Less linear search in DBIter::Seek() when keys are overwritten a lot

Summary:
In one deployment we saw high latencies (presumably from slow iterator operations) and a lot of CPU time reported by perf with this stack:

```
  rocksdb::MergingIterator::Next
  rocksdb::DBIter::FindNextUserEntryInternal
  rocksdb::DBIter::Seek
```

I think what's happening is:
1. we create a snapshot iterator,
2. we do lots of Put()s for the same key x; this creates lots of entries in memtable,
3. we seek the iterator to a key slightly smaller than x,
4. the seek walks over lots of entries in memtable for key x, skipping them because of high sequence numbers.

CC IslamAbdelRahman
Closes https://github.com/facebook/rocksdb/pull/1413

Differential Revision: D4083879

Pulled By: IslamAbdelRahman

fbshipit-source-id: a83ddae

.gitignore

@@ -37,6 +37,7 @@ util/build_version.cc
 build_tools/VALGRIND_LOGS/
 coverage/COVERAGE_REPORT
 .gdbhistory
+.gdb_history
 package/
 .phutil_module_cache
 unity.a

db/db_iter.cc

@@ -339,7 +339,7 @@ void DBIter::Next() {
 //           saved_value_             => the merged value
 //
 // NOTE: In between, saved_key_ can point to a user key that has
-//       a delete marker
+//       a delete marker or a sequence number higher than sequence_
 //
 // The prefix_check parameter controls whether we check the iterated
 // keys against the prefix of the seeked key. Set to false when
@@ -356,90 +356,137 @@ void DBIter::FindNextUserEntryInternal(bool skipping, bool prefix_check) {
   assert(iter_->Valid());
   assert(direction_ == kForward);
   current_entry_is_merged_ = false;
+
+  // How many times in a row we have skipped an entry with user key less than
+  // or equal to saved_key_. We could skip these entries either because
+  // sequence numbers were too high or because skipping = true.
+  // What saved_key_ contains throughout this method:
+  //  - if skipping        : saved_key_ contains the key that we need to skip,
+  //                         and we haven't seen any keys greater than that,
+  //  - if num_skipped > 0 : saved_key_ contains the key that we have skipped
+  //                         num_skipped times, and we haven't seen any keys
+  //                         greater than that,
+  //  - none of the above  : saved_key_ can contain anything, it doesn't matter.
   uint64_t num_skipped = 0;
+
   do {
     ParsedInternalKey ikey;
 
-    if (ParseKey(&ikey)) {
+    if (!ParseKey(&ikey)) {
-      if (iterate_upper_bound_ != nullptr &&
+      // Skip corrupted keys.
-          user_comparator_->Compare(ikey.user_key, *iterate_upper_bound_) >= 0) {
+      iter_->Next();
-        break;
+      continue;
-      }
+    }
 
-      if (prefix_extractor_ && prefix_check &&
+    if (iterate_upper_bound_ != nullptr &&
-          prefix_extractor_->Transform(ikey.user_key).compare(prefix_start_key_) != 0) {
+        user_comparator_->Compare(ikey.user_key, *iterate_upper_bound_) >= 0) {
-        break;
+      break;
-      }
+    }
 
-      if (ikey.sequence <= sequence_) {
+    if (prefix_extractor_ && prefix_check &&
-        if (skipping &&
+        prefix_extractor_->Transform(ikey.user_key)
-           user_comparator_->Compare(ikey.user_key, saved_key_.GetKey()) <= 0) {
+          .compare(prefix_start_key_) != 0) {
-          num_skipped++;  // skip this entry
+      break;
-          PERF_COUNTER_ADD(internal_key_skipped_count, 1);
+    }
-        } else {
+
-          switch (ikey.type) {
+    if (ikey.sequence <= sequence_) {
-            case kTypeDeletion:
+      if (skipping &&
-            case kTypeSingleDeletion:
+          user_comparator_->Compare(ikey.user_key, saved_key_.GetKey()) <= 0) {
+        num_skipped++;  // skip this entry
+        PERF_COUNTER_ADD(internal_key_skipped_count, 1);
+      } else {
+        skipping = false;  // ikey > saved_key_, i.e. saved_key_ is skipped
+        num_skipped = 0;
+        switch (ikey.type) {
+          case kTypeDeletion:
+          case kTypeSingleDeletion:
+            // Arrange to skip all upcoming entries for this key since
+            // they are hidden by this deletion.
+            saved_key_.SetKey(
+                ikey.user_key,
+                !iter_->IsKeyPinned() || !pin_thru_lifetime_ /* copy */);
+            skipping = true;
+            PERF_COUNTER_ADD(internal_delete_skipped_count, 1);
+            break;
+          case kTypeValue:
+            saved_key_.SetKey(
+                ikey.user_key,
+                !iter_->IsKeyPinned() || !pin_thru_lifetime_ /* copy */);
+            if (range_del_agg_.ShouldDelete(ikey)) {
               // Arrange to skip all upcoming entries for this key since
               // they are hidden by this deletion.
-              saved_key_.SetKey(
-                  ikey.user_key,
-                  !iter_->IsKeyPinned() || !pin_thru_lifetime_ /* copy */);
               skipping = true;
               num_skipped = 0;
               PERF_COUNTER_ADD(internal_delete_skipped_count, 1);
-              break;
+            } else {
-            case kTypeValue:
+              valid_ = true;
-              saved_key_.SetKey(
+              return;
-                  ikey.user_key,
+            }
-                  !iter_->IsKeyPinned() || !pin_thru_lifetime_ /* copy */);
+            break;
-              if (range_del_agg_.ShouldDelete(ikey)) {
+          case kTypeMerge:
-                // Arrange to skip all upcoming entries for this key since
+            saved_key_.SetKey(
-                // they are hidden by this deletion.
+                ikey.user_key,
-                skipping = true;
+                !iter_->IsKeyPinned() || !pin_thru_lifetime_ /* copy */);
-                num_skipped = 0;
+            if (range_del_agg_.ShouldDelete(ikey)) {
-                PERF_COUNTER_ADD(internal_delete_skipped_count, 1);
+              // Arrange to skip all upcoming entries for this key since
-              } else {
+              // they are hidden by this deletion.
-                valid_ = true;
+              skipping = true;
-                return;
+              num_skipped = 0;
-              }
+              PERF_COUNTER_ADD(internal_delete_skipped_count, 1);
-              break;
+            } else {
-            case kTypeMerge:
+              // By now, we are sure the current ikey is going to yield a
-              saved_key_.SetKey(
+              // value
-                  ikey.user_key,
+              current_entry_is_merged_ = true;
-                  !iter_->IsKeyPinned() || !pin_thru_lifetime_ /* copy */);
+              valid_ = true;
-              if (range_del_agg_.ShouldDelete(ikey)) {
+              MergeValuesNewToOld();  // Go to a different state machine
-                // Arrange to skip all upcoming entries for this key since
+              return;
-                // they are hidden by this deletion.
+            }
-                skipping = true;
+            break;
-                num_skipped = 0;
+          default:
-                PERF_COUNTER_ADD(internal_delete_skipped_count, 1);
+            assert(false);
-              } else {
+            break;
-                // By now, we are sure the current ikey is going to yield a
-                // value
-                current_entry_is_merged_ = true;
-                valid_ = true;
-                MergeValuesNewToOld();  // Go to a different state machine
-                return;
-              }
-              break;
-            default:
-              assert(false);
-              break;
-          }
         }
       }
+    } else {
+      // This key was inserted after our snapshot was taken.
+      PERF_COUNTER_ADD(internal_recent_skipped_count, 1);
+
+      // Here saved_key_ may contain some old key, or the default empty key, or
+      // key assigned by some random other method. We don't care.
+      if (user_comparator_->Compare(ikey.user_key, saved_key_.GetKey()) <= 0) {
+        num_skipped++;
+      } else {
+        saved_key_.SetKey(
+                ikey.user_key,
+                !iter_->IsKeyPinned() || !pin_thru_lifetime_ /* copy */);
+        skipping = false;
+        num_skipped = 0;
+      }
     }
-    // If we have sequentially iterated via numerous keys and still not
+
-    // found the next user-key, then it is better to seek so that we can
+    // If we have sequentially iterated via numerous equal keys, then it's
-    // avoid too many key comparisons. We seek to the last occurrence of
+    // better to seek so that we can avoid too many key comparisons.
-    // our current key by looking for sequence number 0 and type deletion
+    if (num_skipped > max_skip_) {
-    // (the smallest type).
-    if (skipping && num_skipped > max_skip_) {
       num_skipped = 0;
       std::string last_key;
-      AppendInternalKey(&last_key, ParsedInternalKey(saved_key_.GetKey(), 0,
+      if (skipping) {
-                                                     kTypeDeletion));
+        // We're looking for the next user-key but all we see are the same
+        // user-key with decreasing sequence numbers. Fast forward to
+        // sequence number 0 and type deletion (the smallest type).
+        AppendInternalKey(&last_key, ParsedInternalKey(saved_key_.GetKey(), 0,
+                                                       kTypeDeletion));
+        // Don't set skipping = false because we may still see more user-keys
+        // equal to saved_key_.
+      } else {
+        // We saw multiple entries with this user key and sequence numbers
+        // higher than sequence_. Fast forward to sequence_.
+        // Note that this only covers a case when a higher key was overwritten
+        // many times since our snapshot was taken, not the case when a lot of
+        // different keys were inserted after our snapshot was taken.
+        AppendInternalKey(&last_key,
+                          ParsedInternalKey(saved_key_.GetKey(), sequence_,
+                                            kValueTypeForSeek));
+      }
       iter_->Seek(last_key);
       RecordTick(statistics_, NUMBER_OF_RESEEKS_IN_ITERATION);
     } else {
@@ -503,6 +550,7 @@ void DBIter::MergeValuesNewToOld() {
       // when complete, add result to operands and continue.
       merge_context_.PushOperand(iter_->value(),
                                  iter_->IsValuePinned() /* operand_pinned */);
+      PERF_COUNTER_ADD(internal_merge_count, 1);
     } else {
       assert(false);
     }
@@ -564,6 +612,11 @@ void DBIter::ReverseToBackward() {
     FindParseableKey(&ikey, kReverse);
     while (iter_->Valid() &&
            user_comparator_->Compare(ikey.user_key, saved_key_.GetKey()) > 0) {
+      if (ikey.sequence > sequence_) {
+        PERF_COUNTER_ADD(internal_recent_skipped_count, 1);
+      } else {
+        PERF_COUNTER_ADD(internal_key_skipped_count, 1);
+      }
       iter_->Prev();
       FindParseableKey(&ikey, kReverse);
     }
@@ -676,6 +729,7 @@ bool DBIter::FindValueForCurrentKey() {
           assert(merge_operator_ != nullptr);
           merge_context_.PushOperandBack(
               iter_->value(), iter_->IsValuePinned() /* operand_pinned */);
+          PERF_COUNTER_ADD(internal_merge_count, 1);
         }
         break;
       default:
@@ -760,6 +814,7 @@ bool DBIter::FindValueForCurrentKeyUsingSeek() {
          ikey.type == kTypeMerge && !range_del_agg_.ShouldDelete(ikey)) {
     merge_context_.PushOperand(iter_->value(),
                                iter_->IsValuePinned() /* operand_pinned */);
+    PERF_COUNTER_ADD(internal_merge_count, 1);
     iter_->Next();
     FindParseableKey(&ikey, kForward);
   }
@@ -830,6 +885,11 @@ void DBIter::FindPrevUserKey() {
         ++num_skipped;
       }
     }
+    if (ikey.sequence > sequence_) {
+      PERF_COUNTER_ADD(internal_recent_skipped_count, 1);
+    } else {
+      PERF_COUNTER_ADD(internal_key_skipped_count, 1);
+    }
     iter_->Prev();
     FindParseableKey(&ikey, kReverse);
   }

db/db_iterator_test.cc

@@ -8,10 +8,10 @@
 // found in the LICENSE file. See the AUTHORS file for names of contributors.
 
 #include "db/db_test_util.h"
+#include "port/port.h"
 #include "port/stack_trace.h"
 #include "rocksdb/iostats_context.h"
 #include "rocksdb/perf_context.h"
-#include "port/port.h"
 
 namespace rocksdb {
 
@@ -1778,6 +1778,62 @@ TEST_F(DBIteratorTest, ReadAhead) {
   delete iter;
 }
 
+// Insert a key, create a snapshot iterator, overwrite key lots of times,
+// seek to a smaller key. Expect DBIter to fall back to a seek instead of
+// going through all the overwrites linearly.
+TEST_F(DBIteratorTest, DBIteratorSkipRecentDuplicatesTest) {
+  Options options = CurrentOptions();
+  options.env = env_;
+  options.create_if_missing = true;
+  options.max_sequential_skip_in_iterations = 3;
+  options.prefix_extractor = nullptr;
+  options.write_buffer_size = 1 << 27;  // big enough to avoid flush
+  options.statistics = rocksdb::CreateDBStatistics();
+  DestroyAndReopen(options);
+
+  // Insert.
+  ASSERT_OK(Put("b", "0"));
+
+  // Create iterator.
+  ReadOptions ro;
+  std::unique_ptr<Iterator> iter(db_->NewIterator(ro));
+
+  // Insert a lot.
+  for (int i = 0; i < 100; ++i) {
+    ASSERT_OK(Put("b", std::to_string(i + 1).c_str()));
+  }
+
+#ifndef ROCKSDB_LITE
+  // Check that memtable wasn't flushed.
+  std::string val;
+  ASSERT_TRUE(db_->GetProperty("rocksdb.num-files-at-level0", &val));
+  EXPECT_EQ("0", val);
+#endif
+
+  // Seek iterator to a smaller key.
+  perf_context.Reset();
+  iter->Seek("a");
+  ASSERT_TRUE(iter->Valid());
+  EXPECT_EQ("b", iter->key().ToString());
+  EXPECT_EQ("0", iter->value().ToString());
+
+  // Check that the seek didn't do too much work.
+  // Checks are not tight, just make sure that everything is well below 100.
+  EXPECT_LT(perf_context.internal_key_skipped_count, 4);
+  EXPECT_LT(perf_context.internal_recent_skipped_count, 8);
+  EXPECT_LT(perf_context.seek_on_memtable_count, 10);
+  EXPECT_LT(perf_context.next_on_memtable_count, 10);
+  EXPECT_LT(perf_context.prev_on_memtable_count, 10);
+
+  // Check that iterator did something like what we expect.
+  EXPECT_EQ(perf_context.internal_delete_skipped_count, 0);
+  EXPECT_EQ(perf_context.internal_merge_count, 0);
+  EXPECT_GE(perf_context.internal_recent_skipped_count, 2);
+  EXPECT_GE(perf_context.seek_on_memtable_count, 2);
+  EXPECT_EQ(1, options.statistics->getTickerCount(
+                 NUMBER_OF_RESEEKS_IN_ITERATION));
+}
+
 }  // namespace rocksdb
 
 int main(int argc, char** argv) {

db/memtable.cc

@@ -322,11 +322,13 @@ class MemTableIterator : public InternalIterator {
     valid_ = iter_->Valid();
   }
   virtual void Next() override {
+    PERF_COUNTER_ADD(next_on_memtable_count, 1);
     assert(Valid());
     iter_->Next();
     valid_ = iter_->Valid();
   }
   virtual void Prev() override {
+    PERF_COUNTER_ADD(prev_on_memtable_count, 1);
     assert(Valid());
     iter_->Prev();
     valid_ = iter_->Valid();

include/rocksdb/perf_context.h

@@ -45,8 +45,7 @@ struct PerfContext {
   //    tombstones are not included in this counter, while previous updates
   //    hidden by the tombstones will be included here.
   // 4. symmetric cases for Prev() and SeekToLast()
-  // We sometimes also skip entries of more recent updates than the snapshot
+  // internal_recent_skipped_count is not included in this counter.
-  // we read from, but they are not included in this counter.
   //
   uint64_t internal_key_skipped_count;
   // Total number of deletes and single deletes skipped over during iteration
@@ -57,6 +56,13 @@ struct PerfContext {
   // still older updates invalidated by the tombstones.
   //
   uint64_t internal_delete_skipped_count;
+  // How many times iterators skipped over internal keys that are more recent
+  // than the snapshot that iterator is using.
+  //
+  uint64_t internal_recent_skipped_count;
+  // How many values were fed into merge operator by iterators.
+  //
+  uint64_t internal_merge_count;
 
   uint64_t get_snapshot_time;       // total nanos spent on getting snapshot
   uint64_t get_from_memtable_time;  // total nanos spent on querying memtables
@@ -67,7 +73,12 @@ struct PerfContext {
   // total nanos spent on seeking memtable
   uint64_t seek_on_memtable_time;
   // number of seeks issued on memtable
+  // (including SeekForPrev but not SeekToFirst and SeekToLast)
   uint64_t seek_on_memtable_count;
+  // number of Next()s issued on memtable
+  uint64_t next_on_memtable_count;
+  // number of Prev()s issued on memtable
+  uint64_t prev_on_memtable_count;
   // total nanos spent on seeking child iters
   uint64_t seek_child_seek_time;
   // number of seek issued in child iterators

util/perf_context.cc

@@ -28,6 +28,8 @@ void PerfContext::Reset() {
   block_decompress_time = 0;
   internal_key_skipped_count = 0;
   internal_delete_skipped_count = 0;
+  internal_recent_skipped_count = 0;
+  internal_merge_count = 0;
   write_wal_time = 0;
 
   get_snapshot_time = 0;
@@ -37,6 +39,8 @@ void PerfContext::Reset() {
   get_from_output_files_time = 0;
   seek_on_memtable_time = 0;
   seek_on_memtable_count = 0;
+  next_on_memtable_count = 0;
+  prev_on_memtable_count = 0;
   seek_child_seek_time = 0;
   seek_child_seek_count = 0;
   seek_min_heap_time = 0;
@@ -80,6 +84,8 @@ std::string PerfContext::ToString(bool exclude_zero_counters) const {
   PERF_CONTEXT_OUTPUT(block_decompress_time);
   PERF_CONTEXT_OUTPUT(internal_key_skipped_count);
   PERF_CONTEXT_OUTPUT(internal_delete_skipped_count);
+  PERF_CONTEXT_OUTPUT(internal_recent_skipped_count);
+  PERF_CONTEXT_OUTPUT(internal_merge_count);
   PERF_CONTEXT_OUTPUT(write_wal_time);
   PERF_CONTEXT_OUTPUT(get_snapshot_time);
   PERF_CONTEXT_OUTPUT(get_from_memtable_time);
@@ -88,6 +94,8 @@ std::string PerfContext::ToString(bool exclude_zero_counters) const {
   PERF_CONTEXT_OUTPUT(get_from_output_files_time);
   PERF_CONTEXT_OUTPUT(seek_on_memtable_time);
   PERF_CONTEXT_OUTPUT(seek_on_memtable_count);
+  PERF_CONTEXT_OUTPUT(next_on_memtable_count);
+  PERF_CONTEXT_OUTPUT(prev_on_memtable_count);
   PERF_CONTEXT_OUTPUT(seek_child_seek_time);
   PERF_CONTEXT_OUTPUT(seek_child_seek_count);
   PERF_CONTEXT_OUTPUT(seek_min_heap_time);