tortoise and hare

Author: mlin

loaders/common.hpp

@@ -154,8 +154,8 @@ template <class Item> class BackgroundProducer {
 
     void background_thread() {
         t0_ = chrono::high_resolution_clock::now();
+        long long p = 0;
         do {
-            auto p = p_.load(memory_order_acquire);
             bool ok = false;
             try {
                 ok = Produce(ring_[p % R_]);
@@ -167,14 +167,13 @@ template <class Item> class BackgroundProducer {
                 stop_.store(true, memory_order_release);
             }
             if (ok) {
-                ++p;
-                p_.store(p, memory_order_release);
+                p_.store(++p, memory_order_release);
                 if (p - max(c_.load(memory_order_acquire), 1LL) == R_ - 1) {
                     auto t_spin = chrono::high_resolution_clock::now();
                     do {
-                        // assumption -- producer will usually be faster than the consumer, and
-                        // ringsize_ provides buffer if that's occasionally not the case
-                        this_thread::sleep_for(chrono::milliseconds(1));
+                        // assumption -- producer is usually faster than the consumer, and ringsize
+                        // provides a buffer if that's occasionally not the case
+                        this_thread::sleep_for(chrono::nanoseconds(10000));
                     } while (!stop_.load(memory_order_relaxed) &&
                              (p - max(c_.load(memory_order_acquire), 1LL) == R_ - 1));
                     p_blocked_ += chrono::high_resolution_clock::now() - t_spin;
@@ -204,7 +203,7 @@ template <class Item> class BackgroundProducer {
             }
             worker_.reset(new thread([this]() { this->background_thread(); }));
         }
-        auto c = c_.load(memory_order_acquire), p = p_.load(memory_order_acquire);
+        long long p = p_.load(memory_order_acquire), c = c_.load(memory_order_relaxed);
         if (c == p) {
             auto t_spin = chrono::high_resolution_clock::now();
             while (c == p && !stop_.load(memory_order_relaxed)) {

loaders/sam_into_sqlite.cc

@@ -76,10 +76,9 @@ map<string, int> import_readgroups(const string &table_prefix, sam_hdr_t *hdr, S
 
 // Given tab-split SAM line, write JSON dict of read's tags (aux) into out; return rg_id or -1
 int write_tags_json(const map<string, int> &readgroups, const vector<char *> &sam_fields,
-                    OStringStream &out) {
+                    vector<char *> &tag, OStringStream &out) {
     out << '{';
     int rg_id = -1;
-    vector<char *> tag;
     bool first = true;
     for (int c = 11; c < sam_fields.size(); ++c) {
         tag.clear();
@@ -139,6 +138,7 @@ class SamReader : public BackgroundProducer<SamItem> {
     bam_hdr_t *hdr_;
     const map<string, int> &readgroups_;
     OStringStream tagsbuf_;
+    vector<char *> tagsparsebuf_;
 
     bool Produce(SamItem &it) override {
         it.Clear();
@@ -158,9 +158,9 @@ class SamReader : public BackgroundProducer<SamItem> {
             throw runtime_error("Corrupt SAM record; fields.size() = " +
                                 to_string(it.fields.size()));
         }
-        // formulate tags JSON on here on background thread
+        // formulate tags JSON here on background thread
         tagsbuf_.Clear();
-        it.rg_id = write_tags_json(readgroups_, it.fields, tagsbuf_);
+        it.rg_id = write_tags_json(readgroups_, it.fields, tagsparsebuf_, tagsbuf_);
         it.tags_json = tagsbuf_.Get();
         return true;
     }
@@ -327,8 +327,8 @@ int main(int argc, char *argv[]) {
                                                "reads_tags(rowid,tags_json) VALUES(?,?)");
 
         // stream bam1_t records
-        progress &&cerr << "inserting reads...";
-        SamReader reader(sam.get(), hdr.get(), readgroups, 64);
+        progress &&cerr << "inserting reads..." << endl;
+        SamReader reader(sam.get(), hdr.get(), readgroups, 256);
         while (reader.next()) {
             const SamItem &it = reader.item();
             bam1_t *rec = it.rec.get();