[Performance]: vllm 0.5.4 with enable_chunked_prefill =True, throughput is slightly lower than 0.5.3~0.5.0.
### Your current environment

<details>
<summary>environment</summary>

# Hardware & Nvidia driver & OS
GPU models and configuration: GPU 0: NVIDIA GeForce RTX 4090       

Nvidia driver version: 550.107.02 

OS: Ubuntu 22.04.4 LTS (x86_64) 

# conda env create -f environment_linux.yml
```
name: vllm_xxx
channels:
  - conda-forge
  - pytorch
  - nvidia
  - defaults
dependencies:
  - python=3.11
  - anaconda
  - pip
  - pip:
      - easydict
  
pip install vllm==v0.5.4 / v0.5.3.post1 / v0.5.2 / v0.5.1
```

</details>


### 🐛 Describe the bug

Throughput and latency vary with max_num_seqs。

vllm 0.5.4 with enable_chunked_prefill =True, throughput is slightly lower than 0.5.3~0.5.1. very strange.

![chunked_prefill](https://github.com/user-attachments/assets/0250456a-60b8-45e9-82ad-316204f6e778)

| max_num_seqs | requests/s | disable 0.5.4 | requests/s | disable 0.5.3 | requests/s | disable 0.5.2 | requests/s | disable 0.5.1 | requests/s | enable 0.5.4 | requests/s | enable 0.5.3 | requests/s | enable 0.5.2 | requests/s | enable 0.5.1 |
|--------------|------------|---------------|------------|---------------|------------|---------------|------------|---------------|------------|--------------|------------|--------------|------------|--------------|------------|--------------|
| 1024         | 2.5115     | 36.1          | 2.4747     | 36.69         | 2.4878     | 36.82         | 2.4972     | 36.33         | 3.1797     | 39.72        | 3.1341     | 40.15        | 3.1696     | 39.67        | 3.1745     | 39.61        |
| 768          | 3.2838     | 42.6          | 3.2242     | 43.48         | 3.2608     | 42.93         | 3.2648     | 42.88         | 4.1047     | 43.4         | 3.9708     | 44.42        | 4.0413     | 43.6         | 4.0439     | 43.57        |
| 512          | 4.1063     | 51.93         | 4.0102     | 53.22         | 4.0966     | 52.07         | 4.0998     | 51.97         | 4.6486     | 46.79        | 4.6377     | 46.25        | 4.7419     | 45.15        | 4.747      | 45.13        |
| 384          | 4.1705     | 54.83         | 4.0749     | 56.35         | 4.1538     | 55.07         | 4.1587     | 55            | 4.798      | 49.66        | 4.8605     | 45.93        | 4.9834     | 44.72        | 5.0019     | 44.61        |
| 256          | 4.3613     | 59.37         | 4.2659     | 60.94         | 4.3586     | 59.44         | 4.3632     | 59.36         | 4.9096     | 48.27        | 5.4424     | 42.23        | 5.5876     | 41.1         | 5.5949     | 41.04        |
| 128          | 4.7441     | 42.75         | 4.6511     | 43.76         | 4.7564     | 42.62         | 4.7583     | 42.58         | 4.2047     | 32.77        | 4.0718     | 29.7         | 4.1528     | 29.11        | 4.1544     | 29.1         |
| 64           | 3.7161     | 29.56         | 3.6446     | 30.2          | 3.6972     | 29.71         | 3.7044     | 29.66         | 2.435      | 26.88        | 2.3879     | 25.74        | 2.4141     | 25.45        | 2.4175     | 25.41        |
| 32           | 2.6923     | 20.76         | 2.6465     | 21.16         | 2.6702     | 20.94         | 2.6735     | 20.92         | 1.6103     | 19.83        | 1.5846     | 19.55        | 1.593      | 19.44        | 1.5942     | 19.43        |

```
import os
import random
import numpy as np
import time


def benchmark(args):
    random.seed(args.seed)

    os.environ["VLLM_LOGGING_LEVEL"] = "ERROR"
    os.environ["VLLM_NO_USAGE_STATS"] = "True"

    import vllm
    from vllm import LLMEngine, EngineArgs, SamplingParams, TextPrompt

    print(vllm.__version__)

    engine_args = EngineArgs(
        model=args.model,
        tokenizer=args.tokenizer,
        quantization=args.quantization,
        tensor_parallel_size=args.tensor_parallel_size,
        seed=args.seed,
        trust_remote_code=args.trust_remote_code,
        dtype=args.dtype,
        max_model_len=args.max_model_len,
        gpu_memory_utilization=args.gpu_memory_utilization,
        enforce_eager=args.enforce_eager,
        kv_cache_dtype=args.kv_cache_dtype,
        quantization_param_path=args.quantization_param_path,
        device=args.device,
        enable_prefix_caching=args.enable_prefix_caching,
        download_dir=args.download_dir,
        enable_chunked_prefill=args.enable_chunked_prefill,
        max_num_batched_tokens=args.max_num_batched_tokens,
        max_num_seqs=args.max_num_seqs,
        distributed_executor_backend=args.distributed_executor_backend,
        disable_log_stats=True
    )
    engine = LLMEngine.from_engine_args(engine_args)

    prompt = "hi" * (args.input_len - 1)
    requests = [(prompt, args.input_len, args.output_len)
                for _ in range(args.num_prompts)]

    start = time.perf_counter()
    for request_id, (prompt, _, output_len) in enumerate(requests):
        inputs = TextPrompt(prompt=prompt)
        sampling_params = SamplingParams(
            n=args.n,
            temperature=0.0 if args.use_beam_search else 1.0,
            top_p=1.0,
            use_beam_search=args.use_beam_search,
            ignore_eos=True,
            max_tokens=output_len,
        )
        engine.add_request(str(request_id), inputs, sampling_params)

    out = []
    while engine.has_unfinished_requests():
        request_outputs = engine.step()
        out.append((time.perf_counter(), request_outputs))
    end = time.perf_counter()

    timestamp = {}
    for t, rs in out:
        for r in rs:
            request_id = r.request_id
            if request_id not in timestamp:
                timestamp[request_id] = []
            timestamp[request_id].append(t)

    tpot = []
    for v in timestamp.values():
        dd = [v[i]-v[i-1] for i in range(1, len(v))]
        tpot.extend(dd)

    tpot = np.mean(tpot)
    elapsed_time = end - start

    total_num_tokens = sum(prompt_len + output_len
                           for _, prompt_len, output_len in requests)

    print(f"Throughput: {len(requests) / elapsed_time:.4f} requests/s, "
          f"{total_num_tokens / elapsed_time:.4f} tokens/s, "
          f"Delay {tpot*1000:0.2f} ms")


if __name__ == '__main__':
    from easydict import EasyDict as edict
    args = edict()

    args.dataset = None
    args.input_len = 512
    args.output_len = 512

    args.model = "Qwen/Qwen2-7B-Instruct"
    args.trust_remote_code = False
    args.tokenizer = args.model
    args.quantization = None
    args.quantization_param_path = None
    args.tensor_parallel_size = 1
    args.seed = 0
    args.n = 1
    args.use_beam_search = False
    args.num_prompts = 1000
    args.dtype = 'auto'
    args.max_model_len = 10000
    args.enforce_eager = True
    args.kv_cache_dtype = "auto"
    args.device = "cuda"
    args.enable_prefix_caching = False
    args.gpu_memory_utilization = 0.9
    args.output_json = None
    args.distributed_executor_backend = None
    args.download_dir = None

    import sys
    from concurrent.futures import ProcessPoolExecutor

    def run(args):
        with ProcessPoolExecutor(1) as executor:
            f = executor.submit(benchmark, args)
            f.result()

    max_num_seqs_list = [1024, 768, 512, 384, 256, 128, 64, 32]

    print()
    print("enable_chunked_prefill = False")
    for max_num_seqs in max_num_seqs_list:
        print("max_num_seqs", max_num_seqs)
        args.enable_chunked_prefill = False
        args.max_num_batched_tokens = None
        args.max_num_seqs = max_num_seqs
        run(args)

    print()
    print("enable_chunked_prefill = True")
    for max_num_seqs in max_num_seqs_list:
        print("max_num_seqs", max_num_seqs)
        args.enable_chunked_prefill = True
        args.max_num_seqs = max_num_seqs
        args.max_num_batched_tokens = args.max_num_seqs
        run(args)
```



[Performance]: vllm 0.5.4 with enable_chunked_prefill =True, throughput is slightly lower than 0.5.3~0.5.0.
### Your current environment

<details>
<summary>environment</summary>

# Hardware & Nvidia driver & OS
GPU models and configuration: GPU 0: NVIDIA GeForce RTX 4090       

Nvidia driver version: 550.107.02 

OS: Ubuntu 22.04.4 LTS (x86_64) 

# conda env create -f environment_linux.yml
```
name: vllm_xxx
channels:
  - conda-forge
  - pytorch
  - nvidia
  - defaults
dependencies:
  - python=3.11
  - anaconda
  - pip
  - pip:
      - easydict
  
pip install vllm==v0.5.4 / v0.5.3.post1 / v0.5.2 / v0.5.1
```

</details>


### 🐛 Describe the bug

Throughput and latency vary with max_num_seqs。

vllm 0.5.4 with enable_chunked_prefill =True, throughput is slightly lower than 0.5.3~0.5.1. very strange.

![chunked_prefill](https://github.com/user-attachments/assets/0250456a-60b8-45e9-82ad-316204f6e778)

| max_num_seqs | requests/s | disable 0.5.4 | requests/s | disable 0.5.3 | requests/s | disable 0.5.2 | requests/s | disable 0.5.1 | requests/s | enable 0.5.4 | requests/s | enable 0.5.3 | requests/s | enable 0.5.2 | requests/s | enable 0.5.1 |
|--------------|------------|---------------|------------|---------------|------------|---------------|------------|---------------|------------|--------------|------------|--------------|------------|--------------|------------|--------------|
| 1024         | 2.5115     | 36.1          | 2.4747     | 36.69         | 2.4878     | 36.82         | 2.4972     | 36.33         | 3.1797     | 39.72        | 3.1341     | 40.15        | 3.1696     | 39.67        | 3.1745     | 39.61        |
| 768          | 3.2838     | 42.6          | 3.2242     | 43.48         | 3.2608     | 42.93         | 3.2648     | 42.88         | 4.1047     | 43.4         | 3.9708     | 44.42        | 4.0413     | 43.6         | 4.0439     | 43.57        |
| 512          | 4.1063     | 51.93         | 4.0102     | 53.22         | 4.0966     | 52.07         | 4.0998     | 51.97         | 4.6486     | 46.79        | 4.6377     | 46.25        | 4.7419     | 45.15        | 4.747      | 45.13        |
| 384          | 4.1705     | 54.83         | 4.0749     | 56.35         | 4.1538     | 55.07         | 4.1587     | 55            | 4.798      | 49.66        | 4.8605     | 45.93        | 4.9834     | 44.72        | 5.0019     | 44.61        |
| 256          | 4.3613     | 59.37         | 4.2659     | 60.94         | 4.3586     | 59.44         | 4.3632     | 59.36         | 4.9096     | 48.27        | 5.4424     | 42.23        | 5.5876     | 41.1         | 5.5949     | 41.04        |
| 128          | 4.7441     | 42.75         | 4.6511     | 43.76         | 4.7564     | 42.62         | 4.7583     | 42.58         | 4.2047     | 32.77        | 4.0718     | 29.7         | 4.1528     | 29.11        | 4.1544     | 29.1         |
| 64           | 3.7161     | 29.56         | 3.6446     | 30.2          | 3.6972     | 29.71         | 3.7044     | 29.66         | 2.435      | 26.88        | 2.3879     | 25.74        | 2.4141     | 25.45        | 2.4175     | 25.41        |
| 32           | 2.6923     | 20.76         | 2.6465     | 21.16         | 2.6702     | 20.94         | 2.6735     | 20.92         | 1.6103     | 19.83        | 1.5846     | 19.55        | 1.593      | 19.44        | 1.5942     | 19.43        |

```
import os
import random
import numpy as np
import time


def benchmark(args):
    random.seed(args.seed)

    os.environ["VLLM_LOGGING_LEVEL"] = "ERROR"
    os.environ["VLLM_NO_USAGE_STATS"] = "True"

    import vllm
    from vllm import LLMEngine, EngineArgs, SamplingParams, TextPrompt

    print(vllm.__version__)

    engine_args = EngineArgs(
        model=args.model,
        tokenizer=args.tokenizer,
        quantization=args.quantization,
        tensor_parallel_size=args.tensor_parallel_size,
        seed=args.seed,
        trust_remote_code=args.trust_remote_code,
        dtype=args.dtype,
        max_model_len=args.max_model_len,
        gpu_memory_utilization=args.gpu_memory_utilization,
        enforce_eager=args.enforce_eager,
        kv_cache_dtype=args.kv_cache_dtype,
        quantization_param_path=args.quantization_param_path,
        device=args.device,
        enable_prefix_caching=args.enable_prefix_caching,
        download_dir=args.download_dir,
        enable_chunked_prefill=args.enable_chunked_prefill,
        max_num_batched_tokens=args.max_num_batched_tokens,
        max_num_seqs=args.max_num_seqs,
        distributed_executor_backend=args.distributed_executor_backend,
        disable_log_stats=True
    )
    engine = LLMEngine.from_engine_args(engine_args)

    prompt = "hi" * (args.input_len - 1)
    requests = [(prompt, args.input_len, args.output_len)
                for _ in range(args.num_prompts)]

    start = time.perf_counter()
    for request_id, (prompt, _, output_len) in enumerate(requests):
        inputs = TextPrompt(prompt=prompt)
        sampling_params = SamplingParams(
            n=args.n,
            temperature=0.0 if args.use_beam_search else 1.0,
            top_p=1.0,
            use_beam_search=args.use_beam_search,
            ignore_eos=True,
            max_tokens=output_len,
        )
        engine.add_request(str(request_id), inputs, sampling_params)

    out = []
    while engine.has_unfinished_requests():
        request_outputs = engine.step()
        out.append((time.perf_counter(), request_outputs))
    end = time.perf_counter()

    timestamp = {}
    for t, rs in out:
        for r in rs:
            request_id = r.request_id
            if request_id not in timestamp:
                timestamp[request_id] = []
            timestamp[request_id].append(t)

    tpot = []
    for v in timestamp.values():
        dd = [v[i]-v[i-1] for i in range(1, len(v))]
        tpot.extend(dd)

    tpot = np.mean(tpot)
    elapsed_time = end - start

    total_num_tokens = sum(prompt_len + output_len
                           for _, prompt_len, output_len in requests)

    print(f"Throughput: {len(requests) / elapsed_time:.4f} requests/s, "
          f"{total_num_tokens / elapsed_time:.4f} tokens/s, "
          f"Delay {tpot*1000:0.2f} ms")


if __name__ == '__main__':
    from easydict import EasyDict as edict
    args = edict()

    args.dataset = None
    args.input_len = 512
    args.output_len = 512

    args.model = "Qwen/Qwen2-7B-Instruct"
    args.trust_remote_code = False
    args.tokenizer = args.model
    args.quantization = None
    args.quantization_param_path = None
    args.tensor_parallel_size = 1
    args.seed = 0
    args.n = 1
    args.use_beam_search = False
    args.num_prompts = 1000
    args.dtype = 'auto'
    args.max_model_len = 10000
    args.enforce_eager = True
    args.kv_cache_dtype = "auto"
    args.device = "cuda"
    args.enable_prefix_caching = False
    args.gpu_memory_utilization = 0.9
    args.output_json = None
    args.distributed_executor_backend = None
    args.download_dir = None

    import sys
    from concurrent.futures import ProcessPoolExecutor

    def run(args):
        with ProcessPoolExecutor(1) as executor:
            f = executor.submit(benchmark, args)
            f.result()

    max_num_seqs_list = [1024, 768, 512, 384, 256, 128, 64, 32]

    print()
    print("enable_chunked_prefill = False")
    for max_num_seqs in max_num_seqs_list:
        print("max_num_seqs", max_num_seqs)
        args.enable_chunked_prefill = False
        args.max_num_batched_tokens = None
        args.max_num_seqs = max_num_seqs
        run(args)

    print()
    print("enable_chunked_prefill = True")
    for max_num_seqs in max_num_seqs_list:
        print("max_num_seqs", max_num_seqs)
        args.enable_chunked_prefill = True
        args.max_num_seqs = max_num_seqs
        args.max_num_batched_tokens = args.max_num_seqs
        run(args)
```