CS267 – Lecture 15 Automatic Performance Tuning and Sparse-Matrix-Vector-Multiplication (SpMV)...

CS267 – Lecture 15

Automatic Performance Tuningand

Sparse-Matrix-Vector-Multiplication (SpMV)

James Demmel

www.cs.berkeley.edu/~demmel/cs267_Spr14

Outline

• Motivation for Automatic Performance Tuning• Results for sparse matrix kernels• OSKI = Optimized Sparse Kernel Interface

– pOSKI for multicore

• Tuning Higher Level Algorithms• Future Work, Class Projects

• BeBOP: Berkeley Benchmarking and Optimization Group– Many results shown from current and former members– Meet weekly W 12-1:30, in 380 Soda

Motivation for Automatic Performance Tuning• Writing high performance software is hard

– Make programming easier while getting high speed

• Ideal: program in your favorite high level language (Matlab, Python, PETSc…) and get a high fraction of peak performance

• Reality: Best algorithm (and its implementation) can depend strongly on the problem, computer architecture, compiler,…– Best choice can depend on knowing a lot of applied

mathematics and computer science

• How much of this can we teach?• How much of this can we automate?

Examples of Automatic Performance Tuning (1)

• Dense BLAS– Sequential– PHiPAC (UCB), then ATLAS (UTK) (used in Matlab)– math-atlas.sourceforge.net/– Internal vendor tools

• Fast Fourier Transform (FFT) & variations– Sequential and Parallel– FFTW (MIT)– www.fftw.org

• Digital Signal Processing– SPIRAL: www.spiral.net (CMU)

• Communication Collectives (UCB, UTK)• Rose (LLNL), Bernoulli (Cornell), Telescoping Languages

(Rice), …• More projects, conferences, government reports, …


• What do dense BLAS, FFTs, signal processing, MPI reductions have in common?– Can do the tuning off-line: once per architecture,

algorithm– Can take as much time as necessary (hours, a week…)– At run-time, algorithm choice may depend only on few

parameters• Matrix dimension, size of FFT, etc.

Tuning Register Tile Sizes (Dense Matrix Multiply)

333 MHz Sun Ultra 2i

2-D slice of 3-D space; implementations color-coded by performance in Mflop/s

16 registers, but 2-by-3 tile size fastest

Needle in a haystack

Example: Select a Matmul Implementation

Example: Support Vector Classification

Machine Learning in Automatic Performance Tuning

• References– Statistical Models for Empirical Search-Based

Performance Tuning(International Journal of High Performance Computing Applications, 18 (1), pp. 65-94, February 2004)Richard Vuduc, J. Demmel, and Jeff A. Bilmes.

– Predicting and Optimizing System Utilization and Performance via Statistical Machine Learning (Computer Science PhD Thesis, University of California, Berkeley. UCB//EECS-2009-181 ) Archana Ganapathi

Machine Learning in Automatic Performance Tuning

• More references– Machine Learning for Predictive Autotuning

with Boosted Regression Trees, (Innovative Parallel Computing, 2012) J. Bergstra et al.

– Practical Bayesian Optimization of Machine Learning Algorithms,

(NIPS 2012) J. Snoek et al– OpenTuner: An Extensible Framework for

Program Autotuning, (dspace.mit.edu/handle/1721.1/81958) S.

Amarasinghe et al


• What do dense BLAS, FFTs, signal processing, MPI reductions have in common?– Can do the tuning off-line: once per architecture, algorithm– Can take as much time as necessary (hours, a week…)– At run-time, algorithm choice may depend only on few

parameters• Matrix dimension, size of FFT, etc.

• Can’t always do off-line tuning– Algorithm and implementation may strongly depend

on data only known at run-time– Ex: Sparse matrix nonzero pattern determines both

best data structure and implementation of Sparse-matrix-vector-multiplication (SpMV)

– Part of search for best algorithm just be done (very quickly!) at run-time

Source: Accelerator Cavity Design Problem (Ko via Husbands)

Linear Programming Matrix

…

A Sparse Matrix You Encounter Every Day

Matrix-vector multiply kernel: y(i) y(i) + A(i,j)*x(j)

for each row i

for k=ptr[i] to ptr[i+1]-1 do

y[i] = y[i] + val[k]*x[ind[k]]

SpMV with Compressed Sparse Row (CSR) Storage


for each row i

for k=ptr[i] to ptr[i+1]-1 do


Example: The Difficulty of Tuning

• n = 21200• nnz = 1.5 M• kernel: SpMV

• Source: NASA structural analysis problem




• 8x8 dense substructure

Taking advantage of block structure in SpMV

• Bottleneck is time to get matrix from memory– Only 2 flops for each nonzero in matrix

• Don’t store each nonzero with index, instead store each nonzero r-by-c block with index– Storage drops by up to 2x, if rc >> 1, all 32-bit

quantities– Time to fetch matrix from memory decreases

• Change both data structure and algorithm– Need to pick r and c– Need to change algorithm accordingly

• In example, is r=c=8 best choice?– Minimizes storage, so looks like a good idea…

Speedups on Itanium 2: The Need for Search

Reference

Best: 4x2

Mflop/s

Mflop/s

Register Profile: Itanium 2

190 Mflop/s

1190 Mflop/s

SpMV Performance (Matrix #2): Generation 1

Power3 - 13% Power4 - 14%

Itanium 2 - 31%Itanium 1 - 7%

195 Mflop/s

100 Mflop/s

703 Mflop/s

469 Mflop/s

225 Mflop/s

103 Mflop/s

1.1 Gflop/s

276 Mflop/s

Register Profiles: IBM and Intel IA-64



252 Mflop/s

122 Mflop/s

820 Mflop/s

459 Mflop/s

247 Mflop/s

107 Mflop/s

1.2 Gflop/s

190 Mflop/s

Register Profiles: Sun and Intel x86

Ultra 2i - 11% Ultra 3 - 5%

Pentium III-M - 15%Pentium III - 21%

72 Mflop/s

35 Mflop/s

90 Mflop/s

50 Mflop/s

108 Mflop/s

42 Mflop/s

122 Mflop/s

58 Mflop/s

Another example of tuning challenges

• More complicated non-zero structure in general

• N = 16614• NNZ = 1.1M

Zoom in to top corner


• N = 16614• NNZ = 1.1M

3x3 blocks look natural, but…


• Example: 3x3 blocking– Logical grid of 3x3 cells

• But would lead to lots of “fill-in”

Extra Work Can Improve Efficiency!


• Example: 3x3 blocking– Logical grid of 3x3 cells– Fill-in explicit zeros– Unroll 3x3 block multiplies– “Fill ratio” = 1.5

• On Pentium III: 1.5x speedup!– Actual mflop rate 1.52 =

2.25 higher

Automatic Register Block Size Selection

• Selecting the r x c block size– Off-line benchmark

• Precompute Mflops(r,c) using dense A for each r x c

• Once per machine/architecture– Run-time “search”

• Sample A to estimate Fill(r,c) for each r x c– Run-time heuristic model

• Choose r, c to minimize time ~ Fill(r,c) / Mflops(r,c)

Accurate and Efficient Adaptive Fill Estimation• Idea: Sample matrix

– Fraction of matrix to sample: s [0,1]– Cost ~ O(s * nnz)– Control cost by controlling s

• Search at run-time: the constant matters!• Control s automatically by computing statistical

confidence intervals– Idea: Monitor variance

• Cost of tuning– Lower bound: convert matrix in 5 to 40 unblocked

SpMVs– Heuristic: 1 to 11 SpMVs

Accuracy of the Tuning Heuristics (1/4)

NOTE: “Fair” flops used (ops on explicit zeros not counted as “work”)See p. 375 of Vuduc’s thesis for matrices

Accuracy of the Tuning Heuristics (2/4)DGEMV

Upper Bounds on Performance for blocked SpMV

• P = (flops) / (time)– Flops = 2 * nnz(A)

• Lower bound on time: Two main assumptions– 1. Count memory ops only (streaming)– 2. Count only compulsory, capacity misses: ignore conflicts

• Account for line sizes• Account for matrix size and nnz

• Charge minimum access “latency” i at Li cache & mem

– e.g., Saavedra-Barrera and PMaC MAPS benchmarks

1mem11

1memmem

Misses)(Misses)(Loads

HitsHitsTime

iiii

iii

Example: L2 Misses on Itanium 2

Misses measured using PAPI [Browne ’00]

Example: Bounds on Itanium 2

Summary of Other Sequential Performance Optimizations

• Optimizations for SpMV– Register blocking (RB): up to 4x over CSR– Variable block splitting: 2.1x over CSR, 1.8x over RB– Diagonals: 2x over CSR– Reordering to create dense structure + splitting: 2x over

CSR– Symmetry: 2.8x over CSR, 2.6x over RB– Cache blocking: 2.8x over CSR– Multiple vectors (SpMM): 7x over CSR– And combinations…

• Sparse triangular solve– Hybrid sparse/dense data structure: 1.8x over CSR

• Higher-level kernels– A·AT·x, AT·A·x: 4x over CSR, 1.8x over RB– A·x: 2x over CSR, 1.5x over RB– [A·x, A·x, A·x, .. , Ak·x]

Example: Sparse Triangular Factor

• Raefsky4 (structural problem) + SuperLU + colmmd

• N=19779, nnz=12.6 M

Dense trailing triangle: dim=2268, 20% of total nz

Can be as high as 90+%!1.8x over CSR

Cache Optimizations for AAT*x

• Cache-level: Interleave multiplication by A, AT

– Only fetch A from memory once

• Register-level: aiT to be rc block row, or diag

row

n

i

Tii

Tn

T

nT xaax

a

a

aaxAA1

1

1 )(

dot product“axpy”

…

Example: Combining Optimizations (1/2)

• Register blocking, symmetry, multiple (k) vectors– Three low-level tuning parameters: r, c, v

v

kX

Y A

cr

+=

*

Example: Combining Optimizations (2/2)

• Register blocking, symmetry, and multiple vectors [Ben Lee @ UCB]– Symmetric, blocked, 1 vector

• Up to 2.6x over nonsymmetric, blocked, 1 vector

– Symmetric, blocked, k vectors• Up to 2.1x over nonsymmetric, blocked, k vectors• Up to 7.3x over nonsymmetric, nonblocked, 1 vector

– Symmetric Storage: up to 64.7% savings

Why so much about SpMV?Contents of the “Sparse Motif”

• What is “sparse linear algebra”?• Direct solvers for Ax=b, least squares

– Sparse Gaussian elimination, QR for least squares– How to choose:

crd.lbl.gov/~xiaoye/SuperLU/SparseDirectSurvey.pdf

• Iterative solvers for Ax=b, least squares, Ax=λx, SVD– Used when SpMV only affordable operation on A –

• Krylov Subspace Methods

– How to choose • For Ax=b: www.netlib.org/templates/Templates.html• For Ax=λx: www.cs.ucdavis.edu/~bai/ET/contents.html

• What about Multigrid?– In overlap of sparse and (un)structured grid motifs – details later

How to choose an iterative solver - example

All methods (GMRES, CGS,CG…) depend on SpMV (or variations…)See www.netlib.org/templates/Templates.html for details

Motif/Dwarf: Common Computational Methods(Red Hot Blue Cool)

Potential Impact on Applications: Omega3P• Application: accelerator cavity design [Ko]• Relevant optimization techniques

– Symmetric storage– Register blocking– Reordering, to create more dense blocks

• Reverse Cuthill-McKee ordering to reduce bandwidth– Do Breadth-First-Search, number nodes in reverse order visited

• Traveling Salesman Problem-based ordering to create blocks

– Nodes = columns of A– Weights(u, v) = no. of nonzeros u, v have in common– Tour = ordering of columns– Choose maximum weight tour– See [Pinar & Heath ’97]

• 2.1x speedup on Power 4

Source: Accelerator Cavity Design Problem (Ko via Husbands)

Post-RCM Reordering

100x100 Submatrix Along Diagonal

Before: Green + RedAfter: Green + Blue

“Microscopic” Effect of RCM Reordering

“Microscopic” Effect of Combined RCM+TSP Reordering

Before: Green + RedAfter: Green + Blue

(Omega3P)

How do permutations affect algorithms?

• A = original matrix, AP = A with permuted rows, columns• Naïve approach: permute x, multiply y=APx, permute y• Faster way to solve Ax=b

– Write AP = PTAP where P is a permutation matrix– Solve APxP = PTb for xP, using SpMV with AP, then let x = PxP

– Only need to permute vectors twice, not twice per iteration

• Faster way to solve Ax=λx– A and AP have same eigenvalues, no vectors to permute!– APxP =λxP implies Ax = λx where x = PxP

• Where else do optimizations change higher level algorithms? More later…

55

Tuning SpMV on Multicore

56

Multicore SMPs UsedAMD Opteron 2356 (Barcelona)Intel Xeon E5345 (Clovertown)

IBM QS20 Cell BladeSun T2+ T5140 (Victoria Falls)

Source: Sam Williams

57

Multicore SMPs Used(Conventional cache-based memory hierarchy)

AMD Opteron 2356 (Barcelona)Intel Xeon E5345 (Clovertown)

Sun T2+ T5140 (Victoria Falls) IBM QS20 Cell Blade


58

Multicore SMPs Used(Local store-based memory hierarchy)




59

Multicore SMPs Used(CMT = Chip-MultiThreading)




60

Multicore SMPs Used(threads)



8 threads 8 threads

16* threads128 threads

*SPEs onlySource: Sam Williams

61

Multicore SMPs Used(Non-Uniform Memory Access - NUMA)




62

Multicore SMPs Used(peak double precision flops)



75 GFlop/s 74 Gflop/s

29* GFlop/s19 GFlop/s


63

Multicore SMPs Used(Total DRAM bandwidth)



21 GB/s (read)

10 GB/s (write)21 GB/s

51 GB/s42 GB/s (read)

21 GB/s (write)


64

Results from

“Auto-tuning Sparse Matrix-Vector Multiplication (SpMV)”

Samuel Williams, Leonid Oliker, Richard Vuduc, John Shalf, Katherine Yelick, James Demmel, "Optimization of Sparse Matrix-Vector Multiplication on Emerging Multicore Platforms", Supercomputing (SC), 2007.

65

Test matrices

• Suite of 14 matrices• All bigger than the caches of our SMPs• We’ll also include a median performance number

Dense

ProteinFEM /

SpheresFEM /

CantileverWind

TunnelFEM /Harbor

QCDFEM /Ship

Economics Epidemiology

FEM /Accelerator

Circuit webbase

LP

2K x 2K Dense matrixstored in sparse format

Well Structured(sorted by nonzeros/row)

Poorly Structuredhodgepodge

Extreme Aspect Ratio(linear programming)


SpMV Parallelization• How do we parallelize a matrix-vector multiplication ?• By rows blocks• No inter-thread data dependencies, but random access to x

69

thre

ad

0th

read

1th

read

2th

read

3


70

SpMV Performance(simple parallelization)

• Out-of-the box SpMV performance on a suite of 14 matrices

• Simplest solution = parallelization by rows

• Scalability isn’t great• Can we do better?

Naïve Pthreads

Naïve


Summary of Multicore Optimizations

• NUMA - Non-Uniform Memory Access – pin submatrices to memories close to cores assigned to

them

• Prefetch – values, indices, and/or vectors– use exhaustive search on prefetch distance

• Matrix Compression – not just register blocking (BCSR)– 32 or 16-bit indices, Block Coordinate format for

submatrices

• Cache-blocking– 2D partition of matrix, so needed parts of x,y fit in

cache71

SpMV Performance(Matrix Compression)

80

After maximizing memory bandwidth, the only hope is to minimize memory traffic.

Compression: exploit register blocking other formats smaller indices

Use a traffic minimization heuristic rather than search

Benefit is clearlymatrix-dependent.

Register blocking enables efficient software prefetching (one per cache line)


83

Auto-tuned SpMV Performance(cache and TLB blocking)

• Fully auto-tuned SpMV performance across the suite of matrices

• Why do some optimizations work better on some architectures?

• matrices with naturally small working sets

• architectures with giant caches

+Cache/LS/TLB Blocking

+Matrix Compression

+SW Prefetching

+NUMA/Affinity

Naïve Pthreads

Naïve


84

Auto-tuned SpMV Performance(architecture specific optimizations)


• Included SPE/local store optimized version



+Matrix Compression

+SW Prefetching

+NUMA/Affinity

Naïve Pthreads

Naïve


85

Auto-tuned SpMV Performance(max speedup)


• Included SPE/local store optimized version



+Matrix Compression

+SW Prefetching

+NUMA/Affinity

Naïve Pthreads

Naïve

2.7x2.7x 4.0x4.0x

2.9x2.9x 35x35x


Optimized Sparse Kernel Interface - pOSKI bebop.cs.berkeley.edu/poski• Provides sparse kernels automatically tuned for user’s

matrix & machine– BLAS-style functionality: SpMV, Ax & ATy

– Hides complexity of run-time tuning

• Based on OSKI – bebop.cs.berkeley.edu/oski– Autotuner for sequential sparse matrix operations:

• SpMV (Ax and ATx), ATAx, solve sparse triangular systems, …

– So far pOSKI only does multicore optimizations of SpMV• Class projects!

– Up to 4.5x faster SpMV (Ax) on Intel Sandy Bridge E

• On-going work by the Berkeley Benchmarking and Optimization (BeBop) group

Optimizations in pOSKI, so far

• Fully automatic heuristics for– Sparse matrix-vector multiply (Ax, ATx)

• Register-level blocking, Thread-level blocking• SIMD, software prefetching, software pipelining, loop unrolling• NUMA-aware allocations

• “Plug-in” extensibility– Very advanced users may write their own heuristics, create new

data structures/code variants and dynamically add them to the system, using embedded scripting language Lua

• Other optimizations under development– Cache-level blocking, Reordering (RCM, TSP), variable block structure,

index compressing, Symmetric storage, etc.

How the pOSKI Tunes (Overview)

1. Build forTarget Arch.

2. Benchmark

GeneratedCode

Variants

Library Install-Time (offline) Application Run-Time

Sample Dense Matrix

(r,c)(r,c) = Register Block size(d) = prefetching distance(imp) = SIMD implementation

(r,c,d,imp,…)

BenchmarkData

&Selected

Code Variants

…..

…..2. EvaluateModels

3. SelectData Struct.

& Code

2. EvaluateModels


& Code

User’s Matrix

1. Partition Workloadfrom program

monitoring

Empirical & Heuristic

Search

History

User’s hints

Submatrix thread

Submatrix threadSubmatrixSubmatrix ….

To user: Matrix handle for kernel calls

How the pOSKI Tunes (Overview)• At library build/install-time

– Generate code variants• Code generator (Python) generates code variants for various

implementations – Collect benchmark data

• Measures and records speed of possible sparse data structure and code variants on target architecture

– Select best code variants & benchmark data• prefetching distance, SIMD implementation

– Installation process uses standard, portable GNU AutoTools• At run-time

– Library “tunes” using heuristic models• Models analyze user’s matrix & benchmark data to choose optimized data

structure and code• User may re-collect benchmark data with user’s sparse matrix (under

development) – Non-trivial tuning cost: up to ~40 mat-vecs

• Library limits the time it spends tuning based on estimated workload– provided by user or inferred by library

• User may reduce cost by saving tuning results for application on future runs with same or similar matrix (under development)

How to Call pOSKI: Basic Usage• May gradually migrate existing apps

– Step 1: “Wrap” existing data structures– Step 2: Make BLAS-like kernel calls

int* ptr = …, *ind = …; double* val = …; /* Matrix, in CSR format */

double* x = …, *y = …; /* Let x and y be two dense vectors */

/* Compute y = ·y + ·A·x, 500 times */for( i = 0; i < 500; i++ )

my_matmult( ptr, ind, val, , x, , y );




double* x = …, *y = …; /* Let x and y be two dense vectors *//* Step 1: Create a default pOSKI thread object */poski_threadarg_t *poski_thread = poski_InitThread();

/* Step 2: Create pOSKI wrappers around this data */poski_mat_t A_tunable = poski_CreateMatCSR(ptr, ind, val, nrows, ncols,

nnz, SHARE_INPUTMAT, poski_thread, NULL, …);

poski_vec_t x_view = poski_CreateVecView(x, ncols, UNIT_STRIDE, NULL);

poski_vec_t y_view = poski_CreateVecView(y, nrows, UNIT_STRIDE, NULL);






double* x = …, *y = …; /* Let x and y be two dense vectors *//* Step 1: Create a default pOSKI thread object */poski_threadarg_t *poski_thread = poski_InitThread();

/* Step 2: Create pOSKI wrappers around this data */poski_mat_t A_tunable = poski_CreateMatCSR(ptr, ind, val, nrows, ncols,

nnz, SHARE_INPUTMAT, poski_thread, NULL, …);

poski_vec_t x_view = poski_CreateVecView(x, ncols, UNIT_STRIDE, NULL);

poski_vec_t y_view = poski_CreateVecView(y, nrows, UNIT_STRIDE, NULL);

/* Step 3: Compute y = ·y + ·A·x, 500 times */for( i = 0; i < 500; i++ )

poski_MatMult(A_tunable, OP_NORMAL, , x_view, , y_view);

How to Call pOSKI: Tune with Explicit Hints

• User calls “tune” routine (optional)– May provide explicit tuning hints

poski_mat_t A_tunable = poski_CreateMatCSR( … );

/* … */

/* Tell pOSKI we will call SpMV 500 times (workload hint) */poski_TuneHint_MatMult(A_tunable, OP_NORMAL, , x_view, , y_view,500);/* Tell pOSKI we think the matrix has 8x8 blocks (structural hint) */poski_TuneHint_Structure(A_tunable, HINT_SINGLE_BLOCKSIZE, 8, 8);

/* Ask pOSKI to tune */poski_TuneMat(A_tunable);

for( i = 0; i < 500; i++ )

poski_MatMult(A_tunable, OP_NORMAL, , x_view, , y_view);

How to Call pOSKI: Implicit Tuning• Ask library to infer workload (optional)

– Library profiles all kernel calls– May periodically re-tune

poski_mat_t A_tunable = poski_CreateMatCSR( … );

/* … */

for( i = 0; i < 500; i++ ) {

poski_MatMult(A_tunable, OP_NORMAL, , x_view, , y_view);poski_TuneMat(A_tunable); /* Ask pOSKI to tune */

}

Performance on Intel Sandy Bridge E

4.8x

3.2x

4.5x

2.9x

4.1x4.5x

4.7x

• Jaketown: i7-3960X @ 3.3 GHz• #Cores: 6 (2 threads per core), L3:15MB• pOSKI SpMV (Ax) with double precision float-point• MKL Sparse BLAS Level 2: mkl_dcsrmv()

Is tuning SpMV all we can do?

• Iterative methods all depend on it• But speedups are limited

– Just 2 flops per nonzero– Communication costs dominate

• Can we beat this bottleneck?• Need to look at next level in stack:

– What do algorithms that use SpMV do?– Can we reorganize them to avoid communication?

• Only way significant speedups will be possible

Tuning Higher Level Algorithms than SpMV• We almost always do many SpMVs, not just one

– “Krylov Subspace Methods” (KSMs) for Ax=b, Ax = λx• Conjugate Gradients, GMRES, Lanczos, …

– Do a sequence of k SpMVs to get vectors [x1 , … , xk]

– Find best solution x as linear combination of [x1 , … , xk]

• Main cost is k SpMVs• Since communication usually dominates, can we do better?• Goal: make communication cost independent of k

– Parallel case: O(log P) messages, not O(k log P) - optimal• same bandwidth as before

– Sequential case: O(1) messages and bandwidth, not O(k) - optimal

• Achievable when matrix partitionable with low surface-to-volume ratio

1 2 3 4 … … 32

x

A·x

A2·x

A3·x

Communication Avoiding Kernels:The Matrix Powers Kernel : [Ax, A2x, …, Akx]

• Replace k iterations of y = Ax with [Ax, A2x, …, Akx]

• Example: A tridiagonal, n=32, k=3• Works for any “well-partitioned” A

1 2 3 4 … … 32

x

A·x

A2·x

A3·x



• Example: A tridiagonal, n=32, k=3

1 2 3 4 … … 32

x

A·x

A2·x

A3·x



• Sequential Algorithm


Step 1

1 2 3 4 … … 32

x

A·x

A2·x

A3·x





Step 1 Step 2

1 2 3 4 … … 32

x

A·x

A2·x

A3·x





Step 1 Step 2 Step 3

1 2 3 4 … … 32

x

A·x

A2·x

A3·x





Step 1 Step 2 Step 3 Step 4

1 2 3 4 … … 32

x

A·x

A2·x

A3·x



• Parallel Algorithm


Proc 1 Proc 2 Proc 3 Proc 4

1 2 3 4 … … 32

x

A·x

A2·x

A3·x




• Example: A tridiagonal, n=32, k=3• Each processor communicates once with

neighbors


1 2 3 4 … … 32

x

A·x

A2·x

A3·x





Proc 1

1 2 3 4 … … 32

x

A·x

A2·x

A3·x





Proc 2

1 2 3 4 … … 32

x

A·x

A2·x

A3·x





Proc 3

1 2 3 4 … … 32

x

A·x

A2·x

A3·x





Proc 4

1 2 3 4 … … 32

x

A·x

A2·x

A3·x




• Example: A tridiagonal, n=32, k=3• Each processor works on (overlapping)

trapezoid


Same idea works for general sparse matrices


Simple block-row partitioning (hyper)graph partitioning

Top-to-bottom processing Traveling Salesman Problem

Speedups on Intel Clovertown (8 core)

Performance Results• Measured Multicore (Clovertown) speedups up to 6.4x• Measured/Modeled sequential OOC speedup up to 3x• Modeled parallel Petascale speedup up to 6.9x• Modeled parallel Grid speedup up to 22x

• Sequential speedup due to bandwidth, works for many problem sizes

• Parallel speedup due to latency, works for smaller problems on many processors

• Multicore results used both techniques

Avoiding Communication in Iterative Linear Algebra

• k-steps of typical iterative solver for sparse Ax=b or Ax=λx– Does k SpMVs with starting vector– Finds “best” solution among all linear combinations of these k+1

vectors– Many such “Krylov Subspace Methods”

• Conjugate Gradients, GMRES, Lanczos, Arnoldi, … • Goal: minimize communication in Krylov Subspace Methods

– Assume matrix “well-partitioned,” with modest surface-to-volume ratio

– Parallel implementation• Conventional: O(k log p) messages, because k calls to SpMV• New: O(log p) messages - optimal

– Serial implementation• Conventional: O(k) moves of data from slow to fast memory• New: O(1) moves of data – optimal

• Lots of speed up possible (modeled and measured)– Price: some redundant computation

• Much prior work– See Mark Hoemmen’s PhD thesis, other papers at

bebop.cs.berkeley.edu

Minimizing Communication of GMRES to solve Ax=b• GMRES: find x in span{b,Ab,…,Akb} minimizing || Ax-b ||2

• Cost of k steps of standard GMRES vs new GMRES

Standard GMRES for i=1 to k w = A · v(i-1) MGS(w, v(0),…,v(i-1)) update v(i), H endfor solve LSQ problem with H

Sequential: #words_moved = O(k·nnz) from SpMV + O(k2·n) from MGSParallel: #messages = O(k) from SpMV + O(k2 · log p) from MGS

Communication-avoiding GMRES W = [ v, Av, A2v, … , Akv ] [Q,R] = TSQR(W) … “Tall Skinny QR” Build H from R, solve LSQ problem

Sequential: #words_moved = O(nnz) from SpMV + O(k·n) from TSQRParallel: #messages = O(1) from computing W + O(log p) from TSQR

•Oops – W from power method, precision lost!

“Monomial” basis [Ax,…,Akx] fails to converge

A different polynomial basis does converge: [p1(A)x,…,pk(A)x]

Speed ups of GMRES on 8-core Intel Clovertown

Requires co-tuning kernels [MHDY09]

CA-BiCGStab

“New Algorithm Improves Performance and Accuracy on Extreme-Scale Computing Systems. On modern computer architectures, communication between processors takes longer than the performance of a floating point arithmetic operation by a given processor. ASCR researchers have developed a new method, derived from commonly used linear algebra methods, to minimize communications between processors and the memory hierarchy, by reformulating the communication patterns specified within the algorithm. This method has been implemented in the TRILINOS framework, a highly-regarded suite of software, which provides functionality for researchers around the world to solve large scale, complex multi-physics problems.”

FY 2010 Congressional Budget, Volume 4, FY2010 Accomplishments, Advanced Scientific Computing Research (ASCR), pages 65-67.

President Obama cites Communication-Avoiding Algorithms in the FY 2012 Department of Energy Budget

Request to Congress:

CA-GMRES (Hoemmen, Mohiyuddin, Yelick, JD)“Tall-Skinny” QR (Grigori, Hoemmen, Langou, JD)

Tuning space for Krylov Methods

Explicit (O(nnz)) Implicit (o(nnz))

Explicit (O(nnz))

CSR and variations

Vision, climate, AMR,…

Implicit (o(nnz))

Graph Laplacian Stencils

Nonzero entries

Indices

•Many different algorithms (GMRES, BiCGStab, CG, Lanczos,…), polynomials, preconditioning •Classifications of sparse operators for avoiding communication

• Explicit indices or nonzero entries cause most communication, along with vectors• Ex: With stencils (all implicit) all communication for vectors

• Operations• [x, Ax, A2x,…, Akx ] or [x, p1(A)x, p2(A)x, …, pk(A)x ]• Number of columns in x• [x, Ax, A2x,…, Akx ] and [y, ATy, (AT)2y,…, (AT)ky ], or [y, ATAy, (ATA)2y,…, (ATA)ky ], • return all vectors or just last one

• Cotuning and/or interleaving• W = [x, Ax, A2x,…, Akx ] and {TSQR(W) or WTW or … }• Ditto, but throw away W

Possible Class Projects• Come to BEBOP meetings (W 12 – 1:30, 380

Soda)• Experiment with SpMV on different

architectures– Which optimizations are most effective?

• Try to speed up particular matrices of interest– Data mining, “bottom solver” from AMR

• Explore tuning space of [x,Ax,…,Akx] kernel– Different matrix representations (last slide)– New Krylov subspace methods, preconditioning

• Experiment with new frameworks (SPF, Halide) • More details available

Extra Slides

Extensions

• Other Krylov methods– Arnoldi, CG, Lanczos, …

• Preconditioning– Solve MAx=Mb where preconditioning matrix M chosen to

make system “easier” • M approximates A-1 somehow, but cheaply, to accelerate

convergence

– Cheap as long as contributions from “distant” parts of the system can be compressed

• Sparsity• Low rank

– No implementations yet (class projects!)

Design Space for [x,Ax,…,Akx] (1/3)

• Mathematical Operation– How many vectors to keep

• All: Krylov Subspace Methods • Keep last vector Akx only (Jacobi, Gauss Seidel)

– Improving conditioning of basis• W = [x, p1(A)x, p2(A)x,…,pk(A)x]

• pi(A) = degree i polynomial chosen to reduce cond(W)

– Preconditioning (Ay=b MAy=Mb)• [x,Ax,MAx,AMAx,MAMAx,…,(MA)kx]


• Representation of sparse A– Zero pattern may be explicit or implicit– Nonzero entries may be explicit or implicit

• Implicit save memory, communication

Explicit pattern Implicit pattern

Explicit nonzeros General sparse matrix

Image segmentation

Implicit nonzeros Laplacian(graph)Multigrid (AMR)

“Stencil matrix”Ex: tridiag(-1,2,-1)

• Representation of dense preconditioners M

– Low rank off-diagonal blocks (semiseparable)


• Parallel implementation– From simple indexing, with redundant flops

surface/volume ratio– To complicated indexing, with fewer redundant flops

• Sequential implementation– Depends on whether vectors fit in fast memory

• Reordering rows, columns of A– Important in parallel and sequential cases– Can be reduced to pair of Traveling Salesmen Problems

• Plus all the optimizations for one SpMV!

Summary • Communication-Avoiding Linear Algebra (CALA)• Lots of related work

– Some going back to 1960’s– Reports discuss this comprehensively, not here

• Our contributions– Several new algorithms, improvements on old ones

• Preconditioning

– Unifying parallel and sequential approaches to avoiding communication

– Time for these algorithms has come, because of growing communication costs

– Why avoid communication just for linear algebra motifs?

Optimized Sparse Kernel Interface - OSKI

• Provides sparse kernels automatically tuned for user’s matrix & machine– BLAS-style functionality: SpMV, Ax & ATy, TrSV– Hides complexity of run-time tuning– Includes new, faster locality-aware kernels: ATAx, Akx

• Faster than standard implementations– Up to 4x faster matvec, 1.8x trisolve, 4x ATA*x

• For “advanced” users & solver library writers– Available as stand-alone library (OSKI 1.0.1h, 6/07)– Available as PETSc extension (OSKI-PETSc .1d, 3/06)– Bebop.cs.berkeley.edu/oski

• Under development: pOSKI for multicore

How the OSKI Tunes (Overview)

Benchmarkdata

1. Build forTargetArch.

2. Benchmark

Heuristicmodels

1. EvaluateModels

Generatedcode

variants


& Code

Library Install-Time (offline) Application Run-Time

To user:Matrix handlefor kernelcalls

Workloadfrom program

monitoring

Extensibility: Advanced users may write & dynamically add “Code variants” and “Heuristic models” to system.

HistoryMatrix

How the OSKI Tunes (Overview)• At library build/install-time

– Pre-generate and compile code variants into dynamic libraries

– Collect benchmark data• Measures and records speed of possible sparse data structure

and code variants on target architecture– Installation process uses standard, portable GNU AutoTools

• At run-time– Library “tunes” using heuristic models

• Models analyze user’s matrix & benchmark data to choose optimized data structure and code

– Non-trivial tuning cost: up to ~40 mat-vecs• Library limits the time it spends tuning based on estimated

workload– provided by user or inferred by library

• User may reduce cost by saving tuning results for application on future runs with same or similar matrix

Optimizations in OSKI, so far• Fully automatic heuristics for

– Sparse matrix-vector multiply• Register-level blocking• Register-level blocking + symmetry + multiple vectors• Cache-level blocking

– Sparse triangular solve with register-level blocking and “switch-to-dense” optimization

– Sparse ATA*x with register-level blocking• User may select other optimizations manually

– Diagonal storage optimizations, reordering, splitting; tiled matrix powers kernel (Ak*x)

– All available in dynamic libraries– Accessible via high-level embedded script language

• “Plug-in” extensibility– Very advanced users may write their own heuristics, create new

data structures/code variants and dynamically add them to the system

• pOSKI under construction– Optimizations for multicore – more later

How to Call OSKI: Basic Usage

• May gradually migrate existing apps– Step 1: “Wrap” existing data structures– Step 2: Make BLAS-like kernel calls


double* x = …, *y = …; /* Let x and y be two dense vectors */






double* x = …, *y = …; /* Let x and y be two dense vectors *//* Step 1: Create OSKI wrappers around this data */oski_matrix_t A_tunable = oski_CreateMatCSR(ptr, ind, val, num_rows,

num_cols, SHARE_INPUTMAT, …);

oski_vecview_t x_view = oski_CreateVecView(x, num_cols, UNIT_STRIDE);

oski_vecview_t y_view = oski_CreateVecView(y, num_rows, UNIT_STRIDE);






double* x = …, *y = …; /* Let x and y be two dense vectors *//* Step 1: Create OSKI wrappers around this data */oski_matrix_t A_tunable = oski_CreateMatCSR(ptr, ind, val, num_rows,

num_cols, SHARE_INPUTMAT, …);

oski_vecview_t x_view = oski_CreateVecView(x, num_cols, UNIT_STRIDE);

oski_vecview_t y_view = oski_CreateVecView(y, num_rows, UNIT_STRIDE);


oski_MatMult(A_tunable, OP_NORMAL, , x_view, , y_view);/* Step 2 */

How to Call OSKI: Tune with Explicit Hints

• User calls “tune” routine– May provide explicit tuning hints (OPTIONAL)

oski_matrix_t A_tunable = oski_CreateMatCSR( … );

/* … */

/* Tell OSKI we will call SpMV 500 times (workload hint) */oski_SetHintMatMult(A_tunable, OP_NORMAL, , x_view, , y_view, 500);/* Tell OSKI we think the matrix has 8x8 blocks (structural hint) */oski_SetHint(A_tunable, HINT_SINGLE_BLOCKSIZE, 8, 8);

oski_TuneMat(A_tunable); /* Ask OSKI to tune */

for( i = 0; i < 500; i++ )

oski_MatMult(A_tunable, OP_NORMAL, , x_view, , y_view);

How the User Calls OSKI: Implicit Tuning

• Ask library to infer workload– Library profiles all kernel calls– May periodically re-tune

oski_matrix_t A_tunable = oski_CreateMatCSR( … );

/* … */

for( i = 0; i < 500; i++ ) {

oski_MatMult(A_tunable, OP_NORMAL, , x_view, , y_view);oski_TuneMat(A_tunable); /* Ask OSKI to tune */

}

Quick-and-dirty Parallelism: OSKI-PETSc

• Extend PETSc’s distributed memory SpMV (MATMPIAIJ)

p0

p1

p2

p3

• PETSc– Each process stores

diag (all-local) and off-diag submatrices

• OSKI-PETSc:– Add OSKI wrappers– Each submatrix

tuned independently

OSKI-PETSc Proof-of-Concept Results

• Matrix 1: Accelerator cavity design (R. Lee @ SLAC)– N ~ 1 M, ~40 M non-zeros– 2x2 dense block substructure– Symmetric

• Matrix 2: Linear programming (Italian Railways)– Short-and-fat: 4k x 1M, ~11M non-zeros– Highly unstructured– Big speedup from cache-blocking: no native PETSc

format

• Evaluation machine: Xeon cluster– Peak: 4.8 Gflop/s per node

Accelerator Cavity Matrix

OSKI-PETSc Performance: Accel. Cavity

Linear Programming Matrix

…

OSKI-PETSc Performance: LP Matrix

Tuning SpMV for Multicore: Architectural Review

Cost of memory access in Multicore

• When physically partitioned, cache or memory access is non uniform (latency and bandwidth to memory/cache addresses varies)– NUMA = Non-Uniform Memory Access– NUCA = Non-Uniform Cache Access

• UCA & UMA architecture:

156

CoreCore

DRAMDRAM

CacheCache

CoreCore CoreCore CoreCore


Cost of memory access in Multicore


• UCA & UMA architecture:

157

CoreCore

DRAMDRAM

CacheCache



Cost of Memory Access in Multicore


• NUCA & UMA architecture:

158

CoreCore

CacheCache


CacheCache CacheCache CacheCache

Memory Controller HubMemory Controller Hub

DRAMDRAM Source: Sam Williams



• NUCA & NUMA architecture:

159

CoreCore

CacheCache



DRAMDRAM DRAMDRAM



• Proper cache locality to maximize performance

160

CoreCore

CacheCache



DRAMDRAM DRAMDRAM



• Proper DRAM locality to maximize performance

161

CoreCore

CacheCache



DRAMDRAM DRAMDRAM


Optimizing Communication Complexity of Sparse Solvers

• Need to modify high level algorithms to use new kernel

• Example: GMRES for Ax=b where A= 2D Laplacian– x lives on n-by-n mesh– Partitioned on p½ -by- p½ processor grid– A has “5 point stencil” (Laplacian)

• (Ax)(i,j) = linear_combination(x(i,j), x(i,j±1), x(i±1,j))– Ex: 18-by-18 mesh on 3-by-3 processor grid

Minimizing Communication• What is the cost = (#flops, #words, #mess) of s

steps of standard GMRES?

GMRES, ver.1: for i=1 to s w = A * v(i-1) MGS(w, v(0),…,v(i-1)) update v(i), H endfor solve LSQ problem with H

n/p½

n/p½

• Cost(A * v) = s * (9n2 /p, 4n / p½ , 4 )• Cost(MGS = Modified Gram-Schmidt) = s2/2 * ( 4n2 /p , log p , log p )• Total cost ~ Cost( A * v ) + Cost (MGS)• Can we reduce the latency?

Minimizing Communication• Cost(GMRES, ver.1) = Cost(A*v) + Cost(MGS)

• Cost(W) = ( ~ same, ~ same , 8 )• Latency cost independent of s – optimal

• Cost (MGS) unchanged• Can we reduce the latency more?

= ( 9sn2 /p, 4sn / p½ , 4s ) + ( 2s2n2 /p , s2 log p / 2 , s2 log p / 2 )

• How much latency cost from A*v can you avoid? Almost all

GMRES, ver. 2: W = [ v, Av, A2v, … , Asv ] [Q,R] = MGS(W) Build H from R, solve LSQ problem

s = 3

Minimizing Communication• Cost(GMRES, ver. 2) = Cost(W) + Cost(MGS)

= = ( 9sn2 /p, 4sn / p½ , 8 ) + ( 2s2n2 /p , s2 log p / 2 , s2 log p / 2 )

• How much latency cost from MGS can you avoid? Almost all

• Cost(TSQR) = ( ~ same, ~ same , log p )• Latency cost independent of s - optimal

GMRES, ver. 3: W = [ v, Av, A2v, … , Asv ] [Q,R] = TSQR(W) … “Tall Skinny QR” (See Lecture 11) Build H from R, solve LSQ problem

W = W1

W2

W3

W4

R1

R2

R3

R4

R12

R34

R1234


= ( 9sn2 /p, 4sn / p½ , 8 ) + ( 2s2n2 /p , s2 log p / 2 , s2 log p / 2 )


• Cost(TSQR) = ( ~ same, ~ same , log p )• Oops


W =

W1

W2

W3

W4

R1

R2

R3

R4

R12

R34

R1234


= ( 9sn2 /p, 4sn / p½ , 8 ) + ( 2s2n2 /p , s2 log p / 2 , s2 log p / 2 )


• Cost(TSQR) = ( ~ same, ~ same , log p )• Oops – W from power method, precision lost!


W =

W1

W2

W3

W4

R1

R2

R3

R4

R12

R34

R1234

Minimizing Communication• Cost(GMRES, ver. 3) = Cost(W) + Cost(TSQR)

= = ( 9sn2 /p, 4sn / p½ , 8 ) + ( 2s2n2 /p , s2 log p / 2 , log p )

• Latency cost independent of s, just log p – optimal• Oops – W from power method, so precision lost – What to do?

• Use a different polynomial basis• Not Monomial basis W = [v, Av, A2v, …], instead …• Newton Basis WN = [v, (A – θ1 I)v , (A – θ2 I)(A – θ1 I)v, …] or

• Chebyshev Basis WC = [v, T1(v), T2(v), …]

Tuning Higher Level Algorithms

• So far we have tuned a single sparse matrix kernel• y = AT*A*x motivated by higher level algorithm (SVD)

• What can we do by extending tuning to a higher level?• Consider Krylov subspace methods for Ax=b, Ax = x

• Conjugate Gradients (CG), GMRES, Lanczos, …• Inner loop does y=A*x, dot products, saxpys, scalar ops• Inner loop costs at least O(1) messages• k iterations cost at least O(k) messages

• Our goal: show how to do k iterations with O(1) messages• Possible payoff – make Krylov subspace methods much faster on machines with slow networks• Memory bandwidth improvements too (not discussed)• Obstacles: numerical stability, preconditioning, …

Krylov Subspace Methods for Solving Ax=b

• Compute a basis for a subspace V by doing y = A*x k times

• Find “best” solution in that Krylov subspace V

• Given starting vector x1, V spanned by x2 = A*x1, x3 = A*x2 , … , xk = A*xk-1

• GMRES finds an orthogonal basis of V by Gram-Schmidt, so it actually does a different set of SpMVs than in last bullet

Example: Standard GMRES

r = b - A*x1, = length(r), v1 = r / … length(r) = sqrt( ri2 )

for m= 1 to k do w = A*vm … at least O(1) messages

for i = 1 to m do … Gram-Schmidt him = dotproduct(vi , w ) … at least O(1) messages, or log(p)

w = w – h im * vi

end for hm+1,m = length(w) … at least O(1) messages, or log(p)

vm+1 = w / hm+1,m

end forfind y minimizing length( Hk * y – e1 ) … small, local problem

new x = x1 + Vk * y … Vk = [v1 , v2 , … , vk ]

O(k2), or O(k2 log p), messages altogether

Example: Computing [Ax,A2x,A3x,…,Akx] for A tridiagonal

Different basis for same Krylov subspaceWhat can Proc 1 compute without communication?

x(1:30):

(Ax)(1:30):(A2x)(1:30):

(A8x)(1:30):

Proc 1 Proc 2

. .

.


x(1:30):

(Ax)(1:30):(A2x)(1:30):

. .

.

(A8x)(1:30):

Proc 1 Proc 2

Computing missing entries with 1 communication, redundant work

x(1:30):

(Ax)(1:30):(A2x)(1:30):

. .

.

(A8x)(1:30):

Proc 1 Proc 2

Saving half the redundant work


Example: Computing [Ax,A2x,A3x,…,Akx] for Laplacian

A = 5pt Laplacian in 2D,Communicated point for k=3 shown

Latency-Avoiding GMRES (1)

r = b - A*x1, = length(r), v1 = r / …O(log p) messages

Wk+1 = [v1 , A * v1 , A2 * v1 , … , Ak * v1 ] … O(1) messages

[Q, R] = qr(Wk+1) … QR decomposition, O(log p) messages

Hk = R(:, 2:k+1) * (R(1:k,1:k))-1 … small, local problem

find y minimizing length( Hk * y – e1 ) … small, local problem

new x = x1 + Qk * y … local problemO(log p) messages altogether

Independent of k

Latency-Avoiding GMRES (2)

[Q, R] = qr(Wk+1) … QR decomposition, O(log p) messages

Easy, but not so stable way to do it:

X(myproc) = Wk+1T(myproc) * Wk+1 (myproc)

… local computation Y = sum_reduction(X(myproc)) … O(log p) messages

… Y = Wk+1T* Wk+1

R = (cholesky(Y))T … small, local computation

Q(myproc) = Wk+1 (myproc) * R-1 … local computation

Numerical example (1)

Diagonal matrix with n=1000, Aii from 1 down to 10-5

Instability as k grows, after many iterations

Numerical Example (2)Partial remedy: restarting periodically (every 120 iterations)

Other remedies: high precision, different basis than [v , A * v , … , Ak * v ]

Operation Counts for [Ax,A2x,A3x,…,Akx] on p procs

Problem Per-proc cost

Standard Optimized

1D mesh #messages

2k 2

(tridiagonal)

#words sent

2k 2k

#flops 5kn/p 5kn/p + 5k2

memory (k+4)n/p (k+4)n/p + 8k3D mesh #messages 26k 26

27 pt stencil

#words sent

6kn2p-2/3 + 12knp-1/3

+ O(k)6kn2p-2/3 + 12k2np-1/3

+ O(k3)

#flops 53kn3/p 53kn3/p + O(k2n2p-2/3)

memory (k+28)n3/p+ 6n2p-2/3 + O(np-1/3)

(k+28)n3/p + 168kn2p-2/3 + O(k2np-1/3)

Summary and Future Work

• Dense– LAPACK– ScaLAPACK

• Communication primitives• Sparse

– Kernels, Stencils– Higher level algorithms

• All of the above on new architectures– Vector, SMPs, multicore, Cell, …

• High level support for tuning– Specification language– Integration into compilers

Extra Slides


Who am I?

I am aBig Repository

Of usefulAnd uselessFacts alike.

Who am I?

(Hint: Not your e-mail inbox.)

What about the Google Matrix?

• Google approach– Approx. once a month: rank all pages using connectivity

structure• Find dominant eigenvector of a matrix

– At query-time: return list of pages ordered by rank• Matrix: A = G + (1-)(1/n)uuT

– Markov model: Surfer follows link with probability , jumps to a random page with probability 1-

– G is n x n connectivity matrix [n billions]• gij is non-zero if page i links to page j• Normalized so each column sums to 1• Very sparse: about 7—8 non-zeros per row (power law dist.)

– u is a vector of all 1 values– Steady-state probability xi of landing on page i is solution to x

= Ax

• Approximate x by power method: x = Akx0

– In practice, k 25

Current Work

• Public software release• Impact on library designs: Sparse BLAS, Trilinos, PETSc,

…• Integration in large-scale applications

– DOE: Accelerator design; plasma physics– Geophysical simulation based on Block Lanczos (ATA*X; LBL)

• Systematic heuristics for data structure selection?• Evaluation of emerging architectures

– Revisiting vector micros

• Other sparse kernels– Matrix triple products, Ak*x

• Parallelism• Sparse benchmarks (with UTK) [Gahvari & Hoemmen]• Automatic tuning of MPI collective ops [Nishtala, et al.]

Summary of High-Level Themes

• “Kernel-centric” optimization– Vs. basic block, trace, path optimization, for instance– Aggressive use of domain-specific knowledge

• Performance bounds modeling– Evaluating software quality– Architectural characterizations and consequences

• Empirical search– Hybrid on-line/run-time models

• Statistical performance models– Exploit information from sampling, measuring

Related Work

• My bibliography: 337 entries so far• Sample area 1: Code generation

– Generative & generic programming– Sparse compilers– Domain-specific generators

• Sample area 2: Empirical search-based tuning– Kernel-centric

• linear algebra, signal processing, sorting, MPI, …

– Compiler-centric• profiling + FDO, iterative compilation, superoptimizers,

self-tuning compilers, continuous program optimization

Future Directions (A Bag of Flaky Ideas)

• Composable code generators and search spaces• New application domains

– PageRank: multilevel block algorithms for topic-sensitive search?

• New kernels: cryptokernels– rich mathematical structure germane to performance; lots

of hardware

• New tuning environments– Parallel, Grid, “whole systems”

• Statistical models of application performance– Statistical learning of concise parametric models from

traces for architectural evaluation– Compiler/automatic derivation of parametric models

Possible Future Work

• Different Architectures– New FP instruction sets (SSE2)– SMP / multicore platforms– Vector architectures

• Different Kernels• Higher Level Algorithms

– Parallel versions of kenels, with optimized communication– Block algorithms (eg Lanczos)– XBLAS (extra precision)

• Produce Benchmarks– Augment HPCC Benchmark

• Make it possible to combine optimizations easily for any kernel

• Related tuning activities (LAPACK & ScaLAPACK)

Review of Tuning by Illustration

(Extra Slides)

Splitting for Variable Blocks and Diagonals

• Decompose A = A1 + A2 + … At

– Detect “canonical” structures (sampling)– Split

– Tune each Ai

– Improve performance and save storage

• New data structures– Unaligned block CSR

• Relax alignment in rows & columns

– Row-segmented diagonals

Example: Variable Block Row (Matrix #12)

2.1x over CSR1.8x over RB

Example: Row-Segmented Diagonals

2x over CSR

Mixed Diagonal and Block Structure

Summary

• Automated block size selection– Empirical modeling and search– Register blocking for SpMV, triangular solve, ATA*x

• Not fully automated– Given a matrix, select splittings and transformations

• Lots of combinatorial problems– TSP reordering to create dense blocks (Pinar ’97;

Moon, et al. ’04)

Extra Slides


Who am I?

I am aBig Repository

Of usefulAnd uselessFacts alike.

Who am I?

(Hint: Not your e-mail inbox.)

Problem Context

• Sparse kernels abound– Models of buildings, cars, bridges, economies, …– Google PageRank algorithm

• Historical trends– Sparse matrix-vector multiply (SpMV): 10% of peak– 2x faster with “hand-tuning”– Tuning becoming more difficult over time– Promise of automatic tuning: PHiPAC/ATLAS, FFTW, …

• Challenges to high-performance– Not dense linear algebra!

• Complex data structures: indirect, irregular memory access

• Performance depends strongly on run-time inputs

Key Questions, Ideas, Conclusions

• How to tune basic sparse kernels automatically?– Empirical modeling and search

• Up to 4x speedups for SpMV• 1.8x for triangular solve• 4x for ATA*x; 2x for A2*x• 7x for multiple vectors

• What are the fundamental limits on performance?– Kernel-, machine-, and matrix-specific upper bounds

• Achieve 75% or more for SpMV, limiting low-level tuning• Consequences for architecture?

• General techniques for empirical search-based tuning?– Statistical models of performance

Road Map

• Sparse matrix-vector multiply (SpMV) in a nutshell• Historical trends and the need for search• Automatic tuning techniques• Upper bounds on performance• Statistical models of performance

Matrix-vector multiply kernel: y(i) y(i) + A(i,j)*x(j)Matrix-vector multiply kernel: y(i) y(i) + A(i,j)*x(j)

for each row i

for k=ptr[i] to ptr[i+1] do


Compressed Sparse Row (CSR) Storage


for each row i

for k=ptr[i] to ptr[i+1] do


Road Map

• Sparse matrix-vector multiply (SpMV) in a nutshell• Historical trends and the need for search• Automatic tuning techniques• Upper bounds on performance• Statistical models of performance

Historical Trends in SpMV Performance

• The Data– Uniprocessor SpMV performance since 1987– “Untuned” and “Tuned” implementations– Cache-based superscalar micros; some vectors– LINPACK

SpMV Historical Trends: Mflop/s

Still More Surprises


Still More Surprises


• Example: 3x3 blocking– Logical grid of 3x3 cells

Historical Trends: Mixed News

• Observations– Good news: Moore’s law like behavior– Bad news: “Untuned” is 10% peak or less, worsening– Good news: “Tuned” roughly 2x better today, and

improving– Bad news: Tuning is complex

– (Not really news: SpMV is not LINPACK)

• Questions– Application: Automatic tuning?– Architect: What machines are good for SpMV?

Road Map

• Sparse matrix-vector multiply (SpMV) in a nutshell• Historical trends and the need for search• Automatic tuning techniques

– SpMV [SC’02; IJHPCA ’04b]– Sparse triangular solve (SpTS) [ICS/POHLL ’02]– ATA*x [ICCS/WoPLA ’03]

• Upper bounds on performance• Statistical models of performance

SPARSITY: Framework for Tuning SpMV

• SPARSITY: Automatic tuning for SpMV [Im & Yelick ’99]– General approach

• Identify and generate implementation space• Search space using empirical models & experiments

– Prototype library and heuristic for choosing register block size

• Also: cache-level blocking, multiple vectors

• What’s new?– New block size selection heuristic

• Within 10% of optimal — replaces previous version

– Expanded implementation space• Variable block splitting, diagonals, combinations

– New kernels: sparse triangular solve, ATA*x, A*x

Automatic Register Block Size Selection

• Selecting the r x c block size– Off-line benchmark: characterize the machine

• Precompute Mflops(r,c) using dense matrix for each r x c• Once per machine/architecture

– Run-time “search”: characterize the matrix• Sample A to estimate Fill(r,c) for each r x c

– Run-time heuristic model• Choose r, c to maximize Mflops(r,c) / Fill(r,c)

• Run-time costs– Up to ~40 SpMVs (empirical worst case)


NOTE: “Fair” flops used (ops on explicit zeros not counted as “work”)

DGEMV

Road Map

• Sparse matrix-vector multiply (SpMV) in a nutshell• Historical trends and the need for search• Automatic tuning techniques• Upper bounds on performance

– SC’02

• Statistical models of performance

Motivation for Upper Bounds Model

• Questions– Speedups are good, but what is the speed limit?

• Independent of instruction scheduling, selection

– What machines are “good” for SpMV?

Upper Bounds on Performance: Blocked SpMV

• P = (flops) / (time)– Flops = 2 * nnz(A)

• Lower bound on time: Two main assumptions– 1. Count memory ops only (streaming)– 2. Count only compulsory, capacity misses: ignore conflicts

• Account for line sizes• Account for matrix size and nnz

• Charge min access “latency” i at Li cache & mem

– e.g., Saavedra-Barrera and PMaC MAPS benchmarks

1mem11

1memmem

Misses)(Misses)(Loads

HitsHitsTime

iiii

iii

Example: Bounds on Itanium 2

Fraction of Upper Bound Across Platforms

Achieved Performance and Machine Balance

• Machine balance [Callahan ’88; McCalpin ’95]– Balance = Peak Flop Rate / Bandwidth (flops /

double)

• Ideal balance for mat-vec: 2 flops / double– For SpMV, even less

• SpMV ~ streaming– 1 / (avg load time to stream 1 array) ~ (bandwidth)– “Sustained” balance = peak flops / model bandwidth

i

iii Misses)(Misses)(LoadsTime mem11

Where Does the Time Go?

• Most time assigned to memory• Caches “disappear” when line sizes are equal

– Strictly increasing line sizes

1

memmem HitsHitsTimei

ii

Execution Time Breakdown: Matrix 40

Speedups with Increasing Line Size

Summary: Performance Upper Bounds

• What is the best we can do for SpMV?– Limits to low-level tuning of blocked implementations– Refinements?

• What machines are good for SpMV?– Partial answer: balance characterization

• Architectural consequences?– Example: Strictly increasing line sizes

Road Map

• Sparse matrix-vector multiply (SpMV) in a nutshell• Historical trends and the need for search• Automatic tuning techniques• Upper bounds on performance• Tuning other sparse kernels• Statistical models of performance

– FDO ’00; IJHPCA ’04a

Statistical Models for Automatic Tuning

• Idea 1: Statistical criterion for stopping a search– A general search model

• Generate implementation• Measure performance• Repeat

– Stop when probability of being within of optimal falls below threshold

• Can estimate distribution on-line

• Idea 2: Statistical performance models– Problem: Choose 1 among m implementations at run-

time– Sample performance off-line, build statistical model

Example: Select a Matmul Implementation

Example: Support Vector Classification

Road Map

• Sparse matrix-vector multiply (SpMV) in a nutshell• Historical trends and the need for search• Automatic tuning techniques• Upper bounds on performance• Tuning other sparse kernels• Statistical models of performance• Summary and Future Work

Summary of High-Level Themes

• “Kernel-centric” optimization– Vs. basic block, trace, path optimization, for instance– Aggressive use of domain-specific knowledge

• Performance bounds modeling– Evaluating software quality– Architectural characterizations and consequences

• Empirical search– Hybrid on-line/run-time models

• Statistical performance models– Exploit information from sampling, measuring

Related Work

• My bibliography: 337 entries so far• Sample area 1: Code generation

– Generative & generic programming– Sparse compilers– Domain-specific generators

• Sample area 2: Empirical search-based tuning– Kernel-centric

• linear algebra, signal processing, sorting, MPI, …

– Compiler-centric• profiling + FDO, iterative compilation, superoptimizers,

self-tuning compilers, continuous program optimization

Future Directions (A Bag of Flaky Ideas)

• Composable code generators and search spaces• New application domains

– PageRank: multilevel block algorithms for topic-sensitive search?

• New kernels: cryptokernels– rich mathematical structure germane to performance; lots

of hardware

• New tuning environments– Parallel, Grid, “whole systems”

• Statistical models of application performance– Statistical learning of concise parametric models from

traces for architectural evaluation– Compiler/automatic derivation of parametric models

Acknowledgements

• Super-advisors: Jim and Kathy• Undergraduate R.A.s: Attila, Ben, Jen, Jin,

Michael, Rajesh, Shoaib, Sriram, Tuyet-Linh• See pages xvi—xvii of dissertation.

TSP-based Reordering: Before

(Pinar ’97;Moon, et al ‘04)

TSP-based Reordering: After

(Pinar ’97;Moon, et al ‘04)

Up to 2xspeedupsover CSR

Example: L2 Misses on Itanium 2

Misses measured using PAPI [Browne ’00]

Example: Distribution of Blocked Non-Zeros

Register Profile: Itanium 2

190 Mflop/s

1190 Mflop/s

Register Profiles: Sun and Intel x86

Ultra 2i - 11% Ultra 3 - 5%

Pentium III-M - 15%Pentium III - 21%

72 Mflop/s

35 Mflop/s

90 Mflop/s

50 Mflop/s

108 Mflop/s

42 Mflop/s

122 Mflop/s

58 Mflop/s

Register Profiles: IBM and Intel IA-64



252 Mflop/s

122 Mflop/s

820 Mflop/s

459 Mflop/s

247 Mflop/s

107 Mflop/s

1.2 Gflop/s

190 Mflop/s

Accurate and Efficient Adaptive Fill Estimation

• Idea: Sample matrix– Fraction of matrix to sample: s [0,1]– Cost ~ O(s * nnz)– Control cost by controlling s

• Search at run-time: the constant matters!

• Control s automatically by computing statistical confidence intervals– Idea: Monitor variance

• Cost of tuning– Lower bound: convert matrix in 5 to 40 unblocked

SpMVs– Heuristic: 1 to 11 SpMVs

Sparse/Dense Partitioning for SpTS

• Partition L into sparse (L1,L2) and dense LD:

2

1

2

1

2

1

b

b

x

x

LL

L

D

• Perform SpTS in three steps:

22

1222

111

ˆ)3(

ˆ)2(

)1(

bxL

xLbb

bxL

D

• Sparsity optimizations for (1)—(2); DTRSV for (3)• Tuning parameters: block size, size of dense triangle

SpTS Performance: Power3

Summary of SpTS and AAT*x Results

• SpTS — Similar to SpMV– 1.8x speedups; limited benefit from low-level tuning

• AATx, ATAx– Cache interleaving only: up to 1.6x speedups– Reg + cache: up to 4x speedups

• 1.8x speedup over register only

– Similar heuristic; same accuracy (~ 10% optimal)– Further from upper bounds: 60—80%

• Opportunity for better low-level tuning a la PHiPAC/ATLAS

• Matrix triple products? Ak*x?– Preliminary work

Register Blocking: Speedup

Register Blocking: Performance

Register Blocking: Fraction of Peak

Example: Confidence Interval Estimation

Costs of Tuning

Splitting + UBCSR: Pentium III

Splitting + UBCSR: Power4

Splitting+UBCSR Storage: Power4

Example: Variable Block Row (Matrix #13)

Dense Tuning is Hard, Too

• Even dense matrix multiply can be notoriously difficult to tune

Dense matrix multiply: surprising performance as register tile size varies.

Preliminary Results (Matrix Set 2): Itanium 2

Web/IR

Dense FEM FEM (var) Bio LPEcon Stat

Multiple Vector Performance

What about the Google Matrix?

• Google approach– Approx. once a month: rank all pages using connectivity

structure• Find dominant eigenvector of a matrix

– At query-time: return list of pages ordered by rank• Matrix: A = G + (1-)(1/n)uuT

– Markov model: Surfer follows link with probability , jumps to a random page with probability 1-

– G is n x n connectivity matrix [n 3 billion]• gij is non-zero if page i links to page j• Normalized so each column sums to 1• Very sparse: about 7—8 non-zeros per row (power law dist.)

– u is a vector of all 1 values– Steady-state probability xi of landing on page i is solution to x

= Ax

• Approximate x by power method: x = Akx0

– In practice, k 25

MAPS Benchmark Example: Power4

MAPS Benchmark Example: Itanium 2

Saavedra-Barrera Example: Ultra 2i

Summary of Results: Pentium III

Summary of Results: Pentium III (3/3)

Execution Time Breakdown (PAPI): Matrix 40

Preliminary Results (Matrix Set 1): Itanium 2

LPFEM FEM (var) AssortedDense

Tuning Sparse Triangular Solve (SpTS)

• Compute x=L-1*b where L sparse lower triangular, x & b dense

• L from sparse LU has rich dense substructure– Dense trailing triangle can account for 20—90% of

matrix non-zeros

• SpTS optimizations– Split into sparse trapezoid and dense trailing triangle– Use tuned dense BLAS (DTRSV) on dense triangle– Use Sparsity register blocking on sparse part

• Tuning parameters– Size of dense trailing triangle– Register block size

Sparse Kernels and Optimizations

• Kernels– Sparse matrix-vector multiply (SpMV): y=A*x– Sparse triangular solve (SpTS): x=T-1*b– y=AAT*x, y=ATA*x– Powers (y=Ak*x), sparse triple-product (R*A*RT), …

• Optimization techniques (implementation space)– Register blocking– Cache blocking– Multiple dense vectors (x)– A has special structure (e.g., symmetric, banded, …)– Hybrid data structures (e.g., splitting, switch-to-

dense, …)– Matrix reordering

• How and when do we search?– Off-line: Benchmark implementations– Run-time: Estimate matrix properties, evaluate

performance models based on benchmark data

Cache Blocked SpMV on LSI Matrix: Ultra 2i

A10k x 255k3.7M non-zeros

Baseline:16 Mflop/s

Best block size& performance:16k x 64k28 Mflop/s

Cache Blocking on LSI Matrix: Pentium 4


Baseline:44 Mflop/s


Cache Blocked SpMV on LSI Matrix: Itanium


Baseline:25 Mflop/s


Cache Blocked SpMV on LSI Matrix: Itanium 2


Baseline:170 Mflop/s


Inter-Iteration Sparse Tiling (1/3)

• [Strout, et al., ‘01]• Let A be 6x6 tridiagonal• Consider y=A2x

– t=Ax, y=At

• Nodes: vector elements• Edges: matrix elements

aij

y1

y2

y3

y4

y5

t1

t2

t3

t4

t5

x1

x2

x3

x4

x5



– t=Ax, y=At


aij

• Orange = everything needed to compute y1

– Reuse a11, a12

y1

y2

y3

y4

y5

t1

t2

t3

t4

t5

x1

x2

x3

x4

x5



– t=Ax, y=At


aij

• Orange = everything needed to compute y1

– Reuse a11, a12

• Grey = y2, y3

– Reuse a23, a33, a43

y1

y2

y3

y4

y5

t1

t2

t3

t4

t5

x1

x2

x3

x4

x5

Inter-Iteration Sparse Tiling: Issues

• Tile sizes (colored regions) grow with no. of iterations and increasing out-degree– G likely to have a few

nodes with high out-degree (e.g., Yahoo)

• Mathematical tricks to limit tile size?– Judicious dropping of

edges [Ng’01]

y1

y2

y3

y4

y5

t1

t2

t3

t4

t5

x1

x2

x3

x4

x5

Summary and Questions

• Need to understand matrix structure and machine– BeBOP: suite of techniques to deal with different sparse

structures and architectures• Google matrix problem

– Established techniques within an iteration– Ideas for inter-iteration optimizations– Mathematical structure of problem may help

• Questions– Structure of G?– What are the computational bottlenecks?– Enabling future computations?

• E.g., topic-sensitive PageRank multiple vector version [Haveliwala ’02]

– See www.cs.berkeley.edu/~richie/bebop/intel/google for more info, including more complete Itanium 2 results.

Exploiting Matrix Structure

• Symmetry (numerical or structural)– Reuse matrix entries– Can combine with register blocking, multiple vectors,

…

• Matrix splitting– Split the matrix, e.g., into r x c and 1 x 1– No fill overhead

• Large matrices with random structure– E.g., Latent Semantic Indexing (LSI) matrices– Technique: cache blocking

• Store matrix as 2i x 2j sparse submatrices• Effective when x vector is large• Currently, search to find fastest size

Symmetric SpMV Performance: Pentium 4

SpMV with Split Matrices: Ultra 2i

Cache Blocking on Random Matrices: Itanium

Speedup on four bandedrandom matrices.



• Optimization techniques (implementation space)– Register blocking– Cache blocking– Multiple dense vectors (x)– A has special structure (e.g., symmetric, banded, …)– Hybrid data structures (e.g., splitting, switch-to-dense, …)– Matrix reordering



Register Blocked SpMV: Pentium III

Register Blocked SpMV: Ultra 2i

Register Blocked SpMV: Power3

Register Blocked SpMV: Itanium

Possible Optimization Techniques

• Within an iteration, i.e., computing (G+uuT)*x once– Cache block G*x

• On linear programming matrices and matrices with random structure (e.g., LSI), 1.5—4x speedups

• Best block size is matrix and machine dependent

– Reordering and/or splitting of G to separate dense structure (rows, columns, blocks)

• Between iterations, e.g., (G+uuT)2x– (G+uuT)2x = G2x + (Gu)uTx + u(uTG)x + u(uTu)uTx

• Compute Gu, uTG, uTu once for all iterations• G2x: Inter-iteration tiling to read G only once

Multiple Vector Performance: Itanium



• Optimization techniques (implementation space)– Register blocking– Cache blocking– Multiple dense vectors (x)– A has special structure (e.g., symmetric, banded, …)– Hybrid data structures (e.g., splitting, switch-to-

dense, …)– Matrix reordering



SpTS Performance: Itanium

(See POHLL ’02 workshop paper, at ICS ’02.)



• Optimization techniques (implementation space)– Register blocking– Cache blocking– Multiple dense vectors (x)– A has special structure (e.g., symmetric, banded, …)– Hybrid data structures (e.g., splitting, switch-to-dense, …)– Matrix reordering



Optimizing AAT*x

• Kernel: y=AAT*x, where A is sparse, x & y dense– Arises in linear programming, computation of SVD– Conventional implementation: compute z=AT*x, y=A*z

• Elements of A can be reused:

n

k

Tkk

Tn

T

n xaax

a

a

aay1

1

1 )(

• When ak represent blocks of columns, can apply register blocking.

Optimized AAT*x Performance: Pentium III

Current Directions

• Applying new optimizations– Other split data structures (variable block, diagonal,

…)– Matrix reordering to create block structure– Structural symmetry

• New kernels (triple product RART, powers Ak, …)• Tuning parameter selection• Building an automatically tuned sparse matrix

library– Extending the Sparse BLAS– Leverage existing sparse compilers as code

generation infrastructure– More thoughts on this topic tomorrow

Related Work

• Automatic performance tuning systems– PHiPAC [Bilmes, et al., ’97], ATLAS [Whaley & Dongarra

’98]– FFTW [Frigo & Johnson ’98], SPIRAL [Pueschel, et al.,

’00], UHFFT [Mirkovic and Johnsson ’00]– MPI collective operations [Vadhiyar & Dongarra ’01]

• Code generation– FLAME [Gunnels & van de Geijn, ’01]– Sparse compilers: [Bik ’99], Bernoulli [Pingali, et al., ’97]– Generic programming: Blitz++ [Veldhuizen ’98], MTL

[Siek & Lumsdaine ’98], GMCL [Czarnecki, et al. ’98], …

• Sparse performance modeling– [Temam & Jalby ’92], [White & Saddayappan ’97],

[Navarro, et al., ’96], [Heras, et al., ’99], [Fraguela, et al., ’99], …

More Related Work

• Compiler analysis, models– CROPS [Carter, Ferrante, et al.]; Serial sparse tiling

[Strout ’01]– TUNE [Chatterjee, et al.]– Iterative compilation [O’Boyle, et al., ’98]– Broadway compiler [Guyer & Lin, ’99]– [Brewer ’95], ADAPT [Voss ’00]

• Sparse BLAS interfaces– BLAST Forum (Chapter 3)– NIST Sparse BLAS [Remington & Pozo ’94];

SparseLib++– SPARSKIT [Saad ’94]– Parallel Sparse BLAS [Fillipone, et al. ’96]

Context: Creating High-Performance Libraries

• Application performance dominated by a few computational kernels

• Today: Kernels hand-tuned by vendor or user• Performance tuning challenges

– Performance is a complicated function of kernel, architecture, compiler, and workload

– Tedious and time-consuming

• Successful automated approaches– Dense linear algebra: ATLAS/PHiPAC– Signal processing: FFTW/SPIRAL/UHFFT

Cache Blocked SpMV on LSI Matrix: Itanium

Sustainable Memory Bandwidth

Multiple Vector Performance: Pentium 4

Multiple Vector Performance: Itanium

Multiple Vector Performance: Pentium 4

Optimized AAT*x Performance: Ultra 2i

Optimized AAT*x Performance: Pentium 4

Tuning Pays Off—PHiPAC

Tuning pays off – ATLAS

Extends applicability of PHIPAC; Incorporated in Matlab (with rest of LAPACK)

Register Tile Sizes (Dense Matrix Multiply)

333 MHz Sun Ultra 2i

2-D slice of 3-D space; implementations color-coded by performance in Mflop/s

16 registers, but 2-by-3 tile size fastest

High Precision GEMV (XBLAS)

High Precision Algorithms (XBLAS)• Double-double (High precision word represented as pair of doubles)

– Many variations on these algorithms; we currently use Bailey’s• Exploiting Extra-wide Registers

– Suppose s(1) , … , s(n) have f-bit fractions, SUM has F>f bit fraction– Consider following algorithm for S = i=1,n s(i)

• Sort so that |s(1)| |s(2)| … |s(n)|• SUM = 0, for i = 1 to n SUM = SUM + s(i), end for, sum = SUM

– Theorem (D., Hida) Suppose F<2f (less than double precision)• If n 2F-f + 1, then error 1.5 ulps• If n = 2F-f + 2, then error 22f-F ulps (can be 1)• If n 2F-f + 3, then error can be arbitrary (S 0 but sum = 0 )

– Examples• s(i) double (f=53), SUM double extended (F=64)

– accurate if n 211 + 1 = 2049• Dot product of single precision x(i) and y(i)

– s(i) = x(i)*y(i) (f=2*24=48), SUM double extended (F=64) – accurate if n 216 + 1 = 65537

CS267 – Lecture 15 Automatic Performance Tuning and Sparse-Matrix-Vector-Multiplication (SpMV)...

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