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Hotfix for serializer #273

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merged 5 commits into from
May 11, 2021
Merged

Hotfix for serializer #273

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1690380
Hotfix for serializer
hcho3 May 6, 2021
b9b8cdd
Add test cases to demonstrate the serializer bug
hcho3 May 6, 2021
24e72d4
Reduce amount of time for PyBufferInterfaceRoundTrip.DeepFullTree
hcho3 May 7, 2021
1056b88
Add case PyBufferInterfaceRoundTrip.XGBoostBoston
hcho3 May 7, 2021
561cb0e
Address reviewer's feedback
hcho3 May 11, 2021
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17 changes: 10 additions & 7 deletions include/treelite/tree_impl.h
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Original file line number Diff line number Diff line change
Expand Up @@ -859,7 +859,7 @@ template <typename ThresholdType, typename LeafOutputType>
template <typename HeaderFieldHandlerFunc, typename TreeHandlerFunc>
inline void
ModelImpl<ThresholdType, LeafOutputType>::DeserializeTemplate(
size_t num_tree,
std::size_t num_tree,
HeaderFieldHandlerFunc header_field_handler,
TreeHandlerFunc tree_handler) {
/* Header */
Expand All @@ -870,7 +870,7 @@ ModelImpl<ThresholdType, LeafOutputType>::DeserializeTemplate(
header_field_handler(&param);
/* Body */
trees.clear();
for (size_t i = 0; i < num_tree; ++i) {
for (std::size_t i = 0; i < num_tree; ++i) {
trees.emplace_back();
tree_handler(trees.back());
}
Expand Down Expand Up @@ -917,17 +917,20 @@ ModelImpl<ThresholdType, LeafOutputType>::InitFromPyBuffer(
if (num_frame < kNumFrameInHeader || (num_frame - kNumFrameInHeader) % kNumFramePerTree != 0) {
throw std::runtime_error("Wrong number of frames");
}
const size_t num_tree = (num_frame - kNumFrameInHeader) / kNumFramePerTree;
const std::size_t num_tree = (num_frame - kNumFrameInHeader) / kNumFramePerTree;

auto header_field_handler = [&begin](auto* field) {
InitScalarFromPyBuffer(field, *begin++);
};

auto tree_hanlder = [&begin](Tree<ThresholdType, LeafOutputType>& tree) {
auto tree_handler = [&begin](Tree<ThresholdType, LeafOutputType>& tree) {
// Read the frames in the range [begin, begin + kNumFramePerTree) into the tree
tree.InitFromPyBuffer(begin, begin + kNumFramePerTree);
begin += kNumFramePerTree;
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Since we're capturing begin by reference, won't this iterate begin forward as a side effect of executing the lambda? It's not immediately clear to me why that is the correct thing to do with this handler. Maybe add a comment or refactor such that the lambda returns the next iterator to be processed rather than directly changing begin?

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Since we're capturing begin by reference, won't this iterate begin forward as a side effect of executing the lambda?

Yes, this is intended behavior.

refactor such that the lambda returns the next iterator to be processed

That would not be feasible, since the tree handler for the file stream does not involve iterators.

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Great! Can we get a comment just to make it clear to future developers that the side-effect is intentional?

// Advance the iterator so that the next tree reads the next kNumFramePerTree frames
};

DeserializeTemplate(num_tree, header_field_handler, tree_hanlder);
DeserializeTemplate(num_tree, header_field_handler, tree_handler);
}

template <typename ThresholdType, typename LeafOutputType>
Expand All @@ -940,11 +943,11 @@ ModelImpl<ThresholdType, LeafOutputType>::DeserializeFromFileImpl(FILE* src_fp)
ReadScalarFromFile(field, src_fp);
};

auto tree_hanlder = [src_fp](Tree<ThresholdType, LeafOutputType>& tree) {
auto tree_handler = [src_fp](Tree<ThresholdType, LeafOutputType>& tree) {
tree.DeserializeFromFile(src_fp);
};

DeserializeTemplate(num_tree, header_field_handler, tree_hanlder);
DeserializeTemplate(num_tree, header_field_handler, tree_handler);
}

inline void InitParamAndCheck(ModelParam* param,
Expand Down
238 changes: 212 additions & 26 deletions tests/cpp/test_serializer.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,9 @@ inline void TestRoundTrip(treelite::Model* model) {
auto buffer = model->GetPyBuffer();
std::unique_ptr<treelite::Model> received_model = treelite::Model::CreateFromPyBuffer(buffer);

ASSERT_EQ(TreeliteToBytes(model), TreeliteToBytes(received_model.get()));
// Use ASSERT_TRUE, since ASSERT_EQ will dump all the raw bytes into a string, potentially
// causing an OOM error
ASSERT_TRUE(TreeliteToBytes(model) == TreeliteToBytes(received_model.get()));
}

for (int i = 0; i < 2; ++i) {
Expand All @@ -44,7 +46,9 @@ inline void TestRoundTrip(treelite::Model* model) {
std::unique_ptr<treelite::Model> received_model = treelite::Model::DeserializeFromFile(fp);
std::fclose(fp);

ASSERT_EQ(TreeliteToBytes(model), TreeliteToBytes(received_model.get()));
// Use ASSERT_TRUE, since ASSERT_EQ will dump all the raw bytes into a string, potentially
// causing an OOM error
ASSERT_TRUE(TreeliteToBytes(model) == TreeliteToBytes(received_model.get()));
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@hcho3 hcho3 May 6, 2021 •
edited
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ASSERT_EQ will dump all the raw bytes into a string, leading to OOM error for this test case. So use ASSERT_TRUE instead.

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Maybe add a comment to this effect so that someone doesn't naively reintroduce this problem down the line?

}
}

Expand Down Expand Up @@ -178,7 +182,7 @@ void PyBufferInterfaceRoundTrip_TreeDepth2() {
};
builder->SetModelParam("pred_transform", "sigmoid");
builder->SetModelParam("global_bias", "0.5");
for (int tree_id = 0; tree_id < 2; ++tree_id) {
for (int tree_id = 0; tree_id < 3; ++tree_id) {
std::unique_ptr<frontend::TreeBuilder> tree{
new frontend::TreeBuilder(threshold_type, leaf_output_type)
};
Expand All @@ -189,10 +193,10 @@ void PyBufferInterfaceRoundTrip_TreeDepth2() {
tree->SetCategoricalTestNode(1, 0, {0, 1}, true, 3, 4);
tree->SetCategoricalTestNode(2, 1, {0}, true, 5, 6);
tree->SetRootNode(0);
tree->SetLeafNode(3, frontend::Value::Create<LeafOutputType>(3));
tree->SetLeafNode(4, frontend::Value::Create<LeafOutputType>(1));
tree->SetLeafNode(5, frontend::Value::Create<LeafOutputType>(4));
tree->SetLeafNode(6, frontend::Value::Create<LeafOutputType>(2));
tree->SetLeafNode(3, frontend::Value::Create<LeafOutputType>(tree_id + 3));
tree->SetLeafNode(4, frontend::Value::Create<LeafOutputType>(tree_id + 1));
tree->SetLeafNode(5, frontend::Value::Create<LeafOutputType>(tree_id + 4));
tree->SetLeafNode(6, frontend::Value::Create<LeafOutputType>(tree_id + 2));
Comment on lines +196 to +199
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I crafted the test case so that all the trees will have different leaf outputs. The bug being addressed causes all trees to be identical.

builder->InsertTree(tree.get());
}

Expand All @@ -216,33 +220,35 @@ template <typename ThresholdType, typename LeafOutputType>
void PyBufferInterfaceRoundTrip_DeepFullTree() {
TypeInfo threshold_type = TypeToInfo<ThresholdType>();
TypeInfo leaf_output_type = TypeToInfo<LeafOutputType>();
const int depth = 19;
const int depth = 17;

std::unique_ptr<frontend::ModelBuilder> builder{
new frontend::ModelBuilder(3, 1, false, threshold_type, leaf_output_type)
};
std::unique_ptr<frontend::TreeBuilder> tree{
new frontend::TreeBuilder(threshold_type, leaf_output_type)
};
for (int level = 0; level <= depth; ++level) {
for (int i = 0; i < (1 << level); ++i) {
const int nid = (1 << level) - 1 + i;
tree->CreateNode(nid);
for (int tree_id = 0; tree_id < 3; ++tree_id) {
std::unique_ptr<frontend::TreeBuilder> tree{
new frontend::TreeBuilder(threshold_type, leaf_output_type)
};
for (int level = 0; level <= depth; ++level) {
for (int i = 0; i < (1 << level); ++i) {
const int nid = (1 << level) - 1 + i;
tree->CreateNode(nid);
}
}
}
for (int level = 0; level <= depth; ++level) {
for (int i = 0; i < (1 << level); ++i) {
const int nid = (1 << level) - 1 + i;
if (level == depth) {
tree->SetLeafNode(nid, frontend::Value::Create<LeafOutputType>(1));
} else {
tree->SetNumericalTestNode(nid, (level % 2), "<", frontend::Value::Create<ThresholdType>(0),
true, 2 * nid + 1, 2 * nid + 2);
for (int level = 0; level <= depth; ++level) {
for (int i = 0; i < (1 << level); ++i) {
const int nid = (1 << level) - 1 + i;
if (level == depth) {
tree->SetLeafNode(nid, frontend::Value::Create<LeafOutputType>(tree_id + 1));
} else {
tree->SetNumericalTestNode(nid, (level % 2), "<", frontend::Value::Create<ThresholdType>(0),
true, 2 * nid + 1, 2 * nid + 2);
}
}
}
tree->SetRootNode(0);
builder->InsertTree(tree.get());
}
tree->SetRootNode(0);
builder->InsertTree(tree.get());

std::unique_ptr<Model> model = builder->CommitModel();
TestRoundTrip(model.get());
Expand All @@ -255,4 +261,184 @@ TEST(PyBufferInterfaceRoundTrip, DeepFullTree) {
PyBufferInterfaceRoundTrip_DeepFullTree<double, uint32_t>();
}

TEST(PyBufferInterfaceRoundTrip, XGBoostBoston) {
std::unique_ptr<frontend::ModelBuilder> builder{
new frontend::ModelBuilder(13, 1, false, TypeInfo::kFloat32, TypeInfo::kFloat32)
};
using frontend::Value;
{
std::unique_ptr<frontend::TreeBuilder> tree{
new frontend::TreeBuilder(TypeInfo::kFloat32, TypeInfo::kFloat32)
};
for (int nid = 0; nid <= 18; ++nid) {
tree->CreateNode(nid);
}
tree->SetRootNode(0);
tree->SetNumericalTestNode(0, 5, "<", Value::Create<float>(6.67599964f), true, 1, 2);
tree->SetNumericalTestNode(1, 12, "<", Value::Create<float>(16.0849991f), true, 3, 4);
tree->SetNumericalTestNode(3, 12, "<", Value::Create<float>(9.71500015f), true, 7, 8);
tree->SetNumericalTestNode(7, 0, "<", Value::Create<float>(4.72704506f), true, 15, 16);
tree->SetLeafNode(15, Value::Create<float>(23.1568813f));
tree->SetLeafNode(16, Value::Create<float>(37.125f));
tree->SetLeafNode(8, Value::Create<float>(19.625f));
tree->SetNumericalTestNode(4, 0, "<", Value::Create<float>(7.31708527f), true, 9, 10);
tree->SetLeafNode(9, Value::Create<float>(16.0535717f));
tree->SetNumericalTestNode(10, 0, "<", Value::Create<float>(24.9239006f), true, 17, 18);
tree->SetLeafNode(17, Value::Create<float>(9.96249962f));
tree->SetLeafNode(18, Value::Create<float>(3.20000005f));
tree->SetNumericalTestNode(2, 5, "<", Value::Create<float>(7.43700027f), true, 5, 6);
tree->SetNumericalTestNode(5, 0, "<", Value::Create<float>(8.18112564f), true, 11, 12);
tree->SetLeafNode(11, Value::Create<float>(31.0228577f));
tree->SetLeafNode(12, Value::Create<float>(9.30000019f));
tree->SetNumericalTestNode(6, 0, "<", Value::Create<float>(2.74223518f), true, 13, 14);
tree->SetLeafNode(13, Value::Create<float>(43.8833313f));
tree->SetLeafNode(14, Value::Create<float>(10.6999998f));
builder->InsertTree(tree.get());
}
{
std::unique_ptr<frontend::TreeBuilder> tree{
new frontend::TreeBuilder(TypeInfo::kFloat32, TypeInfo::kFloat32)
};
for (int nid = 0; nid <= 18; ++nid) {
tree->CreateNode(nid);
}
tree->SetRootNode(0);
tree->SetNumericalTestNode(0, 7, "<", Value::Create<float>(1.37205005f), true, 1, 2);
tree->SetNumericalTestNode(1, 12, "<", Value::Create<float>(11.4849997f), true, 3, 4);
tree->SetLeafNode(3, Value::Create<float>(12.3465471f));
tree->SetNumericalTestNode(4, 0, "<", Value::Create<float>(6.57226992f), true, 7, 8);
tree->SetLeafNode(7, Value::Create<float>(-2.63571453f));
tree->SetLeafNode(8, Value::Create<float>(3.13541675f));
tree->SetNumericalTestNode(2, 12, "<", Value::Create<float>(5.43999958f), true, 5, 6);
tree->SetNumericalTestNode(5, 7, "<", Value::Create<float>(2.85050011f), true, 9, 10);
tree->SetLeafNode(9, Value::Create<float>(6.06147718f));
tree->SetNumericalTestNode(10, 6, "<", Value::Create<float>(11.9499998f), true, 13, 14);
tree->SetLeafNode(13, Value::Create<float>(-1.27356553f));
tree->SetLeafNode(14, Value::Create<float>(1.90286708f));
tree->SetNumericalTestNode(6, 9, "<", Value::Create<float>(278.0f), true, 11, 12);
tree->SetNumericalTestNode(11, 7, "<", Value::Create<float>(4.36069965f), true, 15, 16);
tree->SetLeafNode(15, Value::Create<float>(2.3283093f));
tree->SetLeafNode(16, Value::Create<float>(-0.740369797f));
tree->SetNumericalTestNode(12, 5, "<", Value::Create<float>(6.67599964f), true, 17, 18);
tree->SetLeafNode(17, Value::Create<float>(-0.374256492f));
tree->SetLeafNode(18, Value::Create<float>(-3.15714335f));
builder->InsertTree(tree.get());
}
{
std::unique_ptr<frontend::TreeBuilder> tree{
new frontend::TreeBuilder(TypeInfo::kFloat32, TypeInfo::kFloat32)
};
for (int nid = 0; nid <= 30; ++nid) {
tree->CreateNode(nid);
}
tree->SetRootNode(0);
tree->SetNumericalTestNode(0, 10, "<", Value::Create<float>(20.9500008f), true, 1, 2);
tree->SetNumericalTestNode(1, 7, "<", Value::Create<float>(6.22315025f), true, 3, 4);
tree->SetNumericalTestNode(3, 8, "<", Value::Create<float>(2.5f), true, 7, 8);
tree->SetNumericalTestNode(7, 6, "<", Value::Create<float>(62.7999992f), true, 15, 16);
tree->SetLeafNode(15, Value::Create<float>(1.08206058f));
tree->SetLeafNode(16, Value::Create<float>(-2.5734961f));
tree->SetNumericalTestNode(8, 2, "<", Value::Create<float>(3.09500003f), true, 17, 18);
tree->SetLeafNode(17, Value::Create<float>(2.1601212f));
tree->SetLeafNode(18, Value::Create<float>(0.435377121f));
tree->SetNumericalTestNode(4, 5, "<", Value::Create<float>(6.94500017f), true, 9, 10);
tree->SetNumericalTestNode(9, 5, "<", Value::Create<float>(6.67650032f), true, 19, 20);
tree->SetLeafNode(19, Value::Create<float>(-0.727042675f));
tree->SetLeafNode(20, Value::Create<float>(-2.75314689f));
tree->SetNumericalTestNode(10, 12, "<", Value::Create<float>(4.77499962f), true, 21, 22);
tree->SetLeafNode(21, Value::Create<float>(-0.468363762f));
tree->SetLeafNode(22, Value::Create<float>(3.01290059f));
tree->SetNumericalTestNode(2, 5, "<", Value::Create<float>(6.11900043f), true, 5, 6);
tree->SetNumericalTestNode(5, 9, "<", Value::Create<float>(385.5f), true, 11, 12);
tree->SetNumericalTestNode(11, 5, "<", Value::Create<float>(5.51300001f), true, 23, 24);
tree->SetLeafNode(23, Value::Create<float>(0.224628448f));
tree->SetLeafNode(24, Value::Create<float>(-2.32530594f));
tree->SetNumericalTestNode(12, 5, "<", Value::Create<float>(5.91499996f), true, 25, 26);
tree->SetLeafNode(25, Value::Create<float>(-1.16225815f));
tree->SetLeafNode(26, Value::Create<float>(0.610342026f));
tree->SetNumericalTestNode(6, 0, "<", Value::Create<float>(0.448424995f), true, 13, 14);
tree->SetNumericalTestNode(13, 5, "<", Value::Create<float>(6.45600033f), true, 27, 28);
tree->SetLeafNode(27, Value::Create<float>(-1.64520073f));
tree->SetLeafNode(28, Value::Create<float>(-0.275371552f));
tree->SetNumericalTestNode(14, 0, "<", Value::Create<float>(0.681519985f), true, 29, 30);
tree->SetLeafNode(29, Value::Create<float>(1.69765615f));
tree->SetLeafNode(30, Value::Create<float>(-0.246309474f));
builder->InsertTree(tree.get());
}
{
std::unique_ptr<frontend::TreeBuilder> tree{
new frontend::TreeBuilder(TypeInfo::kFloat32, TypeInfo::kFloat32)
};
for (int nid = 0; nid <= 26; ++nid) {
tree->CreateNode(nid);
}
tree->SetRootNode(0);
tree->SetNumericalTestNode(0, 5, "<", Value::Create<float>(6.68949986f), true, 1, 2);
tree->SetNumericalTestNode(1, 5, "<", Value::Create<float>(6.5454998f), true, 3, 4);
tree->SetNumericalTestNode(3, 9, "<", Value::Create<float>(207.5f), true, 7, 8);
tree->SetNumericalTestNode(7, 11, "<", Value::Create<float>(377.880005f), true, 15, 16);
tree->SetLeafNode(15, Value::Create<float>(0.200853109f));
tree->SetLeafNode(16, Value::Create<float>(3.14392781f));
tree->SetNumericalTestNode(8, 0, "<", Value::Create<float>(0.085769996f), true, 17, 18);
tree->SetLeafNode(17, Value::Create<float>(-0.822109044f));
tree->SetLeafNode(18, Value::Create<float>(0.266653359f));
tree->SetNumericalTestNode(4, 5, "<", Value::Create<float>(6.56400013f), true, 9, 10);
tree->SetLeafNode(9, Value::Create<float>(3.40855145f));
tree->SetNumericalTestNode(10, 7, "<", Value::Create<float>(3.29480004f), true, 19, 20);
tree->SetLeafNode(19, Value::Create<float>(2.98598123f));
tree->SetLeafNode(20, Value::Create<float>(0.94572562f));
tree->SetNumericalTestNode(2, 7, "<", Value::Create<float>(1.95050001f), true, 5, 6);
tree->SetNumericalTestNode(5, 5, "<", Value::Create<float>(6.86849976f), true, 11, 12);
tree->SetLeafNode(11, Value::Create<float>(-0.0353970528f));
tree->SetNumericalTestNode(12, 0, "<", Value::Create<float>(0.943544984f), true, 21, 22);
tree->SetLeafNode(21, Value::Create<float>(0.761680603f));
tree->SetLeafNode(22, Value::Create<float>(3.02160382f));
tree->SetNumericalTestNode(6, 6, "<", Value::Create<float>(50.75f), true, 13, 14);
tree->SetNumericalTestNode(13, 10, "<", Value::Create<float>(15.5500002f), true, 23, 24);
tree->SetLeafNode(23, Value::Create<float>(0.743751168f));
tree->SetLeafNode(24, Value::Create<float>(-0.792990744f));
tree->SetNumericalTestNode(14, 11, "<", Value::Create<float>(384.794983f), true, 25, 26);
tree->SetLeafNode(25, Value::Create<float>(0.319963276f));
tree->SetLeafNode(26, Value::Create<float>(-2.88059473f));
builder->InsertTree(tree.get());
}
{
std::unique_ptr<frontend::TreeBuilder> tree{
new frontend::TreeBuilder(TypeInfo::kFloat32, TypeInfo::kFloat32)
};
for (int nid = 0; nid <= 24; ++nid) {
tree->CreateNode(nid);
}
tree->SetRootNode(0);
tree->SetNumericalTestNode(0, 4, "<", Value::Create<float>(0.820500016f), true, 1, 2);
tree->SetNumericalTestNode(1, 10, "<", Value::Create<float>(17.7000008f), true, 3, 4);
tree->SetNumericalTestNode(3, 5, "<", Value::Create<float>(6.5255003f), true, 7, 8);
tree->SetNumericalTestNode(7, 0, "<", Value::Create<float>(0.0687299967f), true, 15, 16);
tree->SetLeafNode(15, Value::Create<float>(0.206869483f));
tree->SetLeafNode(16, Value::Create<float>(1.80078018f));
tree->SetNumericalTestNode(8, 12, "<", Value::Create<float>(3.14499998f), true, 17, 18);
tree->SetLeafNode(17, Value::Create<float>(-0.923567116f));
tree->SetLeafNode(18, Value::Create<float>(0.386075258f));
tree->SetNumericalTestNode(4, 0, "<", Value::Create<float>(0.0301299989f), true, 9, 10);
tree->SetNumericalTestNode(9, 8, "<", Value::Create<float>(3.5f), true, 19, 20);
tree->SetLeafNode(19, Value::Create<float>(1.81692481f));
tree->SetLeafNode(20, Value::Create<float>(0.130609035f));
tree->SetNumericalTestNode(10, 4, "<", Value::Create<float>(0.708999991f), true, 21, 22);
tree->SetLeafNode(21, Value::Create<float>(-0.330942363f));
tree->SetLeafNode(22, Value::Create<float>(1.32937813f));
tree->SetNumericalTestNode(2, 11, "<", Value::Create<float>(347.565002f), true, 5, 6);
tree->SetNumericalTestNode(5, 6, "<", Value::Create<float>(97.25f), true, 11, 12);
tree->SetLeafNode(11, Value::Create<float>(-3.44793344f));
tree->SetLeafNode(12, Value::Create<float>(-1.2536478f));
tree->SetNumericalTestNode(6, 0, "<", Value::Create<float>(2.34980488f), true, 13, 14);
tree->SetNumericalTestNode(13, 0, "<", Value::Create<float>(1.54080999f), true, 23, 24);
tree->SetLeafNode(23, Value::Create<float>(-0.342328072f));
tree->SetLeafNode(24, Value::Create<float>(0.655293167f));
tree->SetLeafNode(14, Value::Create<float>(-1.51396859f));
builder->InsertTree(tree.get());
}
std::unique_ptr<Model> model = builder->CommitModel();
TestRoundTrip(model.get());
}

} // namespace treelite