Fundamentals of Computational Science CISC 810

1. Fundamentals of Computational Science CISC 810 Dr Rob Thacker Dept of Physics (308A) thacker@physics

2. Today’s Lecture • Review of assignment 1 • C/Fortran programming overview

3. Assignment 1 solutions • Printed copies will be handed out on Oct 13 • An electronic version will not be made available

4. Humour – more FORTRAN jokes • Joke, circa 1980 (following the standardization of FORTRAN 77): "Q: What will the scientific programming language of the year 2000 look like?” “... A: Nobody knows, but its name will be FORTRAN." • “Consistently separating words by spaces became a general custom about the tenth century A. D., and lasted until about 1957, when FORTRAN abandoned the practice." • —Sun FORTRAN Reference Manual • “FORTRAN, the infantile disorder, by now nearly 20 years old, is hopelessly inadequate for whatever computer application you have in mind today: it is now too clumsy, too risky, and too expensive to use.” • Edsger W. Dijkstra, circa 1970.

5. A note on these programming lectures • In two lectures I can’t possibly tell you all these is to know about C/FORTRAN programming • You learn programming by doing • Sit down at a terminal and write a program • Then a more complicated program and so on… • Please be prepared to look up additional material on the web • If you have not done any programming in C/FORTRAN before don’t be intimidated • It isn’t hard (C just looks harder because of the “strange” syntax) • I’ll try and teach them together where possible, this may mean being convoluted in some places

6. Style • When reading and writing code, you have to keep a bunch of facts straight for a short period of time • What do this function's parameters mean? • What does this loop's index refer to? • The more odds and ends readers have to keep track of, the more errors they will make • Goal of style rules is therefore to reduce the number of things the reader has to juggle mentally • The greater a difference is, the more likely we are to notice it • So every semantic difference ought to be visually distinct… • …and every difference in naming or layout ought to mean something • Most important thing is to be consistent • Anything consistent is readable after a while • Just watch kids learning to read French, Punjabi, and Korean

7. C/FORTRAN issues • Remember: • C is case sensitive: HELP is not the same as help • FORTRAN isn’t • FORTRAN coding style is idiosyncratic • f77 standard requires you keep line lengths to 72 characters(!) • Must also start each line in the 7th column(!) • f90 repealed these issues • C is more syntatically sophisticated than FORTRAN • C requires you place a semi-colon at the end of each command line • Allows you to write very long single lines

8. Naming • Names of files, classes, methods, variables, and other things are the most visible clue to purpose • A variable called temperature shouldn't be used to store the number of pottery shards found at a dig site • Choose names that are both meaningful and readable • current_surface_temperature_of_probe is meaningful, but not readable • cstp is easier to read, but hard to understand… • …and easy to confuse with ctsp • If you must abbreviate, be consistent • curr_ave_temp instead of current_average_temperature is OK… • …but only if no one else is using curnt_av_tmp • The smaller the scope of a name, the more compact it can be • It's OK to use i and j for indices in tightly-nested for loops • But not OK if the loop bodies are several pages long • Of course, they shouldn't be anyway… • The wider the scope of a name, the more descriptive it has to be

9. Good practices

10. Commenting • This is an extremely valuable part of any coding project • Don’t leave it out because you are lazy • Don’t think that your code “reads like a book” and that comments are unnecessary • Don’t ignore it because you don’t have time • Well placed and thought out comments… • Document the development of the code (in addition to any repository comments you make) • Help out from a functional perspective (you can have “To do” lists embedded within the code) • Explain code, functions and the control flow of the program

11. /*************************************** *************************************** *** This really gets your attention *** *** use it for warning messages *** *************************************** ***************************************/ /*----> Another important message <----*/ /*************************************** * Use boxed comments at the start * * of code sections or the program * * * * Here we explain important details * * about the code and algorithm * ***************************************/ /* * A medium-level comment explaining the * next few lines of code. Can still use * * characters to **emphasize** words. */ /* This comment explains the next line */ ! *************************************** ! *************************************** ! *** This really gets your attention *** ! *** use it for warning messages *** ! *************************************** ! *************************************** ! ----> Another important message <---- ! *************************************** ! * Use boxed comments at the start * ! * of code sections or the program * ! * * ! * Here we explain important details * ! * about the code and algorithm * ! *************************************** ! ! A medium-level comment explaining the ! next few lines of code. Can still use ! * characters to **emphasize** words. ! ! This comment explains the next line Explanative comment hierarchy C FORTRAN If you use FORTRAN get into the habit of using ! for comments

12. Good practice • At the beginning of each subroutine include a comment that describes each of the inputs • Do the same for functions • If multiple people are working on the same project add your initials to each comment • e.g. !rjt I added this code for a reason • If you borrow code from other projects make sure this is noted as well – helps others to track down bugs and gives credit where it is due

13. Resist the temptation to be clever • Don’t worry that you don’t understand the details of the following code, the concepts should be clear • The following C example is unclear even to reasonable programmers: while (‘\n’, != *p++ = *q++); • It would have been much better to write this as while(1) { *dest_ptr = *source_ptr; if (*dest_ptr == ‘\n’) break; /* Exit loop if done */ dest_ptr++; source_ptr++; }

14. C – either cc or gcc gcc is the GNU C compiler cc is frequently linked to gcc, but this is platform dependent the Intel C compiler is often denoted icc Usage: cc myfile.c –o myprog FORTRAN – many types f77 – usually links to FORTRAN 77 compiler f90 – usually links to FORTRAN 90 compiler gfortran – gnu fortran ifort – Intel compiler Usage: f77 myfile.f –o myprog Compiler command line names What is the difference between compilers? Speed. The Intel compilers are typically between 5 and 20% faster than the GNU compilers (but it varies).

15. C #include <stdio.h> main() { printf(“Hello World! \n”); } Fortran program hello print *,”Hello World!” end Hello World Standard IO header New line character Indented into 7th column Semi-colon ends a statement No format is selected by * so just prints free form main is always the name of the first function to be executed. {} must enclose the code to be executed

16. C headers • The #include forces the compiler to include the file stdio.h • It will find it by checking the linking path • Header files contain prototypes, which are abstract function definitions • stdio.h is by far the most common, however math.h contains many mathematical function definitions (log, trig etc) • Lots of headers available to, including time functions, string functions, exception handling …

17. C int a; Can specify whether signed or unsigned Can also specify whether short (2 bytes) or long (8 bytes) float b; 4 byte floating-point double c; 8 byte floating-point FORTRAN integer a signed integer* real b floating-point* double precision c floating-point* with twice the precision real*4 4 byte floating-point real*8 8 byte floating-point complex 8 byte complex pair complex*16 16 byte complex pair Mathematical variable types *99 times out of 100, these correspond to 4 byte words for integer and real and an 8 byte word for double precision. Every now and again you may use a platform where the native words are 8 bytes

18. C char a; a = ‘S’; Strings are created by declaring arrays of characters: e.g. char a[4]; FORTRAN character a a=“S” logical type is available but is essentially same as integer Strings are handle by a character type whose length you define e.g. character*4 a Character & non-numerical types

19. C - example int data[3]; Indices run from 0 to 2 For multiple dimensions int data[3][2]; Fastest changing index in memory is the last one This is called Row-major order FORTRAN – example integer data(3) Indices run from 1 to 3 For multiple dimensions Integer data(3,2) Fastest changing index in memory is the first one This is called column major order Declaring Arrays This is a very important distinction!

20. Avoid implicit variable definitions in FORTRAN • For economy, early versions of FORTRAN assumed if you did not declare a variable that • Variables beginning with i-n are assumed to be integer • Variables beginning with a-h, o-z are assumed to be real • Do NOT use this convention • If you don’t type a variable name correctly the machine creates a new variable for you – can create horrendous bugs • Add the statement “IMPLICIT NONE” to the beginning of your code • Forces you to declare all variable names • Same is true in F90 unfortunately • Thankfully C forces you to do this

21. C int i; for (i=1; i<=10; i++) { printf(“Iteration %d\n”,i); } i++ means i=i+1 %d means print an integer Note the general loop structure for (initial statement; condition; iteration statement) { body } FORTRAN integer i do i=1,10 print*,”Iteration “,i end do Can also specify loop iteration: do i=1,10,2 Would increment in steps of 2 Loops

22. FORTRAN 90 Array Syntax • Really useful feature for minimizing the length of vector operations • Suppose we wish to add two vectors of length 100 • Normally this would require a loop: do i=1,100 a(i)=b(i)+b(i) end do • Can replace this with a=b+c • You can also specify bounds for the operation • a(1:4)=b(1:4)+c(1:4) • Adds elements b(1)+c(1) through to b(4)+c(4)

23. Pick a style and use it – it will pay off Comment your code – not excessively, but make sure it is clear and concise C requires you include header files Simple programs to try if you haven’t written any in C/FORTRAN before: Sum the first n numbers Sum up the values of a 2d grid of numbers where each grid entry a(i,j) is i*j Try doing this with a while loop that exits when the sum exceeds a given value Summary

24. Next Lecture • more on C/Fortran programming