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cleanup
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@karasikov
karasikov committed Jul 19, 2021
1 parent 36698db commit b7f57f9
Showing 1 changed file with 22 additions and 51 deletions.
73 changes: 22 additions & 51 deletions metagraph/src/annotation/row_diff_builder.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -924,13 +924,6 @@ void convert_batch_to_row_diff(const std::string &pred_succ_fprefix,
}
};

// graph::DBGSuccinct graph(2);
// logger->trace("Loading graph...");
// if (!graph.load(pred_succ_fprefix)) {
// logger->error("Cannot load graph from {}", pred_succ_fprefix);
// std::exit(1);
// }

traverse_anno_chunked(
num_rows, pred_succ_fprefix, sources,
[&](uint64_t chunk_size) {
Expand Down Expand Up @@ -962,7 +955,8 @@ void convert_batch_to_row_diff(const std::string &pred_succ_fprefix,
? (with_values ? code_len(matrix::encode_diff(curr_value - succ_value)) : 1)
: 0;
// reduction
__atomic_add_fetch(&row_nbits_block[chunk_idx], n_bits_before - n_bits_after, __ATOMIC_RELAXED);
__atomic_add_fetch(&row_nbits_block[chunk_idx],
n_bits_before - n_bits_after, __ATOMIC_RELAXED);
}
} else {
bool is_anchor = anchor[row_idx];
Expand All @@ -978,55 +972,33 @@ void convert_batch_to_row_diff(const std::string &pred_succ_fprefix,
} else {
v.push_back(row_idx);
}
if (is_anchor)
num_relations_anchored[source_idx][j]++;

if (v.size() == v.capacity()) {
// dump chunk to disk
dump_chunk_to_disk(v, source_idx, j, 0);
v.resize(0);
}
if (is_anchor)
num_relations_anchored[source_idx][j]++;
}
// else {
// if (succ_begin == succ_end) {
// auto edge = graph.kmer_to_boss_index(to_node(row_idx));
// const auto &boss = graph.get_boss();
// logger->trace("Reduction: value {}"
// "\nFrom anchor: {}, only_incoming: {}, only_outgoing: {}"
// "\nTo NULL",
// curr_value, anchor[row_idx], boss.is_single_incoming(edge, boss.get_W()[edge]), boss.is_single_outgoing(edge));
// } else {
// auto edge = graph.kmer_to_boss_index(to_node(row_idx));
// const auto &boss = graph.get_boss();
// logger->trace("Reduction: value {}"
// "\nFrom anchor: {}, only_incoming: {}, only_outgoing: {}",
// curr_value, anchor[row_idx], boss.is_single_incoming(edge, boss.get_W()[edge]), boss.is_single_outgoing(edge));
// for (const uint64_t *it = succ_begin; it != succ_end; ++it) {
// auto next_edge = graph.kmer_to_boss_index(to_node(*it));
// logger->trace("\nTo anchor: {}, only_incoming: {}, only_outgoing: {}",
// anchor[*it], boss.is_single_incoming(next_edge, boss.get_W()[next_edge]), boss.is_single_outgoing(next_edge));
// }
// }
// }
}

if (!curr_value || (!compute_row_reduction && !rd_succ[to_node(row_idx)]))
return;

// check non-anchor predecessor nodes and add them if they are zero
for (const uint64_t *pred_p = pred_begin; pred_p < pred_end; ++pred_p) {
if (!source_col[*pred_p] && (compute_row_reduction || !anchor[*pred_p])) {
auto &v = set_rows_bwd[source_idx][j];
if constexpr(with_values) {
v.emplace_back(*pred_p, -curr_value);
} else {
v.push_back(*pred_p);
}
if (curr_value && (compute_row_reduction || rd_succ[to_node(row_idx)])) {
// check non-anchor predecessor nodes and add them if they are zero
for (const uint64_t *pred_p = pred_begin; pred_p < pred_end; ++pred_p) {
if (!source_col[*pred_p] && (compute_row_reduction || !anchor[*pred_p])) {
auto &v = set_rows_bwd[source_idx][j];
if constexpr(with_values) {
v.emplace_back(*pred_p, -curr_value);
} else {
v.push_back(*pred_p);
}

if (v.size() == v.capacity()) {
std::sort(v.begin(), v.end());
dump_chunk_to_disk(v, source_idx, j, num_chunks[source_idx][j]++);
v.resize(0);
if (v.size() == v.capacity()) {
std::sort(v.begin(), v.end());
dump_chunk_to_disk(v, source_idx, j, num_chunks[source_idx][j]++);
v.resize(0);
}
}
}
}
Expand Down Expand Up @@ -1123,8 +1095,8 @@ void convert_batch_to_row_diff(const std::string &pred_succ_fprefix,
std::vector<uint64_t> ids;
ids.reserve(row_diff_bits[l_idx][j]);
int64_t value = 0;
// Call merge_files<T> with a single template parameter (not pair).
// It can't extract and add counts, so we do this manually.
// merge_files<T> with a single template parameter (not pair)
// can't extract and add counts, so we do this manually.
elias_fano::merge_files<T>(filenames, [&](T v) {
if constexpr(with_values) {
assert(v.second && "zero diffs must have been skipped");
Expand Down Expand Up @@ -1359,8 +1331,7 @@ void convert_batch_to_row_diff_coord(const std::string &pred_succ_fprefix,
const auto diff = get_diff(curr_value, get_value(source_col, s, j, succ_begin, succ_end));
// reduction (zero diff)
__atomic_add_fetch(&row_nbits_block[chunk_idx],
curr_value.size() - diff.size(),
__ATOMIC_RELAXED);
curr_value.size() - diff.size(), __ATOMIC_RELAXED);
},
[&](uint64_t block_begin) {
__atomic_thread_fence(__ATOMIC_ACQUIRE);
Expand Down

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