BUG: service stopped when pivot a 1125138913x5 matrix into 4000 columns on a 160U-4096GBmem machine

[huboqiang]

Describe the bug

Running pivot and service stopped:

To Reproduce

To help us to reproduce this bug, please provide information below:

1. Your Python version 3.11.4
2. The version of Xorbits you use 0.5.1
3. Versions of crucial packages, such as numpy(1.25.2), scipy(1.11.2) and pandas(2.0.3)
4. Full stack of the error.

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/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xorbits/_mars/dataframe/base/pivot.py:72: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  input_data[dtype] = np.nan
/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xorbits/_mars/dataframe/base/pivot.py:72: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  input_data[dtype] = np.nan
/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xorbits/_mars/dataframe/base/pivot.py:72: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  input_data[dtype] = np.nan
2023-10-13 19:20:03,359 xorbits._mars.services.scheduling.worker.execution 337003 ERROR    Failed to run subtask n6Qo8tTl8A6Pn7uCwJHxGAEK on band numa-0
Traceback (most recent call last):
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xorbits/_mars/services/scheduling/worker/execution.py", line 445, in _run_subtask_once
    return await asyncio.shield(aiotask)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xorbits/_mars/services/subtask/api.py", line 70, in run_subtask_in_slot
    return await ref.run_subtask.options(profiling_context=profiling_context).send(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xoscar/backends/context.py", line 226, in send
    result = await self._wait(future, actor_ref.address, send_message)  # type: ignore
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xoscar/backends/context.py", line 115, in _wait
    return await future
           ^^^^^^^^^^^^
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xoscar/backends/core.py", line 84, in _listen
    raise ServerClosed(
xoscar.errors.ServerClosed: Remote server unixsocket:///361854215913472 closed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xorbits/_mars/services/scheduling/worker/execution.py", line 402, in internal_run_subtask
    subtask_info.result = await self._retry_run_subtask(
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xorbits/_mars/services/scheduling/worker/execution.py", line 513, in _retry_run_subtask
    return await _retry_run(subtask, subtask_info, _run_subtask_once)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xorbits/_mars/services/scheduling/worker/execution.py", line 95, in _retry_run
    raise ex
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xorbits/_mars/services/scheduling/worker/execution.py", line 73, in _retry_run
    return await target_async_func(*args)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xorbits/_mars/services/scheduling/worker/execution.py", line 491, in _run_subtask_once
    raise ex
xoscar.errors.ServerClosed: unexpectedly terminated process (Remote server unixsocket:///361854215913472 closed) with address 127.0.0.1:39737, which is highly suspected to be caused by an Out-of-Memory (OOM) problem
2023-10-13 19:20:03,454 xorbits._mars.services.task.execution.mars.stage 337003 ERROR    Subtask n6Qo8tTl8A6Pn7uCwJHxGAEK errored
Traceback (most recent call last):
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xorbits/_mars/services/scheduling/worker/execution.py", line 445, in _run_subtask_once
    return await asyncio.shield(aiotask)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xorbits/_mars/services/subtask/api.py", line 70, in run_subtask_in_slot
    return await ref.run_subtask.options(profiling_context=profiling_context).send(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xoscar/backends/context.py", line 226, in send
    result = await self._wait(future, actor_ref.address, send_message)  # type: ignore
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xoscar/backends/context.py", line 115, in _wait
    return await future
           ^^^^^^^^^^^^
  File "/cluster/home/bqhu_jh/share/miniconda3/envs/bigdata/lib/python3.11/site-packages/xoscar/backends/core.py", line 84, in _listen
    raise ServerClosed(
xoscar.errors.ServerClosed: Remote server unixsocket:///361854215913472 closed
……
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7. Minimized code to reproduce the error.

df = xpd.read_parquet("./merged.pq")
print(df.shape)   # (1125138913, 5)
df_pvt = df.pivot(index=[0,1,2], columns=[4], values=[3])
df_pvt

Expected behavior

A clear and concise description of what you expected to happen.

I think there were some bug for large scale data and the server closed.

Additional context

Add any other context about the problem here. No.

[huboqiang]

Using rechunk(chunk_size=10_000) can adjust partrition policy like spark repartrition.