1 High-Performance Grid Computing and Research Networking Presented by Xing Hang Instructor: S. Masoud Sadjadi sadjadi/Teaching

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High-Performance Grid Computing and High-Performance Grid Computing and Research NetworkingResearch Networking

Presented by Xing Hang

Instructor: S. Masoud Sadjadihttp://www.cs.fiu.edu/~sadjadi/Teaching/

sadjadi At cs Dot fiu Dot edu

Algorithms on a Grid of ProcessorsAlgorithms on a Grid of Processors

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Acknowledgements

The content of many of the slides in this lecture notes have been adopted from the online resources prepared previously by the people listed below. Many thanks!

Henri Casanova Principles of High Performance Computing http://navet.ics.hawaii.edu/~casanova [email protected]

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2-D Torus topology We’ve looked at a ring, but for some applications it’s convenient to

look at a 2-D grid topology

A 2-D grid with “wrap-around” is called a 2-D torus. Advanced parallel linear algebra libraries/languages allow to

combine arbitrary data distribution strategies with arbitrary topologies (ScaLAPACK, HPF)

1-D block to a ring 2-D block to a 2-D grid cyclic or non-cyclic (more on this later)

We can go through all the algorithms we saw on a ring and make them work on a grid

In practice, for many linear algebra kernel, using a 2-D block-cyclic on a 2-D grid seems to work best in most situations

we’ve seen that blocks are good for locality we’ve seen that cyclic is good for load-balancing

√p

√p

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Semantics of a parallel linear algebra routine?

Centralized when calling a function (e.g., LU)

the input data is available on a single “master” machine the input data must then be distributed among workers the output data must be undistributed and returned to the “master” machine

More natural/easy for the user Allows for the library to make data distribution decisions transparently to

the user Prohibitively expensive if one does sequences of operations

and one almost always does so Distributed

when calling a function (e.g., LU) Assume that the input is already distributed Leave the output distributed

May lead to having to “redistributed” data in between calls so that distributions match, which is harder for the user and may be costly as well

For instance one may want to change the block size between calls, or go from a non-cyclic to a cyclic distribution

Most current software adopt distributed more work for the user more flexibility and control

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Matrix-matrix multiply Many people have thought of doing a matrix-multiply on a 2-D torus Assume that we have three matrices A, B, and C, of size NxN Assume that we have p processors, so that p=q2 is a perfect square and our processor grid is qxq We’re looking at a 2-D block distribution, but not cyclic

again, that would obfuscate the code too much

We’re going to look at three “classic” algorithms: Cannon, Fox, SnyderA00 A01 A02 A03

A10 A11 A12 A13

A20 A21 A22 A23

A30 A31 A32 A33

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B00 B01 B02 B03

B10 B11 B12 B13

B20 B21 B22 B23

B30 B31 B32 B33

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Cannon’s Algorithm (1969)

Very simple (from systolic arrays) Starts with a data redistribution for matrices A and B

goal is to have only neighbor-to-neighbor communications A is circularly shifted/rotated “horizontally” so that its

diagonal is on the first column of processors B is circularly shifted/rotated “vertically” so that its diagonal

is on the first row of processors Called preskewing

A00 A01 A02 A03

A11 A12 A13 A10

A22 A23 A20 A21

A33 A30 A31 A32

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B00 B11 B22 B33

B10 B21 B32 B03

B20 B31 B02 B13

B30 B01 B12 B23

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Cannon’s Algorithm

Preskewing of A and B

For k = 1 to q in parallel

Local C = C + A*B

Vertical shift of B

Horizontal shift of A

Postskewing of A and B

Of course, computation and communication could be done in an overlapped fashion locally at each processor

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Execution Steps...

A00 A01 A02 A03

A11 A12 A13 A10

A22 A23 A20 A21

A33 A30 A31 A32

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B00 B11 B22 B33

B10 B21 B32 B03

B20 B31 B02 B13

B30 B01 B12 B23

local computationon proc (0,0)

A01 A02 A03 A00

A12 A13 A10 A11

A23 A20 A21 A22

A30 A31 A32 A33

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B10 B21 B32 B03

B20 B31 B02 B13

B30 B01 B12 B23

B00 B11 B22 B33

Shifts

A01 A02 A03 A00

A12 A13 A10 A11

A23 A20 A21 A22

A30 A31 A32 A33

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B10 B21 B32 B03

B20 B31 B02 B13

B30 B01 B12 B23

B00 B11 B22 B33

local computationon proc (0,0)

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Fox’s Algorithm(1987)

Originally developed for CalTech’s Hypercube

Uses broadcasts and is also called broadcast-multiply-roll algorithm broadcasts diagonals of matrix A

Uses a shift of matrix B No preskewing step

first diagonalsecond diagonalthird diagonal...

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Execution Steps...

A00 A01 A02 A03

A10 A11 A12 A13

A20 A21 A22 A23

A30 A31 A32 A33

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B00 B01 B02 B03

B10 B11 B12 B13

B20 B21 B22 B23

B30 B31 B32 B33

initialstate

A00 A00 A00 A00

A11 A11 A11 A11

A22 A22 A22 A22

A33 A33 A33 A33

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

Broadcast of A’s 1st diagonal

Localcomputation

A00 A00 A00 A00

A11 A11 A11 A11

A22 A22 A22 A22

A33 A33 A33 A33

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B00 B01 B02 B03

B10 B11 B12 B13

B20 B21 B22 B23

B30 B31 B32 B33

B00 B01 B02 B03

B10 B11 B12 B13

B20 B21 B22 B23

B30 B31 B32 B33

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Execution Steps...

A00 A01 A02 A03

A10 A11 A12 A13

A20 A21 A22 A23

A30 A31 A32 A33

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B10 B11 B12 B13

B20 B21 B22 B23

B30 B31 B32 B33

B00 B01 B02 B03

Shift of B

A01 A01 A01 A01

A12 A12 A12 A12

A23 A23 A23 A23

A30 A30 A30 A30

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

Broadcast of A’s 2nd diagonal

Localcomputation

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B10 B11 B12 B13

B20 B21 B22 B23

B30 B31 B32 B33

B00 B01 B02 B03

A01 A01 A01 A01

A12 A12 A12 A12

A23 A23 A23 A23

A30 A30 A30 A30

B10 B11 B12 B13

B20 B21 B22 B23

B30 B31 B32 B33

B00 B01 B02 B03

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Fox’s Algorithm

// No initial data movementfor k = 1 to q-1 in parallel Broadcast A’s kth diagonal Local C = C + A*B Vertical shift of B// No final data movement

Note that there is an additional array to store incoming diagonal block

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Snyder’s Algorithm (1992)

More complex than Cannon’s or

Fox’s

First transposes matrix B

Uses reduction operations (sums) on

the rows of matrix C

Shifts matrix B

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Execution Steps...

A00 A01 A02 A03

A10 A11 A12 A13

A20 A21 A22 A23

A30 A31 A32 A33

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B00 B01 B02 B03

B10 B11 B12 B13

B20 B21 B22 B23

B30 B31 B32 B33

initialstate

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

Transpose B

Localcomputation

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B00 B10 B20 B30

B01 B11 B21 B31

B02 B12 B22 B32

B03 B13 B23 B33

B00 B10 B20 B30

B01 B11 B21 B31

B02 B12 B22 B32

B03 B13 B23 B33

A00 A01 A02 A03

A10 A11 A12 A13

A20 A21 A22 A23

A30 A31 A32 A33

A00 A01 A02 A03

A10 A11 A12 A13

A20 A21 A22 A23

A30 A31 A32 A33

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Execution Steps...

Shift B

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B01 B11 B21 B31

B02 B12 B22 B32

B03 B13 B23 B32

B00 B10 B20 B30

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B01 B11 B21 B31

B02 B12 B22 B32

B03 B13 B23 B32

B00 B10 B20 B30

Global sumon the rowsof C

A00 A01 A02 A03

A10 A11 A12 A13

A20 A21 A22 A23

A30 A31 A32 A33

A00 A01 A02 A03

A10 A11 A12 A13

A20 A21 A22 A23

A30 A31 A32 A33

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B01 B11 B21 B31

B02 B12 B22 B32

B03 B13 B23 B32

B00 B10 B20 B30

A00 A01 A02 A03

A10 A11 A12 A13

A20 A21 A22 A23

A30 A31 A32 A33

Localcomputation

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Execution Steps...

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

A00 A01 A02 A03

A10 A11 A12 A13

A20 A21 A22 A23

A30 A31 A32 A33

Shift B

B02 B12 B22 B32

B03 B13 B23 B33

B00 B10 B20 B30

B01 B11 B21 B31

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

A00 A01 A02 A03

A10 A11 A12 A13

A20 A21 A22 A23

A30 A31 A32 A33

B02 B12 B22 B32

B03 B13 B23 B33

B00 B10 B20 B30

B01 B11 B21 B31

Global sumon the rowsof C

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

A00 A01 A02 A03

A10 A11 A12 A13

A20 A21 A22 A23

A30 A31 A32 A33

B02 B12 B22 B32

B03 B13 B23 B33

B00 B10 B20 B30

B01 B11 B21 B31

Localcomputation

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Complexity Analysis

Very cumbersome Two models

4-port model: every processor can communicate with its 4 neighbors in one step

Can match underlying architectures like the Intel Paragon

1-port model: only one single communication at a time for each processor

Both models are assumed bi-directional communication

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One-port results

Cannon

Fox

Snyder

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Complexity Results

m in these expressions is the block size Expressions for the 4-port model are MUCH more

complicated Remember that this is all for non-cyclic distributions

formulae and code become very complicated for a full-fledge implementation (nothing divides anything, nothing’s a perfect square, etc.)

Performance analysis of real code is known to be hard

It is done in a few restricted cases An interesting approach is to use simulation

Done in ScaLAPACK (Scalable Linear Algebra PACKage) for instance

Essentially: you have written a code so complex you just run a simulation of it to figure out how fast it goes in different cases

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So What?

Are we stuck with these rather cumbersome algorithms?

Fortunately, there is a much simpler algorithm that’s not as clever about as good in practice anyway

That’s the one you’ll implement in your programming assignment

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The Outer-Product Algorithm

Remember the sequential matrix multiplyfor i = 1 to n

for j = 1 to n for k = 1 to n

Cij = Cij + Aik * Bkj

The first two loops are completely parallel, but the third one isn’t i.e., in shared memory, would require a mutex to

protect the writing of shared variable Cij

One solution: view the algorithm as “n sequential steps”for k = 1 to n // done in sequence

for i = 1 to n // done in parallel for j = 1 to n // done in parallel

Cij = Cij + Aik * Bkj

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The Outer-Product Algorithm

for k = 1 to n // done in sequence

for i = 1 to n // done in parallel

for j = 1 to n // done in parallel

Cij = Cij + Aik * Bkj

During the kth step, the processor who “owns” Cij needs Aik and Bkj

Therefore, at the kth step, the kth column on A and the kth row of B must be broadcasted over all processors

Let us assume a 2-D block distribution

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2-D Block distribution

A00 A01 A02 A03

A10 A11 A12 A13

A20 A21 A22 A23

A30 A31 A32 A33

C00 C01 C02 C03

C10 C11 C12 C13

C20 C21 C22 C23

C30 C31 C32 C33

B00 B01 B02 B03

B10 B11 B12 B13

B20 B21 B22 B23

B30 B31 B32 B33

k

k

At each step, n-q processors receive a piece of the kth column and n-q processors receive a piece of the kth row (n=q2 processors)

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Outer-Product Algorithm

Once everybody has received a piece of row k, everybody can add to the Cij’s they are responsible for

And this is repeated n times In your programming assignment:

Implement the outer-product algorithm Do the “theoretical” performance

analysis with assumptions similar to the ones we

have used in class so far

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Further Optimizations

Send blocks of rows/column to avoid too many small transfers What is the optimal granularity?

Overlap communication and computation by using asynchronous communication How much can be gained?

This is a simple and effective algorithm that is not too cumbersome

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Cyclic 2-D distributions

What if I want to run on 6 processors? It’s not a perfect square

In practice, one makes distributions cyclic to accommodate various numbers of processors

How do we do this in 2-D? i.e, how do we do a 2-D block cyclic

distribution?

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The 2-D block cyclic distribution

Goal: try to have all the advantages of both the horizontal and the vertical 1-D block cyclic distribution Works whichever way the computation

“progresses” left-to-right, top-to-bottom, wavefront, etc.

Consider a number of processors p = r * c arranged in a rxc matrix

Consider a 2-D matrix of size NxN Consider a block size b (which divides

N)

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The 2-D block cyclic distribution

b

b

N

P0 P1 P2

P5P4P3

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The 2-D block cyclic distribution

P2

P5

P1

P4

P0

P3

b

b

N

P0 P1 P2

P5P4P3

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The 2-D block cyclic distribution

P2 P0 P1 P2 P0 P1

P5 P3 P4 P5 P3 P4

P1

P4

P0

P3

b

b

N

P0 P1 P2

P5P4P3

P2 P0 P1 P2 P0 P1

P5 P3 P4 P5 P3 P4

P1

P4

P0

P3

P2 P0 P1 P2 P0 P1

P5 P3 P4 P5 P3 P4

P1

P4

P0

P3

P2 P0 P1 P2 P0 P1P1P0

Slight load imbalance Becomes negligible with

many blocks Index computations had

better be implemented in separate functions

Also: functions that tell a process who its neighbors are

Overall, requires a whole infrastructure, but many think you can’t go wrong with this distribution