[Backport release-2.26] Dense reader fails early when tile offsets ar…

…e too large. (#5310) (#5311)

Backport of #5310 to release-2.26.

---
TYPE: IMPROVEMENT
DESC: Dense reader fails early when tile offsets are too large.

---------

Co-authored-by: Luc Rancourt <[email protected]>
Co-authored-by: KiterLuc <[email protected]>

test/src/unit-dense-reader.cc

@@ -889,6 +889,42 @@ TEST_CASE_METHOD(
       "DenseReader: Memory budget is too small to open array");
 }
 
+TEST_CASE_METHOD(
+    CDenseFx,
+    "Dense reader: budget too small for tile offsets",
+    "[dense-reader][budget-too-small-tile-offsets]") {
+  // Create default array.
+  reset_config();
+  create_default_array_1d();
+
+  uint64_t num_frags = GENERATE(1, 2);
+
+  // Write some fragments.
+  int subarray[] = {1, NUM_CELLS};
+  std::vector<int> data(NUM_CELLS);
+  std::iota(data.begin(), data.end(), 1);
+  uint64_t data_size = data.size() * sizeof(int);
+  for (uint64_t f = 0; f < num_frags; f++) {
+    write_1d_fragment(subarray, data.data(), &data_size);
+  }
+
+  // Footer for a fragment is 390 bytes.
+  // Tile offsets for a fragment are 400 bytes.
+  // Tile upper memory limit is more than enough to load 40 bytes tiles.
+  total_budget_ = std::to_string(390 * num_frags + 200);
+  update_config();
+
+  // Try to read.
+  int data_r[NUM_CELLS] = {0};
+  uint64_t data_r_size = sizeof(data_r);
+  read(
+      subarray,
+      data_r,
+      &data_r_size,
+      0,
+      "DenseReader: Cannot load tile offsets, increase memory budget");
+}
+
 TEST_CASE_METHOD(
     CDenseFx,
     "Dense reader: tile budget exceeded, fixed attribute",
@@ -942,7 +978,7 @@ TEST_CASE_METHOD(
   uint64_t data_size = data.size() * sizeof(int);
   write_1d_fragment(subarray, data.data(), &data_size);
 
-  total_budget_ = "420";
+  total_budget_ = "804";
   tile_upper_memory_limit_ = "50";
   update_config();
 
@@ -1025,7 +1061,7 @@ TEST_CASE_METHOD(
 
   // Each tiles are 91 and 100 bytes respectively, this will only allow to
   // load one as the budget is split across two potential reads.
-  total_budget_ = "460";
+  total_budget_ = "840";
   tile_upper_memory_limit_ = "210";
   update_config();
 

tiledb/sm/query/readers/dense_reader.cc

@@ -98,6 +98,9 @@ DenseReader::DenseReader(
 
   // Check the validity buffer sizes.
   check_validity_buffer_sizes();
+
+  // No dense dimensions can be var sized.
+  is_dim_var_size_.resize(array_schema_.dim_num(), false);
 }
 
 /* ****************************** */
@@ -310,6 +313,25 @@ Status DenseReader::dense_read() {
   if (condition_.has_value()) {
     qc_loaded_attr_names_set_ = condition_->field_names();
   }
+  qc_loaded_attr_names_.clear();
+  qc_loaded_attr_names_.reserve(qc_loaded_attr_names_set_.size());
+  for (auto& name : qc_loaded_attr_names_set_) {
+    qc_loaded_attr_names_.emplace_back(name);
+  }
+
+  // Load per fragment tile offsets memory usage.
+  per_frag_tile_offsets_usage_ = tile_offset_sizes();
+
+  // Compute total tile offsets sizes.
+  auto total_tile_offsets_sizes = std::accumulate(
+      per_frag_tile_offsets_usage_.begin(),
+      per_frag_tile_offsets_usage_.end(),
+      static_cast<uint64_t>(0));
+  if (total_tile_offsets_sizes >
+      memory_budget_ - array_memory_tracker_->get_memory_usage()) {
+    throw DenseReaderException(
+        "Cannot load tile offsets, increase memory budget");
+  }
 
   auto&& [names, var_names] = field_names_to_process(qc_loaded_attr_names_set_);
 

tiledb/sm/query/readers/reader_base.cc

@@ -77,6 +77,8 @@ ReaderBase::ReaderBase(
     , memory_tracker_(params.query_memory_tracker())
     , condition_(params.condition())
     , user_requested_timestamps_(false)
+    , deletes_consolidation_no_purge_(
+          buffers_.count(constants::delete_timestamps) != 0)
     , use_timestamps_(false)
     , initial_data_loaded_(false)
     , max_batch_size_(config_.get<uint64_t>("vfs.max_batch_size").value())
@@ -145,6 +147,134 @@ bool ReaderBase::skip_field(
 /*        PROTECTED METHODS       */
 /* ****************************** */
 
+std::vector<uint64_t> ReaderBase::tile_offset_sizes() {
+  auto timer_se = stats_->start_timer("tile_offset_sizes");
+
+  // For easy reference.
+  std::vector<uint64_t> ret(fragment_metadata_.size());
+  const auto dim_num = array_schema_.dim_num();
+
+  // Compute the size of tile offsets per fragments.
+  const auto relevant_fragments = subarray_.relevant_fragments();
+  throw_if_not_ok(parallel_for(
+      &resources_.compute_tp(), 0, relevant_fragments.size(), [&](uint64_t i) {
+        // For easy reference.
+        auto frag_idx = relevant_fragments[i];
+        auto& fragment = fragment_metadata_[frag_idx];
+        const auto& schema = fragment->array_schema();
+        const auto tile_num = fragment->tile_num();
+        const auto dense = schema->dense();
+
+        // Compute the number of dimensions/attributes requiring offsets.
+        uint64_t num = 0;
+
+        // For fragments with version smaller than 5 we have zipped coords.
+        // Otherwise we load each dimensions independently.
+        if (!dense) {
+          if (fragment->version() < 5) {
+            num = 1;
+          } else {
+            for (unsigned d = 0; d < dim_num; ++d) {
+              // Fixed tile (offsets or fixed data).
+              num++;
+
+              // If var size, we load var offsets and var tile sizes.
+              if (is_dim_var_size_[d]) {
+                num += 2;
+              }
+            }
+          }
+        }
+
+        // Process everything loaded for query condition.
+        for (auto& name : qc_loaded_attr_names_) {
+          // Not a member of array schema, this field was added in array
+          // schema evolution, ignore for this fragment's tile offsets.
+          // Also skip dimensions.
+          if (!schema->is_field(name) || schema->is_dim(name)) {
+            continue;
+          }
+
+          // Fixed tile (offsets or fixed data).
+          num++;
+
+          // If var size, we load var offsets and var tile sizes.
+          const auto attr = schema->attribute(name);
+          num += 2 * attr->var_size();
+
+          // If nullable, we load nullable offsets.
+          num += attr->nullable();
+        }
+
+        // Process everything loaded for user requested data.
+        for (auto& it : buffers_) {
+          const auto& name = it.first;
+
+          // Skip dimensions and attributes loaded by query condition as they
+          // are processed above. Special attributes (timestamps, delete
+          // timestamps, etc.) are processed below.
+          if (array_schema_.is_dim(name) || !schema->is_field(name) ||
+              qc_loaded_attr_names_set_.count(name) != 0 ||
+              schema->is_special_attribute(name)) {
+            continue;
+          }
+
+          // Fixed tile (offsets or fixed data).
+          num++;
+
+          // If var size, we load var offsets and var tile sizes.
+          const auto attr = schema->attribute(name);
+          num += 2 * attr->var_size();
+
+          // If nullable, we load nullable offsets.
+          num += attr->nullable();
+        }
+
+        if (!dense) {
+          // Add timestamps if required.
+          if (!timestamps_not_present(constants::timestamps, frag_idx)) {
+            num++;
+          }
+
+          // Add delete metadata if required.
+          if (!delete_meta_not_present(
+                  constants::delete_timestamps, frag_idx)) {
+            num++;
+            num += deletes_consolidation_no_purge_;
+          }
+        }
+
+        // Finally set the size of the loaded data.
+
+        // The expected size of the tile offsets
+        unsigned offsets_size = num * tile_num * sizeof(uint64_t);
+
+        // Other than the offsets themselves, there is also memory used for the
+        // initialization of the vectors that hold them. This initialization
+        // takes place in LoadedFragmentMetadata::resize_offsets()
+
+        // Calculate the number of fields
+        unsigned num_fields = schema->attribute_num() + 1 +
+                              fragment->has_timestamps() +
+                              fragment->has_delete_meta() * 2;
+
+        // If version < 5 we use zipped coordinates, otherwise separate
+        num_fields += (fragment->version() >= 5) ? schema->dim_num() : 0;
+
+        // The additional memory required for the vectors to
+        // store the tile offsets. The number of fields is calculated above.
+        // Each vector requires 32 bytes. Each field requires 4 vectors. These
+        // are: tile_offsets_, tile_var_offsets_, tile_var_sizes_,
+        // tile_validity_offsets_ and are located in loaded_fragment_metadata.h
+        unsigned offsets_init_size = num_fields * 4 * 32;
+
+        ret[frag_idx] = offsets_size + offsets_init_size;
+        return Status::Ok();
+      }));
+
+  return ret;
+}
+
 bool ReaderBase::process_partial_timestamps(FragmentMetadata& frag_meta) const {
   return frag_meta.has_timestamps() &&
          frag_meta.partial_time_overlap(

tiledb/sm/query/readers/reader_base.h

@@ -269,6 +269,9 @@ class ReaderBase : public StrategyBase {
   /** If the user requested timestamps attribute in the query */
   bool user_requested_timestamps_;
 
+  /** Are we doing deletes consolidation (without purge option). */
+  bool deletes_consolidation_no_purge_;
+
   /**
    * If the special timestamps attribute should be loaded to memory for
    * this query
@@ -281,6 +284,12 @@ class ReaderBase : public StrategyBase {
    */
   std::vector<bool> timestamps_needed_for_deletes_and_updates_;
 
+  /** Are dimensions var sized. */
+  std::vector<bool> is_dim_var_size_;
+
+  /** Names of dim/attr loaded for query condition. */
+  std::vector<std::string> qc_loaded_attr_names_;
+
   /** Names of dim/attr loaded for query condition. */
   std::unordered_set<std::string> qc_loaded_attr_names_set_;
 
@@ -305,6 +314,9 @@ class ReaderBase : public StrategyBase {
    * */
   std::unordered_map<std::string, QueryBuffer>& aggregate_buffers_;
 
+  /** Per fragment tile offsets memory usage. */
+  std::vector<uint64_t> per_frag_tile_offsets_usage_;
+
   /* ********************************* */
   /*         PROTECTED METHODS         */
   /* ********************************* */
@@ -338,6 +350,13 @@ class ReaderBase : public StrategyBase {
     return true;
   }
 
+  /**
+   * Computes the required size for loading tile offsets, per fragments.
+   *
+   * @return Required memory for loading tile offsets, per fragments.
+   */
+  std::vector<uint64_t> tile_offset_sizes();
+
   /**
    * Returns if we need to process partial timestamp condition for this
    * fragment.