computer sciences

Introduction

to Scientific Programming in

C++

Ramses van Zon Scott Northrup

SciNet/Compute Canada

April 23, 2012

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Outline of the course

Introduction

2 C review (+make)

3 Running example

C++ as a better C

Big C++

(object oriented programming)

Important libraries

Further reading

. . .

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Part I

Introduction

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Introduction

Programming strategies

1 Procedural programming

2 Structured programming

3 Object oriented programming

Definition

In procedural programming, one takes the view that a sequence of actions
are performed on given data.

Definition

Structured programming uses a systematic break-down of this sequence of
actions down to the simplest task level.

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Introduction – Procedural and structured programming

Procedural

Structured

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Introduction – Procedural and structured programming

Problems

Complex input data

Multiple actions to be performed on data

Separation data+code is bad for reusability

Leads to reinventing the wheel

One would instead like to build “components” with known properties and
known ways to plug them into your program.

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Introduction – Object oriented programming

Definition

Object oriented programming treats data and the procedures that act on
them as single “objects”.

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Introduction – Object oriented programming

Advantages

Complexity can be hidden inside each component.

Can separate interface from the implementation.

Allows a clear separation of tasks in a program.

Reuse of components.

Same interface can be implemented by different kinds of objects.

Helps maintanance.

Gotcha: Mind The Cost!

Complexity may be hidden, but you should know:

• the computational cost of the operations
• what temporary objects may be created

• and how much creating different types of object costs.

On a low level, OOP rules may need to be broken for best performance.

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Introduction – Language choice

You can apply these programming strategies to almost any
programming languages, but:

The amount of work involved in object-oriented or generic
programming differs among languages.

As a result, the extent to which the compiler helps you by forcing you
not to make mistakes differs among languages.

C++

C++ was designed for object oriented and generic programming,

and C++ has better memory management, stricter type checking,
and easier creation of new types than C,

while you can still optimize at a low level when needed.

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Introduction: History of C++

• 1967 Simula 67: First object-oriented language by Dahl & Nygaard.
• 1969 – 1973 C developed by Dennis Ritchie.
• 1979 Bjarne Stroustup writes preprocessor for classes in C
• 1983 Now called C++.
• 1985 1st edition “The C++ Programming Language”

C++ supports: classes, derived classes, public/private,
constructors/descructors, friends, inline, default arguments,
virtual functions, overloading, references, const, new/delete

• 1986 Object Pascal (Apple,Borland)
• 1987 pointers to members, protected members
• 1989 multiple inheritance, abstract classes, static member functions
• 1995 ISO/ANSI C Standard
• 1990 templates
• 1993 namespaces, cast operators, bool, mutable, RTTI
• 1995 Sun releases Java
• 1998 ISO C++ standard
• 2011 New C++11 standard source: www.devx.com/specialreports/article/38900

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Part II

Review of C

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C review: Basics

C was designed for (unix) system programming.

C has a very small base.

Most functionality is in (standard) libraries.

Most basic C program:

int main() {
return 0;

}

main is first called function: must return an int .

C expresses a lot with punctuation.

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C review: Language elements

Variables

Define a variable with
type name;

where type may be a

built-in type:

floating point type:
float, double, long double

integer type:
short, [unsigned] int, [unsigned] long int

character or string of characters:
char, char*

structure
enumerated type
union
array
pointer

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C review: Language elements

Pointers

type *name;

Assignment:

int a,b;
int *ptr = &a;
a = 10;
b = *ptr;

Automatic arrays

type name[number];

Gotcha: limitations on automatic arrays

• There’s an implementation-dependent limit on number.
• C standard only says at least 65535 bytes.

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C review: Language elements

Dynamically allocated arrays

Defined as a pointer to memory:

type *name;

Allocated by a function call:

name = (type*)malloc(sizeof(type)*number);

Deallocated by a function call:

free(name);

System function call can access all available memory.

Can check if allocation failed (name == 0).

Can control when memory is gived back.

Can even resize memory.

Even better in C++
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C review: Language elements

Structures: collection of other variables.

struct name {
type1 name1;
type2 name2;
…

};

Example

struct Info {
char name[100];
unsigned int age;

};
struct

Info myinfo;

myinfo.age = 38;
strcpy(myinfo.name, “Ramses”);

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C review: Language elements

Enums

Used to define integer constants, typically increasing.

enum name {
enumerator[=value], …

};

By default, successive enumerators get successive integer values.

In C, interconvertible with an int.
Useful to reduce number of #define’s.

Unions

Put one variable on top of another; rarely used.

union name {
type1 name1;
type2 name2;
…

};

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C review: Language elements

Typedefs

Used to give a name to an existing data type, or a compound data type.

typedef existingtype newtype;

Similar to existingtype name; but defines a type instead of a variable.

Example (a controversial way to get rid of the struct keyword)

typedef struct Info Info;

Then you can declare a struct Info simply by

Info myinfo;

This works become the name Info in “struct Info” does not live in the
namespace of typenames.

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C review: Language elements

Functions

Function declaration (prototype)

returntype name(argument-spec);

Function definition

returntype name(argument-spec) {
statements

}

Function call

var = name(arguments);
f(name(arguments);

Procedures

Procedures are just functions with return type void and are called without
assignment.

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C review: Language elements

Conditionals

if (condition) {
statements

} else if (other condition) {
statements

} else {
statements

}

switch (integer-expression) {
case integer:

statements
break;

…
default:

statements;
break;

}

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C review: Language elements

Loops

while (condition) {
statements

}

for (initialization;condition;increment) {
statements

}

You can use break to exit the loop.

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C review: Operators

C has many operators

() [] -> .

! ++ — (type) – * &

* / %

+ –

<< >> < <= > >=

== !=

& ^ | && || ?:

= += -= *= /= %= |= &=

Gotcha: Bad precendence

Relying on operator precedence is error-prone and makes code harder to
read and thus maintain (except for +, -, *, / and maybe %).

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C review: Libraries

Usage

Put an include line in the source code, e.g.

#include
#include “mpi.h”

Include the libraries at link time.
(not needed for standard libraries)

Common standard libraries

stdio.h: input/output, e.g.,printf and fwrite

stdlib.h: memory, e.g. malloc

string.h: strings, memory copies, e.g. strcpy

math.h: special function, e.g. sqrt

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Compilation:
Workflow

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Compilation workflow

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Compiling

Scientific computing = performance: Compile with optimization!

Compiling C from the command-line

If the source is in main.c, type

$ gcc main.c -O3 -o main

$ icc main.c -O3 -o main

Compiling C++ from the command-line

If the source is in main.cpp, type

$ g++ main.cpp -O3 -o main

$ icpc main.cpp -O3 -o main

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Compilation:
Using make

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Compiling with make

Single source file

# This file is called

makefile

CC = gcc
CFLAGS = -O3
main: main.c

$(CC) $(CFLAGS) main.c -o main

Multiple source file application

CC = gcc
CFLAGS = -O3
main: main.o mylib.o

$(CC) main.o mylib.o -o main
main.o: main.c mylib.h
mylib.o: mylib.h mylib.c
clean:
\rm main.o mylib.o

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Compiling with make

When typing make at command line:

Checks if main.c or mylib.c or mylib.h were changed.

If so, invokes corresponding rules for object files.

Only compiles changed code files: faster recompilation.

Gotcha:

Make can only detect changes in the dependencies.
It does not detect changes in compiler, or in system.
But .o files are system/compiler dependent, so they should be recompiled.
So always specify a “clean” rule in the makefile, so that moving from one
system or compiler to another, you can do a fresh rebuild:

$ make clean

$ make

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Part III

Our running example, starting in C

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mymatrix.h/main.c/mymatrix.c

#ifndef MYMATRIXH
#define MYMATRIXH
/* struct to hold a matrix */
struct matrix {

int rows,cols; /* matrix dimensions */
double *elements; /* points to elements */

};
/* initialize matrix (needed before usage) */
void matrix construct(struct matrix *m,int r,int c);
/* free memory held by matrix (do after last usage) */
void matrix destructor(struct matrix *m);
/* access matrix elements (through a pointer) */
double * matrix element(struct matrix *m,int i,int j);
/* set all matrix elements to value */
void matrix fill(struct matrix *m,double value);
#endif

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#include
#include “mymatrix.h”
void print(struct matrix *m) {

int i,j;
for (i=0; i < m->rows; i++) {

for (j=0; j < m->cols; j++)
printf(“%8.2g “,*matrix element(m,i,j));

printf(“\n”);
}

}
int main() {

struct matrix A;
matrix construct(&A, 5, 5);
matrix fill(&A, 0.0);
*matrix element(&A, 0, 0) = 1.3;
*matrix element(&A, 4, 3) = -5.2;
*matrix element(&A, 1, 3) = -3.3e-4;
print(&A);
matrix free(&A);

}

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#include
#include “mymatrix.h”
void matrix construct(struct matrix *m,int r,int c) {

m->elements = (double *)malloc(sizeof(double )*r*c);
if (m->elements==0) exit(1); /* exit program */
m->rows = r;
m->cols = c;

}
void matrix free(struct matrix *m) {

free(m->elements);
}
double * matrix element(struct matrix *m,int i,int j) {

return m->elements+i*m->cols+j;
}
void matrix fill(struct matrix *m, double value) {

int i,j;
for (i=0; i < m->rows; i++)

for (j=0; j < m->cols; j++)
*matrix element(m,i,j)=value;

}

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makefile

CC = gcc
CFLAGS = -O3 -march=native
main: main.o mymatrix.o

$(CC) main.o mymatrix.o -o main
main.o: main.c mymatrix.h
mymatrix.o: mymatrix.h mymatrix.c

$ make
gcc -O3 -march=native -c -o main.o main.c
gcc -O3 -march=native -c -o mymatrix.o mymatrix.c
gcc main.o mymatrix.o -o main
$ main 1.3 0 0 0 0
0 0 0 -0.00033 0
0 0 0 0 0
0 0 0 0 0
0 0 0 -5.2 0

Get the code at:
wiki.scinethpc.ca/wiki/images/3/38/Scinetcppexamples.tgz

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Part IV

C++ as a better C

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Nice C++ features

1 Comment style

2 Declare variables anywhere

3 Namespaces

4 Improved I/O approach

5 References

6 Improved memory allocation

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Nice C++ features: Comment style

C comments start with /* and end with */

C++ allows comments which start with // and last until the
end-of-the-line.

In addition, C-style comments are still allowed.

C99 shares this nicety.

Example

/* This is a C comment*/

C++:

// This is a C++ comment

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Nice C++ features: Declare variables anywhere

C: variables are declared at start of function or file.

C++: you can mix statements and variable declarations.

C99 shares this nicety.
Example
C:

double f() {
double a,b;
int c;
a=5.2;
b=3.1;
for (c=0; c < 10; c++)

a+=b;
return a;

}
C++:

double f() {
double a=5.2, b=3.1;
for (int c=0; c < 10; c++)

a+=b;
return a;
}

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Nice C++ features: Namespaces

In larger projects, name clashes can occur.

I had a 3d vector struct called vector. Then came along the Standard
Template Library, which defined vector to be a general array. Before

namespaces, I had to rename vector to Vector in all my code.

No more: put all functions, structs, . . . in a namespace:

namespace nsname {
…

}

Effectively prefixes all of … with nsname::

Many standard functions/classes are in namespace std.

To omit the prefix, do “using namespace nsname;”

Can selectively omit prefix, e.g., “using std::vector”

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Nice C++ features: I/O streams

Standard input/error/output

Streams objects handle input and output.

All in namespace std.

Global stream objects (header: )

cout is for standard output (screen)
cout is the standard error output (screen)
cin is the standard input (keyboard)

Use insertion operator << for output:

std::cout << "Output to screen!" << std::endl;

(endl ends the line and flushes buffer)

Use extraction operator >> for input:

std::cin >> variable;

These operators figure out type of data and format.

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Nice C++ features: I/O streams

File stream objects (header: )

ofstream is for output to file.
Declare with filename: good to go!

std::ofstream file(“name.txt”);
file << "Writing to file";

ifstream is for input from a file.
Declare with filename: good to go!

std::ifstream file(“name.txt”);
int i;
file >> i;

Can also open and close by hand.

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Nice C++ features: I/O streams
Example

C:
double a,b,c;
FILE* f;
scanf(f, “%lf %lf %lf”, &a, &b, &c);
f = fopen(“name.txt”,”w”);
fprintf(f, “%lf %lf %lf\n”, a, b, c);
fclose(f);

C++:

using namespace std;
double a,b,c;
cin >> a >> b >> c;
ofstream f(“name.txt”);
f << a << b << c << endl;

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Nice C++ features: I/O Streams

Formatting (header: )

Set width of next output:

double d = 14.545;
cout << "[" << setw(10) << d << "]" << endl;

[ 14.525]
Set significant digits of output to follow:

cout << "[" << setprecision(3) << d << "]" << endl;

[14.5]

Set precision of next output:

cout << setw(9) << setfill('#') << d << endl;

#####14.5

Change to scientific notation

cout << scientific << d << endl;

1.454e+01(revert with fixed)

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Nice C++ features: I/O Streams

Gotcha: text (ASCII) versus binary I/O

While easy, writing ASCII is rarely the best choice in scientific code.
“What is wrong with ASCII,” you ask, “isn’t it nice that it is readable?”

ASCII typically doesn’t preserve the data’s accuracy.

ASCII typically takes more space than writing binary.

Writing and reading ASCII is much slower than binary:
Writing 128M doubles

Format /scratch (GPFS) /dev/shm (RAM) /tmp (disk)

ASCII 173s 174s 260s
Binary 6s 1s 20s

Writing binary

std::ofstream has a write(char*,int) member function.
std::ifstream has a read(char*,int) member function.
Remember sizeof!

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Nice C++ features: References

A reference gives another name to an existing object.

References are similar to pointers.

Do not use pointer dereferencing (->), but a period .

Cannot be assigned null.

Standalone definition (rare)

type & name = object;

object has to be of type type.

name is a reference to object.

name points to object, i.e., changing name changes object.

Members accessed as name.membername (as you would for object).

Definition as arguments of a function

returntype functionname(type & name, …);

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Nice C++ features: References
Example

To change a function argument, need a pointer in C:

void makefive(int * a) {
*a = 5;

} …
int b = 4;
makefive(&b); /* b now holds 5 */

C++: can pass by reference using &:

void makefive(int & a){
a = 5;

} …
int b = 4;
makefive(b); /* b now holds 5 */

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Nice C++ features: References

Gotcha: Avoid copies of objects in function calls

Compare these two functions

struct Point3D {
double x,y,z;

};
void print1(Point3D a){

std::cout << a.x << ' ' << a.y << ' ' << a.z << std::endl; }

void print2(Point3D& a){

std::cout << a.x << ' ' << a.y << ' ' << a.z << std::endl; }

Calling print1 copies the content of a to the stack (24 bytes).

Calling print2 only copies the address of a to the stack (8 bytes).

Memory copies are not cheap!

If we do this with classes, a so-called constructor is called everytime
print1 is called, whereas print2 still only copies 8 bytes.

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Nice C++ features: Improved memory allocation

Basic allocation
type* name = new type;

Allocation with initialization
type* name = new type(arguments);

Array allocation

type* name = new type[arraysize];

Basic de-allocation
delete name;

Array de-allocation

delete [] name;

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Nice C++ features: Improved memory allocation
Example

struct credit {
long number, balance;

};

No more of this mess:
#include “stdlib.h”
struct credit* a;
double * b;
a = (struct credit*)malloc(sizeof(struct credit));
b = (double *)malloc(sizeof(double )*10000);
…
free(a); free(b);

Instead, simply:

credit* a = new credit;
double * b = new double [10000];
…
delete a; delete[] b;

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HANDS-ON 1:
Use these nice c++ features to rewrite the matrix routines and the main
function.

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Hands-on 1 – instructions

Make a directory for this course in your home directory, e.g.

$ mkdir scinetc++
$ cd scinetc++

Copy the example directory from scinetcppexamples.tgz
This is the matrix example that we looked at after the c review.

Work from that new directory:

$ cd example

Try to build the code

$ make

If successful, try to execute the program

$ ./main

Every with me so far?

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Hands-on 1 – instructions continued

Copy the example directory to example nice, and work there:

$ cd ..
$ cp -r example example nice
$ cd example nice

This will be the first c++ version of the matrix example.

Rename a the .c files to .cpp files:

$ mv main.c main.cpp
$ mv mymatrix.c mymatrix.cpp

Copy the makefile for this set of files from the example nice directory
in scinetcppexamples.tgz.

Try to build and run the code

$ make
$ ./main

Still with me?
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Hands-on 1 – instructions continued

Modify the code to use (one at a time):

1 C++ comment style

2 Declarations of iteration variables in for loops

3 Improved memory allocation

4 Improved I/O

5 References

Test that the code builds and runs after implementing each feature.

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Hands-on 1 – answers

If you did not quite get there, or if you have a few remaining bugs:

Copy the c++ version I made, from the example nice directory in
scinetcppexamples.tgz, so we can continue later.

Test that the code builds and runs.

Be sure to look at the source code and see if it make sense to you.

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Part V

Big C++

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Object oriented programming (OOP)

Non-OOP: functions and data that are accessible from everywhere.

OOP: Data and functions (methods) together in an object.

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Object oriented programming (OOP)

Data is encapsulated and accessed using methods specific for that
(kind of) data.

The interface (collection of methods) should be designed around the
meaning of the actions: abstraction.

Programs typically contain multiple objects of the same type, called
instances.

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Object oriented programming (OOP)

Programs typically contain different types of objects.

Types of objects can be related, and their methods may act in the
same ways, such that the same code can act on different types of
object, without knowing the type: polymorphism.

Types of object may build upon other types through inheritance.

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OOP Example

Example (abstract object hierarchy)

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OOP Languages

C++ was one of the earlier languages which supported OOP.
(it also supports other programming paradigms.)

Not the earliest OOP language though: Simula, Smalltalk

Java, C#, D all came later.

And one can program in an object oriented fashion in almost any
modern programming language (see matrix example in C).

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Aspects of OOP in C++

1 Classes and objects

2 Polymorphism

3 Derived types/

Inheritance

4 Advanced: Generic programming/

Templates

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Big C++: Classes and objects

What are classes and objects?

Objects in C++ are made using ’classes’.

A class is a type of object.

Using a class, one can create one or more instances of that class.

These are the objects.

Syntactically, classes are structs with member functions.

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Classes: Why structs with member functions?

An object should have properties.

1 A struct can already collect properties of different types.

2 It should be possible to declare several objects of the same type, just
as in “int x,y;”. A struct already constitutes a type definition.

3 Functions on structs often pass a pointer to a struct as a parameter.
Embedding functions in structs gives a natural implied parameter.

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Classes: How do we add these member functions?

class classname {
public:

type1 name1;
type2 name2;
type3 name3(arguments); // declare member function
…

};

public allows use of members from outside the class (later more)

Example

class Point2D {
public:

int j;
double x,y;

void set(int aj,double ax,double ay);

};

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 64 / 124

Classes: How do we define these member functions?

The scope operator ::

type3 classname::name3(arguments) {
statements

}
Example

void Point2D::set(int aj,double ax,double ay) {

j = aj;
x = ax;
y = ay;

}

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 65 / 124

Classes: How do we use the class?

Definition

classname objectname;
classname* objectptrname = new classname;

Access operator . and ->

objectname.name // variable access
objectname.name(arguments); // member function access
objectptrname->name // variable access
objectptrname->name(arguments); // member function access

Example

Point2D myobject;
myobject.set(1,-0.5,3.14);
std::cout << myobject.j << std::endl;

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 66 / 124

Classes: How do we use the class?

The this pointer

The member functions of a class know what object to work on
because under the hood, they are passed the pointer to the object.

For those cases where the pointer to the object is needed, its name is
always this.

In other words, in the set function, j and this->j are the same.

this is implicitly the first argument to the member function
(this will become important in operator overloading later).

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Data hiding: The secret agenda of classes

Good components hide implementation data and member functions.

Each member function or data member can be
1 private: only member functions of the same class can access these
2 public: accessible from anywhere
3 protected: only this class and its derived classes have access.

These are specified as sections within the class.

Example (Declaration)

class Point2D {
private:

int j;
double x,y;

public:
void set(int aj,double ax,double ay);
int get j();
double get x();
double get y();

};
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Data hiding: The secret agenda of classes

Example (Definition)

int Point2D::get j() {
return j;

}
double Point2D::get x() {

return x;
}
double Point2D::get y() {

return y;
}

Example (Usage)

Point2D myobject;
myobject.set(1,-0.5,3.14);
std::cout << myobject.get j() << std::endl;

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 69 / 124

Data hiding: The secret agenda of classes
Gotcha:

When hiding the data through these kinds on accessor functions, now,
each time the data is needed, a function has to be called, and there’s an
overhead associate with that.

The overhead of calling this function can sometimes be optimized
away by the compiler, but often it cannot.

Considering making data is that is needed often by an algorithm just
public, or use a friend .

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Constructors and deconstructors

A class defines a type, and when an instance of that type is declared,
memory is allocated for that struct.

A class is more than just a chunk of memory.
For example, arrays may have to be allocated (new . . . ) when the
object is created.

When the object ceases to exist, some clean-up may be required
(delete . . . ).

Constructor

. . . is called when an object is created.

Destructor

. . . is called when an object is destroyed.

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Constructors

Declare constructors as member functions of the class with no return type:

class classname{
…

public:
classname(arguments);
…

}

Define them in the usual way,

classname::classname(arguments) {
statements

}

Use them by defining an object or with new.

classname object(arguments);
classname* object = new classname(arguments);

You usually want a constructor without arguments as well.

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 72 / 124

Constructors
Example
class Point2D {
private:
int j;
double x,y;

public:
Point2D(int aj,double ax,double ay);
int get j();
double get x();
double get y();

};
Point2D::Point2D(int aj,double ax,double ay) {

j = aj;
x = ax;
y = ay;

}
Point2D myobject(1,-0.5,3.14);

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Destructors

Destructor

. . . is called when an object is destroyed.
Occurs when a non-static object goes out-of-scope, or when delete is
used.
Good opportunity to release memory.

Example

classname* object = new classname(arguments);
…
delete object;// object deleted: calls destructor

{
classname object;

}// object goes out of scope: calls destructor

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Destructors

Declare destructor as a member functions of the class with no return type,
with a name which is the class name plus a ˜ attached to the left.

class classname{
…

public:
˜

classname();
…

}

Define a destructor as follows:

classname::˜classname() {
statements

}

A destructor cannot have arguments.

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 75 / 124

Gotcha: Mixing new/delete and malloc/free

Trivial objects (plain structs without constructors) can in principle be
a allocated with new or with malloc.

But pointers allocated with new cannot be freed using free, and for
pointers allocated with malloc, delete should not be used.

Non-trivial objects cannot be allocated with malloc, since the
constructor is not called.

It is best to stick to new and delete .

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More member functions

. . . to support the class as a new type:

Default constructor

The default constructor is a constructor without arguments.
If you have no constructors at all, C++ already knows what to do
upon construction with no arguments (i.e., nothing), and you do
not need to supply a default constructor (but it can still be a good
idea).
If you have any constructors with arguments, omitting a default
constructor severely limits the use of the class.

Copy constructor

Assignment operator

If the constructor allocates memory, the latter two should be
supplied. If there is no memory allocation in the constructor, C++
can generate the copy constructor and assignment operator for
you, performing a bit-wise or shallow copy.

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Default constructor

Declaration
classname {

…
public:

classname();
…
};
Definition

classname::classname() {
statements

}

This function is needed to be able to

Declare an object without parameters: classname name;

Declare an array of objects: name = new classname[number];

Should set elements to values so that destruction or assignment work.

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Copy constructor
Declaration
classname {
…
public:

classname (classname & anobject);
…

};
Definition

classname::classname(classname & anobject) {
statements

}

Used to

Define an object using another object: classname name(existing);

Pass an object by value to a function (often a bad idea).

Return an object from a function.

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 79 / 124

Assignment operator
Declaration
classname {
…
public:

classname& operator=(classname & anobject);
…

};
Definition

classname& classname::operator=(classname & anobject) {
statements
return *this;

}

Used to assign one object to another object: name = existing;
But not in classname name = existing; calls the copy constructor.
Returns a reference to this, to allow for the common C-construction

name = anothername = existing;

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HANDS-ON:
Convert the matrix structure to a proper c++ class, and rewrite main to
use it.

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Hands-on 2 – instructions

Copy the whole example nice directory to example big

$ cp -r example nice example big

Modify the code to use:

1 Classes instead of structs

2 Member functions

3 Constructors and deconstructors

4 Private member variables

Test that the code builds and runs.

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 82 / 124

Hands-on 2 – answers

If you did not quite get there, or if you have a few remaining bugs:

Copy the c++ version I made from the example big directory in
scinetcppexamples.tgz, so we can continue later.

Test that the code builds and runs.
Be sure to look at the source code and see if it make sense to you.

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 83 / 124

Big C++: Polymorphism

Poly what now?

Objects that adhere to a standard set of properties and behaviors can
be used interchangeably.

Implemented by Overloading and Overriding

Why bother?

Avoid code duplication/reuse where not necessary

Simplifies and structures code

Common interface

Consistency of design should be more understandable

Debugging

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 84 / 124

Operator Overloading

Use expected syntax for non-built in Types

A = B + C, regardless of what A, B, or C is.

Syntax

Declaration
classname {
…
public:
classname& operator=(classname & anobject);
…
};
Definition
classname& classname::operator=(classname & anobject) {
statements
return *this;
}

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 85 / 124

Operator Overloading

Example (Matrix Class)

class matrix {
private:

int rows, cols;
double *elements;

public:
matrix(int r, int c);
˜matrix();
matrix& operator= (matrix &m);
int get rows();
int get cols();
void fill(double value);
matrix operator+ (const matrix &C);

};

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Operator Overloading

Example (Add two martices)

matrix A(5,5), B(5,5), C(5,5);
A.fill(1.0); B.fill(1.0); C.fill(1.0);
for (int i=0, i

for (int j=0, j

Example (Add two martices using ”+” operator)

matrix A(5,5), B(5,5), C(5,5);
A.fill(1.0); B.fill(1.0); C.fill(1.0);
A = B + C;

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 87 / 124

Operator Overloading

”+” Operator

matrix matrix::operator+ (const matrix &C) {
matrix Temp(*this);
for (int i=0, i

Temp.elements[i] += C.elements[i];
return Temp;

};

”+=” Operator

matrix& matrix::operator+= (const matrix &C) {
for (int i=0, i

elements[i] += C.elements[i];
};

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 88 / 124

Operator Overloading

const

set a constant variable at compile time

keyword to protect your variables

const references

”+=” Operator with bounds checking

matrix& matrix::operator+= (const matrix &C) {
if ( rows == C.rows && cols == C.cols) {

for (int i=0, i

} else {
cerr<<"Matrix Indicies don't match, can't add"; exit(1);

}
};

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Operator Overloading

”( )” Operator

double & matrix::operator() (int &i, int &j) {
return elements[i*cols + j];

};

A(1,4) = 6;
double y = A(1,4);

”[ ]” Index Operator

double matrix::operator[] (int &i) {
return elements[i];

};

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 90 / 124

Operator Overloading

”<<” ”>>” Stream Operators

std::ostream& operator << (std::ostream& o, matrix& m) { for (int i=0; i

for (int j=0; j

}
o << std::endl;

}
};

std::cout<<"Matrix A = "<< A << std::endl;

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 91 / 124

Operator Overloading

Friends

friend keyword allows non-member functions access to private data.

”<<” ”>>” Stream Operator using friend

class matrix {
…
friend std::ostream& operator<<(std::ostream& o, matrix& m); };

std::ostream& operator<<(std::ostream& o, matrix& m) { for (int i=0; i

for (int j=0; j

}
o << std::endl; } };

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 92 / 124

Operator Overloading

C++ operators available to overload

+ – * / % ^ &

| ~ ! = < > +=

-= *= /= %= ^= &= |

<< >> >> = << = == != <=

>= && || ++ — ->* ,

-> [ ] ( ) new new[ ] delete delete[ ]

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 93 / 124

HANDS-ON:
Overload +=, (), and stream operators for matrix c++ class, and rewrite
main to use it.

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OOP: Inheritance (Derived Classes)

Example (abstract object hierarchy)

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Inheritance
Definition

child classes are derived from other parent classes

automatically include parent’s members

inherit all the accessible members of the base class

Specifics

A derived class inherits every member of a base class except:

its constructor and destructor

its assignment operator

its friends

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Inheritance
Syntax

Base Class
class baseclass {

protected:
…
public:

baseclass ()
…

};

Derived Class
class derivedclass : public baseclass {

…
public:

derivedclass : baseclass ()
…

};

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Inheritance

Example (Matrix Base Class)

class matrix {
protected:

int rows, cols;
double *elements;

public:
matrix(int r, int c);
˜matrix();
int get rows();
int get cols();
void fill(double value);
matrix operator+ (const matrix &C)

};

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 98 / 124

Inheritance

Example (Square Matrix Derived Class)

class squarematrix : public matrix {
private:
protected:
public:

squarematrix(int r, int c) : matrix(r,c) {
if(r!=c) std::cerr<<"not a square matrix"; exit(1);

}
double trace() {

double sum(0.0);
for(int i=0; i

}
};

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Inheritance
Example

matrix P(5,5);
squarematrix Q(5,5);
P.fill(1.6);
Q.fill(1.6);
std::cout<<" Trace = "<

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HANDS-ON:
Come up with a derived class inheriting the matrix class as a base class.

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 101 / 124

Polymorphism in Inheritance

Idea

Use base class as framework for derived classes usage.

Define member functions with virtual keyword.

Override base class functions with new implementations in derived
classes.

If virtual keyword not used, overloading won’t occur.

Polymorphism comes from the fact that you could call the based method
of an object belonging to any class that derived from it, without knowing
which class the object belonged to.

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 102 / 124

Inheritance
Example (Matrix Base Class)
class matrix {
protected:
int rows, cols;
double *elements;

public:
matrix(int r, int c);
˜matrix();
int get rows();
int get cols();
virtual void fill(double value);

};

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 103 / 124

Inheritance
Example (Square Matrix Derived Class)
class squarematrix : public matrix {
private:
protected:
public:
squarematrix(int r, int c) : matrix(r,c) {
if(r!=c) std::cerr<<"not a square matrix"; exit(1);

}
double trace();
void fill(double value) {

for (int i=0; i < rows*cols; i++) elements[i] = value;

}
};

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 104 / 124

Inheritance

Example (non-virtual)

squarematrix Q(5,5);
Q.fill(1.6);
std::cout<<" Trace = "<

Example (virtual)

matrix *Q;
Q = new squarematrix(5,5);
Q->fill(1.6);
std::cout<<" Trace = "<trace();

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 105 / 124

Inheritance
Gotcha:

Virtual functions are run-time determined

Equivalent cost to a pointer dereference

Not as efficient as compile time determined (ie non-virtual)

Should be avoided for many use functions

Gotcha:

Friend keyword allows non-member functions access to private data.

Useful but does break OOP and will cause problems in inheritance.

”friends are your enemies”

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 106 / 124

HANDS-ON:
Modify your derived and base class using the virtual keyword.

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 107 / 124

Generic Programming

Definition: Generic Programming

Programming style in which specific Types are not specified initially, but
instantiated when needed.

Templates

In C++ generic programming is implemented using Templates and
instantiated at compile time.

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Templates
Syntax

Functions
template < typename T > funcname (T &a)

Classes
template < class T >
class classname {

private:
T a, b;

public:
classname ();
…
memberfunction(T &c, T &d);

};

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Templates

Example (Double Matrix Class)

class matrix {
private:
int rows, cols;
double *elements;

public:
matrix(matrix& m);
…
void fill(double value);
matrix& operator= (const matrix &m)

};

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Templates

Example (Templated Matrix Class)

template
class matrix {

private:
int rows, cols;
T *elements;

public:
matrix(matrix& m);
…
void fill(T value);
matrix& operator= (const matrix& m);

};

template
matrix::matrix() {

rows = 0; cols = 0;
elements = new T[0];

}

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 111 / 124

Templates

Example (Calling Templated Class)

matrix A(5,5);
A.fill(0.0);
A(0,0) = 1.3;
A(4,3) = -5.2;

matrix B(5,5);
B.fill(33);
B(0,0) = 1;
B(4,3) = 2;

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 112 / 124

Templates

Explicit Instantiation

Can override generic template abstract-type instantiation for a
specific concrete-type.

Similar to derived class override of base class member function.

template<> matrix::fill(double value){
for (int i=0; i < rows; i++) {

for (int j=0; j < cols; j++){ std::cout<<" I'm used for doubles "; (*this)(i,j)=value;

}
}

}

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Templates
Gotcha:

Compile times can be significantly longer.

Large header files.

Debugging can be a pain.

Syntax can get complicated.

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HANDS-ON:
Template your matrix class.

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Part VI

Important libraries

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Important libraries

Don’t reinvent the wheel

It may be interesting to code your own linear algebra solver (say), but
is it worth your time?

There are some good scientific libraries out there.

The nice thing is, they needn’t be c++ libraries, as you can use c
libraries in c++.

Even for basic functionality, there are libraries.

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 117 / 124

STL: Standard Template Library

Offers a lot of basic functionality

Supplies a lot of data types and containers (templated).

Often presented as part and parcel of the C++ language itself.

Also contains a number of algorithms for e.g., sorting, finding

Efficiency implementation dependent, and generally not great.

Some of the STL data types

vector Relocating, expandable array
list Doubly linked list
deque Like vector, but easy to put something at beginning
map Associates keys with elements
set Only keys
stack LIFO
queue FIFO
. . .

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STL: Standard Template Library
Example

#include “iostream”
#include “vector”
class Grape {

public:
int nseeds;

};
int main() {

using namespace std;
Grape grapes[10];
vector bunch(grapes,grapes+9);
bunch.push back(grapes[9]);
for (int i=0; i

cout << bunch[i].nseeds << endl; vector::iterator i;
for (i=bunch.begin(); i!=bunch.end(); i++)

cout << (*i).nseeds << endl; }

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 119 / 124

STL: Standard Template Library

Gotcha: Performance

The purpose of the STL is not to provide a high performance library,
i.e., runtime speed is not the objective.

Rather it aims to have flexible containers with a uniform usage
pattern.

As a result, using e.g. an std::vector in an inner loop of you
computation, instead of a simple array, can substantially slow down
your code (even with the improvements in the implementation since
the early days).

The STL still does not have higher dimensional arrays, and the last
thing you want is to have vectors of vectors.

Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 120 / 124

Other useful (scientific) libraries

library functionality C++ parallel
MPI distributed parallel program X X

OpenMP shared memory parallelism X X
Blas/Lapack linear algebra (in MKL, ESSL) × X×

Petsc matrices, vectors, linear solvers × X
GSL numerical library × ×

Boost continues where STL left off X ×
(+math, statistics, random, blas) Thread&MPI

IT++ templated matrix implementations X ×
Blitz++ (not exhaustive) X ×

Armadillo X X×
POOMA X X

Eigen X ×
. . .

Again: Don’t reinvent the wheel!
Ramses van Zon, Scott Northrup (SciNet) Intro Scientific Programming in C++ April 23, 2012 121 / 124

Part VII