IN3200/IN4200: Chapter 2

Basic optimization techniques for serial code

Textbook: Hager & Wellein, Introduction to High Performance Computing for Scientists and
Engineers
Objectives of Chapter 2

“Common sense” and simple optimization strategies for serial

code
(Data access optimization will be discussed in Chapter 3)
The role of compilers
Basics of performance profiling
“Common sense” optimizations

Very simple code changes can sometimes lead to significant

performance boost.
The most important “common sense” principle: avoiding
performance pitfalls!
Do less work; example 1
Example: assume A is an array of numerical values, and a
prescribed threshold value: threshold_value.

int flag = 0;
for (i=0; i<N; i++) {
if ( some_function(A[i]) < threshold_value )
flag = 1;
}

Improvement: leave the loop as soon as flag becomes 1.

int flag = 0;
for (i=0; i<N; i++) {
if ( some_function(A[i]) < threshold_value ) {
flag = 1;
break;
}
}
Do less work; example 2

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

for (j=0; j<80; j++)
for (k=0; k<4; k++)
a[i][j][k] = a[i][j][k] + b[i][j][k]*c[i][j][k];

How many times is the k-indexed loop executed? And how many
times for the j-indexed loop?
Do less work; example 2 (cont’d)

If the 3D arrays a, b and c have contiguous memory storage for all

their values, then we can re-code as follows:

double *a_ptr = a[0][0];

double *b_ptr = b[0][0];
double *c_ptr = c[0][0];

for (i=0; i<(500*80*4); i++)

a_ptr[i] = a_ptr[i] + b_ptr[i]*c_ptr[i];

This technique is called loop collapsing. The main motivation is to

reduce loop overhead, may also help other (compiler-supported)
optimizations.
Do less work; example 3

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

a[i] = 0.;
for (j=0; j<ARRAY_SIZE; j++)
a[i] = a[i] + b[j]*d[j]*c[i];
}

Observation: c[i] is independent of the j-indexed loop.

Do less work; example 3 (cont’d)

Improvement:

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

a[i] = 0.;
for (j=0; j<ARRAY_SIZE; j++)
a[i] = a[i] + b[j]*d[j];
a[i] = a[i]*c[i];
}

Can we improve further?

Do less work; example 3 (further simplification)

There is a common factor:

b[0]*d[0]+b[1]*d[1]+...+b[ARRAY_SIZE-1]*d[ARRAY_SIZE-1]
which is unnecessarily re-computed in every i iteration!

t = 0.;
for (j=0; j<ARRAY_SIZE; j++)
t = t + b[j]*d[j];

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

a[i] = t*c[i];

This technique is called loop factoring or elimination of common

subexpressions.
Another example of common subexpression elimination

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

A[i] = A[i] + s + r*sin(x);

tmp = s + r*sin(x);
for (i=0; i<N; i++)
A[i] = A[i] + tmp;
Avoid expensive operations!
Special math functions (such as trigonometric, exponential and
logarithmic functions) are usually very costly to compute.
An example from simulating non-equilibrium spins:

for (i=1; i<Nx-1; i++)

for (j=1; j<Ny-1; j++)
for (k=1; k<Nz-1; k++) {
iL = spin_orientation[i-1][j][k];
iR = spin_orientation[i+1][j][k];
iS = spin_orientation[i][j-1][k];
iN = spin_orientation[i][j+1][k];
iO = spin_orientation[i][j][k-1];
iU = spin_orientation[i][j][k+1];
edelz = iL+iR+iS+iN+iO+iU;
body_force[i][j][k] = 0.5*(1.0+tanh(edelz/tt));
}
Example continued
If the values of iL, iR, iS, iN, iO, iU can only be −1 or +1,
then the value of edelz (which is the sum of iL, iR, iS, iN,
iO, iU) can only be −6, −4, −2, 0, 2, 4, 6.
If tt is a constant, then we can create a lookup table:

double tanh_table[13];
for (i=0; i<=12; i+=2)
tanh_table[i] = 0.5*(1.0+tanh((i-6)/tt));

for (i=1; i<Nx-1; i++)

for (j=1; j<Ny-1; j++)
for (k=1; k<Nz-1; k++) {
....
edelz = iL+iR+iS+iN+iO+iU;
body_force[i][j][k] = tanh_table[edelz+6];
}
Strength reduction

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

y[i] = pow(x[i],3)/s;

double inverse_s = 1.0/s;

for (i=0; i<N; i++)
y[i] = x[i]*x[i]*x[i]*inverse_s;
Strength reduction (another example)

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

y[i] = a*pow(x[i],4)+b*pow(x[i],3)+c*pow(x[i],2)
+d*pow(x[i],1)+e;

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

y[i] = (((a*x[i]+b)*x[i]+c)*x[i]+d)*x[i]+e;

Use of Horner’s rule of polynomial evaluation:

ax 4 + bx 3 + cx 2 + dx + e = (((ax + b)x + c)x + d)x + e

Shrinking the work set!

The work set of a code is the amount of memory it uses (or

touches), also called memory footprint.
In general, shrinking the work set (if possible) is a good thing for
performance, because it raises the probability of cache hit.
One example: The spin_orientation array should store values of
type char instead of type int. (A factor of 4 in the difference of
memory footprint.)
Avoiding branches

“Tight” loops: few operations per iteration, typically optimized by

compiler using some form of pipelining. In case of conditional
branches in the loop body, the compiler optimization will easily fail.

for (j=0; j<N; j++)

for (i=0; i<N; i++) {
if (i>j)
sign = 1.0;
else if (i<j)
sign = -1.0;
else
sign = 0.0;

C[j] = C[j] + sign * A[j][i] * B[i];

}
Avoiding branches (cont’d)

for (j=0; j<N-1; j++)

for (i=j+1; i<N; i++)
C[j] = C[j] + A[j][i] * B[i];

for (j=1; j<N; j++)

for (i=0; i<j; i++)
C[j] = C[j] - A[j][i] * B[i];
}

We have got rid of the if-tests completely!

Another example of avoiding branches

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

if (i==0)
a[i] = b[i+1]-b[i];
else if (i==n-1)
a[i] = b[i]-b[i-1];
else
a[i] = b[i+1]-b[i-1];
}
Another example of avoid branches (cont’d)

Using the technique of loop peeling, we can re-code as follows:

a[0] = b[1]-b[0];
for (i=1; i<n-1; i++)
a[i] = b[i+1]-b[i-1];
a[n-1] = b[n-1]-b[n-2];
Yet anothe example of avoiding branches

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

if (j>0)
x[i] = x[i] + 1;
else
x[i] = 0;
}

if (j>0)
for (i=0; i<n; i++)
x[i] = x[i] + 1;
else
for (i=0; i<n; i++)
x[i] = 0;
Using SIMD instructions

A “vectorizable” loop can potentially run faster if multiple

operations can be performed with a single instruction.
Using SIMD instructions, register-to-register operations will be
greatly accelerated.
Warning: if the code is strongly limited by memory bandwidth, no
SIMD technique can bridge this gap.
Ideal scenario for applying SIMD to a loop

All iterations are independent

There is no branch in the loop body
The arrays are accessed with a stride of one

Example:

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

r[i] = x[i] + y[i];

(We assume here that the memory regions pointed by r, x, y do

not overlap—no aliasing)
An example of applying SIMD

Pseudocode of applying SIMD (assuming that each SIMD register

can store 4 values):

int i, rest = N%4;

for (i=0; i<N-rest; i+=4) {
load R1 = [x[i],x[i+1],x[i+2],x[i+3]];
load R2 = [y[i],y[i+1],y[i+2],y[i+3]];
R3 = ADD(R1,R2);
store [r[i],r[i+1],r[i+2],r[i+3]] = R3;
}
for (i=N-rest; i<N; i++)
r[i] = x[i] + y[i];
Beware of loop dependency!

If a loop iteration depends on the result of another

iteration—loop-carried dependency

for (i=start; i<end; i++)

A[i] = 10.0*A[i+offset];

If offset<0 → real dependency (read-after-write hazard)

If offset>0 → pseudo dependency (write-after-read harzard)
When there is loop-carried dependency...

In case of real dependency, SIMD cannot be applied if the negative

offset size is smaller than the SIMD width. For example,

for (i=start; i<end; i++)

A[i] = 10.0*A[i-1];

In case of pseudo dependency, SIMD can be applied. For example

when offset>0,

for (i=start; i<end; i++)

A[i] = 10.0*A[i+offset];
Risk of aliasing

Is it safe to vectorize the following function?

void compute(int start, int stop, double *a, double *b) {

for (int i=start; i<stop; i++)
a[i] = 10.0*b[i];
}
Risk of aliasing (cont’d)

A problem of “aliasing” will arise if the compute function is called

as follows

compute(0, N-1, &(array_a[1]), array_a);

If a programmer can guarantee that aliasing won’t happen, this hint

can be provided to the compiler.
The role of compilers

A compiler translates a program, which is implemented in a

programming language, to machine code.
A compiler can carry out code optimization of various degrees,
dictated by the compiler options provided by the user. (-O0, -O1,
-O2, ....)
Different compilers probably allow different compiler options,
should refer to the user manual!
Numerical accuracy may suffer from too aggressive compiler
optimizations.
Profiling

Profiling—gather information about a program’s behavior,

especially its use of resourses. The purpose is to pinpoint the “hot
spots”, and more importantly, to identify any performance
optimization opportunities (if any) and/or bugs.
Two apporaches of “information gathering”:

Instrumentation—compiler automatically inserts some code to

log each function call during the actual execution
Sampling—the program execution is interrupted at periodic
intervals, with information being recorded
GNU gprof

One well-known profiler: GNU gprof

https://sourceware.org/binutils/docs/gprof/

Step 1: compile and link the program with profiling enabled;

Step 2: execute the program to generate a profile data file;
Steo 3: run gprof to analyze the profile data.

(There are other profilers, of course.)

Hardware performance counters

Knowing how much time is spent where is the first step. But what
is the actual reason for “a slow code” or by which resource is the
performance limited?
Modern processors feature a small number of performance
counters, which are special on-chip registers that get incremented
each time a certain event occurs.
Possible events that can be monitored:

number of cache line transfers

number of loads and stores
number of floating-point operations
number of branch mispredictions
number of pipeline stalls
number of instructions executed