vector_name);
Expand Down Expand Up @@ -152,6 +152,15 @@ TEMPLATE_TEST_CASE("check if rank on the symbol vectors is working", "[RankVecto
CHECK(vec.rank( 8, 't') == 0);
CHECK(vec.rank( 9, 't') == 0);
CHECK(vec.rank(10, 't') == 1);

// check all other characters have rank 0
auto ignore = std::unordered_set<size_t>{' ', 'H', 'W', 'a', 'e', 'l', 'o', 't'};
for (size_t s{0}; s < 256; ++s) {
if (ignore.contains(s)) continue;
for (size_t i{0}; i < 11; ++i) {
CHECK(vec.rank(i, s) == 0);
}
}
}

SECTION("test complete vec 'H' for prefix_rank()") {
Expand All @@ -161,6 +170,13 @@ TEMPLATE_TEST_CASE("check if rank on the symbol vectors is working", "[RankVecto
CHECK(vec.prefix_rank( 3, ' ') == 0);
CHECK(vec.prefix_rank( 4, ' ') == 0);
CHECK(vec.prefix_rank( 5, ' ') == 0);
size_t a{};
for (size_t s{0}; s < ' '; ++s) {
a += vec.rank(6, s);
INFO(a);
CHECK(a == 0);
}
CHECK(vec.rank(6, ' ' ) == 1);
CHECK(vec.prefix_rank( 6, ' ') == 1);
CHECK(vec.prefix_rank( 7, ' ') == 1);
CHECK(vec.prefix_rank( 8, ' ') == 1);
Expand Down Expand Up @@ -382,7 +398,7 @@ struct Benchs {
}

static auto benchs_256 = Benchs{};
TEMPLATE_TEST_CASE("benchmark vectors c'tor,symbol() and rank() operations", "[RankVector][!benchmark]", ALLRANKVECTORS(256)) {
TEMPLATE_TEST_CASE("benchmark vectors c'tor,symbol() and rank() operations", "[RankVector][!benchmark][256]", ALLRANKVECTORS(256)) {
using Vector = TestType;
if constexpr (std::same_as<Vector, fmindex_collection::rankvector::Naive<256>>) {
return;
Expand Down Expand Up @@ -452,7 +468,7 @@ TEMPLATE_TEST_CASE("benchmark vectors c'tor,symbol() and rank() operations", "[R
}

static auto benchs_5 = Benchs{};
TEMPLATE_TEST_CASE("benchmark vectors c'tor,symbol() and rank() operations, dna4 like", "[RankVector][!benchmark]", ALLRANKVECTORS(5)) {
TEMPLATE_TEST_CASE("benchmark vectors c'tor,symbol() and rank() operations, dna4 like", "[RankVector][!benchmark][5]", ALLRANKVECTORS(5)) {
using Vector = TestType;
if constexpr (std::same_as<Vector, fmindex_collection::rankvector::Naive<5>>) {
return;
Expand Down Expand Up @@ -517,3 +533,128 @@ TEMPLATE_TEST_CASE("benchmark vectors c'tor,symbol() and rank() operations, dna4
}
}
}

static auto benchs_6 = Benchs{};
static auto benchs_6_text = std::vector<uint8_t>{};
TEMPLATE_TEST_CASE("benchmark vectors c'tor,symbol() and rank() operations, on human dna5 data", "[RankVector][bwt][!benchmark][time]", ALLRANKVECTORS(6)) {
using Vector = TestType;
if constexpr (std::same_as<Vector, fmindex_collection::rankvector::Naive<6>>) {
return;
}
auto& [bench_rank, bench_prefix_rank, bench_all_ranks, bench_all_prefix_ranks, bench_symbol, bench_ctor] = benchs_6;


auto vector_name = getName<Vector>();
INFO(vector_name);

SECTION("benchmarking") {
auto rng = ankerl::nanobench::Rng{};

// generates string with values between 1-4
auto& text = benchs_6_text;
if (text.empty()) {
auto fs = std::ifstream{"bwt.bwt"};
std::string line;
std::getline(fs, line);
fs.close();
text.resize(line.size());
std::memcpy(text.data(), line.data(), line.size());
for (auto& c : text) {
switch(c) {
case '$': c = 0; break;
case 'A': c = 1; break;
case 'C': c = 2; break;
case 'G': c = 3; break;
case 'T': c = 4; break;
case 'N': c = 5; break;
default:
throw std::runtime_error{"unknown char " + std::to_string((int)c)};

}
}
std::cout << "done loading file\n";
}

auto vec = Vector{text};


size_t minEpochIterations = 2'000'000;
minEpochIterations = 2'00;
bench_ctor.minEpochIterations(10).batch(text.size()).run(vector_name, [&]() {
auto vec = Vector{text};
ankerl::nanobench::doNotOptimizeAway(const_cast<Vector const&>(vec));
});

bench_symbol.minEpochIterations(minEpochIterations).run(vector_name, [&]() {
auto v = vec.symbol(rng.bounded(text.size()));
ankerl::nanobench::doNotOptimizeAway(v);
});

bench_rank.minEpochIterations(minEpochIterations).run(vector_name, [&]() {
auto v = vec.rank(rng.bounded(text.size()), rng.bounded(5)+1);
ankerl::nanobench::doNotOptimizeAway(v);
});

bench_prefix_rank.minEpochIterations(minEpochIterations).run(vector_name, [&]() {
auto v = vec.prefix_rank(rng.bounded(text.size()), rng.bounded(5)+1);
ankerl::nanobench::doNotOptimizeAway(v);
});

bench_all_ranks.minEpochIterations(minEpochIterations).run(vector_name, [&]() {
auto v = vec.all_ranks(rng.bounded(text.size()));
ankerl::nanobench::doNotOptimizeAway(v);
});

bench_all_prefix_ranks.minEpochIterations(minEpochIterations).run(vector_name, [&]() {
auto v = vec.all_ranks_and_prefix_ranks(rng.bounded(text.size()));
ankerl::nanobench::doNotOptimizeAway(v);
});
}
}

TEMPLATE_TEST_CASE("benchmark vectors c'tor,symbol() and rank() operations, on human dna5 data", "[RankVector][bwt][!benchmark][size]", ALLRANKVECTORS(6)) {
using Vector = TestType;
if constexpr (std::same_as<Vector, fmindex_collection::rankvector::Naive<6>>) {
return;
}

auto vector_name = getName<Vector>();
INFO(vector_name);

SECTION("benchmarking") {
auto rng = ankerl::nanobench::Rng{};

// generates string with values between 1-4
auto& text = benchs_6_text;
if (text.empty()) {
auto fs = std::ifstream{"bwt.bwt"};
std::string line;
std::getline(fs, line);
fs.close();
text.resize(line.size());
std::memcpy(text.data(), line.data(), line.size());
for (auto& c : text) {
switch(c) {
case '$': c = 0; break;
case 'A': c = 1; break;
case 'C': c = 2; break;
case 'G': c = 3; break;
case 'T': c = 4; break;
case 'N': c = 5; break;
default:
throw std::runtime_error{"unknown char " + std::to_string((int)c)};

}
}
std::cout << "done loading file\n";
}

auto vec = Vector{text};

auto ofs = std::stringstream{};
auto archive = cereal::BinaryOutputArchive{ofs};
archive(vec);
auto s = ofs.str().size();
std::cout << vector_name << " - file size: " << s << "bytes, " << s/double(text.size()) << "bytes/char\n";
}
}

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