Performance of sum vs mean on Bool arrays is 10x different

[stakas]

Code Sample

K = 100000000
df = pd.DataFrame(list(range(K)))
mask = df[0] > K/2

%timeit mask.mean()

%timeit mask.sum()

Problem description

Doing "sum" and "mean" on boolean pandas masks is 10x different! This clearly should not be the case, given these are identical operations.

Expected Output

Output of pd.show_versions()

INSTALLED VERSIONS

commit: None
python: 3.6.1.final.0
python-bits: 64
OS: Darwin
OS-release: 16.7.0
machine: x86_64
processor: i386
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8

pandas: 0.20.1
pytest: 3.0.7
pip: 9.0.1
setuptools: 33.1.1
Cython: 0.25.2
numpy: 1.12.0
scipy: 0.19.0
xarray: None
IPython: 5.3.0
sphinx: 1.5.6
patsy: 0.4.1
dateutil: 2.6.1
pytz: 2017.2
blosc: None
bottleneck: 1.2.1
tables: 3.3.0
numexpr: 2.6.2
feather: None
matplotlib: 2.0.2
openpyxl: 2.4.7
xlrd: 1.0.0
xlwt: 1.2.0
xlsxwriter: 0.9.6
lxml: 3.7.3
bs4: 4.6.0
html5lib: 0.9999999
sqlalchemy: 1.1.9
pymysql: None
psycopg2: 2.7.3 (dt dec pq3 ext lo64)
jinja2: 2.9.6
s3fs: None
pandas_gbq: None
pandas_datareader: None

[TomAugspurger]

Could you post the timings you get? And can you try both with / without bottleneck? mean should use it, but sum won't IIRC.

If that doesn't explain the difference, then when you get a chance, could you upgrade to pandas master and maybe profile https://github.com/pandas-dev/pandas/blob/master/pandas/core/nanops.py a bit?

[stakas]

Spot on!
For

K = 100000000
df = pd.DataFrame(list(range(K)))
mask = df[0] > K/2

Without bottleneck: %timeit mask.mean() gives: 10 loops, best of 3: 141 ms per loop and python %timeit mask.sum() gives: python 1 loop, best of 3: 1.06 s per loop .

With bottleneck timings are much more inline: python 10 loops, best of 3: 137 ms per loop
vs python 1 loop, best of 3: 161 ms per loop .

So the solution would be to use Bottleneck ? Thanks

[TomAugspurger]

Thanks.

IIRC, bottleneck.nansum had some overflow issues. see #15507. This may be easier to solve now that #9422 has been settled.

[jbrockmendel]

im seeing indistinguishable timings both with and without bottleneck. this is on a pre-M1 mac. could use confirmation.

[mroeschke]

Same here, closing