Zelazny7 Zelazny7 - 7 months ago 89
Python Question

Large, persistent DataFrame in pandas

I am exploring switching to python and pandas as a long-time SAS user.

However, when running some tests today, I was surprised that python ran out of memory when trying to

a 128mb csv file. It had about 200,000 rows and 200 columns of mostly numeric data.

With SAS, I can import a csv file into a SAS dataset and it can be as large as my hard drive.

Is there something analogous in pandas?

I regularly work with large files and do not have access to a distributed computing network.


In principle it shouldn't run out of memory, but there are currently memory problems with read_csv on large files caused by some complex Python internal issues (this is vague but it's been known for a long time: http://github.com/pydata/pandas/issues/407).

At the moment there isn't a perfect solution (here's a tedious one: you could transcribe the file row-by-row into a pre-allocated NumPy array or memory-mapped file--np.mmap), but it's one I'll be working on in the near future. Another solution is to read the file in smaller pieces (use iterator=True, chunksize=1000) then concatenate then with pd.concat. The problem comes in when you pull the entire text file into memory in one big slurp.