How to read a 6 GB csv file with pandas

Question

I am trying to read a large csv file (aprox. 6 GB) in pandas and i am getting the following memory error:

MemoryError                               Traceback (most recent call last)
<ipython-input-58-67a72687871b> in <module>()
----> 1 data=pd.read_csv('aphro.csv',sep=';')

C:\Python27\lib\site-packages\pandas\io\parsers.pyc in parser_f(filepath_or_buffer, sep, dialect, compression, doublequote, escapechar, quotechar, quoting, skipinitialspace, lineterminator, header, index_col, names, prefix, skiprows, skipfooter, skip_footer, na_values, na_fvalues, true_values, false_values, delimiter, converters, dtype, usecols, engine, delim_whitespace, as_recarray, na_filter, compact_ints, use_unsigned, low_memory, buffer_lines, warn_bad_lines, error_bad_lines, keep_default_na, thousands, comment, decimal, parse_dates, keep_date_col, dayfirst, date_parser, memory_map, nrows, iterator, chunksize, verbose, encoding, squeeze, mangle_dupe_cols, tupleize_cols, infer_datetime_format)
    450                     infer_datetime_format=infer_datetime_format)
    451 
--> 452         return _read(filepath_or_buffer, kwds)
    453 
    454     parser_f.__name__ = name

C:\Python27\lib\site-packages\pandas\io\parsers.pyc in _read(filepath_or_buffer, kwds)
    242         return parser
    243 
--> 244     return parser.read()
    245 
    246 _parser_defaults = {

C:\Python27\lib\site-packages\pandas\io\parsers.pyc in read(self, nrows)
    693                 raise ValueError('skip_footer not supported for iteration')
    694 
--> 695         ret = self._engine.read(nrows)
    696 
    697         if self.options.get('as_recarray'):

C:\Python27\lib\site-packages\pandas\io\parsers.pyc in read(self, nrows)
   1137 
   1138         try:
-> 1139             data = self._reader.read(nrows)
   1140         except StopIteration:
   1141             if nrows is None:

C:\Python27\lib\site-packages\pandas\parser.pyd in pandas.parser.TextReader.read (pandas\parser.c:7145)()

C:\Python27\lib\site-packages\pandas\parser.pyd in pandas.parser.TextReader._read_low_memory (pandas\parser.c:7369)()

C:\Python27\lib\site-packages\pandas\parser.pyd in pandas.parser.TextReader._read_rows (pandas\parser.c:8194)()

C:\Python27\lib\site-packages\pandas\parser.pyd in pandas.parser.TextReader._convert_column_data (pandas\parser.c:9402)()

C:\Python27\lib\site-packages\pandas\parser.pyd in pandas.parser.TextReader._convert_tokens (pandas\parser.c:10057)()

C:\Python27\lib\site-packages\pandas\parser.pyd in pandas.parser.TextReader._convert_with_dtype (pandas\parser.c:10361)()

C:\Python27\lib\site-packages\pandas\parser.pyd in pandas.parser._try_int64 (pandas\parser.c:17806)()

MemoryError: 

Any help on this??

Answer 1

The error shows that the machine does not have enough memory to read the entire CSV into a DataFrame at one time. Assuming you do not need the entire dataset in memory all at one time, one way to avoid the problem would be to process the CSV in chunks (by specifying the chunksize parameter):

chunksize = 10 ** 6
for chunk in pd.read_csv(filename, chunksize=chunksize):
    process(chunk)

Answer 2

You can try sframe, that have the same syntax as pandas but allows you to manipulate files that are bigger than your RAM.

Answer 3

I proceeded like this:

chunks=pd.read_table('aphro.csv',chunksize=1000000,sep=';',\
       names=['lat','long','rf','date','slno'],index_col='slno',\
       header=None,parse_dates=['date'])

df=pd.DataFrame()
%time df=pd.concat(chunk.groupby(['lat','long',chunk['date'].map(lambda x: x.year)])['rf'].agg(['sum']) for chunk in chunks)

Answer 4

The above answer is already satisfying the topic. Anyway, if you need all the data in memory - have a look at bcolz. Its compressing the data in memory. I have had really good experience with it. But its missing a lot of pandas features

Edit: I got compression rates at around 1/10 or orig size i think, of course depending of the kind of data. Important features missing were aggregates.

Answer 5

You can read in the data as chunks and save each chunk as pickle.

import pandas as pd 
import pickle

in_path = "" #Path where the large file is
out_path = "" #Path to save the pickle files to
chunk_size = 400000 #size of chunks relies on your available memory
separator = "~"

reader = pd.read_csv(in_path,sep=separator,chunksize=chunk_size, 
                    low_memory=False)    

i=1
for chunk in reader:
    out_file = out_path + "/data_{}.pkl".format(i)
    with open(out_file, "wb") as f:
        pickle.dump(chunk,f,pickle.HIGHEST_PROTOCOL)
    i+=1

In the next step you read in the pickles and append each pickle to your desired dataframe.

import glob
pickle_path = "" #Same Path as out_path i.e. where the pickle files are

data_p_files=[]
for name in glob.glob(pickle_path + "/data_*.pkl"):
   data_p_files.append(name)


df = pd.DataFrame([])
for i in range(len(data_p_files)):
    df = df.append(pd.read_pickle(data_p_files[i]),ignore_index=True)