Mastering high performance data algorithms I: Group By

Posted by Wes McKinney on May 13, 2012 Leave a comment (6) Go to comments

I’m on my way back from R/Finance 2012. Those guys did a nice job of organizing the conference and was great to meet everyone there.

As part of pandas development, I have had to develop a suite of high performance data algorithms and implementation strategies which are the heart and soul of the library. I get asked a lot why pandas’s performance is much better than R and other data manipulation tools. The reasons are two-fold: careful implementation (in Cython and and C, so minimizing the computational friction) and carefully-thought-out algorithms.

Here are some of the more important tools and ideas that I make use of on a day-to-day basis:

  • Hash tables I use klib. It’s awesome and easy to use. I have this for critical algorithms like unique, factorize (unique + integer label assignment)
  • O(n) sort, known in pandas as groupsort, on integers with known range. This is a variant of counting sort; if you have N integers with known range from 0 to K – 1, this can be sorted in O(N) time. Combining this tool with factorize (hash table-based), you can categorize and sort a large data set in linear time. Failure to understand these two algorithms will force you to pay O(N log N), dominating the runtime of your algorithm.
  • Vectorized data movement and subsetting routines: take, put, putmask, replace, etc.

    • Let me give you a prime example from a commit yesterday of me applying these ideas to great effect. Suppose I had a time series (or DataFrame containing time series) that I want to group by year, month, and day:

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    In [6]: rng = date_range('1/1/2000', periods=20, freq='4h')
    In [7]: ts = Series(np.random.randn(len(rng)), index=rng)
    In [8]: ts
    Out[8]:
    2000-01-01 00:00:00 -0.891761
    2000-01-01 04:00:00 0.204853
    2000-01-01 08:00:00 0.690581
    2000-01-01 12:00:00 0.454010
    2000-01-01 16:00:00 -0.123102
    2000-01-01 20:00:00 0.300111
    2000-01-02 00:00:00 -1.052215
    2000-01-02 04:00:00 0.094484
    2000-01-02 08:00:00 0.318417
    2000-01-02 12:00:00 0.779984
    2000-01-02 16:00:00 -1.514042
    2000-01-02 20:00:00 2.550011
    2000-01-03 00:00:00 0.983423
    2000-01-03 04:00:00 -0.710861
    2000-01-03 08:00:00 -1.350554
    2000-01-03 12:00:00 -0.464388
    2000-01-03 16:00:00 0.817372
    2000-01-03 20:00:00 1.057514
    2000-01-04 00:00:00 0.743033
    2000-01-04 04:00:00 0.925849
    Freq: 4H
    In [9]: by = lambda x: lambda y: getattr(y, x)
    In [10]: ts.groupby([by('year'), by('month'), by('day')]).mean()
    Out[10]:
    2000 1 1 0.105782
    2 0.196106
    3 0.055418
    4 0.834441

    This is a small dataset, but imagine you have millions of observations and thousands or even millions of groups. How does that look algorithmically? I guarantee if you take a naive approach, you will crash and burn when the data increases in size. I know, because I did just that (take a look at the vbenchmarks). Laying down the infrastructure for doing a better job is not simple. Here are the steps for efficiently aggregating data like this:

  • Factorize the group keys, computing integer label arrays (O(N) per key)
  • Compute a “cartesian product number” or group index for each observation (since you could theoretically have K_1 * … * K_p groups observed, where K_i is the number of unique values in key i). This is again O(n) work.
  • If the maximum number of groups is large, “compress” the group index by using the factorize algorithm on it again. imagine you have 1000 uniques per key and 3 keys; most likely you do not actually observe 1 billion key combinations but rather some much smaller number. O(n) work again
  • For simple aggregations, like mean, go ahead and aggregate the data in one linear sweep without moving anything around.
  • Otherwise, for arbitrary user-defined aggregations, we have two options for chopping up the data set: sorting it (O(N) using groupsort!) or create index arrays indicating which observations belong to each group. The latter would be preferable in many cases to sorting a large data set (reordering the data, even though linear time, can be very costly).

    • I worked on speeding up the latter part of this last bullet point yesterday. The resulting code looked like this:

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    def _get_indices_dict(label_list, keys):
    # Accepts factorized labels and unique key values
    shape = [len(x) for x in keys]
    group_index = get_group_index(label_list, shape) # Compute group index
    sorter, _ = lib.groupsort_indexer(com._ensure_int64(group_index),
    np.prod(shape))
    # Reorder key labels and group index
    sorted_labels = [lab.take(sorter) for lab in label_list]
    group_index = group_index.take(sorter)
    # Compute dict of {group tuple -> location NumPy array for group}
    index = np.arange(len(group_index)).take(sorter)
    return lib.indices_fast(index, group_index, keys, sorted_labels)

    The details of lib.indices_fast aren’t that interesting; it chops up np.arange(len(group_index)).take(sorter), the sorted indirect indices, to produce the index dictionary. Running %lprun to get a line profiling on a large-ish data set:

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    In [11]: rng = date_range('1/1/2000', '12/31/2005', freq='H')
    In [12]: year, month, day = rng.year, rng.month, rng.day
    In [13]: ts = Series(np.random.randn(len(rng)), index=rng)
    In [14]: lprun -f gp._get_indices_dict for i in xrange(100): ts.groupby([year, month, day]).indices
    Timer unit: 1e-06 s
    File: pandas/core/groupby.py
    Function: _get_indices_dict at line 1975
    Total time: 0.628506 s
    Line # Hits Time Per Hit % Time Line Contents
    ==============================================================
    1975 def _get_indices_dict(label_list, keys):
    1976 400 695 1.7 0.1 shape = [len(x) for x in keys]
    1977 100 114388 1143.9 18.2 group_index = get_group_index(label_list, shape)
    1978
    1979 100 320 3.2 0.1 sorter, _ = lib.groupsort_indexer(com._ensure_int64(group_index),
    1980 100 62007 620.1 9.9 np.prod(shape))
    1981
    1982 400 53530 133.8 8.5 sorted_labels = [lab.take(sorter) for lab in label_list]
    1983 100 19516 195.2 3.1 group_index = group_index.take(sorter)
    1984 100 20189 201.9 3.2 index = np.arange(len(group_index)).take(sorter)
    1985
    1986 100 357861 3578.6 56.9 return lib.indices_fast(index, group_index, keys, sorted_labels)

    You might say, well, this seems like a lot of work and maybe we should just zip the keys (forming an array of Python tuples) and do a dumb algorithm? The speed difference ends up being something like an order of magnitude or more faster by being careful in this way and working with indirect integer index arrays.

    Anyway, in conclusion, it’s these kinds of algorithms and ideas why pandas is perhaps the best-performing open-source data analysis toolkit for in memory data (I’m going to get to out-of-core data processing and “big data” eventually, just hang tight). It goes beyond language features and data structure internals (though this naturally also has a major impact, a lot of the things I do are easy to express in Python but would be very awkward or impossible to do in, say, R. Maybe I should write a whole article on this.); carefully thought-out algorithms are a major piece of the puzzle.

    pandas, python, ,
    • Bob Hancock

      Nice post, I look forwardt o the book.

      [Reply]

      Hancock Robert Reply:
      May 13th, 2012 at 9:24 pm

      The accuracy of typing on a tablet.

      [Reply]

    • Jorgen

      I really enjoy following pandas development.

      [Reply]

    • http://profiles.google.com/thouis Thouis (Ray) Jones

      Is there a mailing list to discuss development of pandas?

      [Reply]

      Wes McKinney Reply:
      June 12th, 2012 at 10:17 pm

      yes: http://pydata.googlegroups.com

      [Reply]

    • patfla

      It would be helpful if in the following code block

      In [11]: rng = date_range(’1/1/2000′, ’12/31/2005′, freq=’H')

      In [12]: year, month, day = rng.year, rng.month, rng.day

      In [13]: ts = Series(np.random.randn(len(rng)), index=rng)

      In [14]: lprun -f gp._get_indices_dict for i in xrange(100): ts.groupby([year, month, day]).indices

      Timer unit: 1e-06 s

      you would add

      from pandas.core import groupby as gp

      prior to the last statement (where gp. is referenced).

      [Reply]