Fix crash in consolidation due to accessing invalid/empty matrix entry

TileDB-Inc · Apr 22, 2019 · f2f413e · f2f413e
1 parent 86021e6
commit f2f413e
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Showing 2 changed files with 38 additions and 1 deletion.
diff --git a/test/src/unit-cppapi-array.cc b/test/src/unit-cppapi-array.cc
@@ -478,6 +478,42 @@ TEST_CASE(
     vfs.remove_dir(array_name);
 }
 
+TEST_CASE(
+    "C++ API: Consolidation of sequential fragment writes",
+    "[cppapi], [consolidation-sequential]") {
+  Context ctx;
+  VFS vfs(ctx);
+  const std::string array_name = "cpp_unit_array";
+
+  if (vfs.is_dir(array_name))
+    vfs.remove_dir(array_name);
+
+  Domain domain(ctx);
+  domain.add_dimension(Dimension::create<int>(ctx, "", {0, 11}, 12));
+
+  ArraySchema schema(ctx, TILEDB_DENSE);
+  schema.set_domain(domain).set_order({{TILEDB_ROW_MAJOR, TILEDB_ROW_MAJOR}});
+  schema.add_attribute(Attribute::create<int>(ctx, ""));
+
+  tiledb::Array::create(array_name, schema);
+  auto array_w = tiledb::Array(ctx, array_name, TILEDB_WRITE);
+  auto query_w = tiledb::Query(ctx, array_w, TILEDB_WRITE);
+  std::vector<int> data = {0, 1};
+
+  query_w.set_buffer("", data).set_subarray({0, 1}).submit();
+  query_w.set_buffer("", data).set_subarray({2, 3}).submit();
+  // this fragment write caused crash during consolidation
+  //   https://github.com/TileDB-Inc/TileDB/issues/1205
+  //   https://github.com/TileDB-Inc/TileDB/issues/1212
+  query_w.set_buffer("", data).set_subarray({3, 4}).submit();
+  query_w.finalize();
+  array_w.close();
+  Array::consolidate(ctx, array_name);
+
+  if (vfs.is_dir(array_name))
+    vfs.remove_dir(array_name);
+}
+
 TEST_CASE("C++ API: Encrypted array", "[cppapi], [encryption]") {
   Context ctx;
   VFS vfs(ctx);

diff --git a/tiledb/sm/storage_manager/consolidator.cc b/tiledb/sm/storage_manager/consolidator.cc
@@ -662,11 +662,12 @@ Status Consolidator::compute_next_to_consolidate(
       } else if (i + j >= col_num) {  // Non-valid entries
         m_sizes[i][j] = UINT64_MAX;
         m_union[i][j].clear();
+        m_union[i][j].shrink_to_fit();
       } else {  // Every other row is computed using the previous row
         auto ratio = (float)fragments[i + j - 1].fragment_size_ /
                      fragments[i + j].fragment_size_;
         ratio = (ratio <= 1.0f) ? ratio : 1.0f / ratio;
-        if (ratio >= size_ratio) {
+        if (ratio >= size_ratio && (m_sizes[i - 1][j] != UINT64_MAX)) {
           m_sizes[i][j] = m_sizes[i - 1][j] + fragments[i + j].fragment_size_;
           std::memcpy(&m_union[i][j][0], &m_union[i - 1][j][0], domain_size);
           utils::geometry::expand_mbr_with_mbr<T>(