Graph Algebra
Graph operations in the language of linear algebra
1

Graph representation
1 2
3
2

Graph representation
Graph on top of:
1. tables (JanusGraph as on disk storage)
2. documents (ArangoDB)
Formal graph structure:
1. adjacency list (Neo4J, JanusGraph)
2. adjacency matrix (RedisGraph)
3

Adjacency matrix
0 1 1
0 0 1
0 0 0
A[i,j] = 1 if entity i is connected to j
0 otherwise.
4

Binary matrix
• 1 bit per cell
• Matrix addition binary OR
• Matrix multiplication binary AND
5

Binary matrix
1 bit per matrix cell
1,000,000 X 1,000,000
One trillion bits = 125GB
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6

Real world graphs
Most real world graphs are sparse
Facebook’s friendship graph
2 billion users
338 friends for user on average
2,000,000,000 * 338 / 2,000,000,000^2
0.000000169% utilisation
7

Sparse matrix
• Tracks nonzeros
• Assume zero for untracked entries
8

GraphBLAS
• Standard building blocks for graph algorithms in the
language of linear algebra
• Sparse Matrix-Matrix multiply
• Sparse Vector-Matrix multiply
9

SuiteSparse:GraphBLAS
Graph algorithms via sparse linear algebra over semirings
via traditional Breadth-First-Search:
for each i in current level
for each edge (i,j)
if j is new
add j to next level ...
Find next BFS level: just one masked matrix-vector multiply
Tim Davis, Texas A&M University
via semiring:
y<mask>=A*x

SuiteSparse:GraphBLAS
• traversing nodes and edges one a time: no scope for library optimization
• linear algebra: “bulk” work can be given to a library
• let the experts write the library kernels: fast, robust, portable performance
• composable linear algebra: associative, distributive, (AB)T=BTAT, ...
Tim Davis, Texas A&M University
Why GraphBLAS?

Outline
Graph algorithms in the language of linear algebra
Consider C=A*B on a semiring
Semiring: add and multiply operators, and additive identity
Example: with OR-AND semiring: A and B are adjacency matrices of two graphs
C=A*B: contains edge (i, j) if nodes i and j share any neighbor in common
Shortest paths via MIN-PLUS semiring
Graph object is opaque; can exploit lazy evaluation
The GraphBLAS Spec: graphblas.org
SuiteSparse:GraphBLAS implementation and performance

Why graph algorithms with linear algebra?
powerful way of expressing graph algorithms with large, “bulk” operations on
adjaceny matrices. No need to chase nodes and edges.
linear algebra with semirings: composable operations, like (AB)C = A(BC)
lower software complexity: let the experts write the core graph kernels
simple object for complex problems: a sparse matrix with any data type, including
user-defined
security: encrypt/decrypt via linear algebra and binary operators
mathematically well-defined graph object, closed under operations
performance: serial, parallel, GPU, ... let the library optimize large “bulk”
graph/matrix operators

Breadth-first search example
A(i, j) = 1 for edge (j, i)
A is binary; dot (.) is zero for clarity.
. . . 1 . . .
1 . . . . . .
. . . 1 . 1 1
1 . . . . . 1
. 1 . . . . 1
. . 1 . 1 . .
. 1 . . . . .

Breadth-first search: initializations
v = zeros (n,1) ; // result
q = false (n,1) ; // current level
q (source) = true ;
v: q:
. .
. .
. .
. 1
. .
. .
. .

GrB assign (v, q, NULL, level, GrB ALL, n, NULL)
v <q> = level ; // assign level
v: q:
. .
. .
. .
1 1
. .
. .
. .

GrB mxv (q, v, NULL, GxB LOR LAND BOOL, A, q, desc)
first part of q<!v>=A*q:
t = A*q ;

GrB mxv (q, v, NULL, GxB LOR LAND BOOL, A, q, desc)
second part of q<!v>=A*q:
q = false (n,1) ;
q <!v> = t ;
v: t=A*q: q<!v>=t
. 1 1
. . .
. 1 1
1 . .
. . .
. . .
. . .

GrB assign (v, q, NULL, level, GrB ALL, n, NULL)
v <q> = level ; // assign level
v: q:
2 1
. .
2 1
1 .
. .
. .
. .

GrB mxv (q, v, NULL, GxB LOR LAND BOOL, A, q, desc)
first part of q<!v>=A*q:
t = A*q ;

GrB mxv (q, v, NULL, GxB LOR LAND BOOL, A, q, desc)
second part of q<!v>=A*q:
q = false (n,1) ;
q <!v> = t ;
v: t=A*q: q<!v>=t
2 . .
. 1 1
2 . .
1 1 .
. . .
. 1 1
. . .

GrB assign (v, q, NULL, level, GrB ALL, n, NULL)
v <q> = level ; // assign level
v: q:
2 .
3 1
2 .
1 .
. .
3 1
. .

GrB mxv (q, v, NULL, GxB LOR LAND BOOL, A, q, desc)
first part of q<!v>=A*q:
t = A*q ;

GrB mxv (q, v, NULL, GxB LOR LAND BOOL, A, q, desc)
second part of q<!v>=A*q:
q = false (n,1) ;
q <!v> = t ;
v: t=A*q: q<!v>=t
2 . .
3 . .
2 1 .
1 . .
. 1 1
3 . .
. 1 1

GrB assign (v, q, NULL, level, GrB ALL, n, NULL)
v <q> = level ; // assign level
v: q:
2 .
3 .
2 .
1 .
4 1
3 .
4 1

GrB mxv (q, v, NULL, GxB LOR LAND BOOL, A, q, desc)
first part of q<!v>=A*q:
t = A*q ;

GrB mxv (q, v, NULL, GxB LOR LAND BOOL, A, q, desc)
second part of q<!v>=A*q:
q = false (n,1) ;
q <!v> = t ;
v: t=A*q: q<!v>=t
2 . .
3 . .
2 1 .
1 1 .
4 1 .
3 1 .
4 . .

GraphBLAS operations: overview
operation MATLAB GraphBLAS
analog extras
matrix multiplication C=A*B 960 built-in semirings
element-wise, set union C=A+B any operator
element-wise, set intersection C=A.*B any operator
reduction to vector or scalar s=sum(A) any operator
apply unary operator C=-A C=f(A)
transpose C=A’
submatrix extraction C=A(I,J)
submatrix assignment C(I,J)=A zombies and pending tuples
C=A*B with 960 built-in semirings, and each matrix one of 11 types: GraphBLAS has
960 ⇥ 113 = 1, 277, 760 built-in versions of matrix multiply. MATLAB has 4. Arbitrary
user-defined types, operators, monoids, and semirings can be created at run time.

GraphBLAS objects
GrB_Type 11 built-in types, “any” user-defined type
GrB_UnaryOp unary operator such as z = x
GrB_BinaryOp binary operator such as z = x + y
GrB_Monoid associative operator like z = x + y with identity 0
GrB_Semiring a multiply operator and additive monoid
GrB_Vector like an n-by-1 matrix
GrB_Matrix a sparse m-by-n matrix
GrB_Descriptor parameter settings
all objects opaque; allows for internal optimization
matrices in compressed-sparse column (CSC) form, with sorted indices
non-blocking mode; matrix can have pending operations
all operations can take an optional mask: like a bulk if statement, ChMi = ...
and an optional accumulator operator: C = C ...

GraphBLAS operations
GrB_mxm matrix-matrix multiply ChMi = C AB
GrB_vxm vector-matrix multiply w0
hm0
i = w0
u0
A
GrB_mxv matrix-vector multiply whmi = w Au
GrB_eWiseMult element-wise, ChMi = C (A ⌦ B)
set union whmi = w (u ⌦ v)
GrB_eWiseAdd element-wise, ChMi = C (A B)
set intersection whmi = w (u v)
GrB_extract extract submatrix ChMi = C A(i, j)
whmi = w u(i)
GrB_assign assign submatrix C(i, j)hMi = C(i, j) A
w(i)hmi = w(i) u
GrB_apply apply unary operator ChMi = C f (A)
whmi = w f (u)
GrB_reduce reduce to vector whmi = w [ j A(:, j)]
reduce to scalar s = s [ ij A(i, j)]
GrB_transpose transpose ChMi = C A0

Operations: C(I,J)=A, submatrix/subgraph assignment
hardest function to implement
modifies C in place
costly to modify the matrix/graph, so operations are left pending
zombies: edges/entries still in graph/matrix but marked for deletion
pending tuples: unsorted list of edges/entries to be added to graph/matrix

Building a graph: all at once
Creating a matrix from list of tuples: fast in GraphBLAS:
for (int k = 0 ; k < nz ; k++)
{
I [k] = simple_rand_i ( ) % nrows ;
J [k] = simple_rand_i ( ) % ncols ;
X [k] = simple_rand_x ( ) ;
}
GrB_Matrix A ;
GrB_Matrix_new (&A, GrB_FP64, nrows, ncols) ;
GrB_Matrix_build (A, I, J, X, nz, GrB_SECOND_FP64) ;
Just as fast in MATLAB:
for k = 1:nz
I (k) = randi (nrows) ;
J (k) = randi (ncols) ;
X (k) = rand ( ) ;
end
A = sparse (I,J,X, nrows,ncols) ;

Building a graph: incremental
One element at a time: fast in GraphBLAS:
GrB_Matrix A ;
GrB_Matrix_new (&A, GrB_FP64, nrows, ncols) ;
for (int k = 0 ; k < nz ; k++)
{
GrB_Index i = simple_rand_i ( ) % nrows ;
GrB_Index j = simple_rand_i ( ) % ncols ;
double x = simple_rand_x ( ) ;
// A (i,j) = x
GrB_Matrix_setElement (A, x, i, j) ;
}
Impossibly slow in MATLAB:
A = sparse (nrows,ncols) ; % an empty sparse matrix
for k = 1:nz
i = randi (nrows) ;
j = randi (ncols) ;
A (i,j) = rand ( ) ;
end

GraphBLAS performance: C(I,J)=A
Submatrix assignment
Example: C is the Freescale2 matrix, 3 million by 3 million with 14.3 million
nonzeros
I = randperm (n,5500)
J = randperm (n,7000)
A = random sparse matrix with 38,500 nonzeros
C(I,J) = A
87 seconds in MATLAB
0.74 seconds in GraphBLAS, without exploiting blocking mode, via GrB_assign

Summary
GraphBLAS: graph algorithms in the language of linear algebra
“Sparse-anything” matrices, including user-defined types
matrix multiplication with any semiring
operations: C=A*B, C=A+B, reduction, transpose, accumulator/mask, submatrix
extraction and assigment
performance: most operations just as fast as MATLAB, submatrix assignment
100x or faster.
Version 2.0.1 available at suitesparse.com, Debian, Ubuntu, Mac HomeBrew, ...

RedisGraph
37

Friend of friend
MATCH (src)-[:friend]->(f)-[:friend]-(fof)
WHERE src.age > 30
RETURN fof
src f fof
friend friend
38

Execution plan
MATCH
(src)-[:friend]->(f)-[:friend]->(fof)
WHERE src.age > 30
RETURN fof
Index scan
Expand
Expand
Project
src.age > 30
(src)-[:friend]->(f)
(f)-[:friend]->(fof)
RETURN fof
39

Execution plan
Index scan
Expand
Expand
Project
Entity ID 5
40
src.age > 30
(src)-[:friend]->(f)
(f)-[:friend]->(fof)
RETURN fof

Execution plan
Index scan
Expand
Expand
Project
5 connected to 2
41
src.age > 30
(src)-[:friend]->(f)
(f)-[:friend]->(fof)
RETURN fof

Execution plan
Index scan
Expand
Expand
Project
2 connected to 9
42
src.age > 30
(src)-[:friend]->(f)
(f)-[:friend]->(fof)
RETURN fof

Execution plan
Index scan
Expand
Expand
ProjectProject 9
43
src.age > 30
(src)-[:friend]->(f)
(f)-[:friend]->(fof)
RETURN fof

Execution plan
Index scan
Expand
Expand
Project
2 connected to 1
44
src.age > 30
(src)-[:friend]->(f)
(f)-[:friend]->(fof)
RETURN fof

Execution plan
Index scan
Expand
Expand
ProjectProject 1
45
src.age > 30
(src)-[:friend]->(f)
(f)-[:friend]->(fof)
RETURN fof

Execution plan
Index scan
Expand
Expand
Project
2 depleted
46
src.age > 30
(src)-[:friend]->(f)
(f)-[:friend]->(fof)
RETURN fof

Execution plan
Index scan
Expand
Expand
Project
5 depleted
47
src.age > 30
(src)-[:friend]->(f)
(f)-[:friend]->(fof)
RETURN fof

Execution plan
Index scan
Expand
Expand
Project
Entity ID 8
48
src.age > 30
(src)-[:friend]->(f)
(f)-[:friend]->(fof)
RETURN fof

Execution plan
• Serial
• Random memory access
• Discovers one entity at a time
49

RedisGraph &
GraphBLAS
50

OpenCypher
to
linear algebra expression
51

MATCH
(src)-[:friend]->(f)-[:friend]->(fof)
WHERE src.age > 30
RETURN fof
=
Age_Filter * Friendship * Friendship
52

1
5
4
2
63
53

0 0 0 0 0 0
0 1 0 0 0 0
0 0 1 0 0 0
0 0 0 1 0 0
0 0 0 0 0 0
0 0 0 0 0 1
Age Filter
0 1 0 0 1 0
0 0 1 0 0 0
1 0 0 0 1 1
0 0 0 0 1 0
1 0 1 0 0 0
0 1 0 1 0 0
Friendships
0 1 0 0 1 0
0 0 1 0 0 0
1 0 0 0 1 1
0 0 0 0 1 0
1 0 1 0 0 0
0 1 0 1 0 0
Friendships
* *
54

Matrix multiplication
is associative
(A*B)*C = A*(B*C)
55

0 1 0 0 1 0
0 0 1 0 0 0
1 0 0 0 1 1
0 0 0 0 1 0
1 0 1 0 0 0
0 1 0 1 0 0
Friendships
0 1 0 0 1 0
0 0 1 0 0 0
1 0 0 0 1 1
0 0 0 0 1 0
1 0 1 0 0 0
0 1 0 1 0 0
Friendships
*
1 0 1 0 0 0
1 0 0 0 1 1
1 1 1 1 1 0
1 0 1 0 0 0
1 1 0 0 1 1
0 0 1 0 1 0
Friendships ^2
=
NNZ = 18
56

Age Filter
0 1 0 0 1 0
0 0 1 0 0 0
1 0 0 0 1 1
0 0 0 0 1 0
1 0 1 0 0 0
0 1 0 1 0 0
Friendships
0 0 0 0 0 0
0 0 1 0 0 0
1 0 0 0 1 1
0 0 0 0 1 0
0 0 0 0 0 0
0 1 0 1 0 0
Filtered friendships
src > 30
* =
NNZ = 7
0 0 0 0 0 0
0 1 0 0 0 0
0 0 1 0 0 0
0 0 0 1 0 0
0 0 0 0 0 0
0 0 0 0 0 1
57

0 1 0 0 1 0
0 0 1 0 0 0
1 0 0 0 1 1
0 0 0 0 1 0
1 0 1 0 0 0
0 1 0 1 0 0
Friendships
0 0 0 0 0 0
0 0 1 0 0 0
1 0 0 0 1 1
0 0 0 0 1 0
0 0 0 0 0 0
0 1 0 1 0 0
Filtered friendships
src > 30
* =
0 0 0 0 0 0
1 0 0 0 1 1
1 1 1 1 1 0
1 0 1 0 0 0
0 0 0 0 0 0
0 0 1 0 1 0
FOF
58

0 0 0 0 0 0
1 0 0 0 1 1
1 1 1 1 1 0
1 0 1 0 0 0
0 0 0 0 0 0
0 0 1 0 1 0
1
5
4
2
63
59

0 0 0 0 0 0
1 0 0 0 1 1
1 1 1 1 1 0
1 0 1 0 0 0
0 0 0 0 0 0
0 0 1 0 1 0
1
5
4
2
63
60

Friend of friend
variable length
MATCH (src)-[:friend*2..4]->(fof)
WHERE src.age > 30
RETURN fof
src F2 fof
friend
F3 F4
61

MATCH (src)-[:friend*2..4]->(fof)
WHERE src.age > 30
RETURN fof
=
Age_Filter * (Friendship^2 + Friendship^3 + Friendship^4)
=
M = AF;
R = 0;
For i=0; i < 3; i++
M = M*F
R = R+M
62

0 0 0 0 0 0
0 1 0 0 0 0
0 0 1 0 0 0
0 0 0 1 0 0
0 0 0 0 0 0
0 0 0 0 0 1
Age filter
1 1 1 0 1 1
1 1 1 1 1 1
1 1 1 1 1 1
1 1 1 0 1 1
1 1 1 1 1 1
1 0 1 0 1 1
Friendships^2 + Friendships^3
1 1 1 0 1 1
0 0 0 0 0 0
0 0 0 0 0 0
1 1 1 0 1 1
0 0 0 0 0 0
1 0 1 0 1 1
Friendships
* =
63

1
5
4
2
63
1 1 1 0 1 1
0 0 0 0 0 0
0 0 0 0 0 0
1 1 1 0 1 1
0 0 0 0 0 0
1 0 1 0 1 1
64

Additional algorithms
• Connected Components
• Shortest paths
• Minimum spanning tree
65

Graph distribution
Block multiplication
A*B=C
A B C
A1
A3 A4
A2 B1 B2
B4B3
C1 C2
C3 C4
66

Graph distribution
Block multiplication
A*B=C
A B C
A1
A3 A4
A2 B1 B2
B4B3
A1*B1+
A2*B3
A1*B2+
A2*B4
A3*B1+
A4*B3
A3*B2+
A4*B4
67

Parallelize
• CuSPARSE - GPU
• OpenMP - CPU
68

Benchmarks
69
Benchmarking graph databases on the problem of community detection paper
Reports a comprehensive comparative evaluation
between three popular graph databases, Titan, OrientDB and Neo4j.
For evaluation they’ve used real data derived from the SNAP dataset collection.
All experiments were run on an Intel Core i7 at 3.5Ghz with 16GB of main memory
and a 1.4 TB hard disk, the OS being Ubuntu Linux 12.04 (64bit).
We’ve performed the same benchmarks against RedisGraph, using inferior hardware.

Benchmarks
70
Massive Insertion Workload (MIW)
Create the graph database and configure it for massive loading.
Populate it with a particular dataset.
Measure the time for the creation of the whole graph.
All the measurements are in seconds
Dataset contains 1134890 nodes and 2987624 edges
RedisGraph
Titan
OrientDB
Neo4j
0 75 150 225 300
24.69
252.15
104.27
0.53

Benchmarks
71
Query Workload FindNeighbours (FN)
finds the neighbours of all nodes
All the measurements are in seconds
Dataset contains 1134890 nodes and 2987624 edges
RedisGraph
Titan
OrientDB
Neo4j
0 7.5 15 22.5 30
4.51
9.34
20.71
0.05

Benchmarks
72
Query Workload FindAdjacentNodes (FA)
finds the adjacent nodes of all edges.
All the measurements are in seconds
Dataset contains 1134890 nodes and 2987624 edges
RedisGraph
Titan
OrientDB
Neo4j
0 12.5 25 37.5 50
1.46
6.15
42.82
0.05

Benchmarks
73
Query Workload FindShortestPath (FS)
Finds the shortest path between the first node and 100 randomly picked nodes.
All the measurements are in seconds
Dataset contains 1134890 nodes and 2987624 edges
RedisGraph
Titan
OrientDB
Neo4j
0 7.5 15 22.5 30
0.08
23.47
24.87
0.001

Thank You
@roilipman
davis@tamu.edu
74