fix(anthropic): preserve inline system message position for prefix caching by felix0080 · Pull Request #44602 · vllm-project/vllm

felix0080 · 2026-06-05T02:33:48Z

Problem

PR #44283 merged all inline role: system messages from the messages array into a single leading system message. This changes the conversation prefix, breaking KV-cache hits in multi-turn dialogues.

#44048 (currently open) moves the same merge logic to the protocol layer but retains the same prefix-breaking behavior.

Example of the problem

Input:  [user:A, assistant:B, system:new_rule, user:C]
                ↑ prefix cache can hit here

#44283: [system:(all merged), user:A, assistant:B, user:C]
         ↑ prefix completely different → cache miss

This PR: [system:top-level, user:A, assistant:B, system:new_rule, user:C]
              ↑ prefix unchanged → cache hits preserved

Fix

Remove inline system message extraction from _convert_system_message — only handle top-level system field there
In _convert_messages, handle system messages with a dedicated _extract_system_text helper that:
- Strips x-anthropic-billing-header from inline system messages (previously only done for top-level)
- Only emits a system message if there is real content (avoids empty {"role": "system"} messages that _convert_block could produce)
Add 2 new tests for billing header stripping on inline system messages

Why this approach

Minimal and localized: all system handling is explicit, not spread across _convert_block / _convert_message_content
Prefix structure stays intact for all conversation turns
Billing header stripping is consistent between top-level and inline system messages

Test Plan

(AI assistance was used; I reviewed every changed line.)

python -m pytest tests/entrypoints/anthropic/test_anthropic_messages_conversion.py -v

claude

Claude Code Review

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github-actions · 2026-06-05T02:33:55Z

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felix0080 · 2026-06-05T03:00:12Z

Ready for review — could a maintainer add the ready label to trigger CI? Thanks.

chaunceyjiang · 2026-06-05T06:44:32Z

    ) -> None:
        """Convert Anthropic messages to OpenAI format"""
+
+        def _extract_system_text(msg) -> str | None:


Please convert this method into a class method by adding @classmethod.

@chaunceyjiang ok

@chaunceyjiang @chaunceyjiang Done. I've converted it to a class method

felix0080 · 2026-06-05T07:46:42Z

            openai_messages.append({"role": "system", "content": "".join(system_parts)})

+    @classmethod
+    def _extract_system_text(cls, msg) -> str | None:


@chaunceyjiang Done. I've converted it to a class method

You need to DCO.

@chaunceyjiang Thanks for the reminder. DCO fixed

aleksandaryanakiev · 2026-06-05T08:24:08Z

LGTM

chaunceyjiang · 2026-06-05T09:29:39Z

            if msg.role == "system":
+                text = cls._extract_system_text(msg)
+                if text:
+                    openai_messages.append({"role": "system", "content": text})


In fact, after this change, the Qwen3.5/Qwen3.6 series models will no longer be supported.

@chaunceyjiang This change is meant to preserve prefix caching for Anthropic clients like Claude Code that send system messages mid-conversation. The conflict with Qwen's chat template is a template-level limitation — Qwen expects system to appear only at the beginning — and that should be addressed by updating the Qwen template to handle non-leading system messages, not by compromising the conversion layer for all users.

This will impact not only Qwen models - even though many models may allow system messages at any position in the message list it doesn't mean those models were trained on system messages that come after user messages in a conversation. Most are not trained on this kind of data, and expect the system messages (even if more than 1) to come before the user messages.

Are we aware of any open weight model specifically trained on system messages that appear later in a conversation? This feels like we're trading KV cache efficiency for worse overall trajectories in these agentic workflows.

@bbrowning
Anecdotally, we're running GLM-5.1 and Deepseek-v4 in PD-disaggregated setups with inline system messages preserved, and we haven't observed degraded output quality compared to merging them to the front. The trajectories appear consistent.
This suggests the "training gap" may be narrower than assumed — at least for these models, the capability seems to exist even if it wasn't explicitly optimized for.

@bbrowning
But this matters beyond just quality — it directly impacts deployment architecture.
With PD disaggregation and pooling becoming the standard deployment pattern, the prefill node's value is almost entirely in prefix cache hits. In agentic workflows, 99% of the conversation prefix is identical across requests — the system prompt and prior turns rarely change. If merging inline system messages to the front invalidates the prefix, the prefill node essentially loses its purpose, and the whole PD architecture becomes unusable for these workloads.
So the trade-off is not just "cache vs quality" — it's whether PD-pooled deployments can serve agentic Anthropic clients at all.
That said, I don't want to dismiss the training-distribution concern. The question is whether a universal merge is the right default, or if deployers should be able to choose based on their model and infrastructure.
I'm happy to add an opt-in mechanism to this PR, or follow up with a separate one — whichever the maintainers prefer. For example, enable_inline_system_merge defaulting to true for backward compatibility: deployers running Qwen keep it enabled, those serving Claude Code with PD separation can disable it and preserve prefix cache viability.
Does that approach work?

@bbrowning @dr75 Thanks for the review and accepting the approach. Happy to follow up with the opt-in merge flag separately if needed. Let me know if anything else is needed to get this merged.

Backward compatibility is very necessary, so I have always believed that merging by default into the top level and retaining mid-system-prompt when the flag is enabled seems to be the most reasonable solution. This way, at least all models can support claude, and for large-scale deployment, users can be required to explicitly enable the flag to ensure the highest kvcache efficiency

@bbrowning I’m inclined to merge this PR, since this is a Qwen-specific issue.

@chaunceyjiang Friendly ping — just wanted to check if there's anything else needed to move this forward. Thanks!

@chaunceyjiang All checks are green now — ready to go. Thanks!

chaunceyjiang

LGTM

mergify · 2026-06-11T20:48:29Z

This pull request has merge conflicts that must be resolved before it can be
merged. Please rebase the PR, @felix0080.

https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork

mergify · 2026-06-12T02:51:42Z

Hi @felix0080, the pre-commit checks have failed. Please run:

uv pip install pre-commit>=4.5.1
pre-commit install
pre-commit run --all-files

Then, commit the changes and push to your branch.

For future commits, pre-commit will run automatically on changed files before each commit.

mergify · 2026-06-12T05:57:44Z

Hi @felix0080, the pre-commit checks have failed. Please run:

uv pip install pre-commit>=4.5.1
pre-commit install
pre-commit run --all-files

Then, commit the changes and push to your branch.

For future commits, pre-commit will run automatically on changed files before each commit.

mergify · 2026-06-12T07:16:36Z

Hi @felix0080, the pre-commit checks have failed. Please run:

uv pip install pre-commit>=4.5.1
pre-commit install
pre-commit run --all-files

Then, commit the changes and push to your branch.

For future commits, pre-commit will run automatically on changed files before each commit.

…ching PR vllm-project#44283 merged all inline system:role messages into a single leading system message, which changes the conversation prefix and breaks KV-cache hits in multi-turn dialogues. This fix keeps inline system messages at their original position: - Remove inline system extraction from _convert_system_message (only top-level system is handled there) - In _convert_messages, handle system messages with a dedicated _extract_system_text helper that strips billing headers and only emits the message if real content exists — avoiding the _convert_block / _convert_message_content path which does not strip billing headers and may omit the "content" key - Add tests for billing header stripping on inline system messages Unlike vllm-project#44048 which moves the same merge logic to the protocol layer, this approach fundamentally avoids the prefix-breaking merge entirely. Co-authored-by: Hermes Agent Signed-off-by: felix0080 <felix0080@users.noreply.github.com>

Per maintainer review feedback. Signed-off-by: felix0080 <felix0080@users.noreply.github.com>

cxg987 · 2026-06-13T03:04:20Z

LGTM

bbrowning · 2026-06-15T23:34:17Z

I'm ok to merge this, but would like a fast follow-up ready to fix the issues with Qwen (or similar) models that cannot handle multiple system messages. I'm not sure of the best approach there - maybe we construct some messages with system -> user -> system turns, feed it into the chat template, and if it blows up set a flag that tells us to collapse for this model? We have a lot of users that use the Messages API with Qwen models of various sorts, so I'd like us to minimize the time we break them.

felix0080 · 2026-06-17T01:01:38Z

I'm ok to merge this, but would like a fast follow-up ready to fix the issues with Qwen (or similar) models that cannot handle multiple system messages. I'm not sure of the best approach there - maybe we construct some messages with system -> user -> system turns, feed it into the chat template, and if it blows up set a flag that tells us to collapse for this model? We have a lot of users that use the Messages API with Qwen models of various sorts, so I'd like us to minimize the time we break them.

@bbrowning @chaunceyjiang Thanks for approving. Sounds good — I'll submit a follow-up PR with auto-detection once this is merged.

…tem messages When the chat template requires system-first ordering (e.g., Qwen3.5/3.6 with its loop.first guard), inline system messages preserved at their original position by vllm-project#44602 would be rejected at template render time. This adds auto-detection: a [system, user, system, user] conversation is rendered against the template at init time. The detection covers three scenarios: - Template raises → merge inline system into top-level block (compatible with Qwen and similar models) - Template succeeds → preserve inline system in-place (optimal prefix caching for models that support it) - No template → conservative default: merge No flag or configuration needed. Co-authored-by: Hermes Agent Signed-off-by: felix0080 <felix0080@users.noreply.github.com>

felix0080 · 2026-06-18T09:32:46Z

Follow-up PR is now ready: #46025 — auto-detects template support for mid-conversation system messages so Qwen and similar models are automatically compatible.

…ching (vllm-project#44602) Signed-off-by: felix0080 <felix0080@users.noreply.github.com> Co-authored-by: felix0080 <felix0080@users.noreply.github.com>

…tem messages When the chat template requires system-first ordering (e.g., Qwen3.5/3.6 with its loop.first guard), inline system messages preserved at their original position by vllm-project#44602 would be rejected at template render time. This adds auto-detection: a [system, user, system, user] conversation is rendered against the template at init time. The detection covers three scenarios: - Template raises → merge inline system into top-level block (compatible with Qwen and similar models) - Template succeeds → preserve inline system in-place (optimal prefix caching for models that support it) - No template → conservative default: merge No flag or configuration needed. Co-authored-by: Hermes Agent Signed-off-by: felix0080 <felix0080@users.noreply.github.com>

…ching (vllm-project#44602) Signed-off-by: felix0080 <felix0080@users.noreply.github.com> Co-authored-by: felix0080 <felix0080@users.noreply.github.com> Signed-off-by: divineearthly <divineearthly@gmail.com>

…stem merge When a client (e.g. Claude Code) appends a system message to the messages array of a /v1/messages request, the Anthropic compatibility layer could trigger a full prompt recompute (observed as a ~75s TTFT spike) because the entire prefix-cache block chain is invalidated from the system block onward. Root cause: AnthropicServingMessages.__init__ calls _detect_merge_inline_system(chat_template) with the raw --chat-template arg, which is None by default. The detector returns True ("merge inline system into the leading block") whenever the template is falsy — even for templates like GLM that already accept mid-conversation system messages. That merge hoists the trailing system message into the leading system block, changing tokens from offset 0 onward and breaking the chained block hash, so every subsequent block's hash changes and a full recompute is required. Builds on vllm-project#44283 / vllm-project#44602 / vllm-project#46025, which introduced the merge-vs-inplace switch but defaulted to the conservative (merge) path. This closes the gap: resolve the model's actual chat template (via resolve_chat_template, the same call the renderer uses) before deciding, so GLM-like templates are treated as "no merge" and a trailing system message no longer destroys the prefix. Changes: - __init__: when chat_template is None, resolve the model's actual template via resolve_chat_template(tokenizer, None, None, model_config=...) (tokenizer from self.renderer.tokenizer), then feed that to _detect_merge_inline_system. Falls back to the existing conservative behavior only when no template can be resolved. - _detect_merge_inline_system: import jinja2.sandbox / jinja2.ext explicitly (the package __init__ does not pull them in, so jinja2.sandbox.ImmutableSandboxedEnvironment only worked when something else had imported the submodule). Broadened the catch to except Exception so malformed/non-template input falls back cleanly. - tests: add test_glm_template_does_not_merge. Co-Authored-By: Claude <noreply@anthropic.com>

…stem merge When a client (e.g. Claude Code) appends a system message to the messages array of a /v1/messages request, the Anthropic compatibility layer could trigger a full prompt recompute (observed as a ~75s TTFT spike) because the entire prefix-cache block chain is invalidated from the system block onward. Root cause: AnthropicServingMessages.__init__ calls _detect_merge_inline_system(chat_template) with the raw --chat-template arg, which is None by default. The detector returns True ("merge inline system into the leading block") whenever the template is falsy — even for templates like GLM that already accept mid-conversation system messages. That merge hoists the trailing system message into the leading system block, changing tokens from offset 0 onward and breaking the chained block hash, so every subsequent block's hash changes and a full recompute is required. Builds on vllm-project#44283 / vllm-project#44602 / vllm-project#46025, which introduced the merge-vs-inplace switch but defaulted to the conservative (merge) path. This closes the gap: resolve the model's actual chat template (via resolve_chat_template, the same call the renderer uses) before deciding, so GLM-like templates are treated as "no merge" and a trailing system message no longer destroys the prefix. Changes: - __init__: when chat_template is None, resolve the model's actual template via resolve_chat_template(tokenizer, None, None, model_config=...) (tokenizer from self.renderer.tokenizer), then feed that to _detect_merge_inline_system. Falls back to the existing conservative behavior only when no template can be resolved. - _detect_merge_inline_system: import jinja2.sandbox / jinja2.ext explicitly (the package __init__ does not pull them in, so jinja2.sandbox.ImmutableSandboxedEnvironment only worked when something else had imported the submodule). Broadened the catch to except Exception so malformed/non-template input falls back cleanly. - tests: add test_glm_template_does_not_merge. Co-Authored-By: Claude <noreply@anthropic.com> Signed-off-by: Stardust-minus <stardust@fish.audio>

…ching (vllm-project#44602) Signed-off-by: felix0080 <felix0080@users.noreply.github.com> Co-authored-by: felix0080 <felix0080@users.noreply.github.com>

…stem merge When a client (e.g. Claude Code) appends a system message to the messages array of a /v1/messages request, the Anthropic compatibility layer could trigger a full prompt recompute (observed as a ~75s TTFT spike) because the entire prefix-cache block chain is invalidated from the system block onward. Root cause: AnthropicServingMessages.__init__ calls _detect_merge_inline_system(chat_template) with the raw --chat-template arg, which is None by default. The detector returns True ("merge inline system into the leading block") whenever the template is falsy — even for templates like GLM that already accept mid-conversation system messages. That merge hoists the trailing system message into the leading system block, changing tokens from offset 0 onward and breaking the chained block hash, so every subsequent block's hash changes and a full recompute is required. Builds on vllm-project#44283 / vllm-project#44602 / vllm-project#46025, which introduced the merge-vs-inplace switch but defaulted to the conservative (merge) path. This closes the gap: resolve the model's actual chat template (via resolve_chat_template, the same call the renderer uses) before deciding, so GLM-like templates are treated as "no merge" and a trailing system message no longer destroys the prefix. Changes: - __init__: when chat_template is None, resolve the model's actual template via resolve_chat_template(tokenizer, None, None, model_config=...) (tokenizer from self.renderer.tokenizer), then feed that to _detect_merge_inline_system. Falls back to the existing conservative behavior only when no template can be resolved. - _detect_merge_inline_system: import jinja2.sandbox / jinja2.ext explicitly (the package __init__ does not pull them in, so jinja2.sandbox.ImmutableSandboxedEnvironment only worked when something else had imported the submodule). Broadened the catch to except Exception so malformed/non-template input falls back cleanly. - tests: add test_glm_template_does_not_merge. Co-Authored-By: Claude <noreply@anthropic.com> Signed-off-by: Stardust-minus <stardust@fish.audio>

…ching (vllm-project#44602) Signed-off-by: felix0080 <felix0080@users.noreply.github.com> Co-authored-by: felix0080 <felix0080@users.noreply.github.com>

felix0080 requested review from AndreasKaratzas, DarkLight1337, NickLucche, aarnphm, mgoin and robertgshaw2-redhat as code owners June 5, 2026 02:33

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felix0080 force-pushed the fix/anthropic-inline-system-preserve-position branch from 71ef5be to 835f37d Compare June 5, 2026 02:45

This was referenced Jun 5, 2026

[Anthropic] Support system role messages inside messages array #44283

Merged

[Bugfix][Anthropic] Normalize Claude Code system messages #44048

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felix0080 commented Jun 5, 2026

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felix0080 force-pushed the fix/anthropic-inline-system-preserve-position branch from e81f76a to 4439ea4 Compare June 5, 2026 08:00

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felix0080 force-pushed the fix/anthropic-inline-system-preserve-position branch from 99eaa7e to 88f0825 Compare June 12, 2026 02:46

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felix0080 force-pushed the fix/anthropic-inline-system-preserve-position branch 2 times, most recently from b3a8af5 to 231acc1 Compare June 12, 2026 05:52

felix0080 force-pushed the fix/anthropic-inline-system-preserve-position branch from 231acc1 to ff93cd5 Compare June 12, 2026 06:55

felix0080 added 2 commits June 12, 2026 17:10

refactor: convert _extract_system_text to classmethod

7adca21

Per maintainer review feedback. Signed-off-by: felix0080 <felix0080@users.noreply.github.com>

felix0080 force-pushed the fix/anthropic-inline-system-preserve-position branch from ff93cd5 to 7adca21 Compare June 12, 2026 09:10

chaunceyjiang merged commit 1e9f04d into vllm-project:main Jun 18, 2026
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felix0080 mentioned this pull request Jun 18, 2026

fix(anthropic): auto-detect template support for mid-conversation system messages #46021

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felix0080 mentioned this pull request Jun 18, 2026

fix(anthropic): auto-detect template support for mid-conversation system messages #46025

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Stardust-minus mentioned this pull request Jun 19, 2026

fix(anthropic): resolve model chat template before deciding inline-system merge #46196

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wqh17101 mentioned this pull request Jun 25, 2026

[Bug] DeepSeekV4-Flash produces incorrect output with inline system messages after PR #46025 when preserved in-place #46710

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fix(anthropic): preserve inline system message position for prefix caching#44602

fix(anthropic): preserve inline system message position for prefix caching#44602
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