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README.md

pygraphblas

GraphBLAS for Python

Install

pygraphblas is distributed as a docker image on Docker Hub and can be run with a single command:

docker run -it pygraphblas/pygraphblas ipython

In [1]: from pygraphblas import Matrix

# two random 3x3 matrices with 3 random values mod(10)

In [3]: m = Matrix.from_random(int, 3, 3, 3).apply(lambda x: mod(x, 10))

In [4]: n = Matrix.from_random(int, 3, 3, 3).apply(lambda x: mod(x, 10))

In [5]: n @= m  # multiply accumulate

In [8]: n
Out[8]: <Matrix (3x3: 2)>

In [6]: n.to_lists()
Out[6]: [[0, 1], [0, 0], [0, 35]] # only two values in sparse 3x3

Next run the tests:

$ docker run -it pygraphblas/pygraphblas pytest
========================================== test session starts ==========================================
platform linux -- Python 3.7.3, pytest-5.0.1, py-1.8.0, pluggy-0.12.0
rootdir: /pygraphblas, inifile: setup.cfg
plugins: cov-2.7.1
collected 54 items

tests/test_demo.py .                                                                              [  1%]
tests/test_matrix.py ...............................                                              [ 59%]
tests/test_scalar.py ....                                                                         [ 66%]
tests/test_vector.py ..................                                                           [100%]

======================================= 54 passed in 1.04 seconds =======================================

Summary

pygraphblas is a python extension that bridges The GraphBLAS API with the Python programming language using the CFFI library to wrap the low level GraphBLAS API and provide high level Matrix and Vector Python types.

GraphBLAS is a sparse linear algebra API optimized for processing graphs encoded as sparse matrices and vectors. In addition to common real/integer matrix algebra operations, GraphBLAS supports up to 960 different Semiring algebra operations, that can be used as basic building blocks to implement a wide variety of graph algorithms. See Applications from Wikipedia for some specific examples.

pygraphblas leverages the expertise in the field of sparse matrix programming by The GraphBLAS Forum and uses the SuiteSparse:GraphBLAS API implementation. SuiteSparse:GraphBLAS is brought to us by the work of Dr. Tim Davis, professor in the Department of Computer Science and Engineering at Texas A&M University. News and information can provide you with a lot more background information, in addition to the references below.

While it is my goal to make it so that pygraphblas works with any GraphBLAS implementation, it currently only works with SuiteSparse v3.0.1. SuiteSparse provides several "extension" features pre-packaged objects that are very useful for pygraphblas. If there is a GraphBLAS implementation you would like to see support for in pygraphblas, please consider sending me a pull request.

Intro

Matrices can be used as powerful representations of graphs, as described in this mathmatical introduction to GraphBLAS by Dr. Jermey Kepner head and founder of MIT Lincoln Laboratory Supercomputing Center.

There are two useful matrix representations of graphs: Adjacency Matrices and Incidence Matrices. For this introduction we will focus on the adjacency type as they are simpler, but the same ideas apply to both, both are suported by GraphBLAS and pygraphblas, and it is easy to switch back and forth between them.

An example graph and its adjacency matrix

On the left is a graph, and on the right, the adjacency matrix that represents it. The matrix has a row and column for every node in the graph. If there is an edge going from node A to B, then there will be a value present in the intersection of As row with Bs column. How it differs from many other matrix representations is that the matrix is sparse, nothing is stored in computer memory where there are unused elements.

Sparsity is important because one practical problem with matrix-encoding graphs is that most real-world graphs tend to be sparse, as above, only 7 of 36 possible elements have a value. Those that have values tend to be scattered uniformally across the matrix (for "typical" graphs), so dense linear algebra libraries like BLAS or numpy do not encode or operate on them efficiently, as the relevant data is mostly empty memory with actual data elements spaced far apart. This wastes memory and cpu resources, and defeats CPU caching mechanisms.

For example, suppose a fictional social network has 1 billion users, and each user has about 100 friends, which means there are about 100 billion (1e+11) connections in the graph. A dense matrix large enough to hold this graph would need (1 billion)^2 or (1,000,000,000,000,000,000), a "quintillion" elements, but only 1e+11 of them would have meaningful values, leaving only 0.0000001th of the matrix being utilized.

By using a sparse matrix instead of dense, only the elements used are actually stored in memory. The parts of the matrix with no value are interpreted, but not necessarily stored, as an "identity" value, which may or may not be the actual number zero, but possibly other values like positive or negative infinity depending on the particular semiring operations applied to the matrix.

Semirings ecapsulate different algebraic operations and identities that can be used to multiply matrices and vectors. Anyone who has multiplied matrices has used at least one Semiring before, typically referred to as "plus_times". This is the common operation of multiplying two matrices containing real numbers, the coresponding row and column entries are multipled and the results are summed for the final value.

When using matrices to solve graph problems, it's useful to have a wide variety of semirings that replace the multplication and addition operators and identities with other operations and values. For example, finding a shorest path between nodes involves substituting the min() function for the add operation, and the plus function for the times. pygraphblas wraps all 960 distinct built-in semirings that come with the SuiteSparse GraphBLAS implementation.

Semirings can also work over different domains than just numbers, however pygraphblas does not support the GraphBLAS user defined types (UDT) integration yet. This is being actively worked on.

Solving Graph Problems with Semirings

Once encoded as matrices, graph problems can be solved be using matrix multiplication over a variety of semrings. For numerical problems, matrix multiplication with libraries and languages like BLAS, MATLAB and numpy is done with real numbers using the arithmetic plus and times semiring. GraphBLAS can do this as well, of course, but it also abstracts out the numerical type and operators that can be used for "matrix multiplication".

For example, let's consider three different graph problems and the semrings that can solve them. The first is finding the shortest path between nodes in a graph.

Finding the Shortest Path

In this example, the nodes can be cites, the the edge weights distances between the cities in units like kilometers. If travelling from city A to city C, how can we compute the shortest path to take? The process is fairly simple, add the weights along each path, and then use the minimum function to find the shortest distance.

In pygraphblas, the semiring that solves this problem is called pygraphblas.semiring.min_plus_int. There are two different styles for writing this with pygraphblas, one is to use with blocks to specify the operations to be used, and then use standard Python matrix multiplication syntax:

from pygraphblas import Matrix, Vector
from pygraphblas.semiring import min_plus_int64
from pygraphblas.binaryop import min_int64, Accum

def sssp(matrix, start):
    v = Vector.from_type(                  # create a vector
        matrix.gb_type,                    # same type as m
        matrix.nrows                       # same size as rows of m
    )
    v[start] = 0                           # set the starting vertext distance

    with min_plus_int64, Accum(min_int64): # set Semiring, Accumulator
        for _ in range(matrix.nrows):      # for every row in m
            w = Vector.dup(v)              # dup the vector
            v @= matrix                    # multiply accumulate
            if w == v:                     # if nothing changed
                break                      # exit early
        return v

An identical but slightly more verbose approach is to call the multiplication method directly `Vector.vxm' in this case, with explicit semiring and accumulator operations:

def sssp_direct(matrix, start):
    v = Vector.from_type(            # create a vector
        matrix.gb_type,              # same type as m
        matrix.nrows                 # same size as rows of m
    )
    v[start] = 0                     # set the starting vertext distance

    for _ in range(matrix.nrows):    # for every row in m:
        w = Vector.dup(v)            # dup the vector
        v.vxm(                       # multiply vector by matrix
            matrix, out=v,
            semiring=min_plus_int64, # with min_plus,
            accum=min_int64          # acccumulate the minimum
        )
        if w == v:                   # if nothing changed
            break                    # exit early
    return v

API

The pygraphblas package contains the following sub-modules:

  • pygrablas.matrix contains the Matrix type

  • pygrablas.vector contains the Vector type

  • pygrablas.descriptor contains descriptor types

  • pygrablas.semiring contains Semiring types

  • pygrablas.binaryop contains BinaryOp types

  • pygrablas.unaryop contains UnaryOp types

  • pygrablas.base contains low-level API and FFI wrappers.

Full API documentation coming soon, for now, check out the complete tests for usage.

TODO

  • User Defined Types

  • Push for 100% coverage.

  • A lot more documentation.

  • ReadTheDocs site.

  • User defined types.

  • Jupyter Notebook tutorial.

  • optimize construction from numpy.array and scipy.sparse

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