提问者:小点点

将大型熊猫df保存为hdf时发生溢出错误


我有一个大的Pandas数据帧(~15GB,83m行),我有兴趣保存为h5(或feather)文件。一列包含长ID的数字字符串,它们应该具有字符串/对象类型。但即使我确保熊猫将所有列解析为对象

df = pd.read_csv('data.csv', dtype=object)
print(df.dtypes)  # sanity check
df.to_hdf('df.h5', 'df')

> client_id                object
  event_id                 object
  account_id               object
  session_id               object
  event_timestamp          object
  # etc...

我得到这个错误:

  File "foo.py", line 14, in <module>
    df.to_hdf('df.h5', 'df')
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pandas/core/generic.py", line 1996, in to_hdf
    return pytables.to_hdf(path_or_buf, key, self, **kwargs)
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pandas/io/pytables.py", line 279, in to_hdf
    f(store)
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pandas/io/pytables.py", line 273, in <lambda>
    f = lambda store: store.put(key, value, **kwargs)
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pandas/io/pytables.py", line 890, in put
    self._write_to_group(key, value, append=append, **kwargs)
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pandas/io/pytables.py", line 1367, in _write_to_group
    s.write(obj=value, append=append, complib=complib, **kwargs)
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pandas/io/pytables.py", line 2963, in write
    self.write_array('block%d_values' % i, blk.values, items=blk_items)
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pandas/io/pytables.py", line 2730, in write_array
    vlarr.append(value)
  File "/shared_directory/projects/env/lib/python3.6/site-packages/tables/vlarray.py", line 547, in append
    self._append(nparr, nobjects)
  File "tables/hdf5extension.pyx", line 2032, in tables.hdf5extension.VLArray._append
OverflowError: value too large to convert to int

显然它无论如何都试图将其转换为int,但失败了。

运行df.to_feather()时,我也遇到了类似的问题:

df.to_feather('df.feather')
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pandas/core/frame.py", line 1892, in to_feather
    to_feather(self, fname)
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pandas/io/feather_format.py", line 83, in to_feather
    feather.write_dataframe(df, path)
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pyarrow/feather.py", line 182, in write_feather
    writer.write(df)
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pyarrow/feather.py", line 93, in write
    table = Table.from_pandas(df, preserve_index=False)
  File "pyarrow/table.pxi", line 1174, in pyarrow.lib.Table.from_pandas
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pyarrow/pandas_compat.py", line 501, in dataframe_to_arrays
    convert_fields))
  File "/usr/lib/python3.6/concurrent/futures/_base.py", line 586, in result_iterator
    yield fs.pop().result()
  File "/usr/lib/python3.6/concurrent/futures/_base.py", line 425, in result
    return self.__get_result()
  File "/usr/lib/python3.6/concurrent/futures/_base.py", line 384, in __get_result
    raise self._exception
  File "/usr/lib/python3.6/concurrent/futures/thread.py", line 56, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pyarrow/pandas_compat.py", line 487, in convert_column
    raise e
  File "/shared_directory/projects/env/lib/python3.6/site-packages/pyarrow/pandas_compat.py", line 481, in convert_column
    result = pa.array(col, type=type_, from_pandas=True, safe=safe)
  File "pyarrow/array.pxi", line 191, in pyarrow.lib.array
  File "pyarrow/array.pxi", line 78, in pyarrow.lib._ndarray_to_array
  File "pyarrow/error.pxi", line 85, in pyarrow.lib.check_status
pyarrow.lib.ArrowInvalid: ('Could not convert 1542852887489 with type str: tried to convert to double', 'Conversion failed for column session_id with type object')

所以:

  1. 是否有任何看起来像数字的东西被强制转换为存储中的数字?
  2. NaN的存在会影响这里发生的事情吗?
  3. 有替代存储解决方案吗?什么是最好的?

共2个答案

匿名用户

在对这个主题进行了一些阅读之后,问题似乎是处理string类型列。我的string列包含全数字字符串和带字符的字符串的混合。Pandas可以灵活地选择将字符串保留为对象,没有声明的类型,但是当序列化为hdf5feather时,列的内容被转换为类型(例如strdouble)并且不能混合。当遇到足够大的混合类型库时,这两个库都会失败。

将我的混合列强制转换为字符串允许我将其保存在feather中,但在HDF5中,文件膨胀并且当我耗尽磁盘空间时该过程结束。

以下是一个类似案例的答案,其中一位评论者指出(2年前)“这个问题非常标准,但解决方案很少”。

Pandas中的字符串类型称为object,但这掩盖了它们可能是纯字符串或混合dtype(numpy有内置字符串类型,但Pandas从不将它们用于文本)。因此,在这种情况下,首先要做的是将所有字符串强制执行为字符串类型(使用df[coll]. astype(str))。但即便如此,在足够大的文件(16GB,带有长字符串)中,这仍然失败了。为什么?

我遇到这个错误的原因是我有很长的高熵(许多不同的唯一值)字符串的数据。(对于低熵数据,切换到分类dtype可能是值得的。)在我的例子中,我意识到我只需要这些字符串来识别行——所以我可以用唯一的整数替换它们!

df[col] = df[col].map(dict(zip(df[col].unique(), range(df[col].nunique()))))

对于文本数据,除了hdf5/feather之外,还有其他推荐的解决方案,包括:

  • json
  • msgpack(注意在Pandas 0.25中read_msgpack已被弃用)
  • ickle(已知存在安全问题,请小心-但对于数据帧的内部存储/传输应该可以)
  • parquet,Apache Arrow生态系统的一部分。

这是Matthew Rocklin(dask开发人员之一)比较msgpack泡菜的答案。他在博客上写了一个更广泛的比较。

匿名用户

HDF5不是适合这个用例的解决方案。如果你想在单个结构中存储许多数据帧,hdf5是一个更好的解决方案。打开文件时它有更多的开销,然后它允许你有效地加载每个数据帧,也可以轻松地加载它们的切片。它应该被认为是一个存储数据帧的文件系统。

在时间序列事件的单个数据帧的情况下,推荐的格式将是Apache Arrow项目格式之一,即featherparquet。人们应该将它们视为基于列的(压缩的)csv文件。这两者之间的特殊权衡在什么是羽毛和镶木地板之间的区别?下进行了很好的阐述。

需要考虑的一个特殊问题是数据类型。由于feather不是为通过压缩来优化磁盘空间而设计的,因此它可以为更多种数据类型提供支持。虽然parquet试图提供非常有效的压缩,但它只能支持有限的子集,从而可以更好地处理数据压缩。