Pandas segmentation fault

Question

The following lines of code is not being successfully executed because of low memory.

import pandas as pd
import datetime as dt

u_cols=['remote_host', 'dummy1', 'dummy2', 'date', 'timezone', 'get', 'status', 'bytes_sent', 'dummy3', 'logline']

logfile='/var/log/apache2/error.log.1'

info = pd.read_csv(logfile, sep=' ', names=u_cols, low_memory=False)


 In [5]: info = pd.read_csv(logfile, sep=' ', names=u_cols, low_memory=False)
Segmentation fault (core dumped)


# free -m
             total       used       free     shared    buffers     cached
Mem:           590        495         94          0         25         89
-/+ buffers/cache:        380        209
Swap:            0          0          0

How do I exit gracefully? This error is causing Django to stop working.

>>> pd.show_versions()

INSTALLED VERSIONS
------------------
commit: None
python: 2.7.7.final.0
python-bits: 64
OS: Linux
OS-release: 3.2.0-31-virtual
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8

pandas: 0.14.1
nose: 1.3.3
Cython: 0.20.1
numpy: 1.8.1
scipy: 0.14.0
statsmodels: 0.5.0
IPython: 2.1.0
sphinx: 1.2.2
patsy: 0.2.1
scikits.timeseries: None
dateutil: 1.5
pytz: 2014.3
bottleneck: None
tables: 3.1.1
numexpr: 2.3.1
matplotlib: 1.3.1
openpyxl: 1.8.5
xlrd: 0.9.3
xlwt: 0.7.5
xlsxwriter: 0.5.5
lxml: 3.3.5
bs4: 4.3.1
html5lib: None
httplib2: None
apiclient: None
rpy2: None
sqlalchemy: 0.9.4
pymysql: 0.6.2.None
psycopg2: 2.5.4 (dt dec pq3 ext)

You can try this with your own error log or use a test file from:

http://testbyshantanu.s3.amazonaws.com/error.log.1

The file is not correctly formatted but it should not force python to exit :)

Answer 1

need to add "engine" parameter to read_csv method or else get segmentation error.

In [5]: info = pd.read_csv(logfile, sep=' ', names=u_cols, engine='python' )

In [6]: info = pd.read_csv(logfile, sep=' ', names=u_cols )
Segmentation fault (core dumped)