Column storage for wide datasets

The notion of big data is quite a bit overhyped. I do get some exposure to it at work, but many tools like Hadoop are not needed over doing things in chunks on more typical machines. One thing though I have learned more generally about databases, many relational databases (such as postgres) store data under the hood like this:


So they are stacked cumulatively in an underlying file format. And then to access the information the system has to know “ok I need to find Index2 and column 2”, so it calculates offsets for where those pieces of information should be located in the file.

This however is not so nice for databases that have many columns. In particular administrative record databases that have few rows, but many thousands of columns (often with many missing fields and low dimensional categories), this default format is not very friendly. In fact many databases have limits on the number of columns a table can have. (“Few rows” is relative, but really I am contrasting with sensor data that often has billions/trillions of rows, but very few columns.)

In these situations, a columnar database (or data format) makes more sense. Instead of having to calculate many large number of offsets, the database often will represent the key-column pairs in some easier base format, and then will only worry about grabbing specific columns. Both representing the underlying data in a more efficient manner will lower on computer disk space (e.g. only takes up 1 gig instead of many gigabytes) as well as improve input/output operations on the data (e.g. it is faster to read the data/write new data).

I will show some examples via the American Community Survey data for micro areas. I have saved the functions/code here on github to follow along.

So first, I load in pandas and DuckDB. DuckDB is an open source database that uses by default a columnar storage format, but can consider it a very similar drop in replacement for sqllite for persistantly storing data.

import pandas as pd
import duckdb
import os

# my local census functions
# grabbing small area 2019 data
# here defaults to just Texas/Delaware
# still takes a few minutes
import census_funcs
cen2019_small, fields2019 = census_funcs.get_data(year=2019)
print(cen2019_small.shape) # (21868, 17145)

Here I grab the small area data for just Texas/Delaware (this includes mostly census tracts and census block groups in the census FTP data). You can see not so many rows, almost 22k, but quite a few columns, over 17k. This is after some data munging to drop entirely missing/duplicated columns even. The census data just has very many slightly different aggregate categories.

Next I save these data files to disk. For data that does not change very often, you just want to do this process a single time and save that data somewhere you can more easily access it. No need to re-download the data from the internet/census site everytime you want to do a new analysis.

I don’t have timing data here, but you can just experiment to see the parquet data format is quite a bit faster to save (and csv formats are the slowest). DuckDB is smart and just knows to look at your local namespace to find the referenced pandas dataframe in the execute string.

# Save locally to CSV file

# Trying zip compression

# Save to parquet files

# Save to DuckDB, should make the DB if does not exist
con = duckdb.connect(database='census.duckdb',read_only=False)
con.execute('CREATE TABLE census_2019 AS SELECT * FROM cen2019_small')

If we then go and check out the datasizes on disk, csv for just these two states is 0.8 gigs (the full set of data for all 50 states is closer to 20 gigs). Using zip compression reduces this to around 1/4th of the size for the csv file. Using parquet format (which can be considered an alternative fixed file format to CSV although columnar oriented) and gzip compression is pretty much the same as zip compression for this data (not many missing values or repeat categories of numbers), but if you have repeat categorical data with a bit of missing data should be slightly better compression (I am thinking NIBRS here). The entire DuckDB database is actually smaller than the CSV file (I haven’t checked closely, I try to coerce the data to smarter float/int formats before saving, but there are probably even more space to squeeze out of my functions).

# Lets check out the file sizes
files = ['census_test.csv','',

for fi in files:
    file_size = os.path.getsize(fi)
    print(f'File size for {fi} is {file_size/1024**3:,.1f} gigs')

# File size for census_test.csv is 0.8 gigs
# File size for is 0.2 gigs
# File size for census.parquet.gzip is 0.2 gigs
# File size for census.duckdb is 0.7 gigs

The benefit of having a database here like DuckDB is for later SQL querying, as well as the ability to save additional tables. If I scoop up the 2018 data (that has slightly different columns), I can save to an additional table. Then later on downstream applications can select out the limited columns/years as needed (unlikely any real analysis workflow needs all 17,000 columns).

# Can add in another table into duckdb
cen2018_small, fields2018 = census_funcs.get_data(year=2018)
con.execute('CREATE TABLE census_2018 AS SELECT * FROM cen2018_small')

ducksize = os.path.getsize(files[-1])
print(f'File size for {files[-1]} with two tables is {ducksize/1024**3:,.1f} gigs')
# File size for census.duckdb with two tables is 1.5 gigs

Sqllite is nice, as you can basically share a sqllite file and you know your friend will be able to open it. I have not worked with DuckDB that much, but hopefully it has similar functionality and ability to share without too much headache.

I have not worried about doing timing – I don’t really care about write timings of these data formats compared to CSV (slow read timing is annoying, but 10 seconds vs 1 minute to read data is not a big deal). But it is good practice to not be gluttonous with on disk space, which saving a bunch of inefficient csv files can be a bit wasteful.

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  1. Using IO objects in python to read data | Andrew Wheeler

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