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DPL Analysis: fix VLA reading by reading the size branch separetely #7918

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Merged
ktf merged 3 commits into from
Jan 9, 2022
Merged

DPL Analysis: fix VLA reading by reading the size branch separetely #7918

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9b73a91
Revert "DPL Analysis: fall back to per-entry reading of VLA branches …
aalkin Jan 7, 2022
61a332d
separate size branch reading
aalkin Jan 7, 2022
a737b7f
cleanup; update test
aalkin Jan 7, 2022
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255 changes: 62 additions & 193 deletions Framework/Core/src/TableTreeHelpers.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -196,7 +196,7 @@ std::pair<std::shared_ptr<arrow::ChunkedArray>, std::shared_ptr<arrow::Field>> B
while (readEntries < totalEntries) {
auto readLast = mBranch->GetBulkRead().GetBulkEntries(readEntries, *buffer);
readEntries += readLast;
status &= static_cast<arrow::BooleanBuilder*>(mValueBuilder)->AppendValues(reinterpret_cast<uint8_t const*>(buffer->GetCurrent()), (int64_t)readLast * (int64_t)mListSize);
status &= static_cast<arrow::BooleanBuilder*>(mValueBuilder)->AppendValues(reinterpret_cast<uint8_t const*>(buffer->GetCurrent()), readLast * mListSize);
}
if (mListSize > 1) {
status &= static_cast<arrow::FixedSizeListBuilder*>(mListBuilder.get())->AppendValues(readEntries);
Expand All @@ -214,209 +214,78 @@ std::pair<std::shared_ptr<arrow::ChunkedArray>, std::shared_ptr<arrow::Field>> B
}
} else {
// other types: use serialized read to build arrays directly
if (mVLA && totalEntries > 616) {
// special case workaround
auto status = arrow::MakeBuilder(mPool, mArrowType->field(0)->type(), &mBuilder);
if (!status.ok()) {
throw runtime_error("Failed to create value builder");
}
mListBuilder = std::make_unique<arrow::ListBuilder>(mPool, std::move(mBuilder));
mValueBuilder = static_cast<arrow::ListBuilder*>(mListBuilder.get())->value_builder();
void* ptr = nullptr;

switch (mType) {
case EDataType::kUChar_t:
ptr = new uint8_t[255];
break;
case EDataType::kUShort_t:
ptr = new uint16_t[255];
break;
case EDataType::kUInt_t:
ptr = new uint32_t[255];
break;
case EDataType::kULong64_t:
ptr = new uint64_t[255];
break;
case EDataType::kChar_t:
ptr = new int8_t[255];
break;
case EDataType::kShort_t:
ptr = new int16_t[255];
break;
case EDataType::kInt_t:
ptr = new int32_t[255];
break;
case EDataType::kLong64_t:
ptr = new int64_t[255];
break;
case EDataType::kFloat_t:
ptr = new float[255];
break;
case EDataType::kDouble_t:
ptr = new double[255];
break;
default:
throw runtime_error("Unsupported branch type");
}
auto&& result = arrow::AllocateResizableBuffer(mBranch->GetTotBytes(), mPool);
if (!result.ok()) {
throw runtime_error("Cannot allocate values buffer");
}
std::shared_ptr<arrow::Buffer> arrowValuesBuffer = std::move(result).ValueUnsafe();
auto ptr = arrowValuesBuffer->mutable_data();
if (ptr == nullptr) {
throw runtime_error("Invalid buffer");
}

int sz;
auto* mSizeBranch = mBranch->GetTree()->GetBranch((std::string{mBranch->GetName()} + TableTreeHelpers::sizeBranchSuffix).c_str());
mSizeBranch->SetAddress(&sz);
mBranch->SetAddress(ptr);
std::vector<int> offsets;

offsets.push_back(0);
for (auto entry = 0; entry < totalEntries; ++entry) {
mBranch->GetEntry(entry);
mSizeBranch->GetEntry(entry);
offsets.push_back(sz + offsets.back());
arrow::Status status;
switch (mType) {
case EDataType::kUChar_t:
status = static_cast<arrow::UInt8Builder*>(mValueBuilder)->AppendValues(reinterpret_cast<uint8_t const*>(ptr), sz);
break;
case EDataType::kUShort_t:
status = static_cast<arrow::UInt16Builder*>(mValueBuilder)->AppendValues(reinterpret_cast<uint16_t const*>(ptr), sz);
break;
case EDataType::kUInt_t:
status = static_cast<arrow::UInt32Builder*>(mValueBuilder)->AppendValues(reinterpret_cast<uint32_t const*>(ptr), sz);
break;
case EDataType::kULong64_t:
status = static_cast<arrow::UInt64Builder*>(mValueBuilder)->AppendValues(reinterpret_cast<uint64_t const*>(ptr), sz);
break;
case EDataType::kChar_t:
status = static_cast<arrow::Int8Builder*>(mValueBuilder)->AppendValues(reinterpret_cast<int8_t const*>(ptr), sz);
break;
case EDataType::kShort_t:
status = static_cast<arrow::Int16Builder*>(mValueBuilder)->AppendValues(reinterpret_cast<int16_t const*>(ptr), sz);
break;
case EDataType::kInt_t:
status = static_cast<arrow::Int32Builder*>(mValueBuilder)->AppendValues(reinterpret_cast<int32_t const*>(ptr), sz);
break;
case EDataType::kLong64_t:
status = static_cast<arrow::Int64Builder*>(mValueBuilder)->AppendValues(reinterpret_cast<int64_t const*>(ptr), sz);
break;
case EDataType::kFloat_t:
status = static_cast<arrow::FloatBuilder*>(mValueBuilder)->AppendValues(reinterpret_cast<float const*>(ptr), sz);
break;
case EDataType::kDouble_t:
status = static_cast<arrow::DoubleBuilder*>(mValueBuilder)->AppendValues(reinterpret_cast<double const*>(ptr), sz);
break;
default:
throw runtime_error("Unsupported branch type");
}
}
status &= static_cast<arrow::ListBuilder*>(mListBuilder.get())->AppendValues(offsets.data(), totalEntries);
status &= static_cast<arrow::ListBuilder*>(mListBuilder.get())->Finish(&array);

mSizeBranch->SetStatus(false);
mSizeBranch->DropBaskets("all");
mSizeBranch->Reset();
mSizeBranch->GetTransientBuffer(0)->Expand(0);

switch (mType) {
case EDataType::kUChar_t:
delete[] static_cast<uint8_t*>(ptr);
break;
case EDataType::kUShort_t:
delete[] static_cast<uint16_t*>(ptr);
break;
case EDataType::kUInt_t:
delete[] static_cast<uint32_t*>(ptr);
break;
case EDataType::kULong64_t:
delete[] static_cast<uint64_t*>(ptr);
break;
case EDataType::kChar_t:
delete[] static_cast<int8_t*>(ptr);
break;
case EDataType::kShort_t:
delete[] static_cast<int16_t*>(ptr);
break;
case EDataType::kInt_t:
delete[] static_cast<int32_t*>(ptr);
break;
case EDataType::kLong64_t:
delete[] static_cast<int64_t*>(ptr);
break;
case EDataType::kFloat_t:
delete[] static_cast<float*>(ptr);
break;
case EDataType::kDouble_t:
delete[] static_cast<double*>(ptr);
break;
default:
throw runtime_error("Unsupported branch type");
}
} else {
auto&& result = arrow::AllocateResizableBuffer(mBranch->GetTotBytes(), mPool);
auto typeSize = TDataType::GetDataType(mType)->Size();
std::unique_ptr<TBufferFile> offsetBuffer = nullptr;

uint32_t offset = 0;
int count = 0;
std::shared_ptr<arrow::Buffer> arrowOffsetBuffer;
gsl::span<int> offsets;
int size = 0;
uint32_t totalSize = 0;
TBranch* mSizeBranch = nullptr;
if (mVLA) {
mSizeBranch = mBranch->GetTree()->GetBranch((std::string{mBranch->GetName()} + TableTreeHelpers::sizeBranchSuffix).c_str());
offsetBuffer = std::make_unique<TBufferFile>(TBuffer::EMode::kWrite, 4 * 1024 * 1024);
result = arrow::AllocateResizableBuffer((totalEntries + 1) * (int64_t)sizeof(int), mPool);
if (!result.ok()) {
throw runtime_error("Cannot allocate values buffer");
}
std::shared_ptr<arrow::Buffer> arrowValuesBuffer = std::move(result).ValueUnsafe();
auto ptr = arrowValuesBuffer->mutable_data();
if (ptr == nullptr) {
throw runtime_error("Invalid buffer");
}

auto typeSize = TDataType::GetDataType(mType)->Size();
std::unique_ptr<TBufferFile> offsetBuffer;

uint32_t offset = 0;
uint32_t lastOffset;
int count = 0;
std::shared_ptr<arrow::Buffer> arrowOffsetBuffer;
gsl::span<int> offsets;
int size = 0;
uint32_t totalSize = 0;
if (mVLA) {
offsetBuffer = std::make_unique<TBufferFile>(TBuffer::EMode::kWrite, 4 * 1024 * 1024);
result = arrow::AllocateResizableBuffer((int64_t)(sizeof(int) * (totalEntries + 1)), mPool);
if (!result.ok()) {
throw runtime_error("Cannot allocate offset buffer");
}
arrowOffsetBuffer = std::move(result).ValueUnsafe();
unsigned char* ptrOffset = arrowOffsetBuffer->mutable_data();
auto* tPtrOffset = reinterpret_cast<int*>(ptrOffset);
offsets = gsl::span<int>{tPtrOffset, tPtrOffset + totalEntries + 1};
throw runtime_error("Cannot allocate offset buffer");
}
arrowOffsetBuffer = std::move(result).ValueUnsafe();
unsigned char* ptrOffset = arrowOffsetBuffer->mutable_data();
auto* tPtrOffset = reinterpret_cast<int*>(ptrOffset);
offsets = gsl::span<int>{tPtrOffset, tPtrOffset + totalEntries + 1};

// read sizes first
while (readEntries < totalEntries) {
auto readLast = mBranch->GetBulkRead().GetEntriesSerialized(readEntries, *buffer, offsetBuffer.get());
auto readLast = mSizeBranch->GetBulkRead().GetEntriesSerialized(readEntries, *offsetBuffer);
readEntries += readLast;

if (mVLA) {
lastOffset = offset;
for (auto i = 0; i < readLast; ++i) {
offsets[count++] = (int)offset;
offset += swap32_(reinterpret_cast<uint32_t*>(offsetBuffer->GetCurrent())[i]);
}
size = (int)(offset - lastOffset);
} else {
size = readLast * mListSize;
for (auto i = 0; i < readLast; ++i) {
offsets[count++] = (int)offset;
offset += swap32_(reinterpret_cast<uint32_t*>(offsetBuffer->GetCurrent())[i]);
}
swapCopy(ptr, buffer->GetCurrent(), size, typeSize);
ptr += (ptrdiff_t)(size * typeSize);
}
offsets[count] = (int)offset;
totalSize = offset;
readEntries = 0;
}

while (readEntries < totalEntries) {
auto readLast = mBranch->GetBulkRead().GetEntriesSerialized(readEntries, *buffer);
if (mVLA) {
offsets[count] = (int)offset;
totalSize = offset;
size = offsets[readEntries + readLast] - offsets[readEntries];
} else {
totalSize = readEntries * mListSize;
}
std::shared_ptr<arrow::PrimitiveArray> varray;
switch (mListSize) {
case -1:
varray = std::make_shared<arrow::PrimitiveArray>(mArrowType->field(0)->type(), totalSize, arrowValuesBuffer);
array = std::make_shared<arrow::ListArray>(mArrowType, readEntries, arrowOffsetBuffer, varray);
break;
case 1:
array = std::make_shared<arrow::PrimitiveArray>(mArrowType, readEntries, arrowValuesBuffer);
break;
default:
varray = std::make_shared<arrow::PrimitiveArray>(mArrowType->field(0)->type(), totalSize, arrowValuesBuffer);
array = std::make_shared<arrow::FixedSizeListArray>(mArrowType, readEntries, varray);
size = readLast * mListSize;
}
readEntries += readLast;
swapCopy(ptr, buffer->GetCurrent(), size, typeSize);
ptr += (ptrdiff_t)(size * typeSize);
}
if (!mVLA) {
totalSize = readEntries * mListSize;
}
std::shared_ptr<arrow::PrimitiveArray> varray;
switch (mListSize) {
case -1:
varray = std::make_shared<arrow::PrimitiveArray>(mArrowType->field(0)->type(), totalSize, arrowValuesBuffer);
array = std::make_shared<arrow::ListArray>(mArrowType, readEntries, arrowOffsetBuffer, varray);
break;
case 1:
array = std::make_shared<arrow::PrimitiveArray>(mArrowType, readEntries, arrowValuesBuffer);
break;
default:
varray = std::make_shared<arrow::PrimitiveArray>(mArrowType->field(0)->type(), totalSize, arrowValuesBuffer);
array = std::make_shared<arrow::FixedSizeListArray>(mArrowType, readEntries, varray);
}
}

Expand Down
30 changes: 15 additions & 15 deletions Framework/Core/test/test_TreeToTable.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -183,13 +183,13 @@ BOOST_AUTO_TEST_CASE(VariableLists)

int empty[] = {3, 7, 10};
auto count = 0;
for (auto i = 1; i < 11; ++i) {
for (auto i = 1; i < 1000; ++i) {
iv.clear();
fv.clear();
dv.clear();
ui.clear();
if (i != empty[count]) {
for (auto j = 0; j < i; ++j) {
for (auto j = 0; j < i % 10 + 1; ++j) {
iv.push_back(j + 2);
fv.push_back((j + 2) * 0.2134f);
dv.push_back((j + 4) * 0.192873819237);
Expand Down Expand Up @@ -218,22 +218,22 @@ BOOST_AUTO_TEST_CASE(VariableLists)
int i = 1;
count = 0;
for (auto& row : v) {
auto iv = row.ivec();
auto fv = row.fvec();
auto dv = row.dvec();
auto uv = row.uivec();
auto ivr = row.ivec();
auto fvr = row.fvec();
auto dvr = row.dvec();
auto uvr = row.uivec();
if (i != empty[count]) {
for (auto j = 0; j < i; ++j) {
BOOST_CHECK_EQUAL(iv[j], j + 2);
BOOST_CHECK_EQUAL(fv[j], (j + 2) * 0.2134f);
BOOST_CHECK_EQUAL(dv[j], (j + 4) * 0.192873819237);
BOOST_CHECK_EQUAL(uv[j], j);
for (auto j = 0; j < i % 10 + 1; ++j) {
BOOST_CHECK_EQUAL(ivr[j], j + 2);
BOOST_CHECK_EQUAL(fvr[j], (j + 2) * 0.2134f);
BOOST_CHECK_EQUAL(dvr[j], (j + 4) * 0.192873819237);
BOOST_CHECK_EQUAL(uvr[j], j);
}
} else {
BOOST_CHECK_EQUAL(iv.size(), 0);
BOOST_CHECK_EQUAL(fv.size(), 0);
BOOST_CHECK_EQUAL(dv.size(), 0);
BOOST_CHECK_EQUAL(uv.size(), 0);
BOOST_CHECK_EQUAL(ivr.size(), 0);
BOOST_CHECK_EQUAL(fvr.size(), 0);
BOOST_CHECK_EQUAL(dvr.size(), 0);
BOOST_CHECK_EQUAL(uvr.size(), 0);
count++;
}
++i;
Expand Down