Acceleration of scientific computing

using graphics hardware

Graham Pullan
Whittle Lab
Engineering Department, University of Cambridge
28 May 2008 I’ve added some notes that
weren’t on the original slides to
help readers of the online pdf
version.
Coming up...
• Background
• CPUs and GPUs
• GPU programming models
• An example – CFD
• Alternative devices
• Conclusions
Part 1: Background
 Whittle Lab

You are here

 Whittle Lab

I work here

You are here

Turbomachinery
Engine calculation

Courtesy Vicente Jerez

Fidalgo, Whittle Lab
CFD basics

Body-fitted mesh
CFD basics

Body-fitted mesh For each cell, conserve:

• mass
• momentum
• energy
and update flow properties
Approximate compute requirements
“Steady” models (no wake/blade interaction, etc)
1 blade 0.5 Mcells 1 CPU hour
1 stage (2 blades) 1.0 Mcells 3 CPU hours
1 component (5 stages) 5.0 Mcells 20 CPU hours
Approximate compute requirements
“Steady” models (no wake/blade interaction, etc)
1 blade 0.5 Mcells 1 CPU hour
1 stage (2 blades) 1.0 Mcells 3 CPU hours
1 component (5 stages) 5.0 Mcells 20 CPU hours

“Unsteady” models (with wakes, etc)

1 component (1000 blades) 500 Mcells 0.1 M CPU hours
Engine (4000 blades) 2 Gcells 1 M CPU hours
Graham’s coding experience:
• FORTRAN
• C
• MPI
Graham’s coding experience:

• C

•MPI
Part 2: CPUs and GPUs
Moore’s Law
“The complexity for minimum component costs has
increased at a rate of roughly a factor of two per year.
Certainly over the short term this rate can be expected to
continue.”
Gordon Moore (Intel), 1965
Moore’s Law
“The complexity for minimum component costs has
increased at a rate of roughly a factor of two per year.
Certainly over the short term this rate can be expected to
continue.”
Gordon Moore (Intel), 1965

“OK, maybe a factor of two every two years.”

Gordon Moore (Intel), 1975 [paraphrased]
Was Moore right?

Source:
ftp://download.intel.com/resea
rch/silicon/Gordon_Moore_ISSC
C_021003.pdf

Source: Intel
Was Moore right?

Source: Intel
Was Moore right?

Source: Intel
Feature size

Source:
ftp://download.intel.com/resea
rch/silicon/Gordon_Moore_ISSC
C_021003.pdf

Source: Intel
 Clock speed

Source:
http://www.tomshardware.com/2005/11/21/the_mother_of_al
l_cpu_charts_2005/index.html
Power – the Clock speed limiter?
• 1 GHz CPU requires ≈ 25 W
• 3 GHz CPU requires ≈ 100 W
Power – the Clock speed limiter?
• 1 GHz CPU requires ≈ 25 W
• 3 GHz CPU requires ≈ 100 W

“The total of electricity consumed by major search

engines in 2006 approaches 5 GW.” – Wired / AMD

Source:
http://www.hotchips.org/hc19/docs/keynote2.pdf
What to do with all these transistors?
Parallel computing
Multi-core chips are either:

– Instruction parallel
(Multipile Instruction, Multiple Data) – MIMD

or

– Data parallel
(Single Instruction, Multiple Data) – SIMD
Today’s commodity MIMD chips: CPUs
Intel Core 2 Quad
• 4 cores
• 2.4 GHz
• 65nm features
• 582 million transistors
• 8MB on chip memory
Today’s commodity SIMD chips: GPUs
NVIDIA 8800 GTX
• 128 cores
• 1.35 GHz
• 90nm features
• 681 million transistors
• 768MB on board memory
CPUs vs GPUs

Source:
http://www.eng.cam.ac.uk/~gp10006/research/Brandvi
k_Pullan_2008a_DRAFT.pdf
CPUs vs GPUs
Transistor usage:

Source: NVIDIA CUDA SDK

documentation
Graphics pipeline

Source:
ftp://download.nvidia.com/developer/presentations/200
4/Perfect_Kitchen_Art/English_Evolution_of_GPUs.pdf
Graphics pipeline
GPUs and scientific computing

GPUs are designed to apply the

same shading function
to many pixels simultaneously
GPUs and scientific computing

GPUs are designed to apply the

same function
to many data simultaneously

This is what most scientific computing needs!

Part 3: Programming methods
3 Generations of GPGPU (Owens, 2008)
3 Generations of GPGPU (Owens, 2008)
• Making it work at all:
– Primitive functionality and tools (graphics APIs)
– Comparisons with CPU not rigorous
3 Generations of GPGPU (Owens, 2008)
• Making it work at all:
– Primitive functionality and tools (graphics APIs)
– Comparisons with CPU not rigorous
• Making it work better:
– Easier to use (higher level APIs)
– Understanding of how best to do it
3 Generations of GPGPU (Owens, 2008)
• Making it work at all:
– Primitive functionality and tools (graphics APIs)
– Comparisons with CPU not rigorous
• Making it work better:
– Easier to use (higher level APIs)
– Understanding of how best to do it
• Doing it right:
– Stable, portable, modular building blocks

Source:
http://www.ece.ucdavis.edu/~jowens/talks/intel-
santaclara-070420.pdf
 GPU – Programming for graphics
Courtesy, John Owens, UC Davis

Application specifies geometry – GPU

rasterizes

Each fragment is shaded (SIMD)

Shading can use values from memory

(textures)

Image can be stored for re-use

Source:
http://www.ece.ucdavis.edu/~jowens/talks/intel-
santaclara-070420.pdf
 GPGPU programming (“old-school”)

Draw a quad

Run a SIMD program over each

fragment

Gather is permitted from texture memory

Resulting buffer can be stored for re-use

Courtesy, John Owens, UC Davis

NVIDIA G80 hardware implementation
• Vertex/fragment processors replaced by Unified Shaders
• Now view GPU as massively parallel co-processor
• Set of (16) SIMD MultiProcessors (8 cores)

Source:
http://www.ece.wisc.edu/~kati/fpga2008/fpga2008%20wo
rkshop%20-%2006%20NVIDIA%20-%20Kirk.pdf
NVIDIA G80 hardware implementation
Divide 128 cores into
16 Multiprocessors (MPs)

•Each MP has:
–Registers
–Shared memory
–Read only constant
cache
–Read only texture
cache
NVIDIA’s CUDA programming model
• G80 chip supports MANY active threads: 12,288
• Threads are lightweight:
– Little creation overhead
– “instant” switching
– Efficiency achieved through 1000’s of threads
• Threads are organised into blocks (1D, 2D, 3D)
• Blocks are further organised into a grid
Kernels, grids, blocks and threads
Kernels, grids, blocks and threads
• Organisation of threads and blocks is key abstraction
Kernels, grids, blocks and threads
• Organisation of threads and blocks is key abstraction
• Software:
– Threads from one block may cooperate:
• Using data in shared memory
• Through synchronising
Kernels, grids, blocks and threads
• Organisation of threads and blocks is key abstraction
• Software:
– Threads from one block may cooperate:
• Using data in shared memory
• Through synchronising
• Hardware:
– A block runs on one MP
– Hardware free to schedule any block on any MP
– More than one block can reside on one MP
Kernels, grids, blocks and threads
CUDA implementation
• CUDA implemented as extensions to C

• CUDA programs:
– explicitly manage host and device memory:
• allocation
• transfers
– set thread blocks and grid
– launch kernels
– are compiled with the CUDA nvcc compiler
Part 4: An example – CFD
Distribution function

f = f (c, x , t )
c is microscopic velocity

ρ = ∫ f dc

ρ u = ∫ cf d c
u is macroscopic velocity
Boltzmann equation
The evolution of f:

∂f ∂f
+ u ⋅ ∇f =
∂t ∂t collisions

Major simplification:

∂f 1
+ u ⋅ ∇f = − ( f − f )
eq

∂t τ
Lattice Boltzmann Method
Uniform mesh (lattice)
Lattice Boltzmann Method
Uniform mesh (lattice) Restrict microscopic velocities
to a finite set:

ρ = ∑ fα ρu = ∑ fα cα
α α
Macroscopic flow

For 2D, 9 velocities recover

• Isothermal, incompressible Navier-Stokes eqns

⎛ 1 ⎞ Δx 2
• With viscosity: ν = ⎜τ − ⎟
⎝ 2 ⎠ Δt
Solution procedure

1. Evaluate macroscopic properties:

ρ = ∑ fα ρu = ∑ fα cα
α α

2. Evaluate fαeq ( ρ , u )

3. Find

fα = fα −
*

τ
1
( f α − fα
eq
)
Solution procedure
Solution procedure

Simple prescriptions at
boundary nodes
CPU code: main.c
/* Memory allocation */
f0 = (float *)malloc(ni*nj*sizeof(float));
...

/* Main loop */
Stream (...args...);
Apply_BCs (...args...);
Collide (...args...);
GPU code: main.cu
/* allocate memory on host */
f0 = (float *)malloc(ni*nj*sizeof(float));

/* allocate memory on device */

cudaMallocPitch((void **)&f0_data, &pitch,
sizeof(float)*ni, nj);

cudaMallocArray(&f0_array, &desc, ni, nj);

/* Main loop */
Stream (...args...);
Apply_BCs (...args...);
Collide (...args...);
CPU code – collide.c
for (j=0; j<nj; j++) {
for (i=0; i<ni; i++) {
i2d = I2D(ni,i,j);
/* Flow properties */
density = ...function of f’s ...
vel_x = ... “
vel_y = ... “
/* Equilibrium f’s */
f0eq = ... function of density, vel_x, vel_y ...
f1eq = ... “
/* Collisions */
f0[i2d] = rtau1 * f0[i2d] + rtau * f0eq;
f1[i2d] = rtau1 * f1[i2d] + rtau * f1eq;
...
}
}
GPU code – collide.cu – kernel wrapper

void collide( ... args ...)

{
/* Set thread blocks and grid */
dim3 grid = dim3(ni/TILE_I, nj/TILE_J);
dim3 block = dim3(TILE_I, TILE_J);

/* Launch kernel */
collide_kernel<<<grid, block>>>(... args ...);

}
GPU code – collide.cu - kernel
/* Evaluate indices */
i = blockIdx.x*TILE_I + threadIdx.x;
j = blockIdx.y*TILE_J + threadIdx.y;
i2d = i + j*pitch/sizeof(float);
/* Read from device global memory */
f0now = f0_data[i2d];
f1now = f1_data[i2d];

/* Calc flow, feq, collide, as CPU code */

/* Write to device global memory */

f0_data[i2d] = rtau1 * f0now + rtau * f0eq;
f1_data[i2d] = rtau1 * f1now + rtau * f1eq;
GPU code – stream.cu – kernel wrapper
void stream( ... args ...)
{
/* Copy linear memory to CUDA array */
cudaMemcpy2DToArray(f1_array, 0, 0,
(void *)f1_data, pitch,sizeof(float)*ni, nj,
cudaMemcpyDeviceToDevice);
/* Make CUDA array a texture */
f1_tex.filterMode = cudaFilterModePoint;
cudaBindTextureToArray(f1_tex, f1_array));
/* Set threads and launch kernel */
dim3 grid = dim3(ni/TILE_I, nj/TILE_J);
dim3 block = dim3(TILE_I, TILE_J);
stream_kernel<<<grid, block>>>(... args ...);
}
GPU code – stream.cu – kernel
/* indices */

i = blockIdx.x*TILE_I + threadIdx.x;
j = blockIdx.y*TILE_J + threadIdx.y;
i2d = i + j*pitch/sizeof(float);

/* stream using texture fetches */

f1_data[i2d] = tex2D(f1_tex, (i-1), j);
f2_data[i2d] = tex2D(f2_tex, i, (j-1));
...
CPU / GPU demo
Results
• 2D Lattice Boltzmann code: 15x speedup GPU vs CPU

• Real CFD is more complex:

– more kernels
– 3D

• To improve performance, make use of shared memory

3D stencil operations
• Most CFD operations use nearest neighbour lookups
(stencil operations)

• e.g. 7 point stencil: centre point + 6 nearest neighbours

• Load data into shared memory

• Perform stencil ops
• Export results to device global memory
• Read in more data into shared memory
 Stencil operations

3D sub-domain Threads in one plane

Source:
http://www.eng.cam.ac.uk/~gp10006/research/Brandvik_Pullan_2
008a_DRAFT.pdf
CUDA stencil kernel
__global__ void smooth_kernel(float sf, float
*a_data, float *b_data){

/* shared memory array */

__shared__ float a[16][3][5];
/* fetch first planes */
a[i][0][k] = a_data[i0m10];
a[i][1][k] = a_data[i000];
a[i][2][k] = a_data[i0p10];
__syncthreads();
/* compute */
b_data[i000] =
sf1*a[i][1][k] + sfd6*(a[im1][1][k] +
a[ip1][1][k] + a[i][0][k] +
a[i][2][k] + a[i][1][km1] + a[i][1][kp1])
/* load next "j" plane and repeat ...*/
Typical grid – CUDA partitioning
Typical grid – CUDA partitioning

Each colour to a different

multiprocessor
3D results

30x speedup GPU vs CPU

Part 5: NVIDIA – the only show in town?
 NVIDIA

• 4 Tesla HPC GPUs

• 500 GFLOPs peak per GPU
• 1.5GB per GPU
AMD

• Firestream HPC GPU

• 500 GFLOPs
• 2GB
• available?
ClearSpeed

80 GFLOPs
35 W !
IBM Cell BE

25 x 8 GFLOPs
 Chip comparison (Giles 2008)

Source:
http://www.cardiff.ac.uk/arcca/services/events/NovelArchitecture/
Mike-Giles.pdf
Too much choice!
• Each device has
– different hardware characteristics
– different software (C extensions)
– different developer tools

• How can we write code for all SIMD devices for all
applications?
Big picture – all devices, all problems?
Forget the big picture
Tackle the dwarves!
 The View from Berkeley (7 “dwarves”)
1. Dense Linear Algebra
2. Sparse Linear Algebra
3. Spectral Methods
4. N-Body Methods
5. Structured Grids
6. Unstructured Grids
7. MapReduce

Source:
http://view.eecs.berkeley.edu/wiki/Main_Page
The View from Berkeley (13 dwarves?)
1. Dense Linear Algebra
2. Sparse Linear Algebra
3. Spectral Methods
4. N-Body Methods
5. Structured Grids
6. Unstructured Grids
7. MapReduce
8. Combinational Logic
9. Graph Traversal
10. Dynamic Programming
11. Backtrack and Branch-and-Bound
12. Graphical Models
13. Finite State Machines
The View from Berkeley (13 dwarves?)
1. Dense Linear Algebra
2. Sparse Linear Algebra
3. Spectral Methods
4. N-Body Methods
5. Structured Grids
6. Unstructured Grids
7. MapReduce
8. Combinational Logic
9. Graph Traversal
10. Dynamic Programming
11. Backtrack and Branch-and-Bound
12. Graphical Models
13. Finite State Machines
SBLOCK (Brandvik)
• Tackle structured grid, stencil operations dwarf
• Define kernel using high level Python abstraction
• Generate kernel for a range of devices from same
definition: CPU, GPU, Cell
• Use MPI to handle multiple devices
SBLOCK kernel definition
kind = "stencil"
bpin = ["a"]
bpout = ["b"]
lookup = ((1,0, 0), (0, 0, 0), (1,0, 0), (0, 1,0),
(0, 1, 0), (0, 0, 1), (0, 0, 1))
calc = {"lvalue": "b",
"rvalue": """sf1*a[0][0][0] +
sfd6*(a[1][0][0] + a[1][0][0] +
a[0][1][0] + a[0][1][0] +
a[0][0][1] + a[0][0][1])"""}
SBLOCK – CPU implementation (C)
void smooth(float sf, float *a, float *b)
{
for (k=0; k < nk; k++) {
for (j=0; j < nj; j++) {
for (i=0; i < ni; i++) {
/* compute indices i000, im100, etc */
b[i000] = sf1*a[i000] +
sfd6*(a[im100] + a[ip100] +
a[i0m10] + a[i0p10]
+ a[i00m1] + a[i00p1]);
}
}
}
}
SBLOCK – GPU implementation (CUDA)
__global__ void smooth_kernel(float sf, float
*a_data, float *b_data){

/* shared memory array */

__shared__ float a[16][3][5];
/* fetch first planes */
a[i][0][k] = a_data[i0m10];
a[i][1][k] = a_data[i000];
a[i][2][k] = a_data[i0p10];
__syncthreads();
/* compute */
b_data[i000] =
sf1*a[i][1][k] + sfd6*(a[im1][1][k] +
a[ip1][1][k] + a[i][0][k] +
a[i][2][k] + a[i][1][km1] + a[i][1][kp1])
/* load next "j" plane and repeat ...*/
Benefits of SBLOCK

So long as the task fits the dwarf:

• Programmer need not learn every device library

• Optimal device code is produced
• Code is future proofed (so long as back-ends are
available)
Part 6: Conclusions
Conclusions
• Many science applications fit the SIMD model
• GPUs are commodity SIMD chips
• Good speedups (10x – 100x) can be achieved
Conclusions
• Many science applications fit the SIMD model
• GPUs are commodity SIMD chips
• Good speedups (10x – 100x) can be achieved

• GPGPU is evolving (Owens, UC Davis):

1. Making it work at all (graphics APIs)
2. Doing it better (high level APIs)
3. Doing it right (portable, modular building blocks)
Conclusions
• Many science applications fit the SIMD model
• GPUs are commodity SIMD chips
• Good speedups (10x – 100x) can be achieved

• GPGPU is evolving (Owens, UC Davis):

1. Making it work at all (graphics APIs)
2. Doing it better (high level APIs)
3. Doing it right (portable, modular building blocks)
Acknowledgements and info
• Research student: Tobias Brandvik (CUED)
• Donation of GPU hardware: NVIDIA

http://dx.doi.org/10.1109/JPROC.2008.917757

http://www.gpgpu.org

http://www.oerc.ox.ac.uk/research/many-core-and-
reconfigurable-supercomputing