How to create a large pandas dataframe from an sql query without running out of memory?

As mentioned in a comment, starting from pandas 0.15, you have a chunksize option in read_sql to read and process the query chunk by chunk:

sql = "SELECT * FROM My_Table"
for chunk in pd.read_sql_query(sql , engine, chunksize=5):
    print(chunk)

Reference: http://pandas.pydata.org/pandas-docs/version/0.15.2/io.html#querying