[bugfix] Mark draft tokens to rebuilt their embeddings.

[HieDean]

Purpose

Fix an inconsistency between input_ids and is_token_ids when enable_prompt_embeds is used together with speculative decoding.

Speculative draft token IDs are scattered directly into input_ids.gpu, but the corresponding positions in is_token_ids were not marked as token IDs. As a result, the prompt-embedding path treated these positions as external embeddings and reused stale embeddings during target verification, causing incorrect target predictions and very low acceptance lengths.

This change marks spec_flattened_indices as token-ID positions before synchronizing is_token_ids to the GPU.

Test Plan

import torch

from transformers import AutoModelForCausalLM
from datasets import load_dataset
from vllm import LLM, SamplingParams

TARGET_MODEL = "Qwen3-8B"
DRAFT_MODEL = "Qwen3-8B-DFlash-b16"
DATASET = "gsm8k"

# Create a sampling params object.
sampling_params = SamplingParams(temperature=0.0, max_tokens=128)

def main():
    hf_target_model = AutoModelForCausalLM.from_pretrained(TARGET_MODEL)

    # Create an LLM.
    llm = LLM(
        model=TARGET_MODEL,
        enable_prompt_embeds=True,
        speculative_config={"model": DRAFT_MODEL, "num_speculative_tokens": 16},
        disable_log_stats=False,
    )
    tokenizer = llm.get_tokenizer()

    dataset = load_dataset(DATASET, "main")
    dataset = list(dataset["test"])[:10]
    for data in dataset:
        messages = [
            [{"role": "user", "content": f"{data["question"]}"}]
        ]
        input_ids = tokenizer.apply_chat_template(
            messages,
            tokenize=True,
            add_generation_prompt=False,
            return_tensors="pt"
        )

        embeddings = hf_target_model.get_input_embeddings()(input_ids["input_ids"])
        prompt_len = embeddings.shape[1]

        inputs = {
            "prompt_embeds": embeddings,
            "prompt_token_ids": [tokenizer.vocab_size] * prompt_len,
            "prompt_is_token_ids": [False] * prompt_len,
        }
        outputs = llm.generate(inputs, sampling_params, use_tqdm=False)

        # Print the outputs.
        print("\nGenerated Outputs:\n" + "-" * 60)
        for output in outputs:
            prompt = output.prompt
            generated_text = output.outputs[0].text
            print(f"Prompt:    {prompt!r}")
            print(f"Output:    {generated_text!r}")
            print("-" * 60)

        num_drafts = 0
        num_accepted_tokens = 0
        for metric in llm.get_metrics():
            if metric.name == "vllm:spec_decode_num_drafts":
                num_drafts += metric.value
                print(f"{metric.name}: {metric.value:.2f}")
            elif metric.name == "vllm:spec_decode_num_accepted_tokens":
                num_accepted_tokens += metric.value
                print(f"{metric.name}: {metric.value:.2f}")

        acceptance_length = (
            1 + num_accepted_tokens / num_drafts if num_drafts > 0 else 1.0
        )

        print(f"Mean acceptance length: {acceptance_length:.2f}")

if __name__ == "__main__":
    main()

Test Result

Before this PR:
Mean acceptance length: 2.79

After this PR:
Mean acceptance length: 2.95

[claude]

Claude Code Review

This pull request is from a fork — automated review is disabled. A repository maintainer can comment @claude review to run a one-time review.

[github-actions]

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[qthequartermasterman]

@DarkLight1337 who needs to review this PR?

[DarkLight1337]

I'll just stamp this as it only affects prompt embeds path

[DarkLight1337]

/ci run

[github-actions]

❌ This PR is 22 commits behind upstream main. Your branch must contain every commit currently on upstream main. No new CI build was started. Merge or rebase onto the latest main, then rerun /ci run. To test this branch at your own risk, use /ci run --allow-stale.

[DarkLight1337]

/ci run --allow-stale

[github-actions]

✅ Triggered Buildkite CI #89636 for commit bc8ebea9e6ed.

⚠️ This PR is 22 commits behind upstream main. Running CI at your own risk because --allow-stale was requested; outdated CI configuration may cause failures. Before merging, merge or rebase onto the latest main, then rerun /ci run on the latest PR commit.