Skip to content

Commit

Permalink
DOC: Update performance comparison section of io docs (pandas-dev#28890)
Browse files Browse the repository at this point in the history
  • Loading branch information
@WuraolaOyewusi @proost
WuraolaOyewusi authored and proost committed Dec 19, 2019
1 parent 95f5dd2 commit c4e5daa
Showing 1 changed file with 73 additions and 65 deletions.
138 changes: 73 additions & 65 deletions doc/source/user_guide/io.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5576,7 +5576,7 @@ Performance considerations
--------------------------

This is an informal comparison of various IO methods, using pandas
0.20.3. Timings are machine dependent and small differences should be
0.24.2. Timings are machine dependent and small differences should be
ignored.

.. code-block:: ipython
Expand All @@ -5597,11 +5597,18 @@ Given the next test set:

.. code-block:: python
import numpy as np
import os
sz = 1000000
df = pd.DataFrame({'A': np.random.randn(sz), 'B': [1] * sz})
sz = 1000000
np.random.seed(42)
df = pd.DataFrame({'A': np.random.randn(sz), 'B': [1] * sz})
def test_sql_write(df):
if os.path.exists('test.sql'):
Expand All @@ -5610,151 +5617,152 @@ Given the next test set:
df.to_sql(name='test_table', con=sql_db)
sql_db.close()
def test_sql_read():
sql_db = sqlite3.connect('test.sql')
pd.read_sql_query("select * from test_table", sql_db)
sql_db.close()
def test_hdf_fixed_write(df):
df.to_hdf('test_fixed.hdf', 'test', mode='w')
def test_hdf_fixed_read():
pd.read_hdf('test_fixed.hdf', 'test')
def test_hdf_fixed_write_compress(df):
df.to_hdf('test_fixed_compress.hdf', 'test', mode='w', complib='blosc')
def test_hdf_fixed_read_compress():
pd.read_hdf('test_fixed_compress.hdf', 'test')
def test_hdf_table_write(df):
df.to_hdf('test_table.hdf', 'test', mode='w', format='table')
def test_hdf_table_read():
pd.read_hdf('test_table.hdf', 'test')
def test_hdf_table_write_compress(df):
df.to_hdf('test_table_compress.hdf', 'test', mode='w',
complib='blosc', format='table')
def test_hdf_table_read_compress():
pd.read_hdf('test_table_compress.hdf', 'test')
def test_csv_write(df):
df.to_csv('test.csv', mode='w')
def test_csv_read():
pd.read_csv('test.csv', index_col=0)
def test_feather_write(df):
df.to_feather('test.feather')
def test_feather_read():
pd.read_feather('test.feather')
def test_pickle_write(df):
df.to_pickle('test.pkl')
def test_pickle_read():
pd.read_pickle('test.pkl')
def test_pickle_write_compress(df):
df.to_pickle('test.pkl.compress', compression='xz')
def test_pickle_read_compress():
pd.read_pickle('test.pkl.compress', compression='xz')
When writing, the top-three functions in terms of speed are are
``test_pickle_write``, ``test_feather_write`` and ``test_hdf_fixed_write_compress``.
def test_parquet_write(df):
df.to_parquet('test.parquet')
def test_parquet_read():
pd.read_parquet('test.parquet')
When writing, the top-three functions in terms of speed are ``test_feather_write``, ``test_hdf_fixed_write`` and ``test_hdf_fixed_write_compress``.

.. code-block:: ipython
In [14]: %timeit test_sql_write(df)
2.37 s ± 36.6 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [4]: %timeit test_sql_write(df)
3.29 s ± 43.2 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [15]: %timeit test_hdf_fixed_write(df)
194 ms ± 65.9 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [5]: %timeit test_hdf_fixed_write(df)
19.4 ms ± 560 µs per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [26]: %timeit test_hdf_fixed_write_compress(df)
119 ms ± 2.15 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [6]: %timeit test_hdf_fixed_write_compress(df)
19.6 ms ± 308 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [16]: %timeit test_hdf_table_write(df)
623 ms ± 125 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [7]: %timeit test_hdf_table_write(df)
449 ms ± 5.61 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [27]: %timeit test_hdf_table_write_compress(df)
563 ms ± 23.7 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [8]: %timeit test_hdf_table_write_compress(df)
448 ms ± 11.9 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [17]: %timeit test_csv_write(df)
3.13 s ± 49.9 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [9]: %timeit test_csv_write(df)
3.66 s ± 26.2 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [30]: %timeit test_feather_write(df)
103 ms ± 5.88 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [10]: %timeit test_feather_write(df)
9.75 ms ± 117 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
In [31]: %timeit test_pickle_write(df)
109 ms ± 3.72 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [11]: %timeit test_pickle_write(df)
30.1 ms ± 229 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [32]: %timeit test_pickle_write_compress(df)
3.33 s ± 55.2 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [12]: %timeit test_pickle_write_compress(df)
4.29 s ± 15.9 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [13]: %timeit test_parquet_write(df)
67.6 ms ± 706 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
When reading, the top three are ``test_feather_read``, ``test_pickle_read`` and
``test_hdf_fixed_read``.


.. code-block:: ipython
In [18]: %timeit test_sql_read()
1.35 s ± 14.7 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [14]: %timeit test_sql_read()
1.77 s ± 17.7 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [15]: %timeit test_hdf_fixed_read()
19.4 ms ± 436 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [16]: %timeit test_hdf_fixed_read_compress()
19.5 ms ± 222 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [19]: %timeit test_hdf_fixed_read()
14.3 ms ± 438 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
In [17]: %timeit test_hdf_table_read()
38.6 ms ± 857 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [28]: %timeit test_hdf_fixed_read_compress()
23.5 ms ± 672 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [18]: %timeit test_hdf_table_read_compress()
38.8 ms ± 1.49 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [20]: %timeit test_hdf_table_read()
35.4 ms ± 314 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [19]: %timeit test_csv_read()
452 ms ± 9.04 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [29]: %timeit test_hdf_table_read_compress()
42.6 ms ± 2.1 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [20]: %timeit test_feather_read()
12.4 ms ± 99.7 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
In [22]: %timeit test_csv_read()
516 ms ± 27.1 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [21]: %timeit test_pickle_read()
18.4 ms ± 191 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
In [33]: %timeit test_feather_read()
4.06 ms ± 115 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
In [22]: %timeit test_pickle_read_compress()
915 ms ± 7.48 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [34]: %timeit test_pickle_read()
6.5 ms ± 172 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
In [23]: %timeit test_parquet_read()
24.4 ms ± 146 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [35]: %timeit test_pickle_read_compress()
588 ms ± 3.57 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
For this test case ``test.pkl.compress``, ``test.parquet`` and ``test.feather`` took the least space on disk.
Space on disk (in bytes)

.. code-block:: none
34816000 Aug 21 18:00 test.sql
24009240 Aug 21 18:00 test_fixed.hdf
7919610 Aug 21 18:00 test_fixed_compress.hdf
24458892 Aug 21 18:00 test_table.hdf
8657116 Aug 21 18:00 test_table_compress.hdf
28520770 Aug 21 18:00 test.csv
16000248 Aug 21 18:00 test.feather
16000848 Aug 21 18:00 test.pkl
7554108 Aug 21 18:00 test.pkl.compress
29519500 Oct 10 06:45 test.csv
16000248 Oct 10 06:45 test.feather
8281983 Oct 10 06:49 test.parquet
16000857 Oct 10 06:47 test.pkl
7552144 Oct 10 06:48 test.pkl.compress
34816000 Oct 10 06:42 test.sql
24009288 Oct 10 06:43 test_fixed.hdf
24009288 Oct 10 06:43 test_fixed_compress.hdf
24458940 Oct 10 06:44 test_table.hdf
24458940 Oct 10 06:44 test_table_compress.hdf

0 comments on commit c4e5daa

Please sign in to comment.