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Valgrind, Move Semantics, and HDF5: Memory-Safe Serialization with H5CPP

Introduction

Memory leaks? Invalid writes? Not in our house. When you're dealing with zero-copy serialization of C++ POD types into HDF5 packet tables, you'd better be sure the memory management holds up — especially under modern C++ semantics like move assignment.

In this short entry, we explore how h5cpp handles move semantics under stress, and how tools like Valgrind can validate correct cleanup when working with dynamically generated HDF5 compound types.

The Test: Moving Packet Tables

The test project from this commit uses:

  • a generated struct (packet_t) via generated.h and struct.h
  • a simple dataset append test using packettable.cpp
  • a Makefile that wires the H5CPP build chain to produce and inspect the binary

The core test is simple:

packet_t a, b;
b = std::move(a);  // move assignment

Followed by an append operation into an HDF5 Packet Table. We simulate real-world usage where streaming structs get moved during staging, queueing, or I/O flushing — and we want to guarantee correctness, not just behavior.

Memory Safety: Valgrind Results

Compiled with HDF5 debugging symbols and H5CPP, we ran:

valgrind --leak-check=full ./packettable

And here's what we expect to see:

==12345== All heap blocks were freed -- no leaks are possible
==12345== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)

Why this matters: move assignment can easily create subtle dangling references or uninitialized accesses in serialization-heavy code. By testing this path explicitly, we ensure that:

  • all memory is correctly initialized/cleaned up
  • no heap leaks happen during serialization/deserialization
  • HDF5’s internal resources are released cleanly

How H5CPP Helps

Behind the scenes, H5CPP generates type-safe HDF5 compound type definitions and adapters. This ensures:

  • correct alignment and layout matching
  • RAII-wrapped HDF5 resources
  • deterministic destruction of dataset writers/readers

The generated code in generated.h avoids heap allocation altogether unless explicitly requested, so move assignment is just a blit operation with well-defined cleanup.

Takeaways

✅ Always test your serialization stack under move semantics ✅ Use Valgrind or ASan regularly to catch lifetime bugs ✅ Let H5CPP do the heavy lifting of alignment, safety, and type deduction