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update alignment optimizations #52

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merged 2 commits into from
Jun 1, 2024
Merged

update alignment optimizations #52

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7f90f30
Adding NDEBUG to default optimizations in Makefile.am
andrewdavidsmith May 31, 2024
b2d67ac
Updating the pragma guard for optimizations in the alignment code tha…
andrewdavidsmith May 31, 2024
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2 changes: 1 addition & 1 deletion Makefile.am
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ if ENABLE_SHORT
AM_CXXFLAGS += -DENABLE_SHORT
endif

CXXFLAGS = -O3 # default has optimization on
CXXFLAGS = -O3 -DNDEBUG # default has optimization on

noinst_LIBRARIES = libabismal.a

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19 changes: 13 additions & 6 deletions src/AbismalAlign.hpp
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Expand Up @@ -159,11 +159,9 @@ is_insertion(const uint8_t c) {

static inline void
get_traceback(const size_t n_col, const std::vector<score_t> &table,
// const std::vector<uint8_t> &traceback,
const std::vector<int8_t> &traceback,
std::vector<uint32_t> &cigar, size_t &the_row, size_t &the_col) {
int8_t prev_arrow = traceback[the_row * n_col + the_col];
// int8_t prev_arrow = traceback[the_row * n_col + the_col];
const bool is_del = is_deletion(prev_arrow);
const bool is_ins = is_insertion(prev_arrow);
the_row -= !is_ins;
Expand Down Expand Up @@ -211,8 +209,15 @@ get_best_score(const std::vector<score_t> &table, const size_t n_cells,
// ADS: it seems like with g++-13, on macos ventura on intel hardware
// the dynamic vectorized optimization of -O3 might be too aggressive
// and makes this function have strange behavior. Placing this pragma
// here helps, and below we restore it to the `-O3` default.
#pragma GCC optimize("vect-cost-model=very-cheap")
// here helps, and below we restore it to the `-O3` default. Probably
// should move to attribute syntax soon.

#ifdef __APPLE__
#pragma GCC push_options
// ADS: below this won't make sense if the user wants no optimizations
// at all...
#pragma GCC optimize ("O2")
#endif

template<score_t (*scr_fun)(const uint8_t, const uint8_t), class T,
class QueryConstItr>
Expand Down Expand Up @@ -284,7 +289,9 @@ from_left(T left_itr, T target, const T target_end, U traceback) {
}
}

#pragma GCC optimize("vect-cost-model=dynamic")
#ifdef __APPLE__
#pragma GCC pop_options
#endif

inline void
make_default_cigar(const uint32_t len, std::string &cigar) {
Expand Down Expand Up @@ -323,7 +330,7 @@ AbismalAlign<scr_fun, indel_pen>::align(const score_t diffs,

// points to relevant reference sequence positions
genome_iterator t_itr = target + t_beg;
const auto q_itr(std::begin(qseq));
const auto q_itr(std::cbegin(qseq));
auto tb_cur(std::begin(traceback));

// prev and cur point to rows in the alignment matrix
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