Undefined behavior with list columns

[krlmlr]

To reproduce:

• Clone https://github.com/krlmlr/r-4-duckdb
• Run docker run --rm -ti --platform linux/amd64 -v $(pwd):/test ghcr.io/krlmlr/r-4-duckdb:main R -q -f test/test.R

Symptoms:

> duckdb::dbAppendTable(con, "test_list", test_list_tbl)
Error: C stack usage  285199482356 is too close to the limit
Error: rapi_execute: Failed to run query
Error: Invalid Error: std::exception
Execution halted

The number varies, it is high on gitpod and on another Linux host (bare metal), hundreds of MB on macOS + colima, the problem can't be reproduced with Docker Desktop on macOS.

Need to understand if this is specific to R 4.0.5: krlmlr/r-4-duckdb#1.

[krlmlr]

Also an issue with R 4.3.3.

[krlmlr]

Running with valgrind:

> dbWriteTable(con, "test_list_2_alternative", test_list_2_tbl)
Error: C stack usage  134889705540 is too close to the limit
Error: rapi_execute: Failed to run query
Error: Invalid Error: std::exception
Execution halted
==692== Syscall param pwrite64(buf) points to uninitialised byte(s)
==692==    at 0x4DD883F: __libc_pwrite64 (pwrite64.c:25)
==692==    by 0x4DD883F: pwrite (pwrite64.c:23)
==692==    by 0x925A96D0: duckdb::LocalFileSystem::Write(duckdb::FileHandle&, void*, long, unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x9334A773: duckdb::SingleFileBlockManager::ChecksumAndWrite(duckdb::FileBuffer&, unsigned long) const (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x93373080: duckdb::BlockManager::ConvertToPersistent(long, std::shared_ptr<duckdb::BlockHandle>) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x934269F2: duckdb::ColumnSegment::ConvertToPersistent(duckdb::optional_ptr<duckdb::BlockManager>, long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x93430F04: duckdb::PartialBlockForCheckpoint::Flush(unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x9334F776: duckdb::PartialBlockManager::FlushPartialBlocks() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x9336536A: duckdb::SingleFileCheckpointWriter::CreateCheckpoint() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x93365661: duckdb::SingleFileStorageManager::CreateCheckpoint(bool, bool) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x930E73C5: duckdb::AttachedDatabase::Close() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x930E7577: duckdb::DatabaseManager::ResetDatabases(duckdb::unique_ptr<duckdb::TaskScheduler, std::default_delete<duckdb::TaskScheduler>, true>&) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x931021B8: duckdb::DatabaseInstance::~DatabaseInstance() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==  Address 0xa865e731 is 1 bytes inside a block of size 262,144 alloc'd
==692==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==692==    by 0x9259DB4B: duckdb::Allocator::AllocateData(unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x9259DC5F: duckdb::FileBuffer::ReallocBuffer(unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x9259DC90: duckdb::FileBuffer::Resize(unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x93345A44: duckdb::StandardBufferManager::ConstructManagedBuffer(unsigned long, duckdb::unique_ptr<duckdb::FileBuffer, std::default_delete<duckdb::FileBuffer>, true>&&, duckdb::FileBufferType) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x93358E6E: duckdb::StandardBufferManager::RegisterMemory(duckdb::MemoryTag, unsigned long, bool) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x933593C5: duckdb::StandardBufferManager::Allocate(duckdb::MemoryTag, unsigned long, bool, std::shared_ptr<duckdb::BlockHandle>*) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x9342C269: duckdb::ColumnSegment::CreateTransientSegment(duckdb::DatabaseInstance&, duckdb::LogicalType const&, unsigned long, unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x93379B43: duckdb::unique_ptr<duckdb::CompressionState, std::default_delete<duckdb::CompressionState>, true> duckdb::AlpInitCompression<double>(duckdb::ColumnDataCheckpointer&, duckdb::unique_ptr<duckdb::AnalyzeState, std::default_delete<duckdb::AnalyzeState>, true>) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x9343AAAB: duckdb::ColumnDataCheckpointer::WriteToDisk() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x9343C8F4: duckdb::ColumnData::Checkpoint(duckdb::RowGroup&, duckdb::PartialBlockManager&, duckdb::ColumnCheckpointInfo&) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692==    by 0x9343CEB3: duckdb::StandardColumnData::Checkpoint(duckdb::RowGroup&, duckdb::PartialBlockManager&, duckdb::ColumnCheckpointInfo&) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==692== 

[krlmlr]

Another one, very similar:

> duckdb::dbAppendTable(con, "test_list", test_list_tbl)
Error: C stack usage  134847741652 is too close to the limit
Error: rapi_execute: Failed to run query
Error: Invalid Error: std::exception
Execution halted
==824== Syscall param pwrite64(buf) points to uninitialised byte(s)
==824==    at 0x4DD883F: __libc_pwrite64 (pwrite64.c:25)
==824==    by 0x4DD883F: pwrite (pwrite64.c:23)
==824==    by 0x925A96D0: duckdb::LocalFileSystem::Write(duckdb::FileHandle&, void*, long, unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x9334A773: duckdb::SingleFileBlockManager::ChecksumAndWrite(duckdb::FileBuffer&, unsigned long) const (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x93373080: duckdb::BlockManager::ConvertToPersistent(long, std::shared_ptr<duckdb::BlockHandle>) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x934269F2: duckdb::ColumnSegment::ConvertToPersistent(duckdb::optional_ptr<duckdb::BlockManager>, long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x93430F04: duckdb::PartialBlockForCheckpoint::Flush(unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x9334F776: duckdb::PartialBlockManager::FlushPartialBlocks() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x9336536A: duckdb::SingleFileCheckpointWriter::CreateCheckpoint() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x93365661: duckdb::SingleFileStorageManager::CreateCheckpoint(bool, bool) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x930E73C5: duckdb::AttachedDatabase::Close() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x930E7577: duckdb::DatabaseManager::ResetDatabases(duckdb::unique_ptr<duckdb::TaskScheduler, std::default_delete<duckdb::TaskScheduler>, true>&) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x931021B8: duckdb::DatabaseInstance::~DatabaseInstance() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==  Address 0x9fab7f31 is 1 bytes inside a block of size 262,144 alloc'd
==824==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==824==    by 0x9259DB4B: duckdb::Allocator::AllocateData(unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x9259DC5F: duckdb::FileBuffer::ReallocBuffer(unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x9259DC90: duckdb::FileBuffer::Resize(unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x93345A44: duckdb::StandardBufferManager::ConstructManagedBuffer(unsigned long, duckdb::unique_ptr<duckdb::FileBuffer, std::default_delete<duckdb::FileBuffer>, true>&&, duckdb::FileBufferType) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x93358E6E: duckdb::StandardBufferManager::RegisterMemory(duckdb::MemoryTag, unsigned long, bool) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x933593C5: duckdb::StandardBufferManager::Allocate(duckdb::MemoryTag, unsigned long, bool, std::shared_ptr<duckdb::BlockHandle>*) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x9342C269: duckdb::ColumnSegment::CreateTransientSegment(duckdb::DatabaseInstance&, duckdb::LogicalType const&, unsigned long, unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x93379B43: duckdb::unique_ptr<duckdb::CompressionState, std::default_delete<duckdb::CompressionState>, true> duckdb::AlpInitCompression<double>(duckdb::ColumnDataCheckpointer&, duckdb::unique_ptr<duckdb::AnalyzeState, std::default_delete<duckdb::AnalyzeState>, true>) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x9343AAAB: duckdb::ColumnDataCheckpointer::WriteToDisk() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x9343C8F4: duckdb::ColumnData::Checkpoint(duckdb::RowGroup&, duckdb::PartialBlockManager&, duckdb::ColumnCheckpointInfo&) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824==    by 0x9343CEB3: duckdb::StandardColumnData::Checkpoint(duckdb::RowGroup&, duckdb::PartialBlockManager&, duckdb::ColumnCheckpointInfo&) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==824== 

@hannes: Have you recently seen undefined behavior with persisting nested data? I'll check the latest and greatest too.

[krlmlr]

Still an issue with https://github.com/duckdb/duckdb-r/commit/953e7d320c6678109cedb50c721f19c264a839c1 (aka https://github.com/duckdb/duckdb/commit/e5f45238740e8c8fef3d22ee61f6b7faf950c05d), installed from r-universe:

> duckdb::dbAppendTable(con, "test_list_2", test_list_2_tbl)
Error: C stack usage  134807170756 is too close to the limit
Error: rapi_execute: Failed to run query
Error: Invalid Error: std::exception
Execution halted
==948== Syscall param pwrite64(buf) points to uninitialised byte(s)
==948==    at 0x4DD883F: __libc_pwrite64 (pwrite64.c:25)
==948==    by 0x4DD883F: pwrite (pwrite64.c:23)
==948==    by 0x9248CB00: duckdb::LocalFileSystem::Write(duckdb::FileHandle&, void*, long, unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x931EACA4: duckdb::BlockManager::ConvertToPersistent(long, std::shared_ptr<duckdb::BlockHandle>) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x9329D311: duckdb::ColumnSegment::ConvertToPersistent(duckdb::optional_ptr<duckdb::BlockManager>, long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x932A6726: duckdb::PartialBlockForCheckpoint::Flush(unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x931C5F06: duckdb::PartialBlockManager::FlushPartialBlocks() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x931DE01D: duckdb::SingleFileCheckpointWriter::CreateCheckpoint() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x931DE44F: duckdb::SingleFileStorageManager::CreateCheckpoint(bool, bool) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x92F6FD85: duckdb::AttachedDatabase::Close() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x92F702F7: duckdb::DatabaseManager::ResetDatabases(duckdb::unique_ptr<duckdb::TaskScheduler, std::default_delete<duckdb::TaskScheduler>, true>&) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x92F703C4: duckdb::DatabaseInstance::~DatabaseInstance() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x923CF739: std::_Sp_counted_base<(__gnu_cxx::_Lock_policy)2>::_M_release() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==  Address 0xa8524f31 is 1 bytes inside a block of size 262,144 alloc'd
==948==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==948==    by 0x924848F5: duckdb::Allocator::AllocateData(unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x924849FF: duckdb::FileBuffer::ReallocBuffer(unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x92484A30: duckdb::FileBuffer::Resize(unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x931C646C: duckdb::StandardBufferManager::ConstructManagedBuffer(unsigned long, duckdb::unique_ptr<duckdb::FileBuffer, std::default_delete<duckdb::FileBuffer>, true>&&, duckdb::FileBufferType) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x931D7E11: duckdb::StandardBufferManager::RegisterMemory(duckdb::MemoryTag, unsigned long, bool) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x931D7FF5: duckdb::StandardBufferManager::Allocate(duckdb::MemoryTag, unsigned long, bool, std::shared_ptr<duckdb::BlockHandle>*) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x932A1F71: duckdb::ColumnSegment::CreateTransientSegment(duckdb::DatabaseInstance&, duckdb::LogicalType const&, unsigned long, unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x931F2371: duckdb::AlpCompressionState<double>::CreateEmptySegment(unsigned long) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x931F26A4: duckdb::unique_ptr<duckdb::CompressionState, std::default_delete<duckdb::CompressionState>, true> duckdb::AlpInitCompression<double>(duckdb::ColumnDataCheckpointer&, duckdb::unique_ptr<duckdb::AnalyzeState, std::default_delete<duckdb::AnalyzeState>, true>) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x932AB186: duckdb::ColumnDataCheckpointer::WriteToDisk() (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948==    by 0x932AC21C: duckdb::ColumnData::Checkpoint(duckdb::RowGroup&, duckdb::PartialBlockManager&, duckdb::ColumnCheckpointInfo&) (in /usr/local/lib/R/site-library/duckdb/libs/duckdb.so)
==948== 

[krlmlr]

Can't repro with the CLI:

CREATE TABLE test_list_2 (a integer, b STRUCT(c VARCHAR[], d VARCHAR[], e INTEGER[]));
INSERT INTO test_list_2 VALUES (1, row(['a', 'b', 'c', 'd', 'e', 'f'], ['A', 'B'], [1, 5, 9]));
SELECT * FROM test_list_2;

[krlmlr]

But with valgrind :

==25532== Syscall param pwrite64(buf) points to uninitialised byte(s)
==25532==    at 0x4CB083F: __libc_pwrite64 (pwrite64.c:25)
==25532==    by 0x4CB083F: pwrite (pwrite64.c:23)
==25532==    by 0x8ABF00: duckdb::LocalFileSystem::Write(duckdb::FileHandle&, void*, long, unsigned long) (in /duckdb/duckdb)
==25532==    by 0xB578C8: duckdb::BlockManager::ConvertToPersistent(long, std::shared_ptr<duckdb::BlockHandle>) (in /duckdb/duckdb)
==25532==    by 0xC1840F: duckdb::ColumnSegment::ConvertToPersistent(duckdb::optional_ptr<duckdb::BlockManager>, long) (in /duckdb/duckdb)
==25532==    by 0xC2583C: duckdb::PartialBlockForCheckpoint::Flush(unsigned long) (in /duckdb/duckdb)
==25532==    by 0xC57316: duckdb::PartialBlockManager::FlushPartialBlocks() (in /duckdb/duckdb)
==25532==    by 0xC6F9B2: duckdb::SingleFileCheckpointWriter::CreateCheckpoint() (in /duckdb/duckdb)
==25532==    by 0xC6FC58: duckdb::SingleFileStorageManager::CreateCheckpoint(bool, bool) (in /duckdb/duckdb)
==25532==    by 0xAF755E: duckdb::AttachedDatabase::Close() (in /duckdb/duckdb)
==25532==    by 0xAF7AC7: duckdb::DatabaseManager::ResetDatabases(duckdb::unique_ptr<duckdb::TaskScheduler, std::default_delete<duckdb::TaskScheduler>, true>&) (in /duckdb/duckdb)
==25532==    by 0xAF7B64: duckdb::DatabaseInstance::~DatabaseInstance() (in /duckdb/duckdb)
==25532==    by 0xAEB399: duckdb::DuckDB::~DuckDB() (in /duckdb/duckdb)
==25532==  Address 0x5c008c0 is in a rw- anonymous segment

I'll open an issue upstream.

[krlmlr]

@TSchiefer: can you confirm the current development version (installable as a binary from r-universe) fixes the issue?

[TSchiefer]

I installed package version 0.10.1.9001 from r-universe today (I see that version bump is from 3 weeks ago), but it was installed from source, not entirely sure that it's the correct version & error is unfortunately still occurring. I then proceeded to install from source from GitHub directly, but the test script is still failing, albeit it seems that it consistently works until a later step in the script than before.

[hannes]

it might be intentional, AFAIK we don't zero blocks for performance reasons and if there's garbage at the end it just gets written to disk. But need to confirm.

[krlmlr]

@TSchiefer: can you please share a reproducible example for the issues you are seeing now?

[krlmlr]

Thanks, I received an example.

The original test still fails with v0.10.3, testing against bleeding-edge duckdb now.

[krlmlr]

I can confirm that even the original issue still persists after vendoring the most recent duckdb (duckdb/duckdb@c3903e44e0d70f4fae6d9c068c0792ebc62b882f). I'll bring this upstream again.