Tutorials for High Performance Scientific Computing

The Art of HPC, volume 4

Victor Eijkhout

2022, last formatted September 10, 2023

Book and slides download: https://tinyurl.com/vle394course
Public repository: https://bitbucket.org/VictorEijkhout/scientific-computing-public

This book is published under the CC-BY 4.0 license.

Introduction to High-Performance Scientific Computing © Victor Eijkhout, distributed under a Creative
Commons Attribution 4.0 Unported (CC BY 4.0) license and made possible by funding from The Saylor
Foundation http://www.saylor.org.
Preface
The field of high performance scientific computing requires, in addition to a broad of scientific knowledge
and ’computing folkore’, a number of practical skills. Call it the ‘carpentry’ aspect of the craft of scientific
computing.
As a companion to the book ‘Introduction to High Performance Scientific Computing’, which covers back-
ground knowledge, here is then a set of tutorials on those practical skills that are important to becoming
a successful high performance practitioner.
The tutorials should be done while sitting at a computer. Given the practice of scientific computing, they
have a clear Unix bias.

Public draft This book is open for comments. What is missing or incomplete or unclear? Is material
presented in the wrong sequence? Kindly mail me with any comments you may have.
You may have found this book in any of a number of places; the authoritative download location is https:
//theartofhpc.com/ That page also links to lulu.com where you can get a nicely printed copy.

Victor Eijkhout [email protected]

Research Scientist
Texas Advanced Computing Center
The University of Texas at Austin
 4.2 Examples cases 74
4.3 Finding and using external
packages 81
4.4 Customizing the compilation
process 88
4.5 CMake scripting 90
Contents 5 Source code control through
Git 93
5.1 Concepts and overview 93
5.2 Git 94
1 Unix intro 7
5.3 Create and populate a
1.1 Shells 7
repository 95
1.2 Files and such 7
5.4 Adding and changing files 98
1.3 Text searching and regular
expressions 15 5.5 Undoing changes 101
1.4 Other useful commands: tar 17 5.6 Remote repositories and
1.5 Command execution 18 collaboration 104
1.6 Input/output Redirection 23 5.7 Branching 111
1.7 Shell environment variables 25 5.8 Releases 115
1.8 Control structures 27 6 Dense linear algebra: BLAS,
1.9 Scripting 29 LAPACK, SCALAPACK 116
1.10 Expansion 30 6.1 Some general remarks 117
1.11 Startup files 32 6.2 BLAS matrix storage 118
1.12 Shell interaction 33 6.3 Performance issues 119
1.13 The system and other users 33 6.4 Some simple examples 121
1.14 Connecting to other machines: ssh 7 Scientific Data Storage 123
and scp 35 7.1 Introduction to HDF5 123
1.15 The sed and awk tools 35 7.2 Creating a file 124
1.16 Review questions 37 7.3 Datasets 125
2 Compilers and libraries 38 7.4 Writing the data 129
2.1 File types in programming 38 7.5 Reading 131
2.2 Simple compilation 41 8 Parallel I/O 133
2.3 Libraries 46 8.1 Use sequential I/O 133
3 Managing projects with 8.2 MPI I/O 134
Make 52 8.3 Higher level libraries 134
3.1 A simple example 52 9 Plotting with GNUplot 135
3.2 Some general remarks 58 9.1 Usage modes 135
3.3 Variables and template rules 58 9.2 Plotting 136
3.4 Miscellania 64 9.3 Workflow 137
3.5 Shell scripting in a Makefile 66 10 Good coding practices 138
3.6 Practical tips for using Make 67 10.1 Defensive programming 138
3.7 A Makefile for LATEX 68 10.2 Guarding against memory
4 The Cmake build system 70 errors 142
4.1 CMake as build system 70 10.3 Testing 145

4
 Contents

11 Debugging 147 15.3 A worked out example 183

11.1 Compiling for debug 147 15.4 Where to take it from here 190
11.2 Invoking the debugger 149 15.5 Review questions 190
11.3 Finding errors: where, frame, 16 Profiling and
print 150 benchmarking 192
11.4 Stepping through a program 153 16.1 Timers 192
11.5 Inspecting values 155 16.2 Accurate counters 195
11.6 Breakpoints 155 16.3 Parallel timers in MPI and
11.7 Memory debugging 157 OpenMP 195
11.8 Memory debugging with 16.4 Profiling tools 196
Valgrind 158 16.5 Tracing 197
11.9 Further reading 160 16.6 Parallel timing 198
12 Parallel debugging 161 17 TAU 199
12.1 Parallel debugging 161 17.1 Usage modes 199
12.2 MPI debugging with gdb 163 17.2 Instrumentation 200
12.3 Full-screen parallel debugging with
17.3 Running 201
DDT 164
17.4 Output 201
12.4 Further reading 165
17.5 Without instrumentation 202
13 Language
17.6 Examples 202
interoperability 166
18 SLURM 208
13.1 C/Fortran interoperability 166
18.1 Cluster structure 208
13.2 C/C++ linking 168
13.3 Strings 170 18.2 Queues 209
13.4 Subprogram arguments 171 18.3 Job running 209
13.5 Input/output 172 18.4 The script file 210
13.6 Python calling C code 172 18.5 Parallelism handling 212
14 Bit operations 174 18.6 Job running 213
14.1 Construction and display 174 18.7 Scheduling strategies 214
14.2 Bit operations 175 18.8 File systems 214
15 LaTeX for scientific 18.9 Examples 214
documentation 176 18.10 Review questions 215
15.1 The idea behind LATEX, some history 19 SimGrid 217
of TEX 176 20 Bibliography 219
15.2 A gentle introduction to 21 List of acronyms 221
LaTeX 177 22 Index 223

Victor Eijkhout 5
Contents

Exercises
lesson Topic Book Slides in-class homework
1 Unix 1 unix 1.42
2 Git 5
3 Programming2 programming 2.3 2.4
4 Libraries 2 programming
5 Debugging 11 root code
6 LATEX 15 15.13
7 Make 3 3.1, 3.2

Table 1: Timetable for the carpentry section of an HPC course.

A good part of being an effective practitioner of High Performance Scientific Computing is what can be
called ‘HPC Carpentry’: a number of skills that are not scientific in nature, but that are still indispensable
to getting your work done.
The vast majority of scientific programming is done on the Unix platform so we start out with a tutorial
on Unix in chapter 1, followed by an explanation of the how your code is handled by compilers and linkers
and such in chapter 2.
Next you will learn about some tools that will increase your productivity and effectiveness:
• The Make utility is used for managing the building of projects; chapter 3.
• Source control systems store your code in such a way that you can undo changes, or maintain
multiple versions; in chapter 5 you will see the subversion software.
• Storing and exchanging scientific data becomes an important matter once your program starts to
produce results; in chapter 7 you will learn the use of HDF5.
• Visual output of program data is important, but too wide a topic to discuss here in great detail;
chapter 9 teaches you the basics of the gnuplot package, which is suitable for simple data plotting.
We also consider the activity of program development itself: chapter 10 considers how to code to prevent
errors, and chapter 11 teaches you to debug code with gdb. Chapter 13 contains some information on how
to write a program that uses more than one programming language.
Finally, chapter 15 teaches you about the LATEX document system, so that you can report on your work in
beautifully typeset articles.
Many of the tutorials are very hands-on. Do them while sitting at a computer!
Table 1 gives a proposed lesson outline for the carpentry section of a course. The article by Wilson [24]
is a good read on the thinking behind this ‘HPC carpentry’.

6 HPC Carpentry
Chapter 1

Unix intro

Unix is an Operating System (OS), that is, a layer of software between the user or a user program and the
hardware. It takes care of files and screen output, and it makes sure that many processes can exist side by
side on one system. However, it is not immediately visible to the user.
Most of this tutorial will work on any Unix-like platform, however, there is not just one Unix:
• Traditionally there are a few major flavors of Unix: ATT or System V , and BSD. Apple has Darwin
which is close to BSD; IBM and HP have their own versions of Unix, and Linux is yet another
variant. These days many Unix versions adhere to the POSIX standard. The differences between
these are deep down and if you are taking this tutorial you probably won’t see them for quite a
while.
• Within Linux there are various Linux distributions such as Red Hat or Ubuntu. These mainly differ
in the organization of system files and again you probably need not worry about them.
• The issue of command shells will be discussed below. This actually forms the most visible differ-
ence between different computers ‘running Unix’.

1.1 Shells
Most of the time that you use Unix, you are typing commands which are executed by an interpreter called
the shell. The shell makes the actual OS calls. There are a few possible Unix shells available
• Most of this tutorial is focused on the sh or bash shell.
• For a variety of reasons (see for instance section 3.5), bash-like shells are to be preferred over the
csh or tcsh shell. These latter ones will not be covered in this tutorial.
• Recent versions of the Apple Mac OS have the zsh as default. While this shell has many things in
common with bash, we will point out differences explicitly.

1.2 Files and such

Purpose. In this section you will learn about the Unix file system, which consists of di-
rectories that store files. You will learn about executable files and commands for displaying
data files.

7
1. Unix intro

1.2.1 Looking at files

Purpose. In this section you will learn commands for displaying file contents.

Commands learned in this section

ls list files or directories
touch create new/empty file or update existing file
cat > filename enter text into file
cp copy files
mv rename files
rm remove files
file report the type of file
cat filename display file
head,tail display part of a file
less,more incrementally display a file

1.2.1.1 ls
Without any argument, the ls command gives you a listing of files that are in your present location.
Exercise 1.1. Type ls. Does anything show up?
Intended outcome. If there are files in your directory, they will be listed; if there are none,
no output will be given. This is standard Unix behavior: no output does not mean that
something went wrong, it only means that there is nothing to report.
Exercise 1.2. If the ls command shows that there are files, do ls name on one of those. By
using an option, for instance ls -s name you can get more information about name.
Things to watch out for. If you mistype a name, or specify a name of a non-existing file,
you’ll get an error message.
The ls command can give you all sorts of information. In addition to the above ls -s for the size, there
is ls -l for the ‘long’ listing. It shows (things we will get to later such as) ownership and permissions,
as well as the size and creation date.

Remark 1 There are several dates associated with a file, corresponding to changes in content, changes in
permissions, and access of any sort. The stat command gives all of them.

1.2.1.2 cat
The cat command (short for ‘concatenate’) is often used to display files, but it can also be used to create
some simple content.
Exercise 1.3. Type cat > newfilename (where you can pick any filename) and type some
text. Conclude with Control-d on a line by itself: press the Control key and hold it
while you press the d key. Now use cat to view the contents of that file: cat newfilename.

8 HPC Carpentry
 1.2. Files and such

Intended outcome. In the first use of cat, text was appended from the terminal to a file;
in the second the file was cat’ed to the terminal output. You should see on your screen
precisely what you typed into the file.
Things to watch out for. Be sure to type Control-d as the first thing on the last line of
input. If you really get stuck, Control-c will usually get you out. Try this: start creating
a file with cat > filename and hit Control-c in the middle of a line. What are the
contents of your file?

Remark 2 Instead of Control-d you will often see the notation ^D. The capital letter is for historic reasons:
you use the control key and the lowercase letter.

1.2.1.3 man
The primary (though not always the most easily understood) source for unix commands is the man com-
mand, for ‘manual’. The descriptions available this way are referred to as the manual pages.
Exercise 1.4. Read the man page of the ls command: man ls. Find out the size and the time /
date of the last change to some files, for instance the file you just created.
Intended outcome. Did you find the ls -s and ls -l options? The first one lists the
size of each file, usually in kilobytes, the other gives all sorts of information about a file,
including things you will learn about later.
The man command puts you in a mode where you can view long text documents. This viewer is common
on Unix systems (it is available as the more or less system command), so memorize the following ways
of navigating: Use the space bar to go forward and the u key to go back up. Use g to go to the beginning
fo the text, and G for the end. Use q to exit the viewer. If you really get stuck, Control-c will get you out.

Remark 3 If you already know what command you’re looking for, you can use man to get online information
about it. If you forget the name of a command, man -k keyword can help you find it.

1.2.1.4 touch
The touch command creates an empty file, or updates the timestamp of a file if it already exists. Use ls
-l to confirm this behavior.

1.2.1.5 cp, mv, rm

The cp can be used for copying a file (or directories, see below): cp file1 file2 makes a copy of file1
and names it file2.
Exercise 1.5. Use cp file1 file2 to copy a file. Confirm that the two files have the same
contents. If you change the original, does anything happen to the copy?
Intended outcome. You should see that the copy does not change if the original changes
or is deleted.
Things to watch out for. If file2 already exists, you will get an error message.
A file can be renamed with mv, for ‘move’.

Victor Eijkhout 9
1. Unix intro

Exercise 1.6. Rename a file. What happens if the target name already exists?
Files are deleted with rm. This command is dangerous: there is no undo. For this reason you can do rm -i
(for ‘interactive’) which asks your confirmation for every file.
See section 1.2.4 for more aggressive removing.

1.2.1.6 head, tail

There are more commands for displaying a file, parts of a file, or information about a file.
Exercise 1.7. Do ls /usr/share/words or ls /usr/share/dict/words to confirm that a
file with words exists on your system. Now experiment with the commands head, tail,
more, and wc using that file.
Intended outcome. head displays the first couple of lines of a file, tail the last, and
more uses the same viewer that is used for man pages. Read the man pages for these
commands and experiment with increasing and decreasing the amount of output. The
wc (‘word count’) command reports the number of words, characters, and lines in a file.
Another useful command is file: it tells you what type of file you are dealing with.
Exercise 1.8. Do file foo for various ‘foo’: a text file, a directory, or the /bin/ls command.
Intended outcome. Some of the information may not be intelligible to you, but the words
to look out for are ‘text’, ‘directory’, or ‘executable’.
At this point it is advisable to learn to use a text editor, such as emacs or vi.

1.2.2 Directories
Purpose. Here you will learn about the Unix directory tree, how to manipulate it and
how to move around in it.

Commands learned in this section

ls list the contents of directories
mkdir make new directory
cd change directory
pwd display present working directory

A unix file system is a tree of directories, where a directory is a container for files or more directories. We
will display directories as follows:
/..............................................The root of the directory tree
bin ................................................... Binary programs
home ....................................... Location of users directories

The root of the Unix directory tree is indicated with a slash. Do ls / to see what the files and directories
there are in the root. Note that the root is not the location where you start when you reboot your personal
machine, or when you log in to a server.

10 HPC Carpentry
 1.2. Files and such

Exercise 1.9. The command to find out your current working directory is pwd. Your home di-
rectory is your working directory immediately when you log in. Find out your home
directory.
Intended outcome. You will typically see something like /home/yourname or /Users/yourname.
This is system dependent.
Do ls to see the contents of the working directory. In the displays in this section, directory names will be
followed by a slash: dir/ but this character is not part of their name. You can get this output by using ls
-F, and you can tell your shell to use this output consistently by stating alias ls=ls -F at the start of
your session. Example:
/home/you/
adirectory/
afile

The command for making a new directory is mkdir.

Exercise 1.10. Make a new directory with mkdir newdir and view the current directory with
ls.
Intended outcome. You should see this structure:
/home/you/
newdir/..............................................the new directory

Remark 4 If you need to create a directory several levels deep, you could
mkdir sub1
cd sub1
mkdir sub2
cd sub2
## et cetera

but it’s shorter to use the -p option (for ‘parent’) and write:
mkdir -p sub1/sub2/sub3

which creates any needed intermediate levels.

The command for going into another directory, that is, making it your working directory, is cd (‘change
directory’). It can be used in the following ways:
• cd Without any arguments, cd takes you to your home directory.
• cd <absolute path> An absolute path starts at the root of the directory tree, that is, starts
with /. The cd command takes you to that location.
• cd <relative path> A relative path is one that does not start at the root. This form of the cd
command takes you to <yourcurrentdir>/<relative path>.
Exercise 1.11. Do cd newdir and find out where you are in the directory tree with pwd. Con-
firm with ls that the directory is empty. How would you get to this location using an
absolute path?

Victor Eijkhout 11
1. Unix intro

Intended outcome. pwd should tell you /home/you/newdir, and ls then has no output,
meaning there is nothing to list. The absolute path is /home/you/newdir.
Exercise 1.12. Let’s quickly create a file in this directory: touch onefile, and another direc-
tory: mkdir otherdir. Do ls and confirm that there are a new file and directory.
Intended outcome. You should now have:
/home/you/
newdir/...................................................you are here
onefile
otherdir/
The ls command has a very useful option: with ls -a you see your regular files and hidden files, which
have a name that starts with a dot. Doing ls -a in your new directory should tell you that there are the
following files:
/home/you/
newdir/...................................................you are here
.
..
onefile
otherdir/

The single dot is the current directory, and the double dot is the directory one level back.
Exercise 1.13. Predict where you will be after cd ./otherdir/.. and check to see if you were
right.
Intended outcome. The single dot sends you to the current directory, so that does not
change anything. The otherdir part makes that subdirectory your current working di-
rectory. Finally, .. goes one level back. In other words, this command puts your right
back where you started.
Since your home directory is a special place, there are shortcuts for cd’ing to it: cd without arguments,
cd ~, and cd $HOME all get you back to your home.
Go to your home directory, and from there do ls newdir to check the contents of the first directory you
created, without having to go there.
Exercise 1.14. What does ls .. do?
Intended outcome. Recall that .. denotes the directory one level up in the tree: you should
see your own home directory, plus the directories of any other users.
Let’s practice the use of the single and double dot directory shortcuts.
Exercise 1.15. From your home directory:
mkdir -p sub1/sub2/sub3
cd sub1/sub2/sub3
touch a

You now have a file sub1/sub2/sub3/a

12 HPC Carpentry
 1.2. Files and such

1. How do you move it to sub1/sub2/a?

2. Go: cd sub1/sub2
How do you now move the file to sub1/a?
3. Go to your home directory: cd
How do you move sub1/a to here?
Exercise 1.16. Can you use ls to see the contents of someone else’s home directory? In the pre-
vious exercise you saw whether other users exist on your system. If so, do ls ../thatotheruser.
Intended outcome. If this is your private computer, you can probably view the contents of
the other user’s directory. If this is a university computer or so, the other directory may
very well be protected – permissions are discussed in the next section – and you get ls:
../otheruser: Permission denied.
Make an attempt to move into someone else’s home directory with cd. Does it work?
You can make copies of a directory with cp, but you need to add a flag to indicate that you recursively
copy the contents: cp -r. Make another directory somedir in your home so that you have
/home/you/
newdir/..............................you have been working in this one
somedir/ ...................................... you just created this one

What is the difference between cp -r newdir somedir where somedir is an exiting directory, and cp
-r newdir thirddir where thirddir is not an existing directory?

1.2.3 Permissions
Purpose. In this section you will learn about how to give various users on your system
permission to do (or not to do) various things with your files.

Unix files, including directories, have permissions, indicating ‘who can do what with this file’. Actions
that can be performed on a file fall into three categories:
• reading r: any access to a file (displaying, getting information on it) that does not change the file;
• writing w: access to a file that changes its content, or even its metadata such as ‘date modified’;
• executing x: if the file is executable, to run it; if it is a directory, to enter it.
The people who can potentially access a file are divided into three classes too:
• the user u: the person owning the file;
• the group g: a group of users to which the owner belongs;
• other o: everyone else.
(For more on groups and ownership, see section 1.13.1.)
The nine permissions are rendered in sequence
user group other
rwx rwx rwx

Victor Eijkhout 13
1. Unix intro

For instance rw-r--r-- means that the owner can read and write a file, the owner’s group and everyone
else can only read.
Permissions are also rendered numerically in groups of three bits, by letting r = 4, w = 2, x = 1:
rwx
421

Common codes are 7 = rwx and 6 = rw. You will find many files that have permissions 755 which stands
for an executable that everyone can run, but only the owner can change, or 644 which stands for a data file
that everyone can see but again only the owner can alter. You can set permissions by the chmod command:
chmod <permissions> file # just one file
chmod -R <permissions> directory # directory, recursively

Examples:
chmod 766 file # set to rwxrw-rw-
chmod g+w file # give group write permission
chmod g=rx file # set group permissions
chod o-w file # take away write permission from others
chmod o= file # take away all permissions from others.
chmod g+r,o-x file # give group read permission
# remove other execute permission

The man page gives all options.

Exercise 1.17. Make a file foo and do chmod u-r foo. Can you now inspect its contents?
Make the file readable again, this time using a numeric code. Now make the file readable
to your classmates. Check by having one of them read the contents.
Intended outcome. 1. A file is only accessible by others if the surrounding folder is read-
able. Can you figure out how to do this? 2. When you’ve made the file ‘unreadable’ by
yourself, you can still ls it, but not cat it: that will give a ‘permission denied’ message.
Make a file com with the following contents:
#!/bin/sh
echo "Hello world!"

This is a legitimate shell script. What happens when you type ./com? Can you get the script executed?
In the three permission categories it is clear who ‘you’ and ‘others’ refer to. How about ‘group’? We’ll go
into that in section 1.13.
Exercise 1.18. Suppose you’re an instructor and you want to make a ‘dropbox’ directory for
students to deposit homework assignments in. What would be an appropriate mode for
that directory? (Assume that you have co-teachers that are in your group, and who also
need to be able to see the contents. In other words, group permission should be identical
to the owner permission.)

Remark 5 There are more obscure permissions. For instance the setuid bit declares that the program should
run with the permissions of the creator, rather than the user executing it. This is useful for system utilities

14 HPC Carpentry
 1.3. Text searching and regular expressions

such passwd or mkdir, which alter the password file and the directory structure, for which root privileges
are needed. Thanks to the setuid bit, a user can run these programs, which are then so designed that a user
can only make changes to their own password entry, and their own directories, respectively. The setuid bit is
set with chmod: chmod 4ugo file.

1.2.4 Wildcards
You already saw that ls filename gives you information about that one file, and ls gives you all files in
the current directory. To see files with certain conditions on their names, the wildcard mechanism exists.
The following wildcards exist:
* any number of characters
? any character.

Example:
%% ls
s sk ski skiing skill
%% ls ski*
ski skiing skill

The second option lists all files whose name start with ski, followed by any number of other characters’;
below you will see that in different contexts ski* means ‘sk followed by any number of i characters’.
Confusing, but that’s the way it is.
You can use rm with wildcards, but this can be dangerous.
rm -f foo ## remove foo if it exists
rm -r foo ## remove directory foo with everything in it
rm -rf foo/* ## delete all contents of foo

Zsh note. No match Removing with a wildcard rm foo* is an error of there are no such files. Set setopt
+o nomatch to allow no matches to occur.

1.3 Text searching and regular expressions

Purpose. In this section you will learn how to search for text in files.

For this section you need at least one file that contains some amount of text. You can for instance get
random text from http://www.lipsum.com/feed/html.
The grep command can be used to search for a text expression in a file.
Exercise 1.19. Search for the letter q in your text file with grep q yourfile and search for it
in all files in your directory with grep q *. Try some other searches.
Intended outcome. In the first case, you get a listing of all lines that contain a q; in the
second case, grep also reports what file name the match was found in: qfile:this
line has q in it.

Victor Eijkhout 15
1. Unix intro

Things to watch out for. If the string you are looking for does not occur, grep will simply
not output anything. Remember that this is standard behavior for Unix commands if there
is nothing to report.
In addition to searching for literal strings, you can look for more general expressions.
^ the beginning of the line
$ the end of the line
. any character
* any number of repetitions
[xyz] any of the characters xyz

This looks like the wildcard mechanism you just saw (section 1.2.4) but it’s subtly different. Compare the
example above with:
%% cat s
sk
ski
skill
skiing
%% grep "ski*" s
sk
ski
skill
skiing

In the second case you search for a string consisting of sk and any number of i characters, including zero
of them.
Some more examples: you can find
• All lines that contain the letter ‘q’ with grep q yourfile;
• All lines that start with an ‘a’ with grep "^a" yourfile (if your search string contains special
characters, it is a good idea to use quote marks to enclose it);
• All lines that end with a digit with grep "[0-9]$" yourfile.
Exercise 1.20. Construct the search strings for finding
• lines that start with an uppercase character, and
• lines that contain exactly one character.
Intended outcome. For the first, use the range characters [], for the second use the period
to match any character.
Exercise 1.21. Add a few lines x = 1, x = 2, x = 3 (that is, have different numbers of
spaces between x and the equals sign) to your test file, and make grep commands to
search for all assignments to x.
The characters in the table above have special meanings. If you want to search that actual character, you
have to escape it.
Exercise 1.22. Make a test file that has both abc and a.c in it, on separate lines. Try the com-
mands grep "a.c" file, grep a\.c file, grep "a\.c" file.

16 HPC Carpentry
 1.4. Other useful commands: tar

Intended outcome. You will see that the period needs to be escaped, and the search string
needs to be quoted. In the absence of either, you will see that grep also finds the abc
string.

1.3.1 Cutting up lines with cut

Another tool for editing lines is cut, which will cut up a line and display certain parts of it. For instance,
cut -c 2-5 myfile

will display the characters in position 2–5 of every line of myfile. Make a test file and verify this example.
Maybe more useful, you can give cut a delimiter character and have it split a line on occurrences of
that delimiter. For instance, your system will mostly likely have a file /etc/passwd that contains user
information1 , with every line consisting of fields separated by colons. For instance:
daemon:*:1:1:System Services:/var/root:/usr/bin/false
nobody:*:-2:-2:Unprivileged User:/var/empty:/usr/bin/false
root:*:0:0:System Administrator:/var/root:/bin/sh

The seventh and last field is the login shell of the user; /bin/false indicates that the user is unable to
log in.
You can display users and their login shells with:
cut -d ":" -f 1,7 /etc/passwd

This tells cut to use the colon as delimiter, and to print fields 1 and 7.

1.4 Other useful commands: tar

The tar command stands for ‘tape archive’, that is, it was originally meant to package files on a tape.
(The ‘archive’ part derives from the ar command.) These days, it’s used to package files together for
distribution on web sites and such: if you want to publish a library of hundreds of files this bundles them
into a single file.
The two most common options are for
1. creating a tar file:
tar fc package.tar directory_with_stuff

pronounced ‘tar file create’, and

2. unpacking a tar file:
tar fx package.tar
# this creates the directory that was packaged

pronounced ‘tar file extract’.

1. This is traditionally the case; on Mac OS information about users is kept elsewhere and this file only contains system
services.

Victor Eijkhout 17
1. Unix intro

Text files can often be compressed to a large extent, so adding the z compressiong for gzip is a good idea:
tar fcz package.tar.gz directory_with_stuff
tar fx package.tar.gz

Naming the ‘gzipped’ file package.tgz is also common.

1.5 Command execution

If you type something in the shell, you are actually asking the underlying interpreter to execute a com-
mand. Some commands are built-ins, others can be names of programs that are stored somewhere, in a
system location or in your own account. This section will go into the mechanisms.

Remark 6 Like any good programming language, the shell language as comments. Any line starting with
a hash character # is ignored.

Zsh note. In Apple’s zsh, the comment character is disabled. Do

setopt interactivecomments

to enable it.

1.5.1 Search paths

Commands learned in this section

which location of executable command
type description of commands, functions, …
Purpose. In this section you will learn how Unix determines what to do when you type
a command name.

If you type a command such as ls, the shell does not just rely on a list of commands: it will actually go
searching for a program by the name ls. This means that you can have multiple different commands with
the same name, and which one gets executed depends on which one is found first.
Exercise 1.23. What you may think of as ‘Unix commands’ are often just executable files in a
system directory. Do which ls, and do an ls -l on the result.
Intended outcome. The location of ls is something like /bin/ls. If you ls that, you will
see that it is probably owned by root. Its executable bits are probably set for all users.
The locations where unix searches for commands is the search path, which is stored in the environment
variable (for more details see below) PATH.
Exercise 1.24. Do echo $PATH. Can you find the location of cd? Are there other commands in
the same location? Is the current directory ‘.’ in the path? If not, do export PATH=".:$PATH".
Now create an executable file cd in the current director (see above for the basics), and do
cd.

18 HPC Carpentry
 1.5. Command execution

Intended outcome. The path will be a list of colon-separated directories,

for instance /usr/bin:/usr/local/bin:/usr/X11R6/bin. If the working directory
is in the path, it will probably be at the end: /usr/X11R6/bin:. but most likely it will
not be there. If you put ‘.’ at the start of the path, unix will find the local cd command
before the system one.
Some people consider having the working directory in the path a security risk. If your directory is writable,
someone could put a malicious script named cd (or any other system command) in your directory, and
you would execute it unwittingly.
The safest way to execute a program in the current directory is:
./my_program

This holds both for compiled programs and shell scripts; section 1.9.1.

Remark 7 Not all Unix commands correspond to executables. The type command gives more information
than which:
$ type echo
echo is a shell builtin
$ type \ls
ls is an alias for ls -F
$ unalias ls
$ type ls
ls is /bin/ls
$ type module
module is a shell function from /usr/local/Cellar/lmod/8.7.2/init/zsh

1.5.2 Aliases
It is possible to define your own commands as aliases of existing commands.
Exercise 1.25. Do alias chdir=cd and convince yourself that now chdir works just like cd.
Do alias rm='rm -i'; look up the meaning of this in the man pages. Some people find
this alias a good idea; can you see why?
Intended outcome. The -i ‘interactive’ option for rm makes the command ask for confir-
mation before each delete. Since unix does not have a trashcan that needs to be emptied
explicitly (as on Windows or the Mac OS), this can be a good idea.

1.5.3 Command sequencing

There are various ways of having multiple commands on a single commandline.

1.5.3.1 Simple sequencing

First of all, you can type
command1 ; command2

Victor Eijkhout 19
1. Unix intro

This is convenient if you repeat the same two commands a number of times: you only need to up-arrow
once to repeat them both.

There is a problem: if you type

cc -o myprog myprog.c ; ./myprog

and the compilation fails, the program will still be executed, using an old version of the executable if that
exists. This is very confusing.

A better way is:

cc -o myprog myprog.c && ./myprog

which only executes the second command if the first one was successful.

1.5.3.2 Pipelining

Instead of taking input from a file, or sending output to a file, it is possible to connect two commands
together, so that the second takes the output of the first as input. The syntax for this is cmdone | cmdtwo;
this is called a pipeline. For instance, grep a yourfile | grep b finds all lines that contains both an
a and a b.
Exercise 1.26. Construct a pipeline that counts how many lines there are in your file that con-
tain the string th. Use the wc command (see above) to do the counting.

1.5.3.3 Backquoting

There are a few more ways to combine commands. Suppose you want to present the result of wc a bit
nicely. Type the following command
echo The line count is wc -l foo

where foo is the name of an existing file. The way to get the actual line count echoed is by the backquote:
echo The line count is `wc -l foo`

Anything in between backquotes is executed before the rest of the command line is evaluated.
Exercise 1.27. The way wc is used here, it prints the file name. Can you find a way to prevent
that from happening?
There is another mechanism for out-of-order evaluation:
echo "There are $( cat Makefile | wc -l ) lines"

This mechanism makes it possible to nest commands, but for compatibility and legacy purposes back-
quotes may still be preferable when nesting is not neeeded.

20 HPC Carpentry
 1.5. Command execution

1.5.3.4 Grouping in a subshell

Suppose you want to apply output redirection to a couple of commands in a row:
configure ; make ; make install > installation.log 2>&1

This only catches the last command. You could for instance group the three commands in a subshell and
catch the output of that:
( configure ; make ; make install ) > installation.log 2>&1

1.5.4 Exit status

Commands can fail. If you type a single command on the command line, you see the error, and you act
accordingly when you type the next command. When that failing command happens in a script, you have
to tell the script how to act accordingly. For this, you use the exit status of the command: this is a value
(zero for success, nonzero otherwise) that is stored in an internal variable, and that you can access with
$?.
Example. Suppose we have a directory that is not writable
[testing] ls -ld nowrite/
dr-xr-xr-x 2 eijkhout 506 68 May 19 12:32 nowrite//
[testing] cd nowrite/

and write try to create a file there:

[nowrite] cat ../newfile
#!/bin/bash
touch $1
echo "Created file: $1"
[nowrite] newfile myfile
bash: newfile: command not found
[nowrite] ../newfile myfile
touch: myfile: Permission denied
Created file: myfile
[nowrite] ls
[nowrite]

The script reports that the file was created even though it wasn’t.
Improved script:
[nowrite] cat ../betterfile
#!/bin/bash
touch $1
if [ $? -eq 0 ] ; then
echo "Created file: $1"
else
echo "Problem creating file: $1"
fi

[nowrite] ../betterfile myfile

touch: myfile: Permission denied
Problem creating file: myfile

Victor Eijkhout 21
1. Unix intro

1.5.5 Processes and jobs

Commands learned in this section

ps list (all) processes
kill kill a process
CTRL-c kill the foreground job
CTRL-z suspect the foreground job
jobs give the status of all jobs
fg bring the last suspended job to the foreground
fg %3 bring a specific job to the foreground
bg run the last suspended job in the background
The Unix operating system can run many programs at the same time, by rotating through the list and
giving each only a fraction of a second to run each time. The command ps can tell you everything that is
currently running.
Exercise 1.28. Type ps. How many programs are currently running? By default ps gives you
only programs that you explicitly started. Do ps guwax for a detailed list of everything
that is running. How many programs are running? How many belong to the root user,
how many to you?
Intended outcome. To count the programs belonging to a user, pipe the ps command
through an appropriate grep, which can then be piped to wc.
In this long listing of ps, the second column contains the process numbers. Sometimes it is useful to have
those: if a program misbehaves you can kill it with
kill 123456

where 12345 is the process number.

The cut command explained above can cut certain position from a line: type ps guwax | cut -c
10-14.
To get dynamic information about all running processes, use the top command. Read the man page to
find out how to sort the output by CPU usage.
Processes that are started in a shell are known as jobsjob (unix). In addition to the process number, they
have a job number. We will now explore manipulating jobs.
When you type a command and hit return, that command becomes, for the duration of its run, the fore-
ground process. Everything else that is running at the same time is a background process.
Make an executable file hello with the following contents:
#!/bin/sh
while [ 1 ] ; do
sleep 2
date
done

and type ./hello.

22 HPC Carpentry
 1.6. Input/output Redirection

Exercise 1.29. Type Control-z. This suspends the foreground process. It will give you a num-
ber like [1] or [2] indicating that it is the first or second program that has been sus-
pended or put in the background. Now type bg to put this process in the background.
Confirm that there is no foreground process by hitting return, and doing an ls.
Intended outcome. After you put a process in the background, the terminal is available
again to accept foreground commands. If you hit return, you should see the command
prompt. However, the background process still keeps generating output.
Exercise 1.30. Type jobs to see the processes in the current session. If the process you just put
in the background was number 1, type fg %1. Confirm that it is a foreground process
again.
Intended outcome. If a shell is executing a program in the foreground, it will not accept
command input, so hitting return should only produce blank lines.
Exercise 1.31. When you have made the hello script a foreground process again, you can kill
it with Control-c. Try this. Start the script up again, this time as ./hello & which
immediately puts it in the background. You should also get output along the lines of [1]
12345 which tells you that it is the first job you put in the background, and that 12345
is its process ID. Kill the script with kill %1. Start it up again, and kill it by using the
process number.
Intended outcome. The command kill 12345 using the process number is usually enough
to kill a running program. Sometimes it is necessary to use kill -9 12345.

1.5.6 Shell customization

Above it was mentioned that ls -F is an easy way to see which files are regular, executable, or directories;
by typing alias ls='ls -F' the ls command will automatically expanded to ls -F every time it is
invoked. If you would like this behavior in every login session, you can add the alias command to your
.profile file. Other shells than sh/bash have other files for such customizations.

1.6 Input/output Redirection

Purpose. In this section you will learn how to feed one command into another, and how
to connect commands to input and output files.

So far, the unix commands you have used have taken their input from your keyboard, or from a file named
on the command line; their output went to your screen. There are other possibilities for providing input
from a file, or for storing the output in a file.

1.6.1 Input redirection

The grep command had two arguments, the second being a file name. You can also write grep string
< yourfile, where the less-than sign means that the input will come from the named file, yourfile.
This is known as input redirection.

Victor Eijkhout 23
1. Unix intro

1.6.2 Standard files

Unix has three standard files that handle input and output:

Standard file
stdin is the file that provides input for processes.
stdout is the file where the output of a process is written.
stderr is the file where error output is written.

In an interactive session, all three files are connected to the user terminal. Using input or output redirection
then means that the input is taken or the output sent to a different file than the terminal.

1.6.3 Output redirection

Just as with the input, you can redirect the output of your program. In the simplest case, grep string
yourfile > outfile will take what normally goes to the terminal, and redirect the output to outfile.
The output file is created if it didn’t already exist, otherwise it is overwritten. (To append, use grep text
yourfile >> outfile.)
Exercise 1.32. Take one of the grep commands from the previous section, and send its output
to a file. Check that the contents of the file are identical to what appeared on your screen
before. Search for a string that does not appear in the file and send the output to a file.
What does this mean for the output file?
Intended outcome. Searching for a string that does not occur in a file gives no terminal
output. If you redirect the output of this grep to a file, it gives a zero size file. Check this
with ls and wc.
Exercise 1.33. Generate a text file that contains your information:
My user name is:
eijkhout
My home directory is:
/users/eijkhout
I made this script on:
isp.tacc.utexas.edu

where you use the commands whoami, pwd, hostname.

Bonus points if you can get the ‘prompt’ and output on the same line.
Hint: see section 1.5.3.3.
Sometimes you want to run a program, but ignore the output. For that, you can redirect your output to
the system null device: /dev/null.
yourprogram >/dev/null

Here are some useful idioms:

24 HPC Carpentry
 1.7. Shell environment variables

Idiom
program 2>/dev/null send only errors to the null device
program >/dev/null 2>&1 send output to dev-null, and errors to output
Note the counterintuitive sequence of specifica-
tions!
program 2>&1 | less send output and errors to less

1.7 Shell environment variables

Above you encountered PATH, which is an example of an shell, or environment, variable. These are vari-
ables that are known to the shell and that can be used by all programs run by the shell. While PATH is a
built-in variable, you can also define your own variables, and use those in shell scripting.
Shell variables are roughly divided in the following categories:
• Variables that are specific to the shell, such as HOME or PATH.
• Variables that are specific to some program, such as TEXINPUTS for TEX/LATEX.
• Variables that you define yourself; see next.
• Variables that are defined by control structures such as for; see below.
You can see the full list of all variables known to the shell by typing env.

Remark 8 This does not include variables you define yourself, unless you export them; see below.

Exercise 1.34. Check on the value of the PATH variable by typing echo $PATH. Also find the
value of PATH by piping env through grep.
We start by exploring the use of this dollar sign in relation to shell variables.

1.7.1 Use of shell variables

You can get the value of a shell variable by prefixing it with a dollar sign. Type the following and inspect
the output:
echo x
echo $x
x=5
echo x
echo $x

You see that the shell treats everything as a string, unless you explicitly tell it to take the value of a variable,
by putting a dollar in front of the name. A variable that has not been previously defined will print as a
blank string.
Shell variables can be set in a number of ways. The simplest is by an assignment as in other programming
languages.
When you do the next exercise, it is good to bear in mind that the shell is a text based language.

Victor Eijkhout 25
1. Unix intro

Exercise 1.35. Type a=5 on the commandline. Check on its value with the echo command.
Define the variable b to another integer. Check on its value.
Now explore the values of a+b and $a+$b, both by echo’ing them, or by first assigning
them.
Intended outcome. The shell does not perform integer addition here: instead you get
a string with a plus-sign in it. (You will see how to do arithmetic on variables in sec-
tion 1.10.1.)
Things to watch out for. Beware not to have space around the equals sign; also be sure to
use the dollar sign to print the value.

1.7.2 Exporting variables

A variable set this way will be known to all subsequent commands you issue in this shell, but not to
commands in new shells you start up. For that you need the export command. Reproduce the following
session (the square brackets form the command prompt):
[] a=20
[] echo $a
20
[] /bin/bash
[] echo $a

[] exit
exit
[] export a=21
[] /bin/bash
[] echo $a
21
[] exit

You can also temporarily set a variable. Replay this scenario:

1. Find an environment variable that does not have a value:
[] echo $b

[]

2. Write a short shell script to print this variable:

[] cat > echob
#!/bin/bash
echo $b

and of course make it executable: chmod +x echob.

3. Now call the script, preceding it with a setting of the variable b:
[] b=5 ./echob
5

The syntax where you set the value, as a prefix without using a separate command, sets the value
just for that one command.

26 HPC Carpentry
 1.8. Control structures

4. Show that the variable is still undefined:

[] echo $b

[]
That is, you defined the variable just for the execution of a single command.
In section 1.8 you will see that the for construct also defines a variable; section 1.9.1 shows some more
built-in variables that apply in shell scripts.
If you want to un-set an environment variable, there is the unset command.

1.8 Control structures

Like any good programming system, the shell has some control structures. Their syntax takes a bit of
getting used to. (Different shells have different syntax; in this tutorial we only discuss the bash shell.

1.8.1 Conditionals
The conditional of the bash shell is predictably called if, and it can be written over several lines:
if [ $PATH = "" ] ; then
echo "Error: path is empty"
fi

or on a single line:
if [ `wc -l file` -gt 100 ] ; then echo "file too long" ; fi

(The backquote is explained in section 1.5.3.3.) There are a number of tests defined, for instance -f
somefile tests for the existence of a file. Change your script so that it will report -1 if the file does
not exist.
The syntax of this is finicky:
• if and elif are followed by a conditional, followed by a semicolon.
• The brackets of the conditional need to have spaces surrounding them.
• There is no semicolon after then of else: they are immediately followed by some command.
Exercise 1.36. Bash conditionals have an elif keyword. Can you predict the error you get from
this:
if [ something ] ; then
foo
else if [ something_else ] ; then
bar
fi
Code it out and see if you were right.
Zsh note. The zsh shell has an extended conditional syntax with double square brackets. For
instance, pattern matching:
if [[ $myvar == *substring* ]] ; then ....

Victor Eijkhout 27
1. Unix intro

1.8.2 Looping
In addition to conditionals, the shell has loops. A for loop looks like
for var in listofitems ; do
something with $var
done

This does the following:

• for each item in listofitems, the variable var is set to the item, and
• the loop body is executed.
As a simple example:
for x in a b c ; do echo $x ; done
a
b
c

In a more meaningful example, here is how you would make backups of all your .c files:
for cfile in *.c ; do
cp $cfile $cfile.bak
done

Shell variables can be manipulated in a number of ways. Execute the following commands to see that you
can remove trailing characters from a variable:
[] a=b.c
[] echo ${a%.c}
b

(See the section 1.10 on expansion.) With this as a hint, write a loop that renames all your .c files to .x
files.
The above construct loops over words, such as the output of ls. To do a numeric loop, use the command
seq:
[shell:474] seq 1 5
1
2
3
4
5

Looping over a sequence of numbers then typically looks like

for i in `seq 1 ${HOWMANY}` ; do echo $i ; done

Note the backtick, which is necessary to have the seq command executed before evaluating the loop.
You can break out of a loop with break; this can even have a numeric argument indicating how many
levels of loop to break out of.

28 HPC Carpentry
 1.9. Scripting

1.9 Scripting
The unix shells are also programming environments. You will learn more about this aspect of unix in this
section.

1.9.1 How to execute scripts

It is possible to write programs of unix shell commands. First you need to know how to put a program in
a file and have it be executed. Make a file script1 containing the following two lines:
#!/bin/bash
echo "hello world"

and type ./script1 on the command line. Result? Make the file executable and try again.
Zsh note. Bash scripts If you use the zsh, but you have bash scripts that you wrote in the past, they will
keep working. The ‘hash-bang’ line determines which shell executes the script, and it is perfectly possible
to have bash in your script, while using zsh for interactive use.
In order write scripts that you want to invoke from anywhere, people typically put them in a directory
bin in their home directory. You would then add this directory to your search path, contained in PATH;
see section 1.5.1.

1.9.2 Script arguments

You can invoke a shell script with options and arguments:
./my_script -a file1 -t -x file2 file3

You will now learn how to incorporate this functionality in your scripts.
First of all, all commandline arguments and options are available as variables $1,$2 et cetera in the script,
and the number of command line arguments is available as $#:
#!/bin/bash

echo "The first argument is $1"

echo "There were $# arguments in all"

Formally:

variable meaning
$# number of arguments
$0 the name of the script
$1,$2,... the arguments
$*,$@ the list of all arguments

Victor Eijkhout 29
1. Unix intro

Exercise 1.37. Write a script that takes as input a file name argument, and reports how many
lines are in that file.
Edit your script to test whether the file has less than 10 lines (use the foo -lt bar test),
and if it does, cat the file. Hint: you need to use backquotes inside the test.
Add a test to your script so that it will give a helpful message if you call it without any
arguments.
The standard way to parse argument is using the shift command, which pops the first argument off the
list of arguments. Parsing the arguments in sequence then involves looking at $1, shifting, and looking at
the new $1.
Code: Output
[code/shell] arguments:
// arguments.sh
while [ $# -gt 0 ] ; do ./arguments.sh the quick "brown
echo "argument: $1" fox" jumps
shift argument: the
done argument: quick
argument: brown fox
argument: jumps

Exercise 1.38. Write a script say.sh that prints its text argument. However, if you invoke it
with
./say.sh -n 7 "Hello world"

it should be print it as many times as you indicated. Using the option -u:
./say.sh -u -n 7 "Goodbye cruel world"

should print the message in uppercase. Make sure that the order of the arguments does
not matter, and give an error message for any unrecognized option.
The variables $@ and $* have a different behavior with respect to double quotes. Let’s say we evaluate
myscript "1 2" 3, then
• Using $* is the list of arguments after removing quotes: myscript 1 2 3.
• Using "$*" is the list of arguments, with quotes removed, in quotes: myscript "1 2 3".
• Using "$@" preserved quotes: myscript "1 2" 3.

1.10 Expansion
The shell performs various kinds of expansion on a command line, that is, replacing part of the comman-
dline with different text.
Brace expansion:
[] echo a{b,cc,ddd}e
abe acce addde

This can for instance be used to delete all extension of some base file name:
[] rm tmp.{c,s,o} # delete tmp.c tmp.s tmp.o

30 HPC Carpentry
 1.10. Expansion

Tilde expansion gives your own, or someone else’s home directory:

[] echo ~
/share/home/00434/eijkhout
[] echo ~eijkhout
/share/home/00434/eijkhout

Parameter expansion gives the value of shell variables:

[] x=5
[] echo $x
5

Undefined variables do not give an error message:

[] echo $y

There are many variations on parameter expansion. Above you already saw that you can strip trailing
characters:
[] a=b.c
[] echo ${a%.c}
b

Here is how you can deal with undefined variables:

[] echo ${y:-0}
0

The backquote mechanism (section 1.5.3.3 above) is known as command substitution. It allows you to
evaluate part of a command and use it as input for another. For example, if you want to ask what type of
file the command ls is, do
[] file `which ls`

This first evaluates which ls, giving /bin/ls, and then evaluates file /bin/ls. As another example,
here we backquote a whole pipeline, and do a test on the result:
[] echo 123 > w
[] cat w
123
[] wc -c w
4 w
[] if [ `cat w | wc -c` -eq 4 ] ; then echo four ; fi
four

1.10.1 Arithmetic expansion

Unix shell programming is very much oriented towards text manipulation, but it is possible to do arith-
metic. Arithmetic substitution tells the shell to treat the expansion of a parameter as a number:
[] x=1
[] echo $((x*2))
2

Victor Eijkhout 31
1. Unix intro

Integer ranges can be used as follows:

[] for i in {1..10} ; do echo $i ; done
1
2
3
4
5
6
7
8
9
10

(but see also the seq command in section 1.8.2.)

1.11 Startup files

In this tutorial you have seen several mechanisms for customizing the behavior of your shell. For instance,
by setting the PATH variable you can extend the locations where the shell looks for executables. Other en-
vironment variables (section 1.7) you can introduce for your own purposes. Many of these customizations
will need to apply to every session, so you can have shell startup files that will be read at the start of any
session.
Popular things to do in a startup file are defining aliases:
alias grep='grep -i'
alias ls='ls -F'

and setting a custom commandline prompt.

The name of the startup file depends on your shell: .bashrc for Bash, .cshrc for the C-shell, and .zshrc
for the Z-shell. These files are read everytime you log in (see below for details), but you can also source
them directly:
source ~/.bashrc

You would do this, for instance, if you have edited your startup file.
Unfortunately, there are several startup files, and which one gets read is a complicated functions of cir-
cumstances. Here is a good common sense guideline2 :
• Have a .profile that does nothing but read the .bashrc:
# ~/.profile
if [ -f ~/.bashrc ]; then
source ~/.bashrc
fi

• Your .bashrc does the actual customizations:

2. Many thanks to Robert McLay for figuring this out.

32 HPC Carpentry
 1.12. Shell interaction

# ~/.bashrc
# make sure your path is updated
if [ -z "$MYPATH" ]; then
export MYPATH=1
export PATH=$HOME/bin:$PATH
fi

1.12 Shell interaction

Interactive use of Unix, in contrast to script writing (section 1.9), is a complicated conversation between
the user and the shell. You, the user, type a line, hit return, and the shell tries to interpret it. There are
several cases.
• Your line contains one full command, such as ls foo: the shell will execute this command.
• You can put more than one command on a line, separated by semicolons: mkdir foo; cd foo.
The shell will execute these commands in sequence.
• Your input line is not a full command, for instance while [ 1]. The shell will recognize that
there is more to come, and use a different prompt to show you that it is waiting for the remainder
of the command.
• Your input line would be a legitimate command, but you want to type more on a second line. In
that case you can end your input line with a backslash character, and the shell will recognize that
it needs to hold off on executing your command. In effect, the backslash will hide (escape) the
return.
When the shell has collected a command line to execute, by using one or more of your input line or only
part of one, as described just now, it will apply expansion to the command line (section 1.10). It will then
interpret the commandline as a command and arguments, and proceed to invoke that command with the
arguments as found.
There are some subtleties here. If you type ls *.c, then the shell will recognize the wildcard character
and expand it to a command line, for instance ls foo.c bar.c. Then it will invoke the ls command
with the argument list foo.c bar.c. Note that ls does not receive *.c as argument! In cases where you
do want the unix command to receive an argument with a wildcard, you need to escape it so that the shell
will not expand it. For instance, find . -name \*.c will make the shell invoke find with arguments .
-name *.c.

1.13 The system and other users

Unix is a multi-user operating system. Thus, even if you use it on your own personal machine, you are a
user with an account and you may occasionally have to type in your username and password.
If you are on your personal machine, you may be the only user logged in. On university machines or other
servers, there will often be other users. Here are some commands relating to them.
whoami show your login name.
who show the other users currently logged in.

Victor Eijkhout 33
1. Unix intro

finger otheruser get information about another user; you can specify a user’s login name here, or
their real name, or other identifying information the system knows about.
top which processes are running on the system; use top -u to get this sorted the amount of cpu time
they are currently taking. (On Linux, try also the vmstat command.)
uptime how long has it been since your last reboot?

1.13.1 Groups and ownership

In section 1.2.3 you saw that there is a permissions category for ‘group’. This allows you to open up files
to your close collaborators, while leaving them protected from the wide world.
When your account is created, your system administrator will have assigned you to one or more groups.
(If you admin your own machine, you’ll be in some default group; read on for adding yourself to more
groups.)
The command groups tells you all the groups you are in, and ls -l tells you what group a file belongs
to. Analogous to chmod, you can use chgrp to change the group to which a file belongs, to share it with
a user who is also in that group.
Creating a new group, or adding a user to a group needs system privileges. To create a group:
sudo groupadd new_group_name

To add a user to a group:

sudo usermod -a -G thegroup theuser

While you can change the group of a file, at least between groups that you belong to, changing the owning
user of a file with chown needs root priviliges. See section 1.13.2.

1.13.2 The super user

Even if you own your machine, there are good reasons to work as much as possible from a regular user
account, and use root privileges only when strictly needed. (The root account is also known as the super
user.) If you have root privileges, you can also use that to ‘become another user’ and do things with their
privileges, with the sudo (‘superuser do’) command.
• To execute a command as another user:
sudo -u otheruser command arguments

• To execute a command as the root user:

sudo command arguments

• Become another user:

sudo su - otheruser

• Become the super user:

sudo su -

34 HPC Carpentry
 1.14. Connecting to other machines: ssh and scp

Change the owning user of a file is done with chown:

sudo chown somefile someuser
sudo chown -R somedir someuser

1.14 Connecting to other machines: ssh and scp

No man is an island, and no computer is either. Sometimes you want to use one computer, for instance
your laptop, to connect to another, for instance a supercomputer.
If you are already on a Unix computer, you can log into another with the ‘secure shell’ command ssh,
a more secure variant of the old ‘remote shell’ command rsh:
ssh [email protected]

where the yourname can be omitted if you have the same name on both machines.
To only copy a file from one machine to another you can use the ‘secure copy’ scp, a secure variant of
‘remote copy’ rcp. The scp command is much like cp in syntax, except that the source or destination can
have a machine prefix.
To copy a file from the current machine to another, type:
scp localfile yourname@othercomputer:otherdirectory

where yourname can again be omitted, and otherdirectory can be an absolute path, or a path relative
to your home directory:
# absolute path:
scp localfile yourname@othercomputer:/share/
# path relative to your home directory:
scp localfile yourname@othercomputer:mysubdirectory

Leaving the destination path empty puts the file in the remote home directory:
scp localfile yourname@othercomputer:

Note the colon at the end of this command: if you leave it out you get a local file with an ‘at’ in the name.
You can also copy a file from the remote machine. For instance, to copy a file, preserving the name:
scp yourname@othercomputer:otherdirectory/otherfile .

1.15 The sed and awk tools

Apart from fairly small utilities such as tr and cut, Unix has some more powerful tools. In this section
you will see two tools for line-by-line transformations on text files. Of course this tutorial merely touches
on the depth of these tools; for more information see [1, 8].

Victor Eijkhout 35
1. Unix intro

1.15.1 Stream editing with sed

Unix has various tools for processing text files on a line-by-line basis. The stream editor sed is one ex-
ample. If you have used the vi editor, you are probably used to a syntax like s/foo/bar/ for making
changes. With sed, you can do this on the commandline. For instance
sed 's/foo/bar/' myfile > mynewfile

will apply the substitute command s/foo/bar/ to every line of myfile. The output is shown on your
screen so you should capture it in a new file; see section 1.6 for more on output redirection.
• If you have more than one edit, you can specify them with
sed -e 's/one/two/' -e 's/three/four/'

• If an edit needs to be done only on certain lines, you can specify that by prefixing the edit with
the match string. For instance
sed '/^a/s/b/c/'

only applies the edit on lines that start with an a. (See section 1.3 for regular expressions.)
You can also apply it on a numbered line:
sed '25/s/foo/bar'

• The a and i commands are for ‘append’ and ‘insert’ respectively. They are somewhat strange
in how they take their argument text: the command letter is followed by a backslash, with the
insert/append text on the next line(s), delimited by the closing quote of the command.
sed -e '/here/a\
appended text
' -e '/there/i\
inserted text
' -i file

• Traditionally, sed could only function in a stream, so the output file always had to be different
from the input. The GNU version, which is standard on Linux systems, has a flag -i which edits
‘in place’:
sed -e 's/ab/cd/' -e 's/ef/gh/' -i thefile

1.15.2 awk
The awk utility also operates on each line, but it can be described as having a memory. An awk program
consists of a sequence of pairs, where each pair consists of a match string and an action. The simplest
awk program is
cat somefile | awk '{ print }'

where the match string is omitted, meaning that all lines match, and the action is to print the line. Awk
breaks each line into fields separated by whitespace. A common application of awk is to print a certain
field:
awk '{print $2}' file

36 HPC Carpentry
 1.16. Review questions

prints the second field of each line.

Suppose you want to print all subroutines in a Fortran program; this can be accomplished with
awk '/subroutine/ {print}' yourfile.f

Exercise 1.39. Build a command pipeline that prints of each subroutine header only the sub-
routine name. For this you first use sed to replace the parentheses by spaces, then awk
to print the subroutine name field.
Awk has variables with which it can remember things. For instance, instead of just printing the second
field of every line, you can make a list of them and print that later:
cat myfile | awk 'BEGIN {v="Fields:"} {v=v " " $2} END {print v}'

As another example of the use of variables, here is how you would print all lines in between a BEGIN and
END line:
cat myfile | awk '/END/ {p=0} p==1 {print} /BEGIN/ {p=1} '

Exercise 1.40. The placement of the match with BEGIN and END may seem strange. Rearrange
the awk program, test it out, and explain the results you get.

1.16 Review questions

Exercise 1.41. Devise a pipeline that counts how many users are logged onto the system, whose
name starts with a vowel and ends with a consonant.
Exercise 1.42. Pretend that you’re a professor writing a script for homework submission: if a
student invokes this script it copies the student file to some standard location.
submit_homework myfile.txt

For simplicity, we simulate this by making a directory submissions and two different
files student1.txt and student2.txt. After
submit_homework student1.txt
submit_homework student2.txt

there should be copies of both files in the submissions directory. Start by writing a
simple script; it should give a helpful message if you use it the wrong way.
Try to detect if a student is cheating. Explore the diff command to see if the submitted
file is identical to something already submitted: loop over all submitted files and
1. First print out all differences.
2. Count the differences.
3. Test if this count is zero.
Now refine your test by catching if the cheating student randomly inserted some spaces.
For a harder test: try to detect whether the cheating student inserted newlines. This can
not be done with diff, but you could try tr to remove the newlines.

Victor Eijkhout 37
Chapter 2

Compilers and libraries

2.1 File types in programming

Purpose. In this section you will be introduced to the different types of files that you
encounter while programming.

2.1.1 Introduction to file types

Your file system has many files, and for purposes of programming we can roughly divide them into ‘text
file’, which are readable to you, and ‘binary files’, which are not meaningfully readable to you, but which
make sense to the computer.
The unix command file can tell you what type of file you are dealing with.
$$ file README.txt
README.txt: ASCII text
$$ mkdir mydir
$$ file mydir
mydir: directory
$$ which ls

This command can also tell you about binary files. Here the output differs by operating system.
$$ which ls
/bin/ls

# on a Mac laptop:
$$ file /bin/ls
/bin/ls: Mach-O 64-bit x86_64 executable

# on a Linux box
$$ file /bin/ls
/bin/ls: ELF 64-bit LSB executable, x86-64

38
 2.1. File types in programming

Exercise 2.1. Apply the file command to sources for different programming language. Can
you find out how file figures things out?
In figure 2.1 you find a brief summary of file types. We will now discuss them in more detail.

Text files
Source Program text that you write
Header also written by you, but not really program text.
Binary files
Object file The compiled result of a single source file
Library Multiple object files bundled together
Executable Binary file that can be invoked as a command
Data files Written and read by a program

Figure 2.1: Different types of files.

2.1.2 About ‘text’ files

Readable files are sometimes called text files; but this is not a concept with a hard definition. One not-
perfect definition is that text files are ascii files, meaning files where every byte uses ‘7-bit ascii’: the first
bit of every byte is zero.
This definition is incomplete, since modern programming languages can often use unicode, at least in
character strings. (For a tutorial on ascii and unicode, see chapter 6 of [9].)

2.1.3 Source versus program

There are two types of programming languages:
1. In an interpreted language you write human-readable source code and you execute it directly: the
computer translates your source line by line as it encounters it.
2. In a compiled language your code whole source is first compiled to a program, which you then
execute.
Examples of interpreted languages are Python, Matlab, Basic, Lisp. Interpreted languages have some ad-
vantages: often you can write them in an interactive environment that allows you to test code very quickly.
They also allow you to construct code dynamically, during runtime. However, all this flexibility comes at
a price: if a source line is executed twice, it is translated twice. In the context of this book, then, we will
focus on compiled languages, using C and Fortran as prototypical examples.
So now you have a distinction between the readable source code, and the unreadable, but executable,
program code. In this tutorial you will learn about the translation process from the one to the other. The
program doing this translation is known as a compiler. This tutorial will be a ‘user manual’ for compilers,
as it were; what goes on inside a compiler is a different branch of computer science.

Victor Eijkhout 39
2. Compilers and libraries

2.1.4 Binary files

Binary files fall in two categories:
• executable code,
• data
Data files can be really anything: they are typically output from a program, and their format is often
specific to that program, although there are some standards, such as hdf5. You get a binary data file
if you write out the exact bytes of certain integers or floating point numbers, rather than a readable
representation of that number.
Exercise 2.2. Why don’t programs write their results to file in readable form?
Enrichment. How do you write/read a binary file in C and Fortran? Use the function hexdump to
make sense of the binary file. Can you generate the file from Fortran, and read it from C? (Answer:
yes, but it’s not quite straightforward.) What does this tell you about binary data?

[linking:31] make binary // binary_write.c

clang -o binary_write_c binary_write.c FILE *binfile;
./binary_write_c binfile = fopen("binarydata.out","wb");
clang -o binary_read_c binary_read.c for (int i=0; i<10; i++)
./binary_read_c fwrite(&i,sizeof(int),1,binfile);
fclose(binfile);
0 1 2 3 4 5 6 7 8 9
[linking:32] hexdump binarydata.out
// binary_read.c
0000000 00 00 00 00 01 00 00 00 02 \
binfile = fopen("binarydata.out","rb");
00 00 00 03 00 00 00 for (int i=0; i<10; i++) {
0000010 04 00 00 00 05 00 00 00 06 \ int ival;
00 00 00 07 00 00 00 fread(&ival,sizeof(int),1,binfile);
0000020 08 00 00 00 09 00 00 00 printf("%d ",ival);
0000028 }
printf("\n");

Fortran works differently: each record, that is, the output of each Write statement, has the record length (in
bytes) before and after it.

[linking:68] make xbinary 00 00 00 06 00 00 00

gfortran -o binary_write_f binary_write.F90 0000050 04 00 00 00 04 00 00 00 07 \
./binary_write_f 00 00 00 04 00 00 00
hexdump binarydata.out 0000060 04 00 00 00 08 00 00 00 04 \
0000000 04 00 00 00 00 00 00 00 04 \ 00 00 00 04 00 00 00
00 00 00 04 00 00 00 0000070 09 00 00 00 04 00 00 00
0000010 01 00 00 00 04 00 00 00 04 \
00 00 00 02 00 00 00
0000020 04 00 00 00 04 00 00 00 03 \
00 00 00 04 00 00 00
0000030 04 00 00 00 04 00 00 00 04 \
00 00 00 04 00 00 00
0000040 05 00 00 00 04 00 00 00 04 \

40 HPC Carpentry
 2.2. Simple compilation

// binary_write.F90 write(13) i
Open(Unit=13,File="binarydata.out",Form=" end do
unformatted") Close(Unit=13)
do i=0,9

In this tutorial you will mostly be concerned with executable binary files. We then distinguish between:
• program files, which are executable by themselves;
• object files, which are like bit of programs; and
• library files, which combine object files, but are not executable.
Object files come from the fact that your source is often spread over multiple source files, and these can
be compiled separately. In this way, an object file, is a piece of an executable: by itself it does nothing, but
it can be combined with other object files to form an executable.
If you have a collection of object files that you need for more than one program, it is usually a good idea to
make a library: a bundle of object files that can be used to form an executable. Often, libraries are written
by an expert and contain code for specialized purposes such as linear algebra manipulations. Libraries
are important enough that they can be commercial, to be bought if you need expert code for a certain
purpose.
You will now learn how these types of files are created and used.

2.2 Simple compilation

Purpose. In this section you will learn about executables and object files.

2.2.1 Compilers
Your main tool for turning source into a program is the compiler. Compilers are specific to a language:
you use a different compiler for C than for Fortran. You can also have two compilers for the same lan-
guage, but from different ‘vendors’. For instance, while many people use the open source gcc or clang
compiler families, companies like Intel and IBM offer compilers that may give more efficient code on their
processors.

2.2.2 Compile a single file

Let’s start with a simple program that has the whole source in one file.
#include <stdlib.h>
#include <stdio.h>

int main() {
printf("hello world\n");
return 0;
}

Victor Eijkhout 41
2. Compilers and libraries

Figure 2.2: Compiling a single source file.

Compile this program with your favorite compiler; we will use gcc in this tutorial, but substitute your
own as desired.
TACC note. On TACC clusters, the Intel compiler icc is preferred.
As a result of the compilation, a file a.out is created, which is the executable.
%% gcc hello.c
%% ./a.out
hello world

You can get a more sensible program name with the -o option:
%% gcc -o helloprog hello.c
%% ./helloprog
hello world

This process is illustrated in figure 2.2.

2.2.3 Compilation: the nitty gritty

Even for the simple compilation of the previous section some details have been left out. The commandline
gcc -save-temps -o hello hello.c

actually generates the following:

• hello.i: a text file where all preprocessor directives have been inlined. In this case, that’s the
stdlib.h and stdio.h files:
# 0 "hello.c"
# 0 "<built-in>"
# 0 "<command-line>"
# 1 "hello.c"
# 12 "hello.c"
# 1 "/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/stdlib.h" 1 3 4
# 61 "/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/stdlib.h" 3 4
# 1 "/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/Availability.h"
1 3 4

42 HPC Carpentry
 2.2. Simple compilation

et cetera.
• hello.s: the assembly listing of your program. This is a sort of ‘readable machine language’:
.arch armv8-a
.text
.cstring
.align 3
lC0:
.ascii "hello world\0"
.text
.align 2
.globl _main
_main:
LFB10:
stp x29, x30, [sp, -16]!

• hello.o: the object file, containing actual machine language. We will go into this more below.
The object file is not directly readable, but later you’ll see the nm tool that can give you some
information.

2.2.4 Multiple files: compile and link

Figure 2.3: Compiling a program from multiple source files.

Now we move on to a program that is in more than one source file.

Main program: fooprog.c bar("hello world\n");

return 0;
// fooprog.c }
extern void bar(char*);

int main() {

Victor Eijkhout 43
2. Compilers and libraries

Subprogram: foosub.c printf("%s",s);

return;
// foosub.c }
void bar(char *s) {

As before, you can make the program with one command.

Output
[code/compile] makeoneprogram:
clang -o oneprogram fooprog.c foosub.c
./oneprogram
hello world

However, you can also do it in steps, compiling each file separately and then linking them together. This
is illustrated in figure 2.3.
Output
[code/compile] makeseparatecompile:
clang -g -O2 -o oneprogram fooprog.o foosub.o
./oneprogram
hello world

The -c option tells the compiler to compile the source file, giving an object file. The third command then
acts as the linker, tieing together the object files into an executable. (With programs that are spread over
several files there is always the danger of editing a subroutine definition and then forgetting to update all
the places it is used. See the ‘make’ tutorial, section 3, for a way of dealing with this.)
Exercise 2.3.
Exercise for separate compilation. Structure:

Main program: fooprog.c Subprogram: foosub.c

#include <stdlib.h> #include <stdlib.h>
#include <stdio.h> #include <stdio.h>

extern void bar(char*); void bar(char *s) {

printf("%s",s);
int main() { return;
bar("hello world\n"); }
return 0;
} Add a second subroutine in a second file.

• Compile in one:
icc -o program fooprog.c foosub.c

• Compile in steps:
icc -c fooprog.c
icc -c foosub.c
icc -o program fooprog.o foosub.o

44 HPC Carpentry
 2.2. Simple compilation

What files are being produced each time?

Can you write a shell script to automate this?

2.2.5 Looking into binary files: nm

Most of a binary file consists of the same instructions that you coded in C or Fortran, just in machine
language, which is much harder to understand. Fortunately, you don’t need to look at machine language
often. What often interests you about object files is what functions are defined in it, and what functions
are used in it.
For this, we use the nm command.
Each object file defines some routine names, and uses some others that are undefined in it, but that will
be defined in other object files or system libraries. Use the nm command to display this:
[c:264] nm foosub.o
0000000000000000 T _bar
U _printf

Lines with T indicate routines that are defined; lines with U indicate routines that are used but not define
in this file. In this case, printf is a system routine that will be supplied in the linker stage.
(With C++ the function names will look a little strange because of name mangling. However, you’ll still
be able to recognize them.)
Sometimes you will come across stripped binary file, and nm will report No symbols. In that case nm -D
may help, which displays ‘dynamic symbols’.

2.2.6 Compiler options and optimizations

Above you already saw some compiler options:
• Specifying -c tells the compiler to only compile, and not do the linking stage; you would do this
in case of separate compilation.
• The option -o gives you the opportunity to specify the name of the output file; without it, the
default name of an executable is a.out.
There are many other options, some of them a de facto standard, and others specific to certain compilers.

2.2.6.1 Symbol table inclusion

The -g option tells the compiler to include the symbol table in the binary. This allows you to use an inter-
active debugger (section 11) since it relates machine instructions to lines of code, and machine addresses
to variable names.

2.2.6.2 Optimization level

Compilers can apply various levels of optimization to your code. The typical optimization levels are spec-
ified as -O0 ‘minus-oh-zero’, -O1, -O2, -O3. Higher levels will typically give faster execution, as the com-
piler does increasingly sophisticated analysis on your code.

Victor Eijkhout 45
2. Compilers and libraries

The following is a fairly standard set of options:

icc -g -O2 -c myfile.c

As an example, let’s look at Given’s rotations:

// rotate.c
void rotate(double *x,double *y,double alpha) {
double x0 = *x, y0 = *y;
*x = cos(alpha) * x0 - sin(alpha) * y0;
*y = sin(alpha) * x0 + cos(alpha) * y0;
return;
}

Run with optimization level 0,1,2,3 we get:

Done after 8.649492e-02
Done after 2.650118e-02
Done after 5.869865e-04
Done after 6.787777e-04

Exercise 2.4. From level zero to one we get (in the above example; in general this depends on
the compiler) an improvement of 2× to 3×. Can you find an obvious factor of two?
Use the optimization report facility of your compiler to see what other optimizations are
applied. One of them is a good lesson in benchmark design!
Many compilers can generate a report of what optimizations they perform.

compiler reporting option

clang -Rpass=.*
gcc -fopt-info
intel -qopt-report

Generally, optimizations leave the semantics of your code intact. (Makes kinda sense, not?) However, at
higher levels, usually level 3, the compiler is at liberty to make transformations that are not legal according
to the language standard, but that in the majority of cases will still give the right outcome. For instance,
the C language specifies that arithmetic operations are evaluated left-to-right. Rearranging arithmetic
expressions is usually safe, but not always. Be careful when applying higher optimization levels!

2.3 Libraries
Purpose. In this section you will learn about creating libraries.

If you have written some subprograms, and you want to share them with other people (perhaps by selling
them), then handing over individual object files is inconvenient. Instead, the solution is to combine them
into a library. This section shows you the basic Unix mechanisms. You would typically use these in a
Makefile; if you use CMake it’s all done for you.

46 HPC Carpentry
 2.3. Libraries

Figure 2.4: Compiling a single source file.

2.3.1 Static libraries

First we look at static libraries, for which the archive utility ar is used. A static library is linked into your
executable, becoming part of it. This has the advantage that you can give such an executable to someone
else, and it will immediately work. On the other hand, this may lead to large executables; you will learn
about shared libraries next, which do not suffer from this problem.

The use of a library to build a program is illustrated in figure 2.4.

Create a directory to contain your library, and create the library file there. The library can be linked into
your executable by explicitly giving its name, or by specifying a library path:

Victor Eijkhout 47
2. Compilers and libraries

Output
[code/compilecxx] staticprogram:

==== Use of static library ====

for o in foosub.o ; do \
ar cr libs/libfoo.a ${o} ; \
done
clang++ -o staticprogram fooprog.o -Llibs -lfoo
-rwxr-xr-x 1 eijkhout staff 52536 Sep 27 04:57 staticprogram

.. running:

hello world

The nm command tells you what’s in the library, just like it did with object files, but now it also tells you
what object files are in the library:
We show this for C:
Code: Output
[code/compilec] staticlib:
==== Making static library
====
for o in foosub.o ; do ar cr foosub.o:
libs/libfoo.a ${o} ; done 0000000000000000 T bar
nm libs/libfoo.a 0000000000000000 N .debug_info_seg
U printf

For C++ we show the output in figure 2.5, where we note the -C flag for name demangling.

2.3.2 Shared libraries

Although they are somewhat more complicated to use, shared libraries have several advantages. For in-
stance, since they are not linked into the executable but only loaded at runtime, they lead to (much) smaller
executables. They are not created with ar, but through the compiler. For instance:
Output
[code/compile] makedynamiclib:
%%%%
Demonstration: making shared library
%%%%
clang -o libs/libfoo.so -shared foosub.o

You can again use nm:

%% nm ../lib/libfoo.so

../lib/libfoo.so(single module):
00000fc4 t __dyld_func_lookup
00000000 t __mh_dylib_header

48 HPC Carpentry
 2.3. Libraries

Code: Output
[code/compilecxx] staticlib:
==== Making static library
====
for o in foosub.o ; do ar cr foosub.o:
libs/libfoo.a ${o} ; done U __cxa_atexit
nm -C libs/libfoo.a 0000000000000000 N .debug_info_seg
U __dso_handle
U __gxx_personality_v0
0000000000000010 t __sti__$E
0000000000000000 T bar(std::__cxx11::basic_string<char, std::
char_traits<char>, std::allocator<char> >)
0000000000000000 b _INTERNALaee936d8::std::__ioinit
0000000000000000 W std::__cxx11::basic_string<char, std::
char_traits<char>, std::allocator<char> >::data() const
0000000000000000 W std::__cxx11::basic_string<char, std::
char_traits<char>, std::allocator<char> >::size() const
U std::ios_base::Init::Init()
U std::ios_base::Init::~Init()
U std::cout
U std::basic_ostream<char, std::char_traits<
char> >& std::operator<< <char, std::char_traits<char>, std
::allocator<char> >(std::basic_ostream<char, std::
char_traits<char> >&, std::__cxx11::basic_string<char, std
::char_traits<char>, std::allocator<char> > const&)

Figure 2.5: The nm output of a C++ library

00000fd2 T _bar
U _printf
00001000 d dyld__mach_header
00000fb0 t dyld_stub_binding_helper

Shared libraries are not actually linked into the executable; instead, the executable needs the information
where the library is to be found at execution time. One way to do this is with LD_LIBRARY_PATH:

Victor Eijkhout 49
2. Compilers and libraries

Output
[code/compile] dynamicprogram:

Linking to shared library

clang -o libs/libfoo.so -shared foosub.o

clang -o dynamicprogram fooprog.o -Llibs -lfoo
-rwxr-xr-x 1 eijkhout staff 49720 Nov 28 12:00 dynamicprogram

.. note the size of the program

-rwxr-xr-x 1 eijkhout staff 49720 Nov 28 12:00 dynamicprogram

.. note unresolved link to a library

otool -L dynamicprogram | grep libfoo

libs/libfoo.so (compatibility version 0.0.0, current version 0.0.0)

.. running by itself:

clang -o libs/libfoo.so -shared foosub.o

clang -o dynamicprogram fooprog.o -Llibs -lfoo
-rwxr-xr-x 1 eijkhout staff 49720 Nov 28 12:00 dynamicprogram
hello world

.. note resolved with LD_LIBRARY_PATH

LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:./libs otool -L dynamicprogram | grep

libfoo
libs/libfoo.so (compatibility version 0.0.0, current version 0.0.0)

.. running with updated library path:

clang -o libs/libfoo.so -shared foosub.o

clang -o dynamicprogram fooprog.o -Llibs -lfoo
-rwxr-xr-x 1 eijkhout staff 49720 Nov 28 12:00 dynamicprogram
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:./libs dynamicprogram
hello world

Another solution is to have the path be included in the executable:

%% gcc -o foo fooprog.o -L../lib -Wl,-rpath,`pwd`/../lib -lfoo
%% ./foo
hello world

The link line now contains the library path twice:

1. once with the -L directive so that the linker can resolve all references, and
2. once with the linker directive -Wl,-rpath,`pwd`/../lib which stores the path into the exe-
cutable so that it can be found at runtime.

Remark 9 You may also come across a syntax with rpath=:

50 HPC Carpentry
 2.3. Libraries

gcc -o foo fooprog.o -L../lib -Wl,-rpath=`pwd`/../lib -lfoo

but beware that that is a GNU extension.

Remark 10 On Apple OS Ventura the use of LD_LIBRARY_PATH is no longer supported for security reasons,
so using the rpath is the only option.

Use the command ldd to get information about what shared libraries your executable uses. (On Mac OS X,
use otool -L instead.)

Victor Eijkhout 51
Chapter 3

Managing projects with Make

The Make utility helps you manage the building of projects: its main task is to facilitate rebuilding only
those parts of a multi-file project that need to be recompiled or rebuilt. This can save lots of time, since it
can replace a minutes-long full installation by a single file compilation. Make can also help maintaining
multiple installations of a program on a single machine, for instance compiling a library with more than
one compiler, or compiling a program in debug and optimized mode.
Make is a Unix utility with a long history, and traditionally there are variants with slightly different
behavior, for instance on the various flavors of Unix such as HP-UX, AUX, IRIX. These days, it is advisable,
no matter the platform, to use the GNU version of Make which has some very powerful extensions; it is
available on all Unix platforms (on Linux it is the only available variant), and it is a de facto standard. The
manual is available at http://www.gnu.org/software/make/manual/make.html, or you can read the
book [14].
There are other build systems, most notably Scons and Bjam. We will not discuss those here. The examples
in this tutorial will be for the C and Fortran languages, but Make can work with any language, and in fact
with things like TEX that are not really a language at all; see section 3.7.

3.1 A simple example

Purpose. In this section you will see a simple example, just to give the flavor of Make.

The files for this section can be found in the repository.

3.1.1 C++
Make the following files:
foo.cxx
#include <iostream>
using std::cout;

#include "bar.h"

52
 3.1. A simple example

int main()
{
int a=2;
cout << bar(a) << '\n';
return 0;
}

bar.cxx
#include "bar.h"
int bar(int a)
{
int b=10;
return b*a;
}

bar.h
int bar(int);

and a makefile:
Makefile
fooprog : foo.o bar.o
icpc -o fooprog foo.o bar.o
foo.o : foo.cxx
icpc -c foo.cxx
bar.o : bar.cxx
icpc -c bar.cxx
clean :
rm -f *.o fooprog

The makefile has a number of rules like

foo.o : foo.cxx
<TAB>icpc -c foo.cxx

which have the general form

target : prerequisite(s)
<TAB>rule(s)

where the rule lines are indented by a TAB character.

A rule, such as above, states that a ‘target’ file foo.o is made from a ‘prerequisite’ foo.cxx, namely by
executing the command icpc -c foo.cxx. (Here we are using the Intel C++ compiler icpc; your system
could have a different compiler, such as clang++ or g++.)
The precise definition of the rule is:
• if the target foo.o does not exist or is older than the prerequisite foo.cxx,
• then the command part of the rule is executed: icpc -c foo.cxx
• If the prerequisite is itself the target of another rule, than that rule is executed first.

Victor Eijkhout 53
3. Managing projects with Make

Exercise. Call make.

Expected outcome. The above rules are applied: make without arguments tries to build the first
target, fooprog. In order to build this, it needs the prerequisites foo.o and bar.o, which do not
exist. However, there are rules for making them, which make recursively invokes. Hence you see
two compilations, for foo.o and bar.o, and a link command for fooprog.
Caveats. Typos in the makefile or in file names can cause various errors. In particular, make sure
you use tabs and not spaces for the rule lines. Unfortunately, debugging a makefile is not simple.
Make’s error message will usually give you the line number in the make file where the error was
detected.

Exercise. Do make clean, followed by mv foo.cxx boo.cxx and make again. Explain the error mes-
sage. Restore the original file name.
Expected outcome. Make will complain that there is no rule to make foo.cxx. This error was
caused when foo.cxx was a prerequisite for making foo.o, and was found not to exist. Make
then went looking for a rule to make it and no rule for creating .cxx files exists.

Now add a second argument to the function bar. This would require you to edit all of bar.cxx, bar.h,
and foo.cxx, but let’s say we forget to edit the last two, so only edit bar.cxx However, it also requires
you to edit foo.c, but let us for now ‘forget’ to do that. We will see how Make can help you find the
resulting error.

Exercise. Call make to recompile your program. Did it recompile foo.c?

Expected outcome. You see that inclusion of the ‘wrong’ header file does not lead to an error,
because C++ has polymorphism. In C this would definitely give an error. The error only shows
up in the linker stage because of an unresolved reference.

Exercise. Update the header file, and call make again. What happens, and what had you been hoping
would happen?
Expected outcome. Only the linker stage is done, and it gives the same error about an unresolved
reference. Were you hoping that the main program would be recompiled?
Caveats.

The way out of this problem is to tie the header file to the source files in the makefile.
In the makefile, change the line
foo.o : foo.cxx

to
foo.o : foo.cxx bar.h

which adds bar.h as a prerequisite for foo.o. This means that, in this case where foo.o already exists,
Make will check that foo.o is not older than any of its prerequisites. Since bar.h has been edited, it is
younger than foo.o, so foo.o needs to be reconstructed.

Remark 11 As already noted above, in C++ fewer errors are caught by this mechanism than in C, because
of polymorphism. You might wonder if it would be possible to generate header files automatically. This is of
course possible with suitable shell scripts, but tools such as Make (or CMake) do not have this built in.

54 HPC Carpentry
 3.1. A simple example

3.1.2 C
Make the following files:
foo.c
#include "bar.h"
int c=3;
int d=4;
int main()
{
int a=2;
return(bar(a*c*d));
}

bar.c
#include "bar.h"
int bar(int a)
{
int b=10;
return(b*a);
}

bar.h
extern int bar(int);

and a makefile:
Makefile
fooprog : foo.o bar.o
cc -o fooprog foo.o bar.o
foo.o : foo.c
cc -c foo.c
bar.o : bar.c
cc -c bar.c
clean :
rm -f *.o fooprog

The makefile has a number of rules like

foo.o : foo.c
<TAB>cc -c foo.c

which have the general form

target : prerequisite(s)
<TAB>rule(s)

where the rule lines are indented by a TAB character.

A rule, such as above, states that a ‘target’ file foo.o is made from a ‘prerequisite’ foo.c, namely by
executing the command cc -c foo.c. The precise definition of the rule is:
• if the target foo.o does not exist or is older than the prerequisite foo.c,

Victor Eijkhout 55
3. Managing projects with Make

• then the command part of the rule is executed: cc -c foo.c

• If the prerequisite is itself the target of another rule, than that rule is executed first.

Exercise. Call make.

Expected outcome. The above rules are applied: make without arguments tries to build the first
target, fooprog. In order to build this, it needs the prerequisites foo.o and bar.o, which do not
exist. However, there are rules for making them, which make recursively invokes. Hence you see
two compilations, for foo.o and bar.o, and a link command for fooprog.

Caveats. Typos in the makefile or in file names can cause various errors. In particular, make sure
you use tabs and not spaces for the rule lines. Unfortunately, debugging a makefile is not simple.
Make’s error message will usually give you the line number in the make file where the error was
detected.

Exercise. Do make clean, followed by mv foo.c boo.c and make again. Explain the error message.
Restore the original file name.

Expected outcome. Make will complain that there is no rule to make foo.c. This error was caused
when foo.c was a prerequisite for making foo.o, and was found not to exist. Make then went
looking for a rule to make it and no rule for creating .c files exists.

Now add a second argument to the function bar. This requires you to edit bar.c and bar.h: go ahead
and make these edits. However, it also requires you to edit foo.c, but let us for now ‘forget’ to do that.
We will see how Make can help you find the resulting error.

Exercise. Call make to recompile your program. Did it recompile foo.c?

Expected outcome. Even through conceptually foo.c would need to be recompiled since it uses
the bar function, Make did not do so because the makefile had no rule that forced it.

In the makefile, change the line

foo.o : foo.c

to
foo.o : foo.c bar.h

which adds bar.h as a prerequisite for foo.o. This means that, in this case where foo.o already exists,
Make will check that foo.o is not older than any of its prerequisites. Since bar.h has been edited, it is
younger than foo.o, so foo.o needs to be reconstructed.

Exercise. Confirm that the new makefile indeed causes foo.o to be recompiled if bar.h is changed. This
compilation will now give an error, since you ‘forgot’ to edit the use of the bar function.

56 HPC Carpentry
 3.1. A simple example

3.1.3 Fortran
Make the following files:
foomain.F
call func(1,2)

end program

foomod.F
contains

subroutine func(a,b)
integer a,b
print *,a,b,c
end subroutine func

end module

and a makefile:
Makefile
fooprog : foomain.o foomod.o
gfortran -o fooprog foo.o foomod.o
foomain.o : foomain.F
gfortran -c foomain.F
foomod.o : foomod.F
gfortran -c foomod.F
clean :
rm -f *.o fooprog

If you call make, the first rule in the makefile is executed. Do this, and explain what happens.

Exercise. Call make.

Expected outcome. The above rules are applied: make without arguments tries to build the first
target, foomain. In order to build this, it needs the prerequisites foomain.o and foomod.o, which
do not exist. However, there are rules for making them, which make recursively invokes. Hence
you see two compilations, for foomain.o and foomod.o, and a link command for fooprog.
Caveats. Typos in the makefile or in file names can cause various errors. Unfortunately, debugging
a makefile is not simple. You will just have to understand the errors, and make the corrections.

Exercise. Do make clean, followed by mv foomod.c boomod.c and make again. Explain the error mes-
sage. Restore the original file name.
Expected outcome. Make will complain that there is no rule to make foomod.c. This error was
caused when foomod.c was a prerequisite for foomod.o, and was found not to exist. Make then
went looking for a rule to make it, and no rule for making .F files exists.

Now add an extra parameter to func in foomod.F and recompile.

Exercise. Call make to recompile your program. Did it recompile foomain.F?

Victor Eijkhout 57
3. Managing projects with Make

Expected outcome. Even through conceptually foomain.F would need to be recompiled, Make did
not do so because the makefile had no rule that forced it.

Change the line

foomain.o : foomain.F

to
foomain.o : foomain.F foomod.o

which adds foomod.o as a prerequisite for foomain.o. This means that, in this case where foomain.o
already exists, Make will check that foomain.o is not older than any of its prerequisites. Recursively,
Make will then check if foomode.o needs to be updated, which is indeed the case. After recompiling
foomode.F, foomode.o is younger than foomain.o, so foomain.o will be reconstructed.

Exercise. Confirm that the corrected makefile indeed causes foomain.F to be recompiled.

3.2 Some general remarks

3.2.1 Rule interpretation
Probably the best way to interpret a rule is:
• if any prerequisite has changed,
• then the target needs to be remade,
• and that is done by executing the commands of the rule;
• checking the prerequisite requires a recursive application of make:
– if the prerequisite does not exist, find a rule to create it;
– if the prerequisite already exists, check applicable rules to see if it needs to be remade.

3.2.2 Make invocation

If you call make without any arguments, the first rule in the makefile is evaluated. You can execute other
rules by explicitly invoking them, for instance make foo.o to compile a single file.

3.2.3 About the make file

The make file needs to be called makefile or Makefile; it is not a good idea to have files with both
names in the same directory. If you want Make to use a different file as make file, use the syntax make -f
My_Makefile.

3.3 Variables and template rules

Purpose. In this section you will learn various work-saving mechanisms in Make, such
as the use of variables and of template rules.

58 HPC Carpentry
 3.3. Variables and template rules

3.3.1 Makefile variables

It is convenient to introduce variables in your makefile. For instance, instead of spelling out the compiler
explicitly every time, introduce a variable in the makefile:
CC = gcc
FC = gfortran

and use ${CC} or ${FC} on the compile lines:

foo.o : foo.c
${CC} -c foo.c
foomain.o : foomain.F
${FC} -c foomain.F

Exercise. Edit your makefile as indicated. First do make clean, then make foo (C) or make fooprog
(Fortran).
Expected outcome. You should see the exact same compile and link lines as before.
Caveats. Unlike in the shell, where braces are optional, variable names in a makefile have to be in
braces or parentheses. Experiment with what happens if you forget the braces around a variable
name.

One advantage of using variables is that you can now change the compiler from the commandline:
make CC="icc -O2"
make FC="gfortran -g"

Exercise. Invoke Make as suggested (after make clean). Do you see the difference in your screen output?
Expected outcome. The compile lines now show the added compiler option -O2 or -g.

Make also has automatic variables:

$@ The target. Use this in the link line for the main program.
$^ The list of prerequisites. Use this also in the link line for the program.
$< The first prerequisite. Use this in the compile commands for the individual object files.
$* In template rules (section 3.3.2) this matches the template part, the part corresponding to the %.
Using these variables, the rule for fooprog becomes
fooprog : foo.o bar.o
${CC} -o $@ $^

and a typical compile line becomes

foo.o : foo.c bar.h
${CC} -c $<

You can also declare a variable

THEPROGRAM = fooprog

Victor Eijkhout 59
3. Managing projects with Make

and use this variable instead of the program name in your makefile. This makes it easier to change your
mind about the name of the executable later.

Exercise. Edit your makefile to add this variable definition, and use it instead of the literal program name.
Construct a commandline so that your makefile will build the executable fooprog_v2.
Expected outcome. You need to specify the THEPROGRAM variable on the commandline using the
syntax make VAR=value.
Caveats. Make sure that there are no spaces around the equals sign in your commandline.

The full list of these automatic variables can be found at https://www.gnu.org/software/make/

manual/html_node/Automatic-Variables.html.

3.3.2 Template rules

So far, you wrote a separate rule for each file that needed to be compiled. However, the rules for the
various .c files are very similar:
• the rule header (foo.o : foo.c) states that a source file is a prerequisite for the object file with
the same base name;
• and the instructions for compiling (${CC} -c $<) are even character-for-character the same,
now that you are using Make’s built-in variables;
• the only rule with a difference is
foo.o : foo.c bar.h
${CC} -c $<

where the object file depends on the source file and another file.
We can take the commonalities and summarize them in one template rule1 :
%.o : %.c
${CC} -c $<
%.o : %.F
${FC} -c $<

This states that any object file depends on the C or Fortran file with the same base name. To regenerate
the object file, invoke the C or Fortran compiler with the -c flag. These template rules can function as a
replacement for the multiple specific targets in the makefiles above, except for the rule for foo.o.
The dependence of foo.o on bar.h, or foomain.o on foomod.o, can be handled by adding a rule
# C
foo.o : bar.h
# Fortran
foomain.o : foomod.o

1. This mechanism is the first instance you’ll see that only exists in GNU make, though in this particular case there is a similar
mechanism in standard make. That will not be the case for the wildcard mechanism in the next section.

60 HPC Carpentry
 3.3. Variables and template rules

with no further instructions. This rule states, ‘if file bar.h or foomod.o changed, file foo.o or foomain.o
needs updating’ too. Make will then search the makefile for a different rule that states how this updating
is done, and it will find the template rule.

Exercise. Change your makefile to incorporate these ideas, and test.

Figure 3.1: File structure with main program and two library files.

Exercise 3.1. Write a makefile for the following structure:

• There is one main file libmain.cxx, and two library files libf.cxx libg.cxx;
• There is a header file libapi.h that gives the prototypes for the functions in the
library files;
• There is a header file libimpl.h that gives implementation details, only to be used
in the library files.
This is illustrated in figure 3.1.
Here is how you can test it:

Changing a source file only recompiles that files: clang++ -o main libmain.o libf.o
libg.o
clang++ -c libf.cxx
clang++ -o main \ Changing the libapi.h recompiles everything:
libmain.o libf.o libg.o
clang++ -c libmain.cxx
Changing the implementation header only recom- clang++ -c libf.cxx
piles the library: clang++ -c libg.cxx
clang++ -o main libmain.o libf.o
clang++ -c libf.cxx libg.o
clang++ -c libg.cxx

For Fortran we don’t have header files so we use modules everywhere; figure 3.3. If you know how to use
submodules, a Fortran2008 feature, you can make the next exercise as efficient as the C version.
Exercise 3.2. Write a makefile for the following structure:
• There is one main file libmain.f90, that uses a module api.f90;
• There are two low level modules libf.f90 libg.f90 that are used in api.f90.
If you use modules, you’ll likely be doing more compilation than needed. For the optimal
solution, use submodules.

Victor Eijkhout 61
3. Managing projects with Make

Source file mainprog.cxx: Source file libg.cxx:

#include <cstdio> #include "impl.h"
#include "api.h" #include "api.h"
int main() { int g() {
int n = f() + g(); struct impl_struct foo;
printf("%d\n",n); return 2;
return 0; };
}
Source file libf.cxx: Header file api.h:
#include "impl.h" int f();
#include "api.h" int g();

int f() { Header file impl.h:

struct impl_struct foo;
return 1; struct impl_struct {};
};

Figure 3.2: Source files for exercise 3.1.

Figure 3.3: File structure with main program and two library files.

3.3.3 Wildcards
Your makefile now uses one general rule for compiling any source file. Often, your source files will be
all the .c or .F files in your directory, so is there a way to state ‘compile everything in this directory’?
Indeed there is.
Add the following lines to your makefile, and use the variable COBJECTS or FOBJECTS wherever appro-
priate. The command wildcard gives the result of ls, and you can manipulate file names with patsubst.
# wildcard: find all files that match a pattern
CSOURCES := ${wildcard *.c}
# pattern substitution: replace one pattern string by another
COBJECTS := ${patsubst %.c,%.o,${SRC}}

FSOURCES := ${wildcard *.F}

FOBJECTS := ${patsubst %.F,%.o,${SRC}}

62 HPC Carpentry
 3.3. Variables and template rules

3.3.4 More functions

GNU make has more function that you can call inside the makefile. Some examples:
HOSTNAME := $(shell hostname -f)
SOURCES := $(wildcard *.c)
OBJECTS := $(patsubst %.c,%.o,${SOURCES})
RECURSIVE := $(foreach d,${DIRECTORIES},$(wildcard ${d}/*.c))

File name manipulation:

$(dir a/b/c.x) # gives `a/b'
$(dir c.x) # gives `./'
$(notdir a/b/c.x) # gives `c.x'
$(suffix a/b/c.x) # gives `.x'

For the full list see https://www.gnu.org/software/make/manual/html_node/Functions.html.

// Makefile SRC: src/f1.c src/f2.c

SRC := ${wildcard src/*.c}

OBJ := ${patsubst src/%,obj/%,${patsubst %.c OBJ: obj/f1.o obj/f2.o

,%.o,${SRC}}}

PRE := ${addprefix /usr/lib,${SRC} othersrc PRE: /usr/libsrc/f1.c /usr/libsrc/f2.c /usr/

moresrc} libothersrc /usr/libmoresrc

BAK := ${addsuffix .bak,${SRC}} BAK: src/f1.c.bak src/f2.c.bak

3.3.5 Conditionals
There are various ways of making the behavior of a makefile dynamic. You can for instance put a shell
conditional in an action line. However, this can make for a cluttered makefile; an easier way is to use
makefile conditionals. There are two types of conditionals: tests on string equality, and tests on environ-
ment variables.
The first type looks like
ifeq "${HOME}" "/home/thisisme"
# case where the executing user is me
else ifeq "${HOME}" "/home/buddyofmine"
# case for other user
else
# case where it's someone else
endif

and in the second case the test looks like

ifdef SOME_VARIABLE

Victor Eijkhout 63
3. Managing projects with Make

The text in the true and false part can be most any part of a makefile. For instance, it is possible to let one
of the action lines in a rule be conditionally included. However, most of the times you will use conditionals
to make the definition of variables dependent on some condition.

Exercise. Let’s say you want to use your makefile at home and at work. At work, your employer has a
paid license to the Intel compiler icc, but at home you use the open source Gnu compiler gcc. Write a
makefile that will work in both places, setting the appropriate value for CC.

3.4 Miscellania
3.4.1 Phony targets
The example makefile contained a target clean. This uses the Make mechanisms to accomplish some
actions that are not related to file creation: calling make clean causes Make to reason ‘there is no file
called clean, so the following instructions need to be performed’. However, this does not actually cause
a file clean to spring into being, so calling make clean again will make the same instructions being
executed.
To indicate that this rule does not actually make the target, you use the .PHONY keyword:
.PHONY : clean

Most of the time, the makefile will actually work fine without this declaration, but the main benefit of
declaring a target to be phony is that the Make rule will still work, even if you have a file (or folder) named
clean.

3.4.2 Directories
It’s a common strategy to have a directory for temporary material such as object files. So you would have
a rule
obj/%.o : %.c
${CC} -c $< -o $@

and to remove the temporaries:

clean ::
rm -rf obj

This raises the question how the obj directory is created. You could do:
obj/%.o : %.c
mkdir -p obj
${CC} -c $< -o $@

but a better solution is to use order-only prerequisites exist.

64 HPC Carpentry
 3.4. Miscellania

obj :
mkdir -p obj
obj/%.o : %.c | obj
${CC} -c $< -o $@

This only tests for the existence of the object directory, but not its timestamp.

3.4.3 Using the target as prerequisite

Suppose you have two different targets that are treated largely the same. You would want to write:
PROGS = myfoo other
${PROGS} : [email protected] # this is wrong!!
${CC} -o $@ [email protected] ${list of libraries goes here}

and saying make myfoo would cause

cc -c myfoo.c
cc -o myfoo myfoo.o ${list of libraries}

and likewise for make other. What goes wrong here is the use of [email protected] as prerequisite. In Gnu Make,
you can repair this as follows2 :
.SECONDEXPANSION:
${PROGS} : [email protected]
${CC} -o $@ [email protected] ${list of libraries goes here}

Exercise. Write a second main program foosecond.c or foosecond.F, and change your makefile so
that the calls make foo and make foosecond both use the same rule.

3.4.4 Predefined variables and rules

Calling make -p yourtarget causes make to print out all its actions, as well as the values of all variables
and rules, both in your makefile and ones that are predefined. If you do this in a directory where there is
no makefile, you’ll see that make actually already knows how to compile .c or .F files. Find this rule and
find the definition of the variables in it.
You see that you can customize make by setting such variables as CFLAGS or FFLAGS. Confirm this with
some experimentation. If you want to make a second makefile for the same sources, you can call make
-f othermakefile to use this instead of the default Makefile.
Note, by the way, that both makefile and Makefile are legitimate names for the default makefile. It is
not a good idea to have both makefile and Makefile in your directory.

2. Technical explanation: Make will now look at lines twice: the first time $$ gets converted to a single $, and in the second
pass $@ becomes the name of the target.

Victor Eijkhout 65
3. Managing projects with Make

3.5 Shell scripting in a Makefile

Purpose. In this section you will see an example of a longer shell script appearing in a
makefile rule.

In the makefiles you have seen so far, the command part was a single line. You can actually have as many
lines there as you want. For example, let us make a rule for making backups of the program you are
building.
Add a backup rule to your makefile. The first thing it needs to do is make a backup directory:
.PHONY : backup
backup :
if [ ! -d backup ] ; then
mkdir backup
fi

Did you type this? Unfortunately it does not work: every line in the command part of a makefile rule gets
executed as a single program. Therefore, you need to write the whole command on one line:
backup :
if [ ! -d backup ] ; then mkdir backup ; fi

or if the line gets too long:

backup :
if [ ! -d backup ] ; then \
mkdir backup ; \
fi

(Writing a long command on a single is only possible in the bash shell, not in the csh shell. This is one
reason for not using the latter.)
Next we do the actual copy:
backup :
if [ ! -d backup ] ; then mkdir backup ; fi
cp myprog backup/myprog

But this backup scheme only saves one version. Let us make a version that has the date in the name of
the saved program.
The Unix date command can customize its output by accepting a format string. Type the following:
date This can be used in the makefile.

Exercise. Edit the cp command line so that the name of the backup file includes the current date.
Expected outcome. Hint: you need the backquote. Consult the Unix tutorial, section 1.5.3, if you
do not remember what backquotes do.

If you are defining shell variables in the command section of a makefile rule, you need to be aware of the
following. Extend your backup rule with a loop to copy the object files:

66 HPC Carpentry
 3.6. Practical tips for using Make

#### This Script Has An ERROR!

backup :
if [ ! -d backup ] ; then mkdir backup ; fi
cp myprog backup/myprog
for f in ${OBJS} ; do \
cp $f backup ; \
done

(This is not the best way to copy, but we use it for the purpose of demonstration.) This leads to an error
message, caused by the fact that Make interprets $f as an environment variable of the outer process. What
works is:
backup :
if [ ! -d backup ] ; then mkdir backup ; fi
cp myprog backup/myprog
for f in ${OBJS} ; do \
cp $$f backup ; \
done

(In this case Make replaces the double dollar by a single one when it scans the commandline. During the
execution of the commandline, $f then expands to the proper filename.)

3.6 Practical tips for using Make

Here are a couple of practical tips.
• Debugging a makefile is often frustratingly hard. Just about the only tool is the -p option, which
prints out all the rules that Make is using, based on the current makefile.
• You will often find yourself first typing a make command, and then invoking the program. Most
Unix shells allow you to use commands from the shell command history by using the up arrow
key. Still, this may get tiresome, so you may be tempted to write
make myprogram ; ./myprogram -options

and keep repeating this. There is a danger in this: if the make fails, for instance because of com-
pilation problems, your program will still be executed. Instead, write
make myprogram && ./myprogram -options

which executes the program conditional upon make concluding successfully.

3.6.1 What does this makefile do?

Above you learned that issuing the make command will automatically execute the first rule in the makefile.
This is convenient in one sense3 , and inconvenient in another: the only way to find out what possible
actions a makefile allows is to read the makefile itself, or the – usually insufficient – documentation.
A better idea is to start the makefile with a target

3. There is a convention among software developers that a package can be installed by the sequence ./configure ; make ;
make install, meaning: Configure the build process for this computer, Do the actual build, Copy files to some system directory
such as /usr/bin.

Victor Eijkhout 67
3. Managing projects with Make

info :
@echo "The following are possible:"
@echo " make"
@echo " make clean"

Now make without explicit targets informs you of the capabilities of the makefile.
If your makefile gets longer, you might want to document each section like this. This runs into a problem:
you can not have two rules with the same target, info in this case. However, if you use a double colon it
is possible. Your makefile would have the following structure:
info ::
@echo "The following target are available:"
@echo " make install"
install :
# ..... instructions for installing
info ::
@echo " make clean"
clean :
# ..... instructions for cleaning

3.7 A Makefile for LATEX

The Make utility is typically used for compiling programs, but other uses are possible too. In this section,
we will discuss a makefile for LATEX documents.
We start with a very basic makefile:
info :
@echo "Usage: make foo"
@echo "where foo.tex is a LaTeX input file"

%.pdf : %.tex
pdflatex $<

The command make myfile.pdf will invoke pdflatex myfile.tex, if needed, once. Next we repeat
invoking pdflatex until the log file no longer reports that further runs are needed:
%.pdf : %.tex
pdflatex $<
while [ `cat ${basename $@}.log | grep "Rerun to get" \
| wc -l` -gt 0 ] ; do \
pdflatex $< ; \
done

We use the ${basename fn} macro to extract the base name without extension from the target name.
In case the document has a bibliography or index, we run bibtex and makeindex.

68 HPC Carpentry
 3.7. A Makefile for LATEX

%.pdf : %.tex
pdflatex ${basename $@}
-bibtex ${basename $@}
-makeindex ${basename $@}
while [ `cat ${basename $@}.log | grep "Rerun to get" \
| wc -l` -gt 0 ] ; do \
pdflatex ${basename $@} ; \
done

The minus sign at the start of the line means that Make should not exit if these commands fail.
Finally, we would like to use Make’s facility for taking dependencies into account. We could write a
makefile that has the usual rules
mainfile.pdf : mainfile.tex includefile.tex

but we can also discover the include files explicitly. The following makefile is invoked with
make pdf TEXTFILE=mainfile

The pdf rule then uses some shell scripting to discover the include files (but not recursively), and it calls
Make again, invoking another rule, and passing the dependencies explicitly.
pdf :
export includes=`grep "^.input " ${TEXFILE}.tex \
| awk '{v=v FS $$2".tex"} END {print v}'` ; \
${MAKE} ${TEXFILE}.pdf INCLUDES="$$includes"

%.pdf : %.tex ${INCLUDES}

pdflatex $< ; \
while [ `cat ${basename $@}.log \
| grep "Rerun to get" | wc -l` -gt 0 ] ; do \
pdflatex $< ; \
done

This shell scripting can also be done outside the makefile, generating the makefile dynamically.

Victor Eijkhout 69
Chapter 4

The Cmake build system

4.1 CMake as build system

CMake is a general build system that uses other systems such as Make as a back-end. The general workflow
is:
1. The configuration stage. Here the CMakeLists.txt file is parsed, and a build directory populated.
This typically looks like:
mkdir build
cd build
cmake <source location>

Some people create the build directory in the source tree, in which case the CMake command is
cmake ..

Others put the build directory next to the source, in which case:
cmake ../src_directory

2. The build stage. Here the installation-specific compilation in the build directory is performed.
With Make as the ‘generator’ this would be
cd build
make

but more generally

cmake --build <build directory>

Alternatively, you could use generators such as ninja, Visual Studio, or XCode:
cmake -G ninja
## the usual arguments

3. The install stage. This can move binary files to a permanent location, such as putting library files
in /usr/lib:
make install

or

70
 4.1. CMake as build system

General directives
cmake_minimum_required specify minimum cmake version
project name and version number of this project
install specify directory where to install targets
Project building directives
add_executable specify executable name and source files for it
add_library specify library name and files to go into it
add_subdirectory specify subdirectory where cmake also needs to
run
target_link_libraries specify executable and libraries to link into it
target_include_directories specify include directories, privately or publicly
find_package other package to use in this build
Utility stuff
target_compile_options literal options to include
target_compile_features things that will be translated by cmake into op-
tions
target_compile_definitions macro definitions to be set private or publicly
file define macro as file list
message Diagnostic to print, subject to level specification
Control
if() else() endif() conditional

Table 4.1: Cmake commands.

Victor Eijkhout 71
4. The Cmake build system

cmake --install <build directory>

However, the install location already has to be set in the configuration stage. We will see later in
detail how this is done.
Summarizing, the out-of-source workflow as advocated in this tutorial is
ls some_package_1.0.0 # we are outside the source
ls some_package_1.0.0/CMakeLists.txt # source contains cmake file
mkdir builddir && cd builddir # goto build location
cmake -D CMAKE_INSTALL_PREFIX=../installdir \
../some_package_1.0.0
make
make install

The resulting directory structure is illustrated in figure 4.1.

dir dir

src src

build build

install install

Figure 4.1: In-source (left) and out-of-source (right) build schemes.

4.1.1 Target philosophy

Modern CMake works through declaring targets and their requirements. For requirements during build-
ing:
target_some_requirement( the_target PRIVATE the require ments )

Usage requirements:
target_some_requirement( the_target PUBLIC the require ments )

4.1.2 Languages
CMake is largely aimed at C++, but it easily supports C as well. For Fortran support, first do
enable_language(Fortran)

Note that capitalization: this also holds for all variables such as CMAKE_Fortran_COMPILER.

72 HPC Carpentry
 4.1. CMake as build system

4.1.3 Script structure

Commands learned in this section

cmake_minimum_required declare minimum required version for this script
project declare a name for this project

CMake is driven by the CMakeLists.txt file. This needs to be in the root directory of your project. (You
can additionally have files by that name in subdirectories.)
Since CMake has changed quite a bit over the years, and is still evolving, it is a good idea to start each
script with a declaration of the (minimum) required version:
cmake_minimum_required( VERSION 3.12 )

You can query the version of your CMake executable:

$ cmake --version
cmake version 3.19.2

You also need to declare a project name and version, which need not correspond to any file names:
project( myproject VERSION 1.0 )

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4. The Cmake build system

4.2 Examples cases

4.2.1 Executable from sources
(The files for this examples are in tutorials/cmake/single.)

Commands learned in this section

add_executable declare an executable and its sources
install indicate location where to install this project
PROJECT_NAME macro that expands to the project name

If you have a project that is supposed to deliver an executable,

you declare in your CMakeLists.txt: dir
add_executable( myprogram program.cxx )
src
Often, the name of the executable is the name of the project,
so you’d specify: CMakeLists.txt
add_executable( ${PROJECT_NAME} program.cxx )
program.cxx
In order to move the executable to the install location, you
need a clause build
install( TARGETS myprogram DESTINATION . )
CMakeCache.txt
Without the DESTINATION clause, a default bin directory will be
created; specifying DESTINATION foo will put the program in a Makefile
foo sub-directory of the installation directory.
myprogram
In the figure on the right we have also indicated the build
directory, which from now on we will not show again. It con-
tains automatically generated files that are hard to decyper, or lots more
debug. Yes, there is a Makefile, but even for simple projects
this is too complicated to debug by hand if your CMake instal- install
lation misbehaves.
myprogram
Here is the full CMakeLists.txt:
cmake_minimum_required( VERSION 3.12 )
project( singleprogram VERSION 1.0 )

add_executable( program program.cxx )

install( TARGETS program DESTINATION . )

74 HPC Carpentry
 4.2. Examples cases

4.2.2 Making libraries

(The files for this examples are in tutorials/cmake/multiple.)

Commands learned in this section

add_library declare a library and its sources
target_link_libraries indicate that the library belong with an exe-
cutable

If there is only one source file, the previous section is all you
need. However, often you will build libraries. You declare those dir
with an add_library clause:
add_library( auxlib aux.cxx aux.h ) src

Next, you need to link that library into the program: CMakeLists.txt
target_link_libraries( program PRIVATE auxlib )
program.cxx
The PRIVATE clause means that the library is only for purposes
of building the executable. (Use PUBLIC to have the library be aux.cxx
included in the installation; we will explore that in section 4.2.2.2.)
aux.h
The full CMakeLists.txt:
cmake_minimum_required( VERSION 3.12 ) install
project( cmakeprogram VERSION 1.0 )

add_executable( program program.cxx ) program

add_library( auxlib STATIC
aux1.cxx aux2.cxx aux.h )
target_link_libraries( program PRIVATE auxlib )
install( TARGETS program DESTINATION . )

Note that private shared libraries make no sense, as they will give runtime unresolved references.

4.2.2.1 Testing the generated makefiles

In the Make tutorial 3 you learned how Make will only recompile the strictly necessary files when a limited
edit has been made. The makefiles generated by CMake behave similarly. With the structure above, we
first touch the aux.cxx file, which necessitates rebuilding the library:
----------------
touch a source file and make:
Consolidate compiler generated dependencies of target auxlib
[ 25%] Building CXX object CMakeFiles/auxlib.dir/aux.cxx.o
[ 50%] Linking CXX static library libauxlib.a
[ 50%] Built target auxlib
Consolidate compiler generated dependencies of target program
[ 75%] Linking CXX executable program

Victor Eijkhout 75
4. The Cmake build system

[100%] Built target program

On the other hand, if we edit a header file, the main program needs to be recompiled too:
----------------
touch a source file and make:
Consolidate compiler generated dependencies of target auxlib
[ 25%] Building CXX object CMakeFiles/auxlib.dir/aux.cxx.o
[ 50%] Linking CXX static library libauxlib.a
[ 50%] Built target auxlib
Consolidate compiler generated dependencies of target program
[ 75%] Linking CXX executable program
[100%] Built target program

4.2.2.2 Making a library for release

(The files for this example are in tutorials/cmake/withlib.)

Commands learned in this section

SHARED indicated to make shared libraries

In order to create a library we use add_library, and we link it

into the target program with target_link_libraries. dir
By default the library is build as a static .a file, but adding
src
add_library( auxlib SHARED aux.cxx aux.h )

CMakeLists.txt
or adding a runtime flag
cmake -D BUILD_SHARED_LIBS=TRUE program.cxx

changes that to a shared .so type. aux.cxx

Related: the -fPIC compile option is set by CMAKE_POSITION_INDEPENDENT_CODE.
aux.h
The full CMake file:
cmake_minimum_required( VERSION 3.12 ) install
project( cmakeprogram VERSION 1.0 )
program
add_executable( program program.cxx )
add_library( auxlib
aux.cxx aux.h ) libauxlib.a
target_link_libraries( program PUBLIC auxlib )
install( TARGETS program auxlib DESTINATION . )

76 HPC Carpentry
 4.2. Examples cases

4.2.3 Using subdirectories during the build

(The files for this examples are in tutorials/cmake/includedir.)

Commands learned in this section

target_include_directories indicate include directories needed
target_sources specify more sources for a target
CMAKE_CURRENT_SOURCE_DIR variable that expands to the current directory
file define single-name synonym for multiple files
GLOB define single-name synonym for multiple files

Suppose you have a directory with header files, as in the dia-

gram on the right. The main program would have dir
#include <iostream>
using namespace std; src

#include "aux.h"
CMakeLists.txt
int main() {
aux1(); program.cxx
aux2();
return 0;
} src

and which is compiled as: aux.cxx

cc -c program.cxx -I./inc
inc

To make sure the header file gets found during the build, you
aux.h
specify that include path with target_include_directories:
target_include_directories( install
program PRIVATE
"${CMAKE_CURRENT_SOURCE_DIR}/inc" )
program
It is best to make such paths relative to CMAKE_CURRENT_SOURCE_DIR
, or the source root CMAKE_SOURCE_DIR, or equivalently PROJECT_SOURCE_DIR

Usually, when you start making such directory structure, you will also have sources in subdirectories. If
you only need to compile them into the main executable, you could list them into a variable
set( SOURCES program.cxx src/aux.cxx )

and use that variable. However, this is deprecated practice; it is recommended to use target_sources:
target_sources( program PRIVATE src/aux1.cxx src/aux2.cxx )

Use of a wildcard is not trivial:

Victor Eijkhout 77
4. The Cmake build system

file( GLOB AUX_FILES "src/*.cxx" )

target_sources( program PRIVATE ${AUX_FILES} )

Complete CMake file:

cmake_minimum_required( VERSION 3.14 )
project( cmakeprogram VERSION 1.0 )

add_executable( program program.cxx )

#target_sources( program PRIVATE src/aux1.cxx src/aux2.cxx )
file( GLOB AUX_FILES "src/*.cxx" )
target_sources( program PRIVATE ${AUX_FILES} )
target_include_directories(
program PRIVATE
"${CMAKE_CURRENT_SOURCE_DIR}/inc" )

install( TARGETS program DESTINATION . )

78 HPC Carpentry
 4.2. Examples cases

4.2.4 Libraries for release; rpath

(The files for this examples are in tutorials/cmake/publiclib.)

Commands learned in this section

add_subdirectory declare a subdirectory where cmake needs to be
run
CMAKE_CURRENT_SOURCE_DIR directory where this command is evaluated
CMAKE_CURRENT_BINARY_DIR
LIBRARY_OUTPUT_PATH
FILES_MATCHING PATTERN wildcard indicator
If your sources are spread over multiple directories, there needs
to be a CMakeLists.txt file in each, and you need to de- dir
clare the existence of those directories. Let’s start with the ob-
vious choice of putting library files in a lib directory with src
add_subdirectory:
add_subdirectory( lib ) CMakeLists.txt

For instance, a library directory would have a CMakeLists.txt program.cxx

file:
cmake_minimum_required( VERSION 3.14 ) lib
project( auxlib )

add_library( auxlib SHARED CMakeLists.txt

aux.cxx aux.h )
target_include_directories( aux.cxx
auxlib PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}" )
install( TARGETS auxlib DESTINATION lib )
install( FILES aux.h DESTINATION include ) aux.h

to build the library file from the sources indicated, and to in- install
stall it in a lib subdirectory.
We also add a clause to install the header files in an include directory: program
install( FILES aux.h DESTINATION include )
lib
For installing multiple files, use
install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} libauxlib.so
DESTINATION ${LIBRARY_OUTPUT_PATH}
FILES_MATCHING PATTERN "*.h") include
One problem is to tell the executable where to find the library. For this we use the rpath mechanism.
aux.h
By default, CMake sets it so that the executable in the build location can find the library. If you use a
non-trivial install prefix, the following lines work:
set( CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib" )
set( CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE )

Victor Eijkhout 79
4. The Cmake build system

Note that these have to be specified before the target.

The whole file:
cmake_minimum_required( VERSION 3.14 )
project( cmakeprogram VERSION 1.0 )

set( CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib" )

set( CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE )

add_executable( program program.cxx )

add_subdirectory( lib )
target_include_directories(
auxlib PUBLIC "${CMAKE_CURRECT_SOURCE_DIR}" )
target_link_libraries(
program PUBLIC auxlib )

install( TARGETS program DESTINATION . )

80 HPC Carpentry
 4.3. Finding and using external packages

4.2.5 Programs that use other libraries

So far we have discussed executables and libraries that can be used by themselves. What to if your build
result needs external libraries? We will discuss how to find those libraries in section 4.3; here we point
out their use.
The issue is that these libraries need to be findable when someone uses your binary. There are two strate-
gies:
• make sure they have been added to the LD_LIBRARY_PATH;
• have the linker add their location through the rpath mechanism to the binary itself. This second
option is in fact the only one on recent versions of Apple Mac OS because of ‘System Integrity
Protection’.
As an example, assume your binary needs the Catch2 and fmtlib libraries. You would then, in addition
to the target_link_directories specification, have:
set_target_properties(
${PROGRAM_NAME} PROPERTIES
BUILD_RPATH "${CATCH2_LIBRARY_DIRS};${FMTLIB_LIBRARY_DIRS}"
INSTALL_RPATH "${CATCH2_LIBRARY_DIRS};${FMTLIB_LIBRARY_DIRS}"
)

4.2.6 Header-only libraries

Use the INTERFACE keyword.

4.3 Finding and using external packages

If your program depends on other libraries, there is a variety of ways to let CMake find them.

4.3.1 CMake commandline options

(The files for this example are in tutorials/cmake/usepubliclib.)
You can indicate the location of your external library explicitly on the commandline.
cmake -D OTHERLIB_INC_DIR=/some/where/include
-D OTHERLIB_LIB_DIR=/somewhere/lib

Example CMake file:

cmake_minimum_required( VERSION 3.12 )
project( pkgconfiglib VERSION 1.0 )

# with environment variables

# set( AUX_INCLUDE_DIR $ENV{TACC_AUX_INC} )
# set( AUX_LIBRARY_DIR $ENV{TACC_AUX_LIB} )

# with cmake -D options

Victor Eijkhout 81
4. The Cmake build system

option( AUX_INCLUDE_DIR "include dir for auxlib" )

option( AUX_LIBRARY_DIR "lib dir for auxlib" )

add_executable( program program.cxx )

target_include_directories(
program PUBLIC
${AUX_INCLUDE_DIR} )
target_link_libraries( program PUBLIC auxlib )
target_link_directories(
program PUBLIC
${AUX_LIBRARY_DIR} )
install( TARGETS program DESTINATION . )

4.3.2 Package finding through ‘find library’ and ‘find package’

Commands learned in this section

find_library find a library with a FOOConfig.cmake file
CMAKE_PREFIX_PATH location for FOOConfig.cmake files
find_package find a library with a FindFOO module
CMAKE_MODULE_PATH location for FindFOO modules
The find_package command looks for files with a name FindXXX.cmake, which are searched on the
CMAKE_MODULE_PATH. Unfortunately, the working of find_package depend somewhat on the specific pack-
age. For instance, most packages set a variable FooFound that you can test
find_package( Foo )
if ( FooFound )
# do something
else()
# throw an error
endif()

Some libraries come with a FOOConfig.cmake file, which is searched on the CMAKE_PREFIX_PATH through
find_library. If it is found, you can test the variable it is supposed to set:
find_library( FOOLIB foo )
if (FOOLIB)
target_link_libraries( myapp PRIVATE ${FOOLIB} )
else()
# throw an error
endif()

4.3.2.1 Example: MPI

(The files for this example are in tutorials/cmake/mpiprog.)
While many MPI implementations have a .pc file, it’s better to use the FindMPI module. This package
defines a number of variables that can be used to query the MPI found; for details see https://cmake.
org/cmake/help/latest/module/FindMPI.html
C version:

82 HPC Carpentry
 4.3. Finding and using external packages

cmake_minimum_required( VERSION 3.12 )

project( ${PROJECT_NAME} VERSION 1.0 )

find_package( MPI )

add_executable( ${PROJECT_NAME} ${PROJECT_NAME}.c )

target_include_directories(
${PROJECT_NAME} PUBLIC
${MPI_C_INCLUDE_DIRS} ${CMAKE_CURRENT_SOURCE_DIR} )
target_link_libraries(
${PROJECT_NAME} PUBLIC
${MPI_C_LIBRARIES} )

install( TARGETS ${PROJECT_NAME} DESTINATION . )

Fortran version:
cmake_minimum_required( VERSION 3.12 )
project( ${PROJECT_NAME} VERSION 1.0 )

enable_language(Fortran)

find_package( MPI )

if( MPI_Fortran_HAVE_F08_MODULE )
else()
message( FATAL_ERROR "No f08 module for this MPI" )
endif()

add_executable( ${PROJECT_NAME} ${PROJECT_NAME}.F90 )

target_include_directories(
${PROJECT_NAME} PUBLIC
${MPI_Fortran_INCLUDE_DIRS} ${CMAKE_CURRENT_SOURCE_DIR} )
target_link_directories(
${PROJECT_NAME} PUBLIC
${MPI_LIBRARY_DIRS} )
target_link_libraries(
${PROJECT_NAME} PUBLIC
${MPI_Fortran_LIBRARIES} )

install( TARGETS ${PROJECT_NAME} DESTINATION . )

4.3.2.2 Example: OpenMP

find_package(OpenMP)
if(OpenMP_C_FOUND) # or CXX
else()
message( FATAL_ERROR "Could not find OpenMP" )
endif()
# for C:
add_executable( ${program} ${program}.c )
target_link_libraries( ${program} PUBLIC OpenMP::OpenMP_C )
# for C++:
add_executable( ${program} ${program}.cxx )

Victor Eijkhout 83
4. The Cmake build system

target_link_libraries( ${program} PUBLIC OpenMP::OpenMP_CXX)

# for Fortran
enable_language(Fortran)
# test: if( OpenMP_Fortran_FOUND )
add_executable( ${program} ${program}.F90 )
target_link_libraries( ${program} PUBLIC OpenMP::OpenMP_Fortran )

4.3.2.3 Example: MKL

(The files for this example are in tutorials/cmake/mklcmake.)

Intel compiler installations come with CMake support: there is a file MKLConfig.cmake.

Example program using Cblas from MKL:

#include <iostream>
#include <vector>
using namespace std;

#include "mkl_cblas.h"

int main() {
vector<double> values{1,2,3,2,1};
auto maxloc = cblas_idamax ( values.size(),values.data(),1);
cout << "Max abs at: " << maxloc << " (s/b 2)" << '\n';

return 0;
}

The following configuration file lists the various options and such:
cmake_minimum_required( VERSION 3.12 )
project( mklconfigfind VERSION 1.0 )

## https://www.intel.com/content/www/us/en/develop/documentation/onemkl-linux-developer-guide/
top/getting-started/cmake-config-for-onemkl.html

find_package( MKL CONFIG REQUIRED )

add_executable( program program.cxx )

target_compile_options(
program PUBLIC
$<TARGET_PROPERTY:MKL::MKL,INTERFACE_COMPILE_OPTIONS> )
target_include_directories(
program PUBLIC
$<TARGET_PROPERTY:MKL::MKL,INTERFACE_INCLUDE_DIRECTORIES> )
target_link_libraries(
program PUBLIC
$<LINK_ONLY:MKL::MKL>)

install( TARGETS program DESTINATION . )

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 4.3. Finding and using external packages

4.3.3 Use of other packages through ‘pkg config’

These days, many package support the pkgconfig mechanism.
1. Suppose you have a library mylib, installed in /opt/local/mylib.
2. If mylib supports pkgconfig, there is most likely a path /opt/local/mylib/lib/pkgconfig,
containing a file mylib.pc.
3. Add the path that contains the .pc file to the PKG_CONFIG_PATH environment variable.
Cmake is now able to find mylib:
find_package( PkgConfig REQUIRED )
pkg_check_modules( MYLIBRARY REQUIRED mylib )

This defines variables

MYLIBRARY_INCLUDE_DIRS
MYLIBRARY_LIBRARY_DIRS
MYLIBRARY_LIBRARIES

which you can then use in the target_include_directories and target_link_directories target_link_libraries
commands.

4.3.3.1 Example: PETSc

(The files for this example are in tutorials/cmake/petscprog.)
This CMake setup searches for petsc.pc, which is located in $PETSC_DIR/$PETSC_ARCH/lib/pkgconfig:
cmake_minimum_required( VERSION 3.12 )
project( pkgconfiglib VERSION 1.0 )

find_package( PkgConfig REQUIRED )

pkg_check_modules( PETSC REQUIRED petsc )
message( STATUS "PETSc includes: ${PETSC_INCLUDE_DIRS}" )
message( STATUS "PETSc libraries: ${PETSC_LIBRARY_DIRS}" )

add_executable( program program.cxx )

target_include_directories(
program PUBLIC
${PETSC_INCLUDE_DIRS} )
target_link_directories(
program PUBLIC
${PETSC_LIBRARY_DIRS} )
target_link_libraries(
program PUBLIC petsc )

install( TARGETS program DESTINATION . )

4.3.3.2 Example: Eigen

(The files for this example are in tutorials/cmake/eigen.)
The eigen package uses pkgconfig.

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4. The Cmake build system

cmake_minimum_required( VERSION 3.12 )

project( eigentest )

find_package( PkgConfig REQUIRED )

pkg_check_modules( EIGEN REQUIRED eigen3 )

add_executable( eigentest eigentest.cxx )

target_include_directories(
eigentest PUBLIC
${EIGEN_INCLUDE_DIRS})

4.3.3.3 Example: cxxopts

(The files for this example are in tutorials/cmake/cxxopts.)

The cxxopts package uses pkgconfig.

cmake_minimum_required( VERSION 3.12 )
project( pkgconfiglib VERSION 1.0 )

find_package( PkgConfig REQUIRED )

pkg_check_modules( OPTS REQUIRED cxxopts )
message( STATUS "cxxopts includes: ${OPTS_INCLUDE_DIRS}" )

add_executable( program program.cxx )

target_include_directories(
program PUBLIC
${OPTS_INCLUDE_DIRS})

install( TARGETS program DESTINATION . )

4.3.3.4 Example: fmtlib

(The files for this example are in tutorials/cmake/fmtlib.)

In the following example, we use the fmtlib. The main CMake file:
cmake_minimum_required( VERSION 3.12 )
project( pkgconfiglib VERSION 1.0 )

find_package( PkgConfig REQUIRED )

pkg_check_modules( FMTLIB REQUIRED fmt )
message( STATUS "fmtlib includes: ${FMTLIB_INCLUDE_DIRS}" )

add_executable( program program.cxx )

target_include_directories(
program PUBLIC
${FMTLIB_INCLUDE_DIRS})

install( TARGETS program DESTINATION . )

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 4.3. Finding and using external packages

4.3.3.5 Example: fmtlib used in library

(The files for this example are in tutorials/cmake/fmtliblib.)
We continue using the fmtlib library, but now the generated library also has references to this library, so
we use target_link_directories and target_link_library.
Main file:
cmake_minimum_required( VERSION 3.12 )
project( pkgconfiglib VERSION 1.0 )

find_package( PkgConfig REQUIRED )

pkg_check_modules( FMTLIB REQUIRED fmt )
message( STATUS "fmtlib includes : ${FMTLIB_INCLUDE_DIRS}" )
message( STATUS "fmtlib lib dirs : ${FMTLIB_LIBRARY_DIRS}" )
message( STATUS "fmtlib libraries: ${FMTLIB_LIBRARIES}" )

add_executable( program program.cxx )

target_include_directories(
program PUBLIC
${FMTLIB_INCLUDE_DIRS})

add_subdirectory( prolib )
target_link_libraries( program PUBLIC prolib )

install( TARGETS program DESTINATION . )

Library file:
project( prolib )

add_library( prolib SHARED aux.cxx aux.h )

target_include_directories(
prolib PUBLIC
${FMTLIB_INCLUDE_DIRS})
target_link_directories(
prolib PUBLIC
${FMTLIB_LIBRARY_DIRS})
target_link_libraries(
prolib PUBLIC fmt )

4.3.4 Writing your own pkg config

We extend the configuration of section 4.2.4 to generate a .pc file.
First of all we need a template for the .pc file:
prefix="@CMAKE_INSTALL_PREFIX@"
exec_prefix="${prefix}"
libdir="${prefix}/lib"
includedir="${prefix}/include"

Name: @PROJECT_NAME@

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4. The Cmake build system

Description: @CMAKE_PROJECT_DESCRIPTION@
Version: @PROJECT_VERSION@
Cflags: -I${includedir}
Libs: -L${libdir} -l@libtarget@

and we transform this by:

set( libtarget auxlib )
configure_file(
${CMAKE_CURRENT_SOURCE_DIR}/${PROJECT_NAME}.pc.in
${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}.pc
@ONLY
)
install(
FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}.pc
DESTINATION share/pkgconfig
)

4.4 Customizing the compilation process

Commands learned in this section

add_compile_options global compiler options
target_compile_features compiler-independent specification of compile
flags
target_compile_definitions pre-processor flags

4.4.1 Customizing the compiler

It’s probably a good idea to tell CMake explicitly what compiler you are using, otherwise it may find some
default gcc version that came with your system. Use the variables CMAKE_CXX_COMPILER, CMAKE_C_COMPILER,
CMAKE_Fortran_COMPILER, CMAKE_LINKER.

Alternatively, set environment variables CC, CXX, FC by the explicit paths of the compilers. For examples,
for Intel compilers:
export CC=`which icc`
export CXX=`which icpc`
export FC=`which ifort`

4.4.2 Global and target flags

Most of the time, compile options should be associated with a target. For instance, some file could need a
higher or lower optimization level, or a specific C++ standard. In that case, use target_compile_features.
Certain options may need to be global, in which case you use add_compile_options. Example:

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 4.4. Customizing the compilation process

## from https://youtu.be/eC9-iRN2b04?t=1548
if (MVSC)
add_compile_options(/W3 /WX)
else()
add_compile_options(-W -Wall -Werror)
endif()

4.4.2.1 Universal flags

Certain flags have a universal meaning, but compiler-dependent realization. For instance, to specify the
C++ standard:
target_compile_features( mydemo PRIVATE cxx_std_17 )

Alteratively, you can set this one the commandline:

cmake -D CMAKE_CXX_STANDARD=20

The variable CMAKE_CXX_COMPILE_FEATURES contains the list of all features you can set.
Optimization flags can be set by specifying the CMAKE_BUILD_TYPE:
• Debug corresponds to the -g flag;
• Release corresponds to -O3 -DNDEBUG;
• MinSizeRel corresponds to -Os -DNDEBUG
• RelWithDebInfo corresponds to -O2 -g -DNDEBUG.
This variable will often be set from the commandline:
cmake .. -DCMAKE_BUILD_TYPE=Release

Unfortunately, this seems to be the only way to influence optimization flags, other than explicitly setting
compiler flags; see next point.

4.4.2.2 Custom compiler flags

Set the variable CMAKE_CXX_FLAGS or CMAKE_C_FLAGS; also CMAKE_LINKER_FLAGS (but see section 4.2.4 for the
popular rpath options.)

4.4.3 Macro definitions

CMake can provide macro definitions:
target_compile_definitions
( programname PUBLIC
HAVE_HELLO_LIB=1 )

and your source could test these:

#ifdef HAVE_HELLO_LIB
#include "hello.h"
#endif

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4. The Cmake build system

4.5 CMake scripting

Commands learned in this section

option query a commandline option
message trace message during cmake-ing
set set the value of a variable
CMAKE_SYSTEM_NAME variable containing the operating system name
STREQUALS string comparison operator

The CMakeLists.txt file is a script, though it doesn’t much look like it.
• Instructions consist of a command, followed by a parenthesized list of arguments.
• (All arguments are strings: there are no numbers.)
• Each command needs to start on a new line, but otherwise whitespace and line breaks are ignored.
Comments start with a hash character.

4.5.1 System dependencies

if (CMAKE_SYSTEM_NAME STREQUALS "Window")
target_compile_options( myapp PRIVATE /W4 )
elseif (CMAKE_SYSTEM_NAME STREQUALS "Darwin" -Wall -Wextra -Wpedantic)
target_compile_options( myapp PRIVATE /W4 )
endif()

4.5.2 Messages, errors, and tracing

The message command can be used to write output to the console. This command has two arguments:
message( STATUS "We are rolling!")

Instead of STATUS you can specify other logging levels (this parameter is actually called ‘mode’ in the
documentation); running for instance
cmake --log-level=NOTICE

will display only messages of ‘notice’ status or higher.

The possibilities here are: FATAL_ERROR, SEND_ERROR, WARNING, AUTHOR_WARNING, DEPRECATION, NOTICE, STATUS,
VERBOSE, DEBUG, TRACE.

The NOTICE, VERBOSE, DEBUG, TRACE options were added in CMake-3.15.

For a complete trace of everything CMake does, use the commandline option --trace.
You can get a verbose make file by using the option
-D CMAKE_VERBOSE_MAKEFILE=ON

on the CMake invocation. You still need make V=1.

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 4.5. CMake scripting

4.5.3 Variables
Variables are set with set, or can be given on the commandline:
cmake -D MYVAR=myvalue

where the space after -D is optional.

Using the variable by itself gives the value, except in strings, where a shell-like notation is needed:
set(SOME_ERROR "An error has occurred")
message(STATUS "${SOME_ERROR}")
set(MY_VARIABLE "This is a variable")
message(STATUS "Variable MY_VARIABLE has value ${MY_VARIABLE}")

Variables can also be queried by the CMake script using the option command:
option( SOME_FLAG "A flag that has some function" defaultvalue )

Some variables are set by other commands. For instance the project command sets PROJECT_NAME and
PROJECT_VERSION.

4.5.3.1 Environment variables

Environment variables can be queried with the ENV command:
set( MYDIR $ENV{MYDIR} )

4.5.3.2 Numerical variables

math( EXPR lhs_var "math expr" )

4.5.4 Control structures

4.5.4.1 Conditionals
if ( MYVAR MATCHES "value$" )
message( NOTICE "Variable ended in 'value'" )
elseif( stuff )
message( stuff )
else()
message( NOTICE "Variable was otherwise" )
endif()

4.5.4.2 Looping
while( myvalue LESS 50 )
message( stuff )
endwhile()

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4. The Cmake build system

foreach ( var IN ITEMS item1 item2 item3 )

## something wityh ${var}
endforeach()
foreach ( var IN LISTS list1 list2 list3 )
## something wityh ${var}
endforeach()

Integer range, with inclusive bounds, upper bound zero by default:

foreach ( idx RANGE 10 )
foreach ( idx RANGE 5 10 )
foreach ( idx RANGE 5 10 2 )
endforeach()

4.5.4.3 Things not to do

Do not use macros that affect all targets: include_directories, add_definitions, link_libraries.
Do not use target_include_directories outside your project: that should be found through some of the
above mechanisms.

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Chapter 5

Source code control through Git

In this tutorial you will learn git, the currently most popular version control (also source code control or
revision control) systems. Other similar systems are Mercurial and Microsoft Sharepoint. Earlier systems
were SCCS, CVS, Subversion, Bitkeeper.
Version control is a system that tracks the history of a software project, by recording the successive
versions of the files of the project. These versions are recorded in a repository, either on the machine you
are working on, or remotely.
This has many practical advantages:
• It becomes possible to undo changes;
• Sharing a repository with another developer makes collaboration possible, including multiple
edits on the same file.
• A repository records the history of the project.
• You can have multiple versions of the project, for instance for exploring new features, or for
customization for certain users.
The use of a version control system is industry standard practice, and git is by far the most popular system
these days.

5.1 Concepts and overview

Older systems were based on having one central repository, that all developers coordinated with. These
days a setup is popular where each developer (or a small group) has a local repository, which gets syn-
chronized to a remoterepository. In so-called distributed version control systems there can even be multiple
remote repositories to synchronize with.
It is possible to track the changes of a single file, but often it makes sense to bundle a group of changes
together in a commit. That also makes it easy to roll back such a group of changes.
If a project is in a state that constitutes some sort of a milestone, it is possible to attach a tag, or mark the
state as a release.

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5. Source code control through Git

Modern version control systems allow you to have multiple branches, even in the same local repository.
This way you can have a main branch for the release version of the project, and one or more development
branches for exploring new features.

5.2 Git
This lab should be done two people, to simulate a group of programmers working on a joint project. You
can also do this on your own by using two clones of the repository, preferably opening two windows on
your computer.
Best practices for distributed version control: https://homes.cs.washington.edu/~mernst/advice/
version-control.html

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 5.3. Create and populate a repository

5.3 Create and populate a repository

Purpose. In this section you will create a repository and make a local copy to work on.

You can create a repository two different ways:

1. Create the remote repository and do a clone.
2. Create the repository locally, and then connect it to a remote; this is a lot more work.

5.3.1 Create a repository by cloning

If you want to work on a repository that you have found (or created!) on some site such as github.com,
you can use
git clone URL [ localname ]

This gives you a directory with the contents of the repository. If you leave out the local name, the directory
will have the name of the repository.
Cmd >> git clone https://github.com/TACC/empty.git
↪empty
Out >>
Cloning into 'empty'...
warning: You appear to have cloned an empty repository.
Cmd >> cd empty
Cmd >> ls -a
Out >>
. Clone an empty repository and
.. check that it is indeed empty
.git
Cmd >> git status
Out >>
On branch main
No commits yet
nothing to commit (create/copy files and use "git add"
↪to track)

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5. Source code control through Git

5.3.2 Create a repository locally

You can also create a directory for your repository, and connect it to a remote site later. For this you do
git init in the directory that is either empty, or already contains the material that you want to add later.
Here, we start with an empty directory.
Cmd >> mkdir newrepo
Cmd >> cd newrepo
Cmd >> git init
Out >>
Initialized empty Git repository in
↪/users/demo/git/newrepo/.git/
Cmd >> ls -a
Out >>
. Create a directory, and nake it into a
.. repository
.git
Cmd >> git status
Out >>
On branch master
No commits yet
nothing to commit (create/copy files and use "git add"
↪to track)

The disadvantage of this method, over cloning an empty repo, is that you now have to connect your
directory to a remote repository. See section 5.6.

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 5.3. Create and populate a repository

5.3.3 Main vs master

It used to be that the default branch (yes, I know, we haven’t discussed branches yet) was called ‘master’.
In a shift of terminology, the preferred name is now ‘main’. Sites such as github and gitlab may already
create this name by default; the git software does not do this, as of this writing in 2022.
Renaming a branch is possible. Use git status to see what branch you are on,
==== Branch renaming
%%
%% See what the main branch is
%%
Cmd >> git status
Out >>
On branch master
No commits yet
nothing to commit (create/copy files and use "git add"
↪to track)
%%
See what the main branch is
%% Rename this branch
%%
Cmd >> git branch -m main
Cmd >> git status
Out >>
On branch main
No commits yet
nothing to commit (create/copy files and use "git add"
↪to track)

Move the current branch with

git branch -m newbranchname

and for good measure check with git status.

Cmd >> git branch -m main
Cmd >> git status
Out >>
On branch main Rename this branch.
No commits yet
nothing to commit (create/copy files and use "git add"
↪to track)

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5. Source code control through Git

5.4 Adding and changing files

5.4.1 Creating a new file
If you create a file it does not automatically become part of your repository. This takes a sequence of steps.
If you create a new file, and you run git status, you’ll see that the file is listed as ‘untracked’.
Cmd >> echo foo > firstfile
Cmd >> git status
Out >>
On branch main
No commits yet
Untracked files: Create a file; it will initually be un-
(use "git add <file>..." to include in what will be tracked
↪committed)
firstfile
nothing added to commit but untracked files present
↪(use "git add" to track)

You need to git add on your file to tell git that the file belongs to the repository. (You can add a single
file, or use a wildcard to add multiple.) However, this does not actually add the file: it moves it to the
staging area. The status now says that it is a change to be committed.
Cmd >> git add firstfile
Cmd >> git status
Out >>
On branch main
No commits yet
Add the file to the local repository
Changes to be committed:
(use "git rm --cached <file>..." to unstage)
new file: firstfile

Use git commit to add these changes to the repository.

Cmd >> git commit -m "adding first file"
Out >>
[main (root-commit) f968ac6] adding first file
1 file changed, 1 insertion(+)
create mode 100644 firstfile Commit these changes
Cmd >> git status
Out >>
On branch main
nothing to commit, working tree clean

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 5.4. Adding and changing files

5.4.2 Changes to a file in the repository

The git add and git commit commands need to be repeated if you make any changes to a file in the
repository:

When you make changes to a file that has previous been added and committed, the git status command
will list it as ‘modified’.
Cmd >> echo bar >> firstfile
Cmd >> cat firstfile
Out >>
foo
bar
Cmd >> git status
Out >>
On branch main
Changes not staged for commit:
Make changes to a file that is
(use "git add <file>..." to update what will be tracked.
↪committed)
(use "git restore <file>..." to discard changes in
↪working directory)
modified: firstfile
no changes added to commit (use "git add" and/or "git
↪commit -a")

If you need to check what changes you have made, git diff on that file will tell you the differences the
between the edited, but not yet added or committed, file and the previous commit version.
Cmd >> git diff firstfile
Out >>
diff --git a/firstfile b/firstfile
index 257cc56..3bd1f0e 100644
--- a/firstfile See what the changes were wrt the
+++ b/firstfile previously commit version.
@@ -1 +1,2 @@
foo
+bar

You now need to repeat git add and git commit on that file.
Cmd >> git add firstfile
Cmd >> git commit -m "changes to first file"
Out >>
[main b1edf77] changes to first file
1 file changed, 1 insertion(+) Commit the changes to the local
Cmd >> git status repo.
Out >>
On branch main
nothing to commit, working tree clean

Doing git log will give you the history of the repository, listing the commit numbers, and the messages
that you entered on those commits.

Victor Eijkhout 99
5. Source code control through Git

Cmd >> git log

Out >>
commit b1edf778c17b7c7e6cb1a8ac73fa9b61464eba14
Author: Victor Eijkhout <[email protected]>
Date: Sat Jan 29 14:14:40 2022 -0600
changes to first file
Get the log of all commits so far.
commit f968ac6c05dd877db84705a4dcdadbc0bed2c535
Author: Victor Eijkhout <[email protected]>
Date: Sat Jan 29 14:14:39 2022 -0600
adding first file

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 5.5. Undoing changes

5.5 Undoing changes

There are various levels of undo, depending on whether you have added or committed those changes.

5.5.1 Undo uncommitted change

Scenario: you have edited a file that is in the repo, you want to undo that change, and you have not yet
committed the change.
First of all, do git diff to confirm:
Cmd >> echo bar >> firstfile
Cmd >> cat firstfile
Out >>
foo
bar
bar
Cmd >> git status
Out >>
On branch main
Changes not staged for commit:
(use "git add <file>..." to update what will be
↪committed)
(use "git restore <file>..." to discard changes in
↪working directory) Make regrettable changes.
modified: firstfile
no changes added to commit (use "git add" and/or "git
↪commit -a")
Cmd >> git diff firstfile
Out >>
diff --git a/firstfile b/firstfile
index 3bd1f0e..58ba28e 100644
--- a/firstfile
+++ b/firstfile
@@ -1,2 +1,3 @@
foo
bar
+bar

Doing git checkout on that file gets the last committed version and puts it back in your working direc-
tory.
Cmd >> git checkout firstfile
Out >>
Updated 1 path from the index
Cmd >> cat firstfile
Out >>
foo Restore previously committed ver-
bar sion.
Cmd >> git status
Out >>
On branch main
nothing to commit, working tree clean

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5. Source code control through Git

5.5.2 Restore a file from a previous commit

A more complicated scenario is where you have committed the change. Then you need to find the commit
id.
You can use git log to get the ids of all commits. This is useful if you want to roll back to pretty far in
the past. However, if you only want to roll back the last commit, use git show HEAD to get a description
of just that last commit.
Cmd >> git log
Out >>
commit e411fad261fd82eb93c328c44978699e946abc0d
Author: Victor Eijkhout <[email protected]>
Date: Sat Jan 29 14:14:42 2022 -0600
changes to first file
commit 63d6ad16beb4e2d12574fb238c29e8ba11fc6732
Author: Victor Eijkhout <[email protected]>
Date: Sat Jan 29 14:14:41 2022 -0600
adding first file
Cmd >> git show HEAD
Out >> Find the commit id that you want to
commit e411fad261fd82eb93c328c44978699e946abc0d roll back.
Author: Victor Eijkhout <[email protected]>
Date: Sat Jan 29 14:14:42 2022 -0600
changes to first file
diff --git a/firstfile b/firstfile
index 257cc56..3bd1f0e 100644
--- a/firstfile
+++ b/firstfile
@@ -1 +1,2 @@
foo
+bar

Now do:
git checkout sdf234987238947 -- myfile myotherfile

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 5.5. Undoing changes

5.5.3 Undo a commit

As above, find the commit number.
Then do git revert sdlksdfkl2343 (with the right id). This will normally open an editor for you to
leave comments; you can prevent this with the --no-edit option.
Cmd >> git revert $commit --no-edit
Out >>
[main 3dca724] Revert "changes to first file" Use ’git revert’ to roll back.
Date: Sat Jan 29 14:14:42 2022 -0600
1 file changed, 1 deletion(-)

This will restore the file to its state before the last add and commit, and it will in generally leave the
repository back in the state it was before that commit.
Cmd >> cat firstfile
Out >>
foo
Cmd >> git status See that we have indeed undone the
Out >> commit.
On branch main
nothing to commit, working tree clean

However, the log will show that you have reverted a certain commit.
Cmd >> git log
Out >>
commit 3dca724a1902e8a5e3dba007c325542c6753a424
Author: Victor Eijkhout <[email protected]>
Date: Sat Jan 29 14:14:42 2022 -0600
Revert "changes to first file"

This reverts commit

↪e411fad261fd82eb93c328c44978699e946abc0d. But there will be an entry in the log.
commit e411fad261fd82eb93c328c44978699e946abc0d
Author: Victor Eijkhout <[email protected]>
Date: Sat Jan 29 14:14:42 2022 -0600
changes to first file
commit 63d6ad16beb4e2d12574fb238c29e8ba11fc6732
Author: Victor Eijkhout <[email protected]>
Date: Sat Jan 29 14:14:41 2022 -0600
adding first file

The git reset command can also be used for various types of undo.

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5. Source code control through Git

5.6 Remote repositories and collaboration

The repository where you have been adding files and changes with git commit is the local repository. This
is great for tracking changes, and reverting them when needed, but a major reason for using source code
control is collaboration with others. For this you need a remote repository. This involves a set of commands
git remote [ other keywords ] [ arguments ]

We have some changes, added to the local repository with git add and git commit
Cmd >> git add newfile && git commit -m "adding first
↪file"
Out >>
[main 8ce1de4] adding first file
Committed changes.
1 file changed, 1 insertion(+)
create mode 100644 newfile

We connect to some remote repository with

git remote add servername url

If you want to see what your remote is, do

git remote -v

Cmd >> git remote add mainserver

↪[email protected]:TACC/tinker.git
Cmd >> git remote -v
Out >>
Connect local repo to a remote one.
mainserver [email protected]:TACC/tinker.git (fetch)
mainserver [email protected]:TACC/tinker.git (push)

Finally, you can git push committed changes to this remote. Git doesn’t just push everything here: since
you can have multiple branches locally, and multiple upstreams remotely, you intially specify both:
git push -u servername branchname

Cmd >> git push -u mainserver main

Out >>
To github.com:TACC/tinker.git
8333bc1..8ce1de4 main -> main
Push changes.
Branch 'main' set up to track remote branch 'main'
↪from 'mainserver'.

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 5.6. Remote repositories and collaboration

5.6.1 Changing the transport

You may have made your clone with
git clone https://....

but when you git push for the first time you get some permission-related errors.
Do
git remote -v
# output: origin https://[email protected]/username/reponame.git
git remote set-url origin [email protected]:username/reponame.git

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5. Source code control through Git

5.6.2 Collaboration on the same repository

Let’s see how changes from one clone of a repository can propagate to another clone. This can be because
more than one person is working on a project, or because one person is working from more than one
machine.
We make one local repository in directory person1.
Cmd >> git clone [email protected]:TACC/tinker.git person1
Out >> Person 1 makes a clone.
Cloning into 'person1'...

Create another clone in person2. Normally the cloned repositories would be two user accounts, or the
accounts of one user on two machines.
Cmd >> git clone [email protected]:TACC/tinker.git person2
Out >> Person 2 makes a clone.
Cloning into 'person2'...

Now the first user creates a file, adds, commits, and pushes it. (This of course requires an upstream to be
set, but since we did a git clone, this is automatically done.)
Cmd >> ( cd person1 && echo 123 >> p1 && git add p1 &&
↪git commit -m "add p1" && git push )
Out >>
[main 6f6b126] add p1
1 file changed, 1 insertion(+)
Person 1 adds a file and pushes it.
create mode 100644 p1
To github.com:TACC/tinker.git
8863559..6f6b126 main -> main

The second user now does

git pull

to get these changes. Again, because we create the local repository by git clone it is clear where the pull
is coming from. The pull message will tell us what new files are created, or how many other files were
changes.
Cmd >> ( cd person2 && git pull )
Out >>
From github.com:TACC/tinker
8863559..6f6b126 main -> origin/main
Updating 8863559..6f6b126 Person 2 pulls, getting the new file.
Fast-forward
p1 | 1 +
1 file changed, 1 insertion(+)
create mode 100644 p1

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 5.6. Remote repositories and collaboration

5.6.3 Merging changes

If you work with someone else, or even if you work solo on a project, but from more than one machine,
it may happen that there will be multiple changes on a single file. That is, two local repositories have
changes committed, and are now pushing to the same remote.
In the following script we start with the same situation of the previous example, where we have two local
repositories, as a stand-in for two users, or two different machines.
We have a file of four lines.
Cmd >> cat person1/fourlines
Out >>
1
2
We have a four line file.
3
4

The first user makes an edit on the first line; we confirm the state of the file;
Cmd >> ( cd person1 && sed -i -e '1s/1/one/' fourlines
↪&& cat fourlines )
Out >>
one Person 1 makes a change.
2
3
4

This user pushes the change.

Cmd >> ( cd person1 && git add fourlines && git commit
↪-m "edit line one" && git push )
Out >>
[main 6767e3f] edit line one Person 1 pushes the change.
1 file changed, 1 insertion(+), 1 deletion(-)
To github.com:TACC/tinker.git
fdd70b7..6767e3f main -> main

The other user also makes a change, but on line 4, so that there is no conflict;
Cmd >> ( cd person2 && sed -i -e '4s/4/four/'
↪fourlines && cat fourlines )
Out >>
1 Person 2 makes a different change to
2 the same file.
3
four

This change is added with git add and git commit, but we proceed more cautiously in pushing: first we
pull any changes made by others with
git pull --no-edit
git push

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5. Source code control through Git

Cmd >> ( cd person2 && git add fourlines && git commit
↪-m "edit line four" && git pull --no-edit && git
↪push )
Out >>
[main 27fb2b2] edit line four
1 file changed, 1 insertion(+), 1 deletion(-)
From github.com:TACC/tinker
fdd70b7..6767e3f main -> origin/main
This change does not conflict, we can
Auto-merging fourlines pull/push.
Merge made by the 'recursive' strategy.
fourlines | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
To github.com:TACC/tinker.git
6767e3f..62bd424 main -> main

Now if the first user does a pull, they see all the merged changes.
Cmd >> ( cd person1 && git pull && cat fourlines )
Out >>
From github.com:TACC/tinker
6767e3f..62bd424 main -> origin/main
Updating 6767e3f..62bd424
Fast-forward
fourlines | 2 +-
Person 1 pulls to get all the changes.
1 file changed, 1 insertion(+), 1 deletion(-)
one
2
3
four

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 5.6. Remote repositories and collaboration

5.6.4 Conflicting changes

There can be various reasons for git to report a conflict.
• You are trying to pull changes from another developer, but you have changes yourself that you
haven’t yet committed. If you don’t want to commit your changes (maybe you’re still busy editing)
you can use git stash to set your edits aside. You can later retrieve them with git stash pop, or
decide to forget all about them with git stash drop.
• There is a conflict between your changes, and those you are trying to pull from another developer,
or from yourself on another machine. This is the case we will look at here.
• Very similar, there can also be conflicts between two branches you try to merge. We will look at
that in section 5.7.1.
As before, we have directories person1 and person2 containing independent clones of a repository. We
have a file of four lines long, but contrary to above, we now make edits that are too close together for
git’s auto-merge to deal with them.
Cmd >> cat person1/fourlines
Out >>
1
2
The original file.
3
4

Now developer 1 makes a change on line 1.

Cmd >> ( cd person1 && sed -i -e '1s/1/one/' fourlines
↪&& git add fourlines && git commit -m "edit line
↪one" && git push )
Out >>
[main a10216d] edit line one
With apologies for some scripting
1 file changed, 1 insertion(+), 1 deletion(-) trickery, we use an edit by sed,
To github.com:TACC/tinker.git changing 1 on line 1 to one. We add,
4955e50..a10216d main -> main commit, and push this change.

In the meantime, developer 2 makes another change, to the original file. This change can be added and
committed to the local repository without any problem.
Cmd >> ( cd person2 && sed -i -e '2s/2/two/' fourlines
↪&& cat fourlines && git add fourlines && git
↪commit -m "edit line two" )
Out >>
1
two
Change the 2 on line two to two.
3 We add and commit this to the local
4 repository.
[main c9b6ded] edit line two
1 file changed, 1 insertion(+), 1 deletion(-)

However, if we try to git push this change to the remote repository, we get an error that the remote is
ahead of the local repository. So we first pull the state of the remote repository. In the previous section
this led to an automatic merge; not so here.

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5. Source code control through Git

Cmd >> ( cd person2 && git pull --no-edit || echo )

Out >>
From github.com:TACC/tinker
4955e50..a10216d main -> origin/main
Auto-merging fourlines
The git pull call results in a mes-
CONFLICT (content): Merge conflict in fourlines sage that the automatic mere failed,
Automatic merge failed; fix conflicts and then commit indicating what file was the prob-
↪the result. lem.
You can now edit the file by hand, or using some merge tool.
Cmd >> ( cd person2 && cat fourlines )
Out >>
<<<<<<< HEAD
1
two
======= In between the chevron’ed lines you
one first get the HEAD, that is the local
2
>>>>>>> a10216da358649df80aaaeb94f1ceef909c2ed83
state, followed by the pulled remote
3 state. Edit this file, commit the merge
4 and push.

5.6.5 Pull requests

The previous sections described collaboration on a repository that you have write permission for. For
large projects you may not have this: the owner of the project may want a safer mechanism where you
submit changes for approval in the form of a pull request, and they will do the merge of your changes into
the repository.
This involves the following steps:
1. You make a fork of the repository;
2. you clone this fork;
3. make a branch with your changes;

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 5.7. Branching

5.7 Branching
With a branch you can keep a completely separate version of all the files in your project.
Initially we have a file on the main branch.
Cmd >> cat firstfile
Out >>
foo
Cmd >> git status We have a file, committed and all.
Out >>
On branch main
nothing to commit, working tree clean

We create a new branch, named dev and check it out

git branch dev
git checkout dev

This initially has the same content.

Cmd >> git branch dev && git branch -a
Out >>
dev
* main
Cmd >> git checkout dev && git branch -a Make a development branch.
Out >>
Switched to branch 'dev'
* dev
main

We make changes, and commit them to the current branch.

Cmd >> cat firstfile
Out >>
foo
Cmd >> echo bar > firstfile && cat firstfile
Out >>
bar
Cmd >> git status
Out >>
On branch dev
Changes not staged for commit:
(use "git add <file>..." to update what will be Make changes and commit them to
↪committed) the dev branch.
(use "git restore <file>..." to discard changes in
↪working directory)
modified: firstfile
no changes added to commit (use "git add" and/or "git
↪commit -a")
Cmd >> git add firstfile && git commit -m "dev changes"
Out >>
[dev b07cd2e] dev changes
1 file changed, 1 insertion(+), 1 deletion(-)

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5. Source code control through Git

If we switch back to the main branch, everything is as before when we made the dev branch.
Cmd >> git checkout main && cat firstfile && git status
Out >>
Switched to branch 'main'
foo
The other branch is still unchanged.
On branch main
nothing to commit, working tree clean

The first time you try to push a new branch you need to establish it upstream:
git push --set-upstream origin mynewbranch

We can inspect differences between branches with

git diff branch1 branch2

Cmd >> git diff main dev

Out >>
diff --git a/firstfile b/firstfile
index 257cc56..5716ca5 100644
--- a/firstfile We can check differences between
+++ b/firstfile branches.
@@ -1 +1 @@
-foo
+bar

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 5.7. Branching

5.7.1 Branch merging

One of the points of having branches is to merge them after you have done some development in one
branch.
We start with the four line file from before.
Cmd >> cat fourlines
Out >>
1
2
3
4
The main branch is up to date.
Cmd >> git status
Out >>
On branch main
nothing to commit, working tree clean

Also as before, we have a dev branch that contains these contents.

We switch back to the main branch and make a change. This will not be visible in the dev branch.
Cmd >> git checkout main
Out >>
Switched to branch 'main'
Cmd >> sed -i -e '1s/1/one/' fourlines && cat fourlines
Out >>
one
2 On line 1, change 1 to one.
3
4
Cmd >> git add fourlines && git commit -m "edit line 1"
Out >>
[main c51d4ff] edit line 1
1 file changed, 1 insertion(+), 1 deletion(-)

We switch to the dev branch and make another file. The change in the main branch is indeed not here.
Cmd >> git checkout dev
Out >>
Switched to branch 'dev'
Cmd >> sed -i -e '4s/4/four/' fourlines && cat
↪fourlines
Out >>
1
2
On line 4, change 4 to four. This
3 change is far enough away from the
four other change, that there should be no
Cmd >> git add fourlines && git commit -m "edit line 4" conflict.
Out >>
[dev dbb0c03] edit line 4
1 file changed, 1 insertion(+), 1 deletion(-)

Switching back to the main branch, we use

git merge dev

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5. Source code control through Git

to merge the dev changes into main.

Cmd >> git checkout main
Out >>
Switched to branch 'main'
Cmd >> git merge dev
Out >>
Auto-merging fourlines
Merge made by the 'recursive' strategy.
fourlines | 2 +- Merge the dev branch into the main
1 file changed, 1 insertion(+), 1 deletion(-) one with git merge. Note the ‘auto-
Cmd >> cat fourlines
Out >>
merge’ message, and confirm that
one both changes to the file are there.
2
3
four

If two developers make changes on the same line, or on adjacent lines, git will not be able to merge and
you have to edit the file as in section 5.6.4.

remote repo
git fe

local repo

git pull [origin] git merge origin/m

working directory

Figure 5.1: Add local changes to the remote repository (left); Get changes that were made to the remote
repository (right).

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 5.8. Releases

5.8 Releases
At certain point in your development process you may want to mark the current state of the repository
as ‘finished’. You can do this by
1. Attaching tag to the state of the repository, or
2. Creating an archive: a released version that has the repo information stripped.

5.8.1 Tags
A tag is a marked state of the repository. There are two types of tags:
1. light-weight tags are no more than a synonym for a commit:
git tag v0.09

2. annotated tags, which carry an information message:

git tag -a v0.1 "base classes finished"

You list all tags with git tag, you get information on a tag with git show v0.1, and you push a tag to a
remote server with
git push origin v0.1

You can retrieve the tagged state of the repository with

git checkout v0.1

but beware that changes you now make can not be pushed to anything: this is a ‘detached HEAD’ state.
If you want to fix bugs in a tagged state, you can create a branch based on the tag:
git checkout -b version0.2 v0.1

5.8.2 Archives, releases

If you want to make a released version of your software, that can be downloaded and does not rely on the
git software, use the archive command:
git archive master --format=tgz --prefix=MyProject-v1 -o MyProject-v1.tgz

Victor Eijkhout 115

Chapter 6

Dense linear algebra: BLAS, LAPACK, SCALAPACK

In this section we will discuss libraries for dense linear algebra operations.
Dense linear algebra, that is linear algebra on matrices that are stored as two-dimensional arrays (as
opposed to sparse linear algebra; see HPC book, section 5.4, as well as the tutorial on PETSc Parallel
Programming book, part III) has been standardized for a considerable time. The basic operations are defined
by the three levels of Basic Linear Algebra Subprograms (BLAS):
• Level 1 defines vector operations that are characterized by a single loop [13].
• Level 2 defines matrix vector operations, both explicit such as the matrix-vector product, and
implicit such as the solution of triangular systems [7].
• Level 3 defines matrix-matrix operations, most notably the matrix-matrix product [6].
The name ‘BLAS’ suggests a certain amount of generality, but the original authors were clear [13] that
these subprograms only covered dense linear algebra. Attempts to standardize sparse operations have
never met with equal success.
Based on these building blocks, libraries have been built that tackle the more sophisticated problems such
as solving linear systems, or computing eigenvalues or singular values. Linpack 1 and Eispack were the first
to formalize these operations involved, using Blas Level 1 and Blas Level 2 respectively. A later develop-
ment, Lapack uses the blocked operations of Blas Level 3. As you saw in section HPC book, section 1.6.1,
this is needed to get high performance on cache-based CPUs.

Remark 12 The reference implementation https://netlib.org/blas/index.html of the BLAS [3]

will not give good performance with any compiler; most platforms have vendor-optimized implementations,
such as the MKL library from Intel.

With the advent of parallel computers, several projects arose that extended the Lapack functionality to
distributed computing, most notably Scalapack [4, 2], PLapack [23, 22], and most recently Elemental [19].
These packages are harder to use than Lapack because of the need for a two-dimensional cyclic distri-
bution; sections HPC book, section 7.2.3 and HPC book, section 7.3.2. We will not go into the details
here.

1. The linear system solver from this package later became the Linpack benchmark; see section HPC book, section 2.11.5.

116
 6.1. Some general remarks

6.1 Some general remarks

6.1.1 The Fortran heritage
The original BLAS routines were written in Fortran, and the reference implementation is still in Fortran.
For this reason you will see the routine definitions first in Fortran in this tutorial It is possible to use the
Fortran routines from a C/C++ program:
• You typically need to append an underscore to the Fortran name;
• You need to include a prototype file in your source, for instance mkl.h;
• Every argument needs to be a ‘star’-argument, so you can not pass literal constants: you need to
pass the address of a variable.
• You need to create a column-major matrix.
There are also C/C++ interfaces:
• The C routine names are formed by prefixing the original name with cblas_; for instance dasum
becomes cblas_dasum.
• Fortran character arguments have been replaced by enumerated constants, for instance CblasNoTrans
instead of the 'N' parameter.
• The Cblas interface can accommodate both row-major and column-major storage.
• Array indices are 1-based, rather than 0-based; this mostly becomes apparent in error messages
and when specifying pivot indices.

6.1.2 Routine naming

Routines conform to a general naming scheme: XYYZZZ where
X precision: S,D,C,Z stand for single and double, single complex and double complex, respectively.
YY storage scheme: general rectangular, triangular, banded.
ZZZ operation. See the manual for a list.

6.1.3 Data formats

Lapack and Blas use a number of data formats, including
GE General matrix: stored two-dimensionally as A(LDA,*)
SY/HE Symmetric/Hermitian: general storage; UPLO parameter to indicate upper or lower (e.g. SPOTRF)
GB/SB/HB General/symmetric/Hermitian band; these formats use column-major storage; in SGBTRF
overallocation needed because of pivoting
PB Symmetric of Hermitian positive definite band; no overallocation in SPDTRF

6.1.4 Lapack operations

For Lapack, we can further divide the routines into an organization with three levels:
• Drivers. These are powerful top level routine for problems such as solving linear systems or
computing an SVD. There are simple and expert drivers; the expert ones have more numerical
sophistication.

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6. Dense linear algebra: BLAS, LAPACK, SCALAPACK

• Computational routines. These are the routines that drivers are built up out of. A user may have
occasion to call them by themselves.
• Auxiliary routines.
Expert driver names end on ’X’.
• Linear system solving. Simple drivers: -SV (e.g., DGESV) Solve 𝐴𝑋 = 𝐵, overwrite A with LU (with
pivoting), overwrite B with X.
Expert driver: -SVX Also transpose solve, condition estimation, refinement, equilibration
• Least squares problems. Drivers:
xGELS using QR or LQ under full-rank assumption
xGELSY ”complete orthogonal factorization”
xGELSS using SVD
xGELSD using divide-conquer SVD (faster, but more workspace than xGELSS)
Also: LSE & GLM linear equality constraint & general linear model
• Eigenvalue routines. Symmetric/Hermitian: xSY or xHE (also SP, SB, ST)
simple driver -EV
expert driver -EVX
divide and conquer -EVD
relative robust representation -EVR
General (only xGE)
Schur decomposition -ES and -ESX
eigenvalues -EV and -EVX
SVD (only xGE)
simple driver -SVD
divide and conquer SDD
Generalized symmetric (SY and HE; SP, SB)
simple driver GV
expert GVX
divide-conquer GVD
Nonsymmetric:
Schur: simple GGES, expert GGESX
eigen: simple GGEV, expert GGEVX
svd: GGSVD

6.2 BLAS matrix storage

There are a few points to bear in mind about the way matrices are stored in the BLAS and LAPACK2 :

6.2.1 Array indexing

Since these libraries originated in a Fortran environment, they use 1-based indexing. Users of languages
such as C/C++ are only affected by this when routines use index arrays, such as the location of pivots in
LU factorizations.

2. We are not going into band storage here.

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 6.3. Performance issues

Figure 6.1: Column-major storage of an array in Fortran.

6.2.2 Fortran column-major ordering

Since computer memory is one-dimensional, some conversion is needed from two-dimensional matrix
coordinates to memory locations. The Fortran language uses column-major storage, that is, elements in
a column are stored consecutively; see figure 6.1. This is also described informally as ‘the leftmost index
varies quickest’.
Arrays in C, on the other hand, are laid out in row-major order.

6.2.3 Submatrices and the LDA parameter

Using the storage scheme described above, it is clear how to store an 𝑚 ×𝑛 matrix in 𝑚𝑛 memory locations.
However, there are many cases where software needs access to a matrix that is a subblock of another,
larger, matrix. As you see in figure 6.2 such a subblock is no longer contiguous in memory. The way to
describe this is by introducing a third parameter in addition to M,N: we let LDA be the ‘leading dimension
of A’, that is, the allocated first dimension of the surrounding array. This is illustrated in figure 6.3. To pass
the subblock to a routine, you would specify it as
call routine( A(3,2), /* M= */ 2, /* N= */ 3, /* LDA= */ Mbig, ... )

6.3 Performance issues

The collection of BLAS and LAPACK routines are a de facto standard: the Application Programmer Inter-
face (API) is fixed, but the implementation is not. You can find reference implementations on the netlib
website (netlib.org), but these will be very low in performance.

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6. Dense linear algebra: BLAS, LAPACK, SCALAPACK

Figure 6.2: A subblock out of a larger matrix.

Figure 6.3: A subblock out of a larger matrix, using LDA.

On the other hand, many LAPACK routines can be based on the matrix-matrix product (BLAS routine
gemm), which you saw in section HPC book, section 7.4.1 has the potential for a substantial fraction of
peak performance. To achieve this, you should use an optimized version, such as

• MKL, the Intel math-kernel library;

• OpenBlas (http://www.openblas.net/), an open source version of the original Goto BLAS; or
• blis (https://code.google.com/p/blis/), a BLAS replacement and extension project.

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 6.4. Some simple examples

6.4 Some simple examples

Let’s look at some simple examples.
The routine xscal scales a vector in place.
! Fortran
subroutine dscal(integer N, double precision DA,
double precision, dimension(*) DX, integer INCX )
// C
void cblas_dscal (const MKL_INT n, const double a,
double *x, const MKL_INT incx);

A simple example:
// example1.F90
do i=1,n
xarray(i) = 1.d0
end do
call dscal(n,scale,xarray,1)
do i=1,n
if (.not.assert_equal( xarray(i),scale )) print *,"Error in index",i
end do

The same in C:
// example1c.cxx
xarray = new double[n]; yarray = new double[n];

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

xarray[i] = 1.;
cblas_dscal(n,scale,xarray,1);
for (int i=0; i<n; i++)
if (!assert_equal( xarray[i],scale ))
printf("Error in index %d",i);

Many routines have an increment parameter. For xscale that’s the final parameter:
// example2.F90
integer :: inc=2
call dscal(n/inc,scale,xarray,inc)
do i=1,n
if (mod(i,inc)==1) then
if (.not.assert_equal( xarray(i),scale )) print *,"Error in index",i
else
if (.not.assert_equal( xarray(i),1.d0 )) print *,"Error in index",i
end if
end do

The matrix-vector product xgemv computes 𝑦 ← 𝛼𝐴𝑥 + 𝛽𝑦, rather than 𝑦 ← 𝐴𝑥. The specification of
the matrix takes the M,N size parameters, and a character argument 'N' to indicate that the matrix is not
transposed. Both of the vectors have an increment argument.
subroutine dgemv(character TRANS,

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6. Dense linear algebra: BLAS, LAPACK, SCALAPACK

integer M,integer N,
double precision ALPHA,
double precision, dimension(lda,*) A,integer LDA,
double precision, dimension(*) X,integer INCX,
double precision BETA,double precision, dimension(*) Y,integer INCY
)

An example of the use of this routine:

// example3.F90
do j=1,n
xarray(j) = 1.d0
do i=1,m
matrix(i,j) = 1.d0
end do
end do

alpha = 1.d0; beta = 0.d0

call dgemv( 'N',M,N, alpha,matrix,M, xarray,1, beta,yarray,1)
do i=1,m
if (.not.assert_equal( yarray(i),dble(n) )) &
print *,"Error in index",i,":",yarray(i)
end do

The same example in C has an extra parameter to indicate whether the matrix is stored in row or column
major storage:
// example3c.cxx
for (int j=0; j<n; j++) {
xarray[j] = 1.;
for (int i=0; i<m; i++)
matrix[ i+j*m ] = 1.;
}

alpha = 1.; beta = 0.;

cblas_dgemv(CblasColMajor,
CblasNoTrans,m,n, alpha,matrix,m, xarray,1, beta,yarray,1);

for (int i=0; i<m; i++)

if (!assert_equal( yarray[i],(double)n ))
printf("Error in index %d",i);

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Chapter 7

Scientific Data Storage

There are many ways of storing data, in particular data that comes in arrays. A surprising number of
people stores data in spreadsheets, then exports them to ascii files with comma or tab delimiters, and
expects other people (or other programs written by themselves) to read that in again. Such a process is
wasteful in several respects:
• The ascii representation of a number takes up much more space than the internal binary repre-
sentation. Ideally, you would want a file to be as compact as the representation in memory.
• Conversion to and from ascii is slow; it may also lead to loss of precision.
For such reasons, it is desirable to have a file format that is based on binary storage. There are a few more
requirements on a useful file format:
• Since binary storage can differ between platforms, a good file format is platform-independent.
This will, for instance, prevent the confusion between big-endian and little-endian storage, as
well as conventions of 32 versus 64 bit floating point numbers.
• Application data can be heterogeneous, comprising integer, character, and floating point data.
Ideally, all this data should be stored together.
• Application data is also structured. This structure should be reflected in the stored form.
• It is desirable for a file format to be self-documenting. If you store a matrix and a right-hand side
vector in a file, wouldn’t it be nice if the file itself told you which of the stored numbers are the
matrix, which the vector, and what the sizes of the objects are?
This tutorial will introduce the HDF5 library, which fulfills these requirements. HDF5 is a large and com-
plicated library, so this tutorial will only touch on the basics. For further information, consult http:
//www.hdfgroup.org/HDF5/. While you do this tutorial, keep your browser open on http://www.
hdfgroup.org/HDF5/doc/ or http://www.hdfgroup.org/HDF5/RM/RM_H5Front.html for the ex-
act syntax of the routines.

7.1 Introduction to HDF5

As described above, HDF5 is a file format that is machine-independent and self-documenting. Each HDF5
file is set up like a directory tree, with subdirectories, and leaf nodes which contain the actual data. This
means that data can be found in a file by referring to its name, rather than its location in the file. In this

123
7. Scientific Data Storage

section you will learn to write programs that write to and read from HDF5 files. In order to check that the
files are as you intend, you can use the h5dump utility on the command line.1
Just a word about compatibility. The HDF5 format is not compatible with the older version HDF4, which
is no longer under development. You can still come across people using hdf4 for historic reasons. This
tutorial is based on HDF5 version 1.6. Some interfaces changed in the current version 1.8; in order to use
1.6 APIs with 1.8 software, add a flag -DH5_USE_16_API to your compile line.
Many HDF5 routines are about creating objects: file handles, members in a dataset, et cetera. The general
syntax for that is
hid_t h_id;
h_id = H5Xsomething(...);

Failure to create the object is indicated by a negative return parameter, so it would be a good idea to create
a file myh5defs.h containing:
#include "hdf5.h"
#define H5REPORT(e) \
{if (e<0) {printf("\nHDF5 error on line %d\n\n",__LINE__); \
return e;}}

and use this as:

#include "myh5defs.h"

hid_t h_id;
h_id = H5Xsomething(...); H5REPORT(h_id);

7.2 Creating a file

First of all, we need to create an HDF5 file.
hid_t file_id;
herr_t status;

file_id = H5Fcreate( filename, ... );

...
status = H5Fclose(file_id);

This file will be the container for a number of data items, organized like a directory tree.

Exercise. Create an HDF5 file by compiling and running the create.c example below.

1. In order to do the examples, the h5dump utility needs to be in your path, and you need to know the location of the hdf5.h
and libhdf5.a and related library files.

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 7.3. Datasets

Expected outcome. A file file.h5 should be created.

Caveats. Be sure to add HDF5 include and library directories:
cc -c create.c -I. -I/opt/local/include
and
cc -o create create.o -L/opt/local/lib -lhdf5. The include and lib directories will be
system dependent.
/*
* File: create.c
* Author: Victor Eijkhout
*/
#include "myh5defs.h"
#define FILE "file.h5"

main() {

hid_t file_id; /* file identifier */

herr_t status;

/* Create a new file using default properties. */

file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
H5REPORT(file_id);

/* Terminate access to the file. */

status = H5Fclose(file_id);
}

You can display the created file on the commandline:

%% h5dump file.h5
HDF5 "file.h5" {
GROUP "/" {
}
}

Note that an empty file corresponds to just the root of the directory tree that will hold the data.

7.3 Datasets
Next we create a dataset, in this example a 2D grid. To describe this, we first need to construct a dataspace:
dims[0] = 4; dims[1] = 6;
dataspace_id = H5Screate_simple(2, dims, NULL);
dataset_id = H5Dcreate(file_id, "/dset", dataspace_id, .... );
....
status = H5Dclose(dataset_id);

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7. Scientific Data Storage

status = H5Sclose(dataspace_id);

Note that datasets and dataspaces need to be closed, just like files.

Exercise. Create a dataset by compiling and running the dataset.c code below
Expected outcome. This creates a file dset.h that can be displayed with h5dump.
/*
* File: dataset.c
* Author: Victor Eijkhout
*/
#include "myh5defs.h"
#define FILE "dset.h5"

main() {

hid_t file_id, dataset_id, dataspace_id; /* identifiers */

hsize_t dims[2];
herr_t status;

/* Create a new file using default properties. */

file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

/* Create the data space for the dataset. */

dims[0] = 4;
dims[1] = 6;
dataspace_id = H5Screate_simple(2, dims, NULL);

/* Create the dataset. */

dataset_id = H5Dcreate(file_id, "/dset", H5T_NATIVE_INT,
dataspace_id, H5P_DEFAULT);
/*H5T_STD_I32BE*/

/* End access to the dataset and release resources used by it. */

status = H5Dclose(dataset_id);

/* Terminate access to the data space. */

status = H5Sclose(dataspace_id);

/* Close the file. */

status = H5Fclose(file_id);
}

We again view the created file online:

%% h5dump dset.h5
HDF5 "dset.h5" {
GROUP "/" {

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 7.3. Datasets

DATASET "dset" {
DATATYPE H5T_STD_I32BE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
DATA {
(0,0): 0, 0, 0, 0, 0, 0,
(1,0): 0, 0, 0, 0, 0, 0,
(2,0): 0, 0, 0, 0, 0, 0,
(3,0): 0, 0, 0, 0, 0, 0
}
}
}
}

The datafile contains such information as the size of the arrays you store. Still, you may want to add
related scalar information. For instance, if the array is output of a program, you could record with what
input parameter was it generated.
parmspace = H5Screate(H5S_SCALAR);
parm_id = H5Dcreate
(file_id,"/parm",H5T_NATIVE_INT,parmspace,H5P_DEFAULT);

Exercise. Add a scalar dataspace to the HDF5 file, by compiling and running the parmwrite.c code
below.
Expected outcome. A new file wdset.h5 is created.
/*
* File: parmdataset.c
* Author: Victor Eijkhout
*/
#include "myh5defs.h"
#define FILE "pdset.h5"

main() {

hid_t file_id, dataset_id, dataspace_id; /* identifiers */

hid_t parm_id,parmspace;
hsize_t dims[2];
herr_t status;

/* Create a new file using default properties. */

file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

/* Create the data space for the dataset. */

dims[0] = 4;
dims[1] = 6;
dataspace_id = H5Screate_simple(2, dims, NULL);

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7. Scientific Data Storage

/* Create the dataset. */

dataset_id = H5Dcreate
(file_id, "/dset", H5T_STD_I32BE, dataspace_id, H5P_DEFAULT);

/* Add a descriptive parameter */

parmspace = H5Screate(H5S_SCALAR);
parm_id = H5Dcreate
(file_id,"/parm",H5T_NATIVE_INT,parmspace,H5P_DEFAULT);

/* End access to the dataset and release resources used by it. */

status = H5Dclose(dataset_id);
status = H5Dclose(parm_id);

/* Terminate access to the data space. */

status = H5Sclose(dataspace_id);
status = H5Sclose(parmspace);

/* Close the file. */

status = H5Fclose(file_id);
}

%% h5dump wdset.h5
HDF5 "wdset.h5" {
GROUP "/" {
DATASET "dset" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
DATA {
(0,0): 0.5, 1.5, 2.5, 3.5, 4.5, 5.5,
(1,0): 6.5, 7.5, 8.5, 9.5, 10.5, 11.5,
(2,0): 12.5, 13.5, 14.5, 15.5, 16.5, 17.5,
(3,0): 18.5, 19.5, 20.5, 21.5, 22.5, 23.5
}
}
DATASET "parm" {
DATATYPE H5T_STD_I32LE
DATASPACE SCALAR
DATA {
(0): 37
}
}
}
}

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7.4 Writing the data

The datasets you created allocate the space in the hdf5 file. Now you need to put actual data in it. This is
done with the H5Dwrite call.
/* Write floating point data */
for (i=0; i<24; i++) data[i] = i+.5;
status = H5Dwrite
(dataset,H5T_NATIVE_DOUBLE,H5S_ALL,H5S_ALL,H5P_DEFAULT,
data);
/* write parameter value */
parm = 37;
status = H5Dwrite
(parmset,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,
&parm);

/*
* File: parmwrite.c
* Author: Victor Eijkhout
*/
#include "myh5defs.h"
#define FILE "wdset.h5"

main() {

hid_t file_id, dataset, dataspace; /* identifiers */

hid_t parmset,parmspace;
hsize_t dims[2];
herr_t status;
double data[24]; int i,parm;

/* Create a new file using default properties. */

file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

/* Create the dataset. */

dims[0] = 4; dims[1] = 6;
dataspace = H5Screate_simple(2, dims, NULL);
dataset = H5Dcreate
(file_id, "/dset", H5T_NATIVE_DOUBLE, dataspace, H5P_DEFAULT);

/* Add a descriptive parameter */

parmspace = H5Screate(H5S_SCALAR);
parmset = H5Dcreate
(file_id,"/parm",H5T_NATIVE_INT,parmspace,H5P_DEFAULT);

/* Write data to file */

for (i=0; i<24; i++) data[i] = i+.5;
status = H5Dwrite
(dataset,H5T_NATIVE_DOUBLE,H5S_ALL,H5S_ALL,H5P_DEFAULT,
data); H5REPORT(status);

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7. Scientific Data Storage

/* write parameter value */

parm = 37;
status = H5Dwrite
(parmset,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,
&parm); H5REPORT(status);

/* End access to the dataset and release resources used by it. */

status = H5Dclose(dataset);
status = H5Dclose(parmset);

/* Terminate access to the data space. */

status = H5Sclose(dataspace);
status = H5Sclose(parmspace);

/* Close the file. */

status = H5Fclose(file_id);
}

%% h5dump wdset.h5
HDF5 "wdset.h5" {
GROUP "/" {
DATASET "dset" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
DATA {
(0,0): 0.5, 1.5, 2.5, 3.5, 4.5, 5.5,
(1,0): 6.5, 7.5, 8.5, 9.5, 10.5, 11.5,
(2,0): 12.5, 13.5, 14.5, 15.5, 16.5, 17.5,
(3,0): 18.5, 19.5, 20.5, 21.5, 22.5, 23.5
}
}
DATASET "parm" {
DATATYPE H5T_STD_I32LE
DATASPACE SCALAR
DATA {
(0): 37
}
}
}
}

If you look closely at the source and the dump, you see that the data types are declared as ‘native’, but
rendered as LE. The ‘native’ declaration makes the datatypes behave like the built-in C or Fortran data
types. Alternatively, you can explicitly indicate whether data is little-endian or big-endian. These terms
describe how the bytes of a data item are ordered in memory. Most architectures use little endian, as you
can see in the dump output, but, notably, IBM uses big endian.

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 7.5. Reading

7.5 Reading
Now that we have a file with some data, we can do the mirror part of the story: reading from that file.
The essential commands are
h5file = H5Fopen( .... )
....
H5Dread( dataset, .... data .... )

where the H5Dread command has the same arguments as the corresponding H5Dwrite.

Exercise. Read data from the wdset.h5 file that you create in the previous exercise, by compiling and
running the allread.c example below.
Expected outcome. Running the allread executable will print the value 37 of the parameter, and
the value 8.5 of the (1,2) data point of the array.
Caveats. Make sure that you run parmwrite to create the input file.
/*
* File: allread.c
* Author: Victor Eijkhout
*/
#include "myh5defs.h"
#define FILE "wdset.h5"

main() {

hid_t file_id, dataset, parmset;

herr_t status;
double data[24]; int parm;

/* Open an existing file */

file_id = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
H5REPORT(file_id);

/* Locate the datasets. */

dataset = H5Dopen(file_id, "/dset"); H5REPORT(dataset);
parmset = H5Dopen(file_id,"/parm"); H5REPORT(parmset);

/* Read data back */

status = H5Dread
(parmset,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,
&parm); H5REPORT(status);
printf("parameter value: %d\n",parm);

status = H5Dread
(dataset,H5T_NATIVE_DOUBLE,H5S_ALL,H5S_ALL,H5P_DEFAULT,
data); H5REPORT(status);
printf("arbitrary data point [1,2]: %e\n",data[1*6+2]);

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7. Scientific Data Storage

/* Terminate access to the datasets */

status = H5Dclose(dataset); H5REPORT(status);
status = H5Dclose(parmset); H5REPORT(status);

/* Close the file. */

status = H5Fclose(file_id);
}

%% ./allread
parameter value: 37
arbitrary data point [1,2]: 8.500000e+00

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Chapter 8

Parallel I/O

Parallel I/O is a tricky subject. You can try to let all processors jointly write one file, or to write a file per
process and combine them later. With the standard mechanisms of your programming language there are
the following considerations:
• On clusters where the processes have individual file systems, the only way to write a single file
is to let it be generated by a single processor.
• Writing one file per process is easy to do, but
– You need a post-processing script;
– if the files are not on a shared file system (such as Lustre), it takes additional effort to bring
them together;
– if the files are on a shared file system, writing many files may be a burden on the metadata
server.
• On a shared file system it is possible for all files to open the same file and set the file pointer
individually. This can be difficult if the amount of data per process is not uniform.
Illustrating the last point:
// pseek.c
FILE *pfile;
pfile = fopen("pseek.dat","w");
fseek(pfile,procid*sizeof(int),SEEK_CUR);
// fseek(pfile,procid*sizeof(char),SEEK_CUR);
fprintf(pfile,"%d\n",procid);
fclose(pfile);

MPI also has its own portable I/O: MPI I/O, for which see chapter Parallel Programming book, section 10.
Alternatively, one could use a library such as hdf5; see 7.
For a great discussion see [15], from which figures here are taken.

8.1 Use sequential I/O

MPI processes can do anything a regular process can, including opening a file. This is the simplest form
of parallel I/O: every MPI process opens its own file. To prevent write collisions,

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8. Parallel I/O

• you use MPI_Comm_rank to generate a unique file name, or

• you use a local file system, typically /tmp, that is unique per process, or at least per the group of
processes on a node.
For reading it is actually possible for all processes to open the same file, but for reading this is not really
feasible. Hence the unique files.

8.2 MPI I/O

In chapter Parallel Programming book, section 10 we discuss MPI I/O. This is a way for all processes on a
communicator to open a single file, and write to it in a coordinated fashion. This has the big advantage
that the end result is an ordinary Unix file.

8.3 Higher level libraries

Libraries such as NetCDF or HDF5 (see 7) offer advantages over MPI I/O:
• Files can be OS-independent, removing worries such as about little-endian storage.
• Files are self-documenting: they contain the metadata describing their contents.

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Chapter 9

Plotting with GNUplot

The gnuplot utility is a simple program for plotting sets of points or curves. This very short tutorial will
show you some of the basics. For more commands and options, see the manual http://www.gnuplot.
info/docs/gnuplot.html.

9.1 Usage modes

The two modes for running gnuplot are interactive and from file. In interactive mode, you call gnuplot
from the command line, type commands, and watch output appear; you terminate an interactive session
with quit. If you want to save the results of an interactive session, do save "name.plt". This file can
be edited, and loaded with load "name.plt".
Plotting non-interactively, you call gnuplot <your file>.
The output of gnuplot can be a picture on your screen, or drawing instructions in a file. Where the
output goes depends on the setting of the terminal. By default, gnuplot will try to draw a picture. This
is equivalent to declaring
set terminal x11

or aqua, windows, or any choice of graphics hardware.

For output to file, declare
set terminal pdf

or fig, latex, pbm, et cetera. Note that this will only cause the pdf commands to be written to your
screen: you need to direct them to file with
set output "myplot.pdf"

or capture them with

gnuplot my.plt > myplot.pdf

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9. Plotting with GNUplot

9.2 Plotting
The basic plot commands are plot for 2D, and splot (‘surface plot’) for 3D plotting.

9.2.1 Plotting curves

By specifying
plot x**2

you get a plot of 𝑓 (𝑥) = 𝑥 2 ; gnuplot will decide on the range for 𝑥. With
set xrange [0:1]
plot 1-x title "down", x**2 title "up"

you get two graphs in one plot, with the 𝑥 range limited to [0, 1], and the appropriate legends for the
graphs. The variable x is the default for plotting functions.
Plotting one function against another – or equivalently, plotting a parametric curve – goes like this:
set parametric
plot [t=0:1.57] cos(t),sin(t)

which gives a quarter circle.

To get more than one graph in a plot, use the command set multiplot.

9.2.2 Plotting data points

It is also possible to plot curves based on data points. The basic syntax is plot 'datafile', which takes
two columns from the data file and interprets them as (𝑥, 𝑦) coordinates. Since data files can often have
multiple columns of data, the common syntax is plot 'datafile' using 3:6 for columns 3 and 6.
Further qualifiers like with lines indicate how points are to be connected.
Similarly, splot "datafile3d.dat" 2:5:7 will interpret three columns as specifying (𝑥, 𝑦, 𝑧) coordi-
nates for a 3D plot.
If a data file is to be interpreted as level or height values on a rectangular grid, do splot "matrix.dat"
matrix for data points; connect them with
split "matrix.dat" matrix with lines

9.2.3 Customization
Plots can be customized in many ways. Some of these customizations use the set command. For instance,

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 9.3. Workflow

set xlabel "time"

set ylabel "output"
set title "Power curve"

You can also change the default drawing style with

set style function dots

(dots, lines, dots, points, et cetera), or change on a single plot with

plot f(x) with points

9.3 Workflow
Imagine that your code produces a dataset that you want to plot, and you run your code for a number
of inputs. It would be nice if the plotting can be automated. Gnuplot itself does not have the facilities for
this, but with a little help from shell programming this is not hard to do.
Suppose you have data files
data1.dat data2.dat data3.dat

and you want to plot them with the same gnuplot commands. You could make a file plot.template:
set term pdf
set output "FILENAME.pdf"
plot "FILENAME.dat"

The string FILENAME can be replaced by the actual file names using, for instance sed:
for d in data1 data2 data3 ; do
cat plot.template | sed s/FILENAME/$d/ > plot.cmd
gnuplot plot.cmd
done

Variations on this basic idea are many.

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Chapter 10

Good coding practices

Sooner or later, and probably sooner than later, every programmer is confronted with code not behaving
as intended. In this section you will learn some techniques of dealing with this problem. At first we will see
a number of techniques for preventing errors; in the next chapter we will discuss debugging, the process
of finding the inevitable errors in a program, once they have occurred.

10.1 Defensive programming

In this section we will discuss a number of techniques that are aimed at preventing the likelihood of
programming errors, or increasing the likelihood of them being found at runtime. We call this defensive
programming.
Scientific codes are often large and involved, so it is a good practice to code knowing that you are going
to make mistakes and prepare for them. Another good coding practice is the use of tools: there is no point
in reinventing the wheel if someone has already done it for you. Some of these tools are be described in
other sections:
• Build systems, such as Make, Scons, Bjam; see section 3.
• Source code management with Git; see section 5.
• Regression testing and designing with testing in mind (unit testing)
First we will have a look at runtime sanity checks, where you test for things that can not or should not
happen.

10.1.1 Assertions
In the things that can go wrong with a program we can distinguish between errors and bugs. Errors are
things that legitimately happen but that should not. File systems are common sources of errors: a program
wants to open a file but the file doesn’t exist because the user mistyped the name, or the program writes
to a file but the disk is full. Other errors can come from arithmetic, such as overflow errors.
On the other hand, a bug in a program is an occurrence that cannot legitimately occur. Of course, ‘le-
gitimately’ here means ‘according to the programmer’s intentions’. Bugs can often be described as ‘the
computer always does what you ask, not necessarily what you want’.

138
 10.1. Defensive programming

Assertions serve to detect bugs in your program: an assertion is a predicate that should be true at a certain
point in your program. Thus, an assertion failing means that you didn’t code what you intended to code.
An assertion is typically a statement in your programming language, or a preprocessor macro; upon failure
of the assertion, your program will stop.
Some examples of assertions:
• If a subprogram has an array argument, it is a good idea to test whether the actual argument is a
null pointer before indexing into the array.
• Similarly, you could test a dynamically allocated data structure for not having a null pointer.
• If you calculate a numerical result for which certain mathematical properties hold, for instance
you are writing a sine function, for which the result has to be in [−1, 1], you should test whether
this property indeed holds for the result.
Assertions are often disabled in a program once it’s sufficiently tested. The reason for this is that assertions
can be expensive to execute. For instance, if you have a complicated data structure, you could write a
complicated integrity test, and perform that test in an assertion, which you put after every access to the
data structure.
Because assertions are often disabled in the ‘production’ version of a code, they should not affect any
stored data . If they do, your code may behave differently when you’re testing it with assertions, versus
how you use it in practice without them. This is also formulated as ‘assertions should not have side-effects’.

10.1.1.1 The C assert macro

The C standard library has a file assert.h which provides an assert() macro. Inserting assert(foo)
has the following effect: if foo is zero (false), a diagnostic message is printed on standard error:
Assertion failed: foo, file filename, line line-number

which includes the literal text of the expression, the file name, and line number; and the program is
subsequently stopped. Here is an example:
#include<assert.h>

void open_record(char *record_name)

{
assert(record_name!=NULL);
/* Rest of code */
}

int main(void)
{
open_record(NULL);
}

The assert macro can be disabled by defining the NDEBUG macro.

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10. Good coding practices

10.1.1.2 An assert macro for Fortran

(Thanks to Robert Mclay for this code.)
#if (defined( GFORTRAN ) || defined( G95 ) || defined ( PGI) )
# define MKSTR(x) "x"
#else
# define MKSTR(x) #x
#endif
#ifndef NDEBUG
# define ASSERT(x, msg) if (.not. (x) ) \
call assert( FILE , LINE ,MKSTR(x),msg)
#else
# define ASSERT(x, msg)
#endif
subroutine assert(file, ln, testStr, msgIn)
implicit none
character(*) :: file, testStr, msgIn
integer :: ln
print *, "Assert: ",trim(testStr)," Failed at ",trim(file),":",ln
print *, "Msg:", trim(msgIn)
stop
end subroutine assert

which is used as
ASSERT(nItemsSet.gt.arraySize,"Too many elements set")

10.1.2 Use of error codes

In some software libraries (for instance MPI or PETSc) every subprogram returns a result, either the
function value or a parameter, to indicate success or failure of the routine. It is good programming practice
to check these error parameters, even if you think that nothing can possibly go wrong.
It is also a good idea to write your own subprograms in such a way that they always have an error
parameter. Let us consider the case of a function that performs some numerical computation.
float compute(float val)
{
float result;
result = ... /* some computation */
return result;
}

float value,result;
result = compute(value);

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 10.1. Defensive programming

Looks good? What if the computation can fail, for instance:

result = ... sqrt(val) ... /* some computation */

How do we handle the case where the user passes a negative number?
float compute(float val)
{
float result;
if (val<0) { /* then what? */
} else
result = ... sqrt(val) ... /* some computation */
return result;
}

We could print an error message and deliver some result, but the message may go unnoticed, and the
calling environment does not really receive any notification that something has gone wrong.
The following approach is more flexible:
int compute(float val,float *result)
{
float result;
if (val<0) {
return -1;
} else {
*result = ... sqrt(val) ... /* some computation */
}
return 0;
}

float value,result; int ierr;

ierr = compute(value,&result);
if (ierr!=0) { /* take appropriate action */
}

You can save yourself a lot of typing by writing

#define CHECK_FOR_ERROR(ierr) \
if (ierr!=0) { \
printf("Error %d detected\n",ierr); \
return -1 ; }
....
ierr = compute(value,&result); CHECK_FOR_ERROR(ierr);

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10. Good coding practices

Using some cpp macros you can even define

#define CHECK_FOR_ERROR(ierr) \
if (ierr!=0) { \
printf("Error %d detected in line %d of file %s\n",\
ierr,__LINE__,__FILE__); \
return -1 ; }

Note that this macro not only prints an error message, but also does a further return. This means that, if
you adopt this use of error codes systematically, you will get a full backtrace of the calling tree if an error
occurs. (In the Python language this is precisely the wrong approach since the backtrace is built-in.)

10.2 Guarding against memory errors

In scientific computing it goes pretty much without saying that you will be working with large amounts
of data. Some programming languages make managing data easy, others, one might say, make making
errors with data easy.
The following are some examples of memory violations.
• Writing outside array bounds. If the address is outside the user memory, your code may exit with
an error such as segmentation violation, and the error is reasonably easy to find. If the address
is just outside an array, it will corrupt data but not crash the program; such an error may go
undetected for a long time, as it can have no effect, or only introduce subtly wrong values in your
computation.
• Reading outside array bounds can be harder to find than errors in writing, as it will often not stop
your code, but only introduce wrong values.
• The use of uninitialized memory is similar to reading outside array bounds, and can go undetected
for a long time. One variant of this is through attaching memory to an unallocated pointer.
This particular kind of error can manifest itself in interesting behavior. Let’s say you notice that
your program misbehaves, you recompile it with debug mode to find the error, and now the error
no longer occurs. This is probably due to the effect that, with low optimization levels, all allocated
arrays are filled with zeros. Therefore, your code was originally reading a random value, but is
now getting a zero.
This section contains some techniques to prevent errors in dealing with memory that you have reserved
for your data.

10.2.1 Array bound checking and other memory techniques

Array bound checking, that is, detecting whether an array access is indeed to a legal location, carries
runtime overhead. For that reason you may want to do this only in the testing phrase of a code, or keep
it out of compute-intensive loops.

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 10.2. Guarding against memory errors

10.2.1.1 C
The C language has arrays, but they suffer from ‘pointer decay’: they behave largely like pointers in
memory. Thus, bounds checking is hard, other than with external tools like Valgrind.

10.2.1.2 C++
C++ has the containers such as std::vector which support bound checking:
vector<float> x(25);
x.at(26) = y; // throws an exception

On the other hand, the C-style x[26] does not perform such checks.

10.2.1.3 Fortran
Fortran arrays are more restricted than C arrays, so compilers often support a flag for activating runtime
bounds checking. For gfortran that is -fbounds-check.

10.2.2 Memory leaks

We say that a program has a memory leak, if it allocates memory, and subsequently loses track of that
memory. The operating system then thinks the memory is in use, while it is not, and as a result the
computer memory can get filled up with allocated memory that serves no useful purpose.
In this example data is allocated inside a lexical scope:
for (i=.... ) {
real *block = malloc( /* large number of bytes */ )
/* do something with that block of memory */
/* and forget to call "free" on that block */
}

The block of memory is allocated in each iteration, but the allocation of one iteration is no longer available
in the next. A similar example can be made with allocating inside a conditional.
It should be noted that this problem is far less serious in Fortran, where memory is deallocated automat-
ically as a variable goes out of scope.
There are various tools for detecting memory errors: Valgrind, DMALLOC, Electric Fence. For valgrind,
see section 11.8.

10.2.3 Roll-your-own malloc

Many programming errors arise from improper use of dynamically allocated memory: the program writes
beyond the bounds, or writes to memory that has not been allocated yet, or has already been freed. While
some compilers can do bound checking at runtime, this slows down your program. A better strategy is to
write your own memory management. Some libraries such as PETSc already supply an enhanced malloc;

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10. Good coding practices

if this is available you should certainly make use of it. (The gcc compiler has a function mcheck, defined in
mcheck.h, that has a similar function.)
If you write in C, you will probably know the malloc and free calls:
int *ip;
ip = (int*) malloc(500*sizeof(int));
if (ip==0) {/* could not allocate memory */}
..... do stuff with ip .....
free(ip);

You can save yourself some typing by

#define MYMALLOC(a,b,c) \
a = (c*)malloc(b*sizeof(c)); \
if (a==0) {/* error message and appropriate action */}

int *ip;
MYMALLOC(ip,500,int);

Runtime checks on memory usage (either by compiler-generated bounds checking, or through tools like
valgrind or Rational Purify) are expensive, but you can catch many problems by adding some functionality
to your malloc. What we will do here is to detect memory corruption after the fact.
We allocate a few integers to the left and right of the allocated object (line 1 in the code below), and put
a recognizable value in them (line 2 and 3), as well as the size of the object (line 2). We then return the
pointer to the actually requested memory area (line 4).
#define MEMCOOKIE 137
#define MYMALLOC(a,b,c) { \
char *aa; int *ii; \
aa = malloc(b*sizeof(c)+3*sizeof(int)); /* 1 */ \
ii = (int*)aa; ii[0] = b*sizeof(c); \
ii[1] = MEMCOOKIE; /* 2 */ \
aa = (char*)(ii+2); a = (c*)aa ; /* 4 */ \
aa = aa+b*sizesof(c); ii = (int*)aa; \
ii[0] = MEMCOOKIE; /* 3 */ \
}

Now you can write your own free, which tests whether the bounds of the object have not been written
over.
#define MYFREE(a) { \
char *aa; int *ii,; ii = (int*)a; \
if (*(--ii)!=MEMCOOKIE) printf("object corrupted\n"); \
n = *(--ii); aa = a+n; ii = (int*)aa; \
if (*ii!=MEMCOOKIE) printf("object corrupted\n"); \

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 10.3. Testing

You can extend this idea: in every allocated object, also store two pointers, so that the allocated memory
areas become a doubly linked list. You can then write a macro CHECKMEMORY which tests all your allocated
objects for corruption.
Such solutions to the memory corruption problem are fairly easy to write, and they carry little overhead.
There is a memory overhead of at most 5 integers per object, and there is practically no performance
penalty.
(Instead of writing a wrapper for malloc, on some systems you can influence the behavior of the system
routine. On linux, malloc calls hooks that can be replaced with your own routines; see http://www.
gnu.org/s/libc/manual/html_node/Hooks-for-Malloc.html.)

10.3 Testing
There are various philosophies for testing the correctness of a code.
• Correctness proving: the programmer draws up predicates that describe the intended behavior of
code fragments and proves by mathematical techniques that these predicates hold [10, 5].
• Unit testing: each routine is tested separately for correctness. This approach is often hard to do
for numerical codes, since with floating point numbers there is essentially an infinity of possible
inputs, and it is not easy to decide what would constitute a sufficient set of inputs.
• Integration testing: test subsystems
• System testing: test the whole code. This is often appropriate for numerical codes, since we often
have model problems with known solutions, or there are properties such as bounds that need to
hold on the global solution.
• Test-driven design: the program development process is driven by the requirement that testing
is possible at all times.
With parallel codes we run into a new category of difficulties with testing. Many algorithms, when exe-
cuted in parallel, will execute operations in a slightly different order, leading to different roundoff behav-
ior. For instance, the parallel computation of a vector sum will use partial sums. Some algorithms have an
inherent damping of numerical errors, for instance stationary iterative methods (section HPC book, sec-
tion 5.5.1), but others have no such built-in error correction (nonstationary methods; section HPC book,
section 5.5.8). As a result, the same iterative process can take different numbers of iterations depending
on how many processors are used.

10.3.1 Unit testing

Unit testing is a way to ensure correctness of a code. For that it’s necessary that the tests have full coverage
of the code: all statements in your code should be part of a test.
Unit tests are also a way to document the use of a code: they show the intended use of the code.
A few notes:

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10. Good coding practices

• Global state in your program makes it hard to test, since it carries information between tests.
• Tests should not reproduce the logic of your code: if the program logic is faulty, the test will be
too.
• Tests should be short, and obey the single-responsibility principle. Naming your tests is good to
keep them focused.

10.3.2 Test-driven design and development

In test-driven design there is a strong emphasis on the code always being testable. The basic ideas are as
follows.
• Both the whole code and its parts should always be testable.
• When extending the code, make only the smallest change that allows for testing.
• With every change, test before and after.
• Assure correctness before adding new features.
Volume 3 of this series discusses Test-Drive Development (TDD) and Unit Testing, using the Catch2 frame-
work. See Introduction to Scientific Programming book, chapter 68.

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Chapter 11

Debugging

Debugging is like being the detective in a crime movie where you are also the murderer.
(Filipe Fortes, 2013)
When a program misbehaves, debugging is the process of finding out why. There are various strategies
of finding errors in a program. The crudest one is debugging by print statements. If you have a notion of
where in your code the error arises, you can edit your code to insert print statements, recompile, rerun,
and see if the output gives you any suggestions. There are several problems with this:
• The edit/compile/run cycle is time consuming, especially since
• often the error will be caused by an earlier section of code, requiring you to edit, compile, and
rerun repeatedly. Furthermore,
• the amount of data produced by your program can be too large to display and inspect effectively,
and
• if your program is parallel, you probably need to print out data from all processors, making the
inspection process very tedious.
For these reasons, the best way to debug is by the use of an interactive debugger, a program that allows
you to monitor and control the behavior of a running program. In this section you will familiarize yourself
with gdb and lldb, the open source debuggers of the GNU and clang projects respectively. Other debuggers
are proprietary, and typically come with a compiler suite. Another distinction is that gdb is a commandline
debugger; there are graphical debuggers such as ddd (a frontend to gdb) or DDT and TotalView (debuggers
for parallel codes). We limit ourselves to gdb, since it incorporates the basic concepts common to all
debuggers.
In this tutorial you will debug a number of simple programs with gdb and valgrind. The files can be found
in the repository in the directory code/gdb.

11.1 Compiling for debug

You often need to recompile your code before you can debug it. A first reason for this is that the binary
code typically knows nothing about what variable names corresponded to what memory locations, or
what lines in the source to what instructions. In order to make the binary executable know this, you have
to include the symbol table in it, which is done by adding the -g option to the compiler line.

147
11. Debugging

Table 11.1: List of common gdb / lldb commands.

gdb lldb
Starting a debugger run
$ gdb program $ lldb program
(gdb) run (lldb) run
Displaying a stack trace
(gdb) where (lldb) thread backtrace
Investigate a specific frame
frame 2 frame select 2
Run/step
run / step / continue thread continue / step-in/over/out
Set a breakpoint at a line
break foo.c:12 breakpoint set [ -f foo.c ] -l 12
break foo.c:12 if n>0
info breakpoints
Set a breakpoint for exceptions
catch throw break set -E C++

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 11.2. Invoking the debugger

Usually, you also need to lower the compiler optimization level: a production code will often be compiled
with flags such as -O2 or -Xhost that try to make the code as fast as possible, but for debugging you need
to replace this by -O0 (‘oh-zero’). The reason is that higher levels will reorganize your code, making it
hard to relate the execution to the source1 .

11.2 Invoking the debugger

There are three ways of using gdb: using it to start a program, attaching it to an already running program,
or using it to inspect a core dump. We will only consider the first possibility.
Starting a debugger run
gdb lldb
$ gdb program $ lldb program
(gdb) run (lldb) run
Here is an example of how to start gdb with program that has no arguments (Fortran users, use hello.F):

tutorials/gdb/c/hello.c
#include <stdlib.h>
#include <stdio.h>
int main() {
printf("hello world\n");
return 0;
}

%% cc -g -o hello hello.c
# regular invocation:
%% ./hello
hello world
# invocation from gdb:
%% gdb hello
GNU gdb 6.3.50-20050815 # ..... [version info]
Copyright 2004 Free Software Foundation, Inc. .... [copyright info] ....
(gdb) run
Starting program: /home/eijkhout/tutorials/gdb/hello
Reading symbols for shared libraries +. done
hello world

Program exited normally.

(gdb) quit
%%

1. Typically, actual code motion is done by -O3, but at level -O2 the compiler will inline functions and make other simplifica-
tions.

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11. Debugging

Important note: the program was compiled with the debug flag -g. This causes the symbol table (that is,
the translation from machine address to program variables) and other debug information to be included
in the binary. This will make your binary larger than strictly necessary, but it will also make it slower, for
instance because the compiler will not perform certain optimizations2 .
To illustrate the presence of the symbol table do
%% cc -g -o hello hello.c
%% gdb hello
GNU gdb 6.3.50-20050815 # ..... version info
(gdb) list

and compare it with leaving out the -g flag:

%% cc -o hello hello.c
%% gdb hello
GNU gdb 6.3.50-20050815 # ..... version info
(gdb) list

For a program with commandline input we give the arguments to the run command (Fortran users use
say.F):

tutorials/gdb/c/say.c %% cc -o say -g say.c

%% ./say 2
hello world
hello world
%% gdb say
.... the usual messages ...
#include <stdlib.h> (gdb) run 2
#include <stdio.h> Starting program: /home/eijkhout/tutorials/gdb/
int main(int argc,char **argv) { Reading symbols for shared libraries +. done
int i;
hello world
for (i=0; i<atoi(argv[1]); i++)
printf("hello world\n");
hello world
return 0;
} Program exited normally.

11.3 Finding errors: where, frame, print

Let us now consider some programs with errors.

2. Compiler optimizations are not supposed to change the semantics of a program, but sometimes do. This can lead to the
nightmare scenario where a program crashes or gives incorrect results, but magically works correctly with compiled with debug
and run in a debugger.

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 11.3. Finding errors: where, frame, print

11.3.1 C programs
The following code has several errors. We will use the debugger to uncover them.
// square.c
int nmax,i;
float *squares,sum;

fscanf(stdin,"%d",nmax);
for (i=1; i<=nmax; i++) {
squares[i] = 1./(i*i); sum += squares[i];
}
printf("Sum: %e\n",sum);

%% cc -g -o square square.c
%% ./square
5000
Segmentation fault

The segmentation fault (other messages are possible too) indicates that we are accessing memory that we
are not allowed to, making the program exit. A debugger will quickly tell us where this happens:
%% gdb square
(gdb) run
50000

Program received signal EXC_BAD_ACCESS, Could not access memory.

Reason: KERN_INVALID_ADDRESS at address: 0x000000000000eb4a
0x00007fff824295ca in __svfscanf_l ()

Apparently the error occurred in a function __svfscanf_l, which is not one of ours, but a system func-
tion. Using the backtrace (or bt, also where or w) command we display the call stack. This usually allows
us to find out where the error lies:
Displaying a stack trace
gdb lldb
(gdb) where (lldb) thread backtrace
(gdb) where
#0 0x00007fff824295ca in __svfscanf_l ()
#1 0x00007fff8244011b in fscanf ()
#2 0x0000000100000e89 in main (argc=1, argv=0x7fff5fbfc7c0) at square.c:7

We inspect the actual problem:

Investigate a specific frame
gdb clang
frame 2 frame select 2

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11. Debugging

We take a close look at line 7, and see that we need to change nmax to &nmax.
There is still an error in our program:
(gdb) run
50000

Program received signal EXC_BAD_ACCESS, Could not access memory.

Reason: KERN_PROTECTION_FAILURE at address: 0x000000010000f000
0x0000000100000ebe in main (argc=2, argv=0x7fff5fbfc7a8) at square1.c:9
9 squares[i] = 1./(i*i); sum += squares[i];

We investigate further:
(gdb) print i
$1 = 11237
(gdb) print squares[i]
Cannot access memory at address 0x10000f000
(gdb) print squares
$2 = (float *) 0x0

and we quickly see that we forgot to allocate squares.

By the way, we were lucky here: this sort of memory errors is not always detected. Starting our programm
with a smaller input does not lead to an error:
(gdb) run
50
Sum: 1.625133e+00

Program exited normally.

Memory errors can also occur if we have a legitimate array, but we access it outside its bounds. The
following program fills an array, forward, and reads it out, backward. However, there is an indexing error
in the second loop.
// up.c
int nlocal = 100,i;
double s, *array = (double*) malloc(nlocal*sizeof(double));
for (i=0; i<nlocal; i++) {
double di = (double)i;
array[i] = 1/(di*di);
}
s = 0.;
for (i=nlocal-1; i>=0; i++) {
double di = (double)i;
s += array[i];
}

Program received signal EXC_BAD_ACCESS, Could not access memory.

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 11.4. Stepping through a program

Reason: KERN_INVALID_ADDRESS at address: 0x0000000100200000

0x0000000100000f43 in main (argc=1, argv=0x7fff5fbfe2c0) at up.c:15
15 s += array[i];
(gdb) print array
$1 = (double *) 0x100104d00
(gdb) print i
$2 = 128608

You see that the index where the debugger finally complains is quite a bit larger than the size of the array.

Exercise 11.1. Can you think of a reason why indexing out of bounds is not immediately fatal?
What would determine where it does become a problem? (Hint: how is computer memory
structured?)
In section 11.8 you will see a tool that spots any out-of-bound indexing.

11.3.2 Fortran programs

Compile and run the following program:
MISSING SNIPPET gdb-squaref
It should end prematurely with a message such as ‘Illegal instruction’. Running the program in gdb quickly
tells you where the problem lies:
(gdb) run
Starting program: tutorials/gdb//fsquare
Reading symbols for shared libraries ++++. done

Program received signal EXC_BAD_INSTRUCTION,

Illegal instruction/operand.
0x0000000100000da3 in square () at square.F:7
7 sum = sum + squares(i)

We take a close look at the code and see that we did not allocate squares properly.

11.4 Stepping through a program

Stepping through a program
gdb lldb meaning
run start a run
cont continue from breakpoint
next next statement on same level
step next statement, this level or next

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11. Debugging

Often the error in a program is sufficiently obscure that you need to investigate the program run in detail.
Compile the following program
// roots.c
float root(int n)
{
float r;
r = sqrt(n);
return r;
}

int main() {
feenableexcept(FE_INVALID | FE_OVERFLOW);
int i;
float x=0;
for (i=100; i>-100; i--)
x += root(i+5);
printf("sum: %e\n",x);

and run it:

%% ./roots
sum: nan

Start it in gdb as before:

%% gdb roots
GNU gdb 6.3.50-20050815
Copyright 2004 Free Software Foundation, Inc.
....

but before you run the program, you set a breakpoint at main. This tells the execution to stop, or ‘break’,
in the main program.
(gdb) break main
Breakpoint 1 at 0x100000ea6: file root.c, line 14.

Now the program will stop at the first executable statement in main:
(gdb) run
Starting program: tutorials/gdb/c/roots
Reading symbols for shared libraries +. done

Breakpoint 1, main () at roots.c:14

14 float x=0;

Most of the time you will set a breakpoint at a specific line:

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 11.5. Inspecting values

Set a breakpoint at a line

gdb lldb
break foo.c:12 breakpoint set [ -f foo.c ] -l 12

If execution is stopped at a breakpoint, you can do various things, such as issuing the step command:
Breakpoint 1, main () at roots.c:14
14 float x=0;
(gdb) step
15 for (i=100; i>-100; i--)
(gdb)
16 x += root(i);
(gdb)

(if you just hit return, the previously issued command is repeated). Do a number of steps in a row by
hitting return. What do you notice about the function and the loop?
Switch from doing step to doing next. Now what do you notice about the loop and the function?
Set another breakpoint: break 17 and do cont. What happens?
Rerun the program after you set a breakpoint on the line with the sqrt call. When the execution stops
there do where and list.
• If you set many breakpoints, you can find out what they are with info breakpoints.
• You can remove breakpoints with delete n where n is the number of the breakpoint.
• If you restart your program with run without leaving gdb, the breakpoints stay in effect.
• If you leave gdb, the breakpoints are cleared but you can save them: save breakpoints <file>.
Use source <file> to read them in on the next gdb run.

11.5 Inspecting values

Run the previous program again in gdb: set a breakpoint at the line that does the sqrt call before you
actually call run. When the program gets to line 8 you can do print n. Do cont. Where does the program
stop?
If you want to repair a variable, you can do set var=value. Change the variable n and confirm that the
square root of the new value is computed. Which commands do you do?

11.6 Breakpoints
If a problem occurs in a loop, it can be tedious keep typing cont and inspecting the variable with print.
Instead you can add a condition to an existing breakpoint. First of all, you can make the breakpoint subject
to a condition: with

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11. Debugging

condition 1 if (n<0)

breakpoint 1 will only obeyed if n<0 is true.

You can also have a breakpoint that is only activated by some condition. The statement
break 8 if (n<0)

means that breakpoint 8 becomes (unconditionally) active after the condition n<0 is encountered.
Set a breakpoint
gdb lldb
break foo.c:12 breakpoint set [ -f foo.c ] -l 12
break foo.c:12 if n>0

Remark 13 You can break on NaN with the following trick:

break foo.c:12 if x!=x

using the fact that NaN is the only number not equal to itself.

Another possibility is to use ignore 1 50, which will not stop at breakpoint 1 the next 50 times.
Remove the existing breakpoint, redefine it with the condition n<0 and rerun your program. When the
program breaks, find for what value of the loop variable it happened. What is the sequence of commands
you use?
You can set a breakpoint in various ways:
• break foo.c to stop when code in a certain file is reached;
• break 123 to stop at a certain line in the current file;
• break foo to stop at subprogram foo
• or various combinations, such as break foo.c:123.
Information about breakpoints:
• If you set many breakpoints, you can find out what they are with info breakpoints.
• You can remove breakpoints with delete n where n is the number of the breakpoint.
• If you restart your program with run without leaving gdb, the breakpoints stay in effect.
• If you leave gdb, the breakpoints are cleared but you can save them: save breakpoints <file>.
Use source <file> to read them in on the next gdb run.
• In languages with exceptions, such as C++, you can set a catchpoint:
Set a breakpoint for exceptions
gdb clang
catch throw break set -E C++
Finally, you can execute commands at a breakpoint:

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 11.7. Memory debugging

break 45
command
print x
cont
end

This states that at line 45 variable x is to be printed, and execution should immediately continue.
If you want to run repeated gdb sessions on the same program, you may want to save an reload break-
points. This can be done with
save-breakpoint filename
source filename

11.7 Memory debugging

Many problems in programming stem from memory errors. We start with a sort description of the most
common types, and then discuss tools that help you detect them.

11.7.1 Type of memory errors

11.7.1.1 Invalid pointers
Dereferencing a pointer that does not point to an allocated object can lead to an error. If your pointer
points into valid memory anyway, your computation will continue but with incorrect results.
However, it is more likely that your program will probably exit with a segmentation violation or a bus
error.

11.7.1.2 Out-of-bounds errors

Addressing outside the bounds of an allocated object is less likely to crash your program and more likely
to give incorrect results.
Exceeding bounds by a large enough amount will again give a segmentation violation, but going out of
bounds by a small amount may read invalid data, or corrupt data of other variables, giving incorrect results
that may go undetected for a long time.

11.7.1.3 Memory leaks

We speak of a memory leak if allocated memory becomes unreachable. Example:
if (something) {
double *x = malloc(10*sizeofdouble);
// do something with x
}

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11. Debugging

After the conditional, the allocated memory is not freed, but the pointer that pointed to has gone away.
This last type especially can be hard to find. Memory leaks will only surface in that your program runs
out of memory. That in turn is detectable because your allocation will fail. It is a good idea to always
check the return result of your malloc or allocate statement!

11.8 Memory debugging with Valgrind

Errors leading to memory problems are easy to make. In this section we will see how valgrind makes it
possible to track down these errors. The use of valgrind is simplicity itself:
valgrind yourprogram yourargs

As a first example, consider out of bound addressing, also known as buffer overflow:
MISSING SNIPPET corruptbound
This is unlikely to crash your code, but the results are unpredictable, and this is certainly a failure of your
program logic.
Valgrind indicates that this is an invalid read, what line it occurs on, and where the block was allocated:
==9112== Invalid read of size 4
==9112== at 0x40233B: main (outofbound.cpp:10)
==9112== Address 0x595fde8 is 0 bytes after a block of size 40 alloc'd
==9112== at 0x4C2A483: operator new(unsigned long) (vg_replace_malloc.c:344)
==9112== by 0x4023CD: allocate (new_allocator.h:111)
==9112== by 0x4023CD: allocate (alloc_traits.h:436)
==9112== by 0x4023CD: _M_allocate (stl_vector.h:296)
==9112== by 0x4023CD: _M_create_storage (stl_vector.h:311)
==9112== by 0x4023CD: _Vector_base (stl_vector.h:260)
==9112== by 0x4023CD: _Vector_base (stl_vector.h:258)
==9112== by 0x4023CD: vector (stl_vector.h:415)
==9112== by 0x4023CD: main (outofbound.cpp:9)

Remark 14 Buffer overflows are a well-known security risk, typically associated with reading string input
from a user source. Buffer overflows can be largely avoided by using C++ constructs such as cin and string
instead of sscanf and character arrays.

Valgrind is informative but cryptic, since it works on the bare memory, not on variables. Thus, these error
messages take some exegesis. They state that line 10 reads a 4-byte object immediately after a block of 40
bytes that was allocated. In other words: the code is writing outside the bounds of an allocated array.
The next example performs a read on an array that has already been free’d. In this simple case you will
actually get the expected output, but if the read comes much later than the free, the output can be anything.
MISSING SNIPPET corruptfree
Valgrind again states that this is an invalid read; it gives both where the block was allocated and where it
was freed.

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 11.8. Memory debugging with Valgrind

==11431== Invalid read of size 4

==11431== at 0x40230C: main (free.cpp:13)
==11431== Address 0x595fdcc is 12 bytes inside a block of size 40,000 free'd
==11431== at 0x4C2B5CF: operator delete(void*, unsigned long) (vg_replace_malloc.c:595)
==11431== by 0x402301: main (free.cpp:12)
==11431== Block was alloc'd at
==11431== at 0x4C2AB28: operator new[](unsigned long) (vg_replace_malloc.c:433)
==11431== by 0x4022E0: main (free.cpp:10)

On the other hand, if you forget to free memory you have a memory leak (just imagine allocation, and
not free’ing, in a loop)
MISSING SNIPPET corruptleak
which valgrind reports on:
==283234== LEAK SUMMARY:
==283234== definitely lost: 40,000 bytes in 1 blocks
==283234== indirectly lost: 0 bytes in 0 blocks
==283234== possibly lost: 0 bytes in 0 blocks
==283234== still reachable: 8 bytes in 1 blocks
==283234== suppressed: 0 bytes in 0 blocks

Memory leaks are much more rare in C++ than in C because of containers such as std::vector. However,
in sophisticated cases you may still do your own memory management, and you need to be aware of the
danger of memory leaks.
If you do your own memory management, there is also a danger of writing to an array pointer that has
not been allocated yet:
MISSING SNIPPET corruptinit
The behavior of this code depends on all sorts of things: if the pointer variable is zero, the code will crash.
On the other hand, if it contains some random value, the write may succeed; provided you are not writing
too far from that location.
The output here shows both the valgrind diagnosis, and the OS message when the program aborted:
==283234== LEAK SUMMARY:
==283234== definitely lost: 40,000 bytes in 1 blocks
==283234== indirectly lost: 0 bytes in 0 blocks
==283234== possibly lost: 0 bytes in 0 blocks
==283234== still reachable: 8 bytes in 1 blocks
==283234== suppressed: 0 bytes in 0 blocks

11.8.1 Electric fence

The electric fence library is one of a number of tools that supplies a new malloc with debugging support.
These are linked instead of the malloc of the standard libc.
cc -o program program.c -L/location/of/efence -lefence

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11. Debugging

Suppose your program has an out-of-bounds error. Running with gdb, this error may only become appar-
ent if the bounds are exceeded by a large amount. On the other hand, if the code is linked with libefence,
the debugger will stop at the very first time the bounds are exceeded.

11.9 Further reading

A good tutorial: http://www.dirac.org/linux/gdb/.
Reference manual: http://www.ofb.net/gnu/gdb/gdb_toc.html.

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Chapter 12

Parallel debugging

When a program misbehaves, debugging is the process of finding out why. There are various strategies
of finding errors in a program. The crudest one is debugging by print statements. If you have a notion of
where in your code the error arises, you can edit your code to insert print statements, recompile, rerun,
and see if the output gives you any suggestions. There are several problems with this:
• The edit/compile/run cycle is time consuming, especially since
• often the error will be caused by an earlier section of code, requiring you to edit, compile, and
rerun repeatedly. Furthermore,
• the amount of data produced by your program can be too large to display and inspect effectively,
and
• if your program is parallel, you probably need to print out data from all proccessors, making the
inspection process very tedious.
For these reasons, the best way to debug is by the use of an interactive debugger, a program that allows you
to monitor and control the behaviour of a running program. In this section you will familiarize yourself
with gdb, which is the open source debugger of the GNU project. Other debuggers are proprietary, and
typically come with a compiler suite. Another distinction is that gdb is a commandline debugger; there
are graphical debuggers such as ddd (a frontend to gdb) or DDT and TotalView (debuggers for parallel
codes). We limit ourselves to gdb, since it incorporates the basic concepts common to all debuggers.
In this tutorial you will debug a number of simple programs with gdb and valgrind. The files can be found
in the repository in the directory tutorials/debug_tutorial_files.

12.1 Parallel debugging

Debugging parallel programs is harder than than sequential programs, because every sequential bug may
show up, plus a number of new types, caused by the interaction of the various processes.
Here are a few possible parallel bugs:
• Processes can deadlock because they are waiting for a message that never comes. This typically
happens with blocking send/receive calls due to an error in program logic.
• If an incoming message is unexpectedly larger than anticipated, a memory error can occur.
• A collective call will hang if somehow one of the processes does not call the routine.

161
12. Parallel debugging

There are few low-budget solutions to parallel debugging. The main one is to create an xterm for each
process. We will describe this next. There are also commercial packages such as DDT and TotalView, that
offer a GUI. They are very convenient but also expensive. The Eclipse project has a parallel package, Eclipse
PTP, that includes a graphic debugger.

Figure 12.1: Display of 16 processes in the DDT debugger.

Debugging in parallel is harder than sequentially, because you will run errors that are only due to inter-
action of processes such as deadlock; see section HPC book, section 2.6.3.6.
As an example, consider this segment of MPI code:
MPI_Init(0,0);
// set comm, ntids, mytid
for (int it=0; ; it++) {
double randomnumber = ntids * ( rand() / (double)RAND_MAX );
printf("[%d] iteration %d, random %e\n",mytid,it,randomnumber);
if (randomnumber>mytid && randomnumber<mytid+1./(ntids+1))
MPI_Finalize();
}
MPI_Finalize();

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 12.2. MPI debugging with gdb

Each process computes random numbers until a certain condition is satisfied, then exits. However, con-
sider introducing a barrier (or something that acts like it, such as a reduction):
for (int it=0; ; it++) {
double randomnumber = ntids * ( rand() / (double)RAND_MAX );
printf("[%d] iteration %d, random %e\n",mytid,it,randomnumber);
if (randomnumber>mytid && randomnumber<mytid+1./(ntids+1))
MPI_Finalize();
MPI_Barrier(comm);
}
MPI_Finalize();

Now the execution will hang, and this is not due to any particular process: each process has a code path
from init to finalize that does not develop any memory errors or other runtime errors. However as soon as
one process reaches the finalize call in the conditional it will stop, and all other processes will be waiting
at the barrier.

Figure 12.1 shows the main display of the Allinea DDT debugger (http://www.allinea.com/products/
ddt) at the point where this code stops. Above the source panel you see that there are 16 processes, and
that the status is given for process 1. In the bottom display you see that out of 16 processes 15 are calling
MPI_Barrier on line 19, while one is at line 18. In the right display you see a listing of the local variables:
the value specific to process 1. A rudimentary graph displays the values over the processors: the value of
ntids is constant, that of mytid is linearly increasing, and it is constant except for one process.
Exercise 12.1. Make and run ring_1a. The program does not terminate and does not crash. In
the debugger you can interrupt the execution, and see that all processes are executing a
receive statement. This is probably a case of deadlock. Diagnose and fix the error.
Exercise 12.2. The author of ring_1c was very confused about how MPI works. Run the pro-
gram. While it terminates without a problem, the output is wrong. Set a breakpoint at
the send and receive statements to figure out what is happening.

12.2 MPI debugging with gdb

You can not run parallel programs in gdb, but you can start multiple gdb processes that behave just like
MPI processes! The command
mpirun -np <NP> xterm -e gdb ./program

create a number of xterm windows, each of which execute the commandline gdb ./program. And be-
cause these xterms have been started with mpirun, they actually form a communicator.

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12. Parallel debugging

12.3 Full-screen parallel debugging with DDT

In this tutorial you will run and diagnose a few incorrect MPI programs using DDT. You can start a
session with ddt yourprogram &, or use File > New Session > Run to specify a program name,
and possibly parameters. In both cases you get a dialog where you can specify program parameters. It is
also important to check the following:
• You can specify the number of cores here;
• It is usually a good idea to turn on memory checking;
• Make sure you specify the right MPI.
When DDT opens on your main program, it halts at the MPI_Init statement, and need to press the
forward arrow, top left of the main window.

Problem1 This program has every process independently generate random numbers, and if the number
meets a certain condition, stops execution. There is no problem with this code as such, so let’s suppose
you simply want to monitor its execution.
• Compile abort.c. Don’t forget about the -g -O0 flags; if you use the makefile they are included
automatically.
• Run the program with DDT, you’ll see that it concludes succesfully.
• Set a breakpoint at the Finalize statement in the subroutine, by clicking to the left of the line
number. Now if you run the program you’ll get a message that all processes are stopped at a
breakpoint. Pause the execution.
• The ‘Stacks’ tab will tell you that all processes are the same point in the code, but they are not in
fact in the same iteration.
• You can for instance use the ‘Input/Output’ tabs to see what every process has been doing.
• Alternatively, use the variables pane on the right to examine the it variable. You can do that
for individual processes, but you can also control click on the it variable and choose View as
Array. Set up the display as a one-dimensional array and check the iteration numbers.
• Activate the barrier statement and rerun the code. Make sure you have no breakpoints. Reason
that the code will not complete, but just hang.
• Hit the general Pause button. Now what difference do you see in the ‘Stacks’ tab?

Problem2 Compile problem1.c and run it in DDT. You’ll get a dialog warning about an error condition.
• Pause the program in the dialog. Notice that only the root process is paused. If you want to inspect
other processes, press the general pause button. Do this.
• In the bottom panel click on Stacks. This gives you the ‘call stack’, which tells you what the
processes were doing when you paused them. Where is the root process in the execution? Where
are the others?
• From the call stack it is clear what the error was. Fix it and rerun with File > Restart Session.

Problem2

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 12.4. Further reading

12.3.1 DDT running modes

DDT can be run several different ways.
1. If you are on a cluster with login nodes, compute nodes, and a batch system, you can run the
DDT Graphical User Interface (GUI) and let it submit a batch job to the queue. The GUI will then
pause until your job starts.
2. If your system does not have the login/compute node distinction, or if you are interactively on
a compute node (such as with the idev command at TACC) you can start the GUI and let it run
your program, bypassing the queue.
3. Using the DDT reverse connect mode you
(a) Start the GUI, telling it to wait for a connection
(b) Submit a batch job, adding an option for the connection.
4. Finally, you can run DDT completely off-line in a batch job, letting it output its result as an HTML
file.

12.4 Further reading

A good tutorial: http://www.dirac.org/linux/gdb/.
Reference manual: http://www.ofb.net/gnu/gdb/gdb_toc.html.

Victor Eijkhout 165

Chapter 13

Language interoperability

Most of the time, a program is written is written in a single language, but in some circumstances it is
necessary or desirable to mix sources in more than one language for a single executable. One such case
is when a library is written in one language, but used by a program in another. In such a case, the library
writer will probably have made it easy for you to use the library; this section is for the case that you find
yourself in the place of the library writer. We will focus on the common case of interoperability between
C/C++ and Fortran or Python.
This issue is complicated by the fact that both languages have been around for a long time, and various
recent language standards have introduced mechanisms to facilitate interoperability. However, there is
still a lot of old code around, and not all compilers support the latest standards. Therefore, we discuss
both the old and the new solutions.

13.1 C/Fortran interoperability

13.1.1 Linker conventions
As explained above, a compiler turns a source file into a binary, which no longer has any trace of the
source language: it contains in effect functions in machine language. The linker will then match up calls
and definitions, which can be in different files. The problem with using multiple languages is then that
compilers have different notions of how to translate function names from the source file to the binary file.
Let’s look at codes (you can find example files in tutorials/linking):
// C:
void foo() {
return;
}
! Fortran
Subroutine foo()
Return
End Subroutine

166
 13.1. C/Fortran interoperability

After compilation you can use nm to investigate the binary object file:
%% nm fprog.o
0000000000000000 T _foo_
....
%% nm cprog.o
0000000000000000 T _foo
....

You see that internally the foo routine has different names: the Fortran name has an underscore appended.
This makes it hard to call a Fortran routine from C, or vice versa. The possible name mismatches are:
• The Fortran compiler appends an underscore. This is the most common case.
• Sometimes it can append two underscores.
• Typically the routine name is lowercase in the object file, but uppercase is a possibility too.
Since C is a popular language to write libraries in, this means that the problem is often solved in the C
library by:
• Appending an underscore to all C function names; or
• Including a simple wrapper call:
int SomeCFunction(int i,float f)
{
// this is the actual function
}
int SomeCFunction_(int i,float f)
{
return SomeCFunction(i,f);
}

13.1.2 Complex numbers

The complex data types in C/C++ and Fortran are compatible with each other. Here is an example of a C++
program linking to Lapack’s complex vector scaling routine zscal.
// zscale.cxx
extern "C" {
void zscal_(int*,double complex*,double complex*,int*);
}
complex double *xarray,*yarray, scale=2.;
xarray = new double complex[n]; yarray = new double complex[n];
zscal_(&n,&scale,xarray,&ione);

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13. Language interoperability

13.1.3 C bindings in Fortran 2003

With the latest Fortran standard there are explicit C bindings, making it possible to declare the external
name of variables and routines:
module operator
real, bind(C) :: x
contains
subroutine s() bind(C,name='s')
return
end subroutine
end module

%% ifort -c fbind.F90
%% nm fbind.o
.... T _s
.... C _x

It is also possible to declare data types to be C-compatible:

Program fdata

use iso_c_binding

type, bind(C) :: c_comp

real (c_float) :: data
integer (c_int) :: i
type (c_ptr) :: ptr
end type

end Program fdata

The latest version of Fortran, unsupported by many compilers at this time, has mechanisms for interfacing
to C.
• There is a module that contains named kinds, so that one can declare
INTEGER,KIND(C_SHORT) :: i

• Fortran pointers are more complicated objects, so passing them to C is hard; Fortran2003 has a
mechanism to deal with C pointers, which are just addresses.
• Fortran derived types can be made compatible with C structures.

13.2 C/C++ linking

Libraries written in C++ offer further problems. The C++ compiler makes external symbols by combining
the names a class and its methods, in a process known as name mangling.

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 13.2. C/C++ linking

13.2.1 Mangling and demangling

Consider a simple C program:
#include <stdlib.h>
#include <stdio.h>
void bar(char *s) {
printf("%s",s);
return;
}

If you compile this and inspect the output with nm you get:
$ gcc -c foochar.c && nm foochar.o | grep bar
0000000000000000 T _bar

That is, apart from a leading underscore the symbol name is clear.
On the other hand, the identical program compiled as C++ gives
$ g++ -c foochar.c && nm foochar.o | grep bar
0000000000000000 T __Z3barPc

Why is this? Well, because of polymorphism, and the fact that methods can be included in classes, you can
not have a unique linker symbol for each function name. Instead this mangled symbol includes enough
information to make the symbol unique.
You can retrieve the meaning of this mangled symbol a number of ways. First of all, there is a demangling
utility c++filt:
c++filt __Z3barPc
bar(char*)

But maybe easier is to use the -C flag on nm

$ g++ -c foochar.c && nm -C foochar.o | grep bar
0000000000000000 T bar(char*)

13.2.2 Extern naming

You can force the compiler to generate names that are intelligible to other languages by
#ifdef __cplusplus
extern"C" {
#endif
.
.
place declarations here

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13. Language interoperability

.
.
#ifdef __cplusplus
}
#endif

You again get the same linker symbols as for C, so that the routine can be called from both C and Fortran.
If your main program is in C, you can use the C++ compiler as linker. If the main program is in Fortran,
you need to use the Fortran compiler as linker. It is then necessary to link in extra libraries for the C++
system routines. For instance, with the Intel compiler -lstdc++ -lc needs to be added to the link line.
The use of extern is also needed if you link other languages to a C++ main program. For instance, a
Fortran subprogram foo should be declared as
extern "C" {
void foo_();
}

In that case, you again use the C++ compiler as linker.

13.3 Strings
Programming languages differ widely in how they handle strings.
• In C, a string is an array of characters; the end of the string is indicated by a null character, that
is the ascii character zero, which has an all zero bit pattern. This is called null termination.
• In Fortran, a string is an array of characters. The length is maintained in a internal variable, which
is passed as a hidden parameter to subroutines.
• In Pascal, a string is an array with an integer denoting the length in the first position. Since only
one byte is used for this, strings can not be longer than 255 characters in Pascal.
As you can see, passing strings between different languages is fraught with peril. This situation is made
even worse by the fact that passing strings as subroutine arguments is not standard.
Example: the main program in Fortran passes a string
Program Fstring
character(len=5) :: word = "Word"
call cstring(word)
end Program Fstring

and the C routine accepts a character string and its length:

#include <stdlib.h>
#include <stdio.h>

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 13.4. Subprogram arguments

void cstring_(char *txt,int txtlen) {

printf("length = %d\n",txtlen);
printf("<<");
for (int i=0; i<txtlen; i++)
printf("%c",txt[i]);
printf(">>\n");
}

which produces:
length = 5
<<Word >>

To pass a Fortran string to a C program you need to append a null character:

call cfunction ('A string'//CHAR(0))

Some compilers support extensions to facilitate this, for instance writing

DATA forstring /'This is a null-terminated string.'C/

Recently, the ‘C/Fortran interoperability standard’ has provided a systematic solution to this.

13.4 Subprogram arguments

In C, you pass a float argument to a function if the function needs its value, and float* if the function
has to modify the value of the variable in the calling environment. Fortran has no such distinction: every
variable is passed by reference. This has some strange consequences: if you pass a literal value 37 to a
subroutine, the compiler will allocate a nameless variable with that value, and pass the address of it,
rather than the value1 .
For interfacing Fortran and C routines, this means that a Fortran routine looks to a C program like all its
argument are ‘star’ arguments. Conversely, if you want a C subprogram to be callable from Fortran, all
its arguments have to be star-this or that. This means on the one hand that you will sometimes pass a
variable by reference that you would like to pass by value.
Worse, it means that C subprograms like
void mysub(int **iarray) {
*iarray = (int*)malloc(8*sizeof(int));
return;
}

can not be called from Fortran. There is a hack to get around this (check out the Fortran77 interface to
the Petsc routine VecGetValues) and with more cleverness you can use POINTER variables for this.

1. With a bit of cleverness and the right compiler, you can have a program that says print *,7 and prints 8 because of this.

Victor Eijkhout 171

13. Language interoperability

13.5 Input/output
Both languages have their own system for handling input/output, and it is not really possible to meet in
the middle. Basically, if Fortran routines do I/O, the main program has to be in Fortran. Consequently, it
is best to isolate I/O as much as possible, and use C for I/O in mixed language programming.

13.6 Python calling C code

Because of its efficiency of computing, C is a logical language to use for the lowest layers of a program.
On the other hand, because of its expressiveness, Python is a good candidate for the top layers. It is then a
logical thought to want to call C routines from a python program. This is possible using the python ctypes
module.
1. You write your C code, and compile it to a dynamic library as indicated above;
2. The python code loads the library dynamically, for instance for libc:
path_libc = ctypes.util.find_library("c")
libc = ctypes.CDLL(path_libc)
libc.printf(b"%s\n", b"Using the C printf function from Python ... ")

3. You need to declare what the types are of the C routines in python:
test_add = mylib.test_add
test_add.argtypes = [ctypes.c_float, ctypes.c_float]
test_add.restype = ctypes.c_float
test_passing_array = mylib.test_passing_array
test_passing_array.argtypes = [ctypes.POINTER(ctypes.c_int), ctypes.c_int]
test_passing_array.restype = None

4. Scalars can be passed simply; arrays need to be constructed:

data = (ctypes.c_int * Nelements)(*[x for x in range(numel)])

13.6.1 Boost
Another way to let C and python interact is through the Boost library.
Let’s start with a C/C++ file that was written for some other purpose, and with no knowledge of Python
or interoperability tools:
char const* greet()
{
return "hello, world";
}

With it, you should have a .h header file with the function signatures.
Next, you write a C++ file that uses the Boost tools:

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 13.6. Python calling C code

#include <boost/python.hpp>

#include "hello.h"

BOOST_PYTHON_MODULE(hello_ext)
{
using namespace boost::python;
def("greet", greet);
}

The crucial step is compiling both C/C++ files together into a dynamic library:
icpc -shared -o hello_ext.so hello_ext.o hello.o \
-Wl,-rpath,/pythonboost/lib -L/pythonboost/lib -lboost_python39 \
-Wl,-rpath,/python/lib -L/python/lib -lpython3

You can now import this library in python, giving you access to the C function:
import hello_ext
print(hello_ext.greet())

Victor Eijkhout 173

Chapter 14

Bit operations

In most of this book we consider numbers, such as integer or floating point representations of real num-
bers, as our lowest building blocks. Sometimes, however, it is necessary to dig deeper and consider the
actual representation of such numbers in terms of bits.
Various programming languages have support for bit operations. We will explore the various options. For
details on C++ and Fortran, see Introduction to Scientific Programming book, section 5.2.1 and Introduction
to Scientific Programming book, section 30.7 respectively.

14.1 Construction and display

14.1.1 C/C++
The built-in possibilities for display are limited:
printf("Octal: %o",i);
printf("Hex : %x",i);

gives octal and hexadecimal representation, but there is no format specifier for binary. Instead use the
following bit of magic:
void printBits(size_t const size, void const * const ptr)
{
unsigned char *b = (unsigned char*) ptr;
unsigned char byte;
for (int i=size-1; i>=0; i--) {
for (int j=7; j>=0; j--) {
byte = (b[i] >> j) & 1;
printf("%u", byte);
}
}
}
/* ... */
printBits(sizeof(i),&i);

174
 14.2. Bit operations

14.1.2 Python
• The python int function converts a string to int. A second argument can indicate what base the
string is to be interpreted in:
five = int('101',2)
maxint32 = int('0xffffffff',16)

• Function bin hex convert an int to a string in base 2,8,16 respectively.

• Since python integers can be of unlimited length, there is a function to determine the bit length
(Python version 3.1): i.bit_length().

14.2 Bit operations

Boolean operations are usually applied to the boolean datatype of the programming language. Some lan-
guages allow you to apply them to actual bits.

boolean bitwise (C) bitwise (Py)

and && & &
or || | |
not ! ~
xor ^

Additionally, there are operations on the bit string as such:

left shift <<

right shift >>
Exercise 14.1. Use bit operations to test whether a number is odd or even.
The shift operations are sometimes used as an efficient shorthand for arithmetic. For instance, a left shift
by one position corresponds to a multiplication by two.
Exercise 14.2. Given an integer 𝑛, find the largest multiple of 8 that is ≤ 𝑛.
This mechanism is sometimes used to allocate aligned memory. Write a routine
aligned_malloc( int Nbytes, int aligned_bits );

that allocates Nbytes of memory, where the first byte has an address that is a multiple
of aligned_bits.

Victor Eijkhout 175

Chapter 15

LaTeX for scientific documentation

15.1 The idea behind LATEX, some history of TEX

TEX is a typesetting system that dates back to the late 1970s. In those days, graphics terminals where you
could design a document layout and immediately view it, the way you can with for instance Microsoft
Word, were rare. Instead, TEX uses a two-step workflow, where you first type in your document with
formatting instructions in an ascii document, using your favorite text editor. Next, you would invoke the
latex program, as a sort of compiler, to translate this document to a form that can be printed or viewed.
%% edit mydocument.tex
%% latex mydocument
%% # print or view the resulting output

The process is comparable to making web pages by typing HTML commands.

This way of working may seem clumsy, but it has some advantages. For instance, the TEX input files are
plain ascii, so they can be generated automatically, for instance from a database. Also, you can edit them
with whatever your favorite editor happens to be.
Another point in favor of TEX is the fact that the layout is specified by commands that are written in a
sort of programming language. This has some important consequences:
• Separation of concerns: when you are writing your document, you do not have to think about
layout. You give the ‘chapter’ command, and the implementation of that command will be decided
independently, for instance by you choosing a document style.
• Changing the layout of a finished document is then done by choosing a different realization of
the layout commands in the input file: the same ‘chapter’ command is used, but by choosing a
different style the resulting layout is different. This sort of change can be as simple as a one-line
change to the document style declaration.
• If you have unusual typesetting needs, it is possible to write new TEX commands for this. For
many needs such extensions have in fact already been written; see section 15.4.
The commands in TEX are fairly low level. For this reason, a number of people have written systems
on top of TEX that offer powerful features, such as automatic cross-referencing, or generation of a table
of contents. The most popular of these systems is LATEX. Since TEX is an interpreted system, all of its
mechanisms are still available to the user, even though LATEX is loaded on top of it.

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 15.2. A gentle introduction to LaTeX

15.1.1 Installing LATEX

The easiest way to install LATEX on your system is by downloading the TEXlive distribution from http:
//tug.org/texlive. Apple users can also use fink or macports. Various front-ends to TEX exist, such
as TEXshop on the Mac.

15.1.2 Running LATEX

Purpose. In this section you will run the LATEX compiler

Originally, the latex compiler would output a device independent file format, named dvi, which could
then be translated to PostScript or PDF, or directly printed. These days, many people use the pdflatex
program which directly translates .tex files to .pdf files. This has the big advantage that the generated
PDF files have automatic cross linking and a side panel with table of contents. An illustration is found
below.
Let us do a simple example.

\documentclass{article}
\begin{document}
Hello world!
\end{document}

Figure 15.1: A minimal LATEX document.

Exercise 15.1. Create a text file minimal.tex with the content as in figure 15.1. Try the com-
mand pdflatex minimal or latex minimal. Did you get a file minimal.pdf in the
first case or minimal.dvi in the second case? Use a pdf viewer, such as Adobe Reader,
or dvips respectively to view the output.
Things to watch out for. If you make a typo, TEX can be somewhat unfriendly. If you get
an error message and TEX is asking for input, typing x usually gets you out, or Ctrl-C.
Some systems allow you to type e to go directly into the editor to correct the typo.

15.2 A gentle introduction to LaTeX

Here you will get a very brief run-through of LATEX features. There are various more in-depth tutorials
available, such as the one by Oetiker [18].

15.2.1 Document structure

Each LATEX document needs the following lines:

Victor Eijkhout 177

15. LaTeX for scientific documentation

\documentclass{ .... } % the dots will be replaced

\begin{document}

\end{document}

The ‘documentclass’ line needs a class name in between the braces; typical values are ‘article’ or ‘book’.
Some organizations have their own styles, for instance ‘ieeeproc’ is for proceedings of the IEEE.
All document text goes between the \begin{document} and \end{document} lines. (Matched ‘begin’
and ‘end’ lines are said to denote an ‘environment’, in this case the document environment.)
The part before \begin{document} is called the ‘preamble’. It contains customizations for this particular
document. For instance, a command to make the whole document double spaced would go in the preamble.
If you are using pdflatex to format your document, you want a line
\usepackage{hyperref}

here.
Have you noticed the following?
• The backslash character is special: it starts a LATEX command.
• The braces are also special: they have various functions, such as indicating the argument of a
command.
• The percent character indicates that everything to the end of the line is a comment.

15.2.2 Some simple text

Purpose. In this section you will learn some basics of text formatting.

Exercise 15.2. Create a file first.tex with the content of figure 15.1 in it. Type some text in
the preamble, that is, before the \begin{document} line and run pdflatex on your file.
Intended outcome. You should get an error message because you are not allowed to
have text in the preamble. Only commands are allowed there; all text has to go after
\begin{document}.
Exercise 15.3. Edit your document: put some text in between the \begin{document} and
\end{document} lines. Let your text have both some long lines that go on for a while,
and some short ones. Put superfluous spaces between words, and at the beginning or end
of lines. Run pdflatex on your document and view the output.
Intended outcome. You notice that the white space in your input has been collapsed in
the output. TEX has its own notions about what space should look like, and you do not
have to concern yourself with this matter.
Exercise 15.4. Edit your document again, cutting and pasting the paragraph, but leaving a blank
line between the two copies. Paste it a third time, leaving several blank lines. Format, and
view the output.

178 HPC Carpentry

 15.2. A gentle introduction to LaTeX

Intended outcome. TEX interprets one or more blank lines as the separation between
paragraphs.
Exercise 15.5. Add \usepackage{pslatex} to the preamble and rerun pdflatex on your
document. What changed in the output?
Intended outcome. This should have the effect of changing the typeface from the default
to Times Roman.
Things to watch out for. Typefaces are notoriously unstandardized. Attempts to use dif-
ferent typefaces may or may not work. Little can be said about this in general.
Add the following line before the first paragraph:
\section{This is a section}

and a similar line before the second. Format. You see that LATEX automatically numbers the sections, and
that it handles indentation different for the first paragraph after a heading.
Exercise 15.6. Replace article by artikel3 in the documentclass declaration line and refor-
mat your document. What changed?
Intended outcome. There are many documentclasses that implement the same commands
as article (or another standard style), but that have their own layout. Your document
should format without any problem, but get a better looking layout.
Things to watch out for. The artikel3 class is part of most distributions these days,
but you can get an error message about an unknown documentclass if it is missing or
if your environment is not set up correctly. This depends on your installation. If the file
seems missing, download the files from http://tug.org/texmf-dist/tex/latex/
ntgclass/ and put them in your current directory; see also section 15.2.9.

15.2.3 Math
Purpose. In this section you will learn the basics of math typesetting

One of the goals of the original TEX system was to facilitate the setting of mathematics. There are two
ways to have math in your document:
• Inline math is part of a paragraph, and is delimited by dollar signs.
• Display math is, as the name implies, displayed by itself.
Exercise 15.7. Put $x+y$ somewhere in a paragraph and format your document. Put \[x+y\]
somewhere in a paragraph and format.
Intended outcome. Formulas between single dollars are included in the paragraph where
you declare them. Formulas between \[...\] are typeset in a display.
For display equations with a number, use an equation environment. Try this.
Here are some common things to do in math. Make sure to try them out.
• Subscripts and superscripts: $x_i^2$. If the sub or superscript is more than a single symbol, it
needs to be grouped: $x_{i+1}^{2n}$. If you need a brace in a formula, use $\{ \}$.

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15. LaTeX for scientific documentation

• Greek letters and other symbols: $\alpha\otimes\beta_i$.

• Combinations of all these $\int_{t=0}^\infty tdt$.
Exercise 15.8. Take the last example and typeset it as display math. Do you see a difference
with inline math?
Intended outcome. TEX tries not to include the distance between text lines, even if there is
math in a paragraph. For this reason it typesets the bounds on an integral sign differently
from display math.

15.2.4 Referencing
Purpose. In this section you will see TEX’s cross referencing mechanism in action.

So far you have not seen LATEX do much that would save you any work. The cross referencing mechanism
of LATEX will definitely save you work: any counter that LATEX inserts (such as section numbers) can be
referenced by a label. As a result, the reference will always be correct.
Start with an example document that has at least two section headings. After your first section heading,
put the command \label{sec:first}, and put \label{sec:other} after the second section heading.
These label commands can go on the same line as the section command, or on the next. Now put
As we will see in section~\ref{sec:other}.

in the paragraph before the second section. (The tilde character denotes a non-breaking space.)
Exercise 15.9. Make these edits and format the document. Do you see the warning about an
undefined reference? Take a look at the output file. Format the document again, and
check the output again. Do you have any new files in your directory?
Intended outcome. On a first pass through a document, the TEX compiler will gather all
labels with their values in a .aux file. The document will display a double question mark
for any references that are unknown. In the second pass the correct values will be filled
in.
Things to watch out for. If after the second pass there are still undefined references, you
probably made a typo. If you use the bibtex utility for literature references, you will
regularly need three passes to get all references resolved correctly.
Above you saw that the equation environment gives displayed math with an equation number. You can
add a label to this environment to refer to the equation number.
Exercise 15.10. Write a formula in an equation environment, and add a label. Refer to this
label anywhere in the text. Format (twice) and check the output.
Intended outcome. The \label and \ref command are used in the same way for formulas
as for section numbers. Note that you must use \begin/end{equation} rather than
\[...\] for the formula.

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 15.2. A gentle introduction to LaTeX

15.2.5 Lists
Purpose. In this section you will see the basics of lists.

Bulleted and numbered lists are provided through an environment.

\begin{itemize}
\item This is an item;
\item this is one too.
\end{itemize}
\begin{enumerate}
\item This item is numbered;
\item this one is two.
\end{enumerate}

Exercise 15.11. Add some lists to your document, including nested lists. Inspect the output.
Intended outcome. Nested lists will be indented further and the labeling and numbering
style changes with the list depth.
Exercise 15.12. Add a label to an item in an enumerate list and refer to it.
Intended outcome. Again, the \label and \ref commands work as before.

15.2.6 Source code and algorithms

As a computer scientist, you will often want to include algorithms in your writings; sometimes even source
code.
In this tutorial so far you have seen that some characters have special meaning to LATEX, and just can not
just type them and expect them to show up in the output. Since funny characters appear quite regularly
in programming languages, we need a tool for this: the verbatim mode.
To display bits of code inside a paragraph, you use the \verb command. This command delimits its ar-
gument with two identical characters that can not appear in the verbatim text. For instance, the output
if (x%5>0) { ... } is produced by \verb+if (x%5>0) { ... }+. (Exercise: how did the author of
this book get that verbatim command in the text?)
For longer stretches of verbatim text, that need to be displayed by themselves you use
\begin{verbatim}
stuff
\end{verbatim}
Finally, in order to include a whole file as verbatim listing, use .
Verbatim text is one way of displaying algorithms, but there are more elegant solutions. For instance, in
this book the following is used:
\usepackage[algo2e,noline,noend]{algorithm2e}

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15. LaTeX for scientific documentation

15.2.7 Graphics
Since you can not immediately see the output of what you are typing, sometimes the output may come
as a surprise. That is especially so with graphics. LATEX has no standard way of dealing with graphics, but
the following is a common set of commands:
\usepackage{graphicx} % this line in the preamble

\includegraphics{myfigure} % in the body of the document

The figure can be in any of a number of formats, except that PostScript figures (with extension .ps or
.eps) can not be used if you use pdflatex.
Since your figure is often not the right size, the include line will usually have something like:
\includegraphics[scale=.5]{myfigure}

A bigger problem is that figures can be too big to fit on the page if they are placed where you declare them.
For this reason, they are usually treated as ‘floating material’. Here is a typical declaration of a figure:
\begin{figure}[ht]
\includegraphics{myfigure}
\caption{This is a figure.}
\label{fig:first}
\end{figure}

It contains the following elements:

• The figure environment is for ‘floating’ figures; they can be placed right at the location where
they are declared, at the top or bottom of the next page, at the end of the chapter, et cetera.
• The [ht] argument of the \begin{figure} line states that your figure should be attempted to
be placed here; it that does not work, it should go top of the next page. The remaining possible
specifications are b for placement at the bottom of a page, or p for placement on a page by itself.
For example
\begin{figure}[hbp]

declares that the figure has to be placed here if possible, at the bottom of the page if that’s not
possible, and on a page of its own if it is too big to fit on a page with text.
• A caption to be put under the figure, including a figure number;
• A label so that you can refer to the figure number by its label: figure~\ref{fig:first}.
• And of course the figure material. There are various ways to fine-tune the figure placement. For
instance
\begin{center}
\includegraphics{myfigure}
\end{center}

gives a centered figure.

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 15.3. A worked out example

15.2.8 Bibliography references

The mechanism for citing papers and books in your document is a bit like that for cross referencing. There
are labels involved, and there is a \cite{thatbook} command that inserts a reference, usually numeric.
However, since you are likely to refer to a paper or book in more than one document your write, LATEX
allows you to have a database of literature references in a file by itself, rather than somewhere in your
document.
Make a file mybibliography.bib with the following content:
@article{JoeDoe1985,
author = {Joe Doe},
title = {A framework for bibliography references},
journal = {American Library Assoc. Mag.},
year = {1985}
}

In your document mydocument.tex, put

For details, refer to Doe~\cite{JoeDoe1985} % somewhere in the text

\bibliography{mybibliography} % at the end of the document

\bibliographystyle{plain}

Format your document, then type on the commandline

bibtex mydocument

and format your document two more times. There should now be a bibliography in it, and a correct
citation. You will also see that files mydocument.bbl and mydocument.blg have been created.

15.2.9 Environment variables

On Unix systems, TEX investigates the TEXINPUTS environment variable when it tries to find an include
file. Consequently, you can create a directory for your styles and other downloaded include files, and set
this variable to the location of that directory. Similarly, the BIBINPUTS variable indicates the location of
bibliography files for bibtex (section 15.2.8).

15.3 A worked out example

The following example demo.tex contains many of the elements discussed above.

You also need the file math.bib:

Victor Eijkhout 183

15. LaTeX for scientific documentation

The following sequence of commands

pdflatex demo
bibtex demo
pdflatex demo
pdflatex demo

gives the output of figures 15.2, 15.3.

15.3.1 Listings
The ‘listings’ package is makes it possible to have source code included, with coloring and indentation
automatically taken care of.

\documentclass{article} MPI_Recv,MPI_Irecv,MPI_Mrecv,
MPI_Sendrecv,MPI_Sendrecv_replace,
\usepackage[pdftex]{hyperref} },emphstyle={\color{red!70!black}\bfseries
\usepackage{pslatex} }
}
\lstset{emph={[2] %% constants
%%%% MPI_COMM_WORLD,MPI_STATUS_IGNORE,
%%%% Import the listings package MPI_STATUSES_IGNORE,MPI_STATUS_SIZE,
%%%% MPI_INT,MPI_INTEGER,
\usepackage{listings,xcolor} },emphstyle={[2]\color{green!40!black}}
}
%%%% \lstset{emph={[3] %% types
%%%% Set a basic code style MPI_Aint,MPI_Comm,MPI_Count,MPI_Datatype
%%%% (see documentation for more options} ,MPI_Errhandler,MPI_File,MPI_Group,
%%%% },emphstyle={[3]\color{yellow!30!brown}\
\lstdefinestyle{reviewcode}{ bfseries},
belowcaptionskip=1\baselineskip, }
breaklines=true, frame=L,
xleftmargin=\parindent, showstringspaces= \begin{document}
false, \title{SSC 335: listings demo}
basicstyle=\footnotesize\ttfamily, \author{Victor Eijkhout}
keywordstyle=\bfseries\color{blue}, \date{today}
commentstyle=\color{red!60!black}, \maketitle
identifierstyle=\slshape\color{black},
stringstyle=\color{green!60!black}, \section{C examples}
columns=fullflexible,
keepspaces=true,tabsize=8, \lstset{language=C}
} \begin{lstlisting}
\lstset{style=reviewcode} int main() {
MPI_Init();
\lstset{emph={ %% MPI commands MPI_Comm comm = MPI_COMM_WORLD;
MPI_Init,MPI_Initialized,MPI_Finalize, if (x==y)
MPI_Finalized,MPI_Abort, MPI_Send( &x,1,MPI_INT,0,0,comm);
MPI_Comm_size,MPI_Comm_rank, else
MPI_Send,MPI_Isend,MPI_Rsend,MPI_Irsend, MPI_Recv( &y,1,MPI_INT,1,1,comm,
MPI_Ssend,MPI_Issend, MPI_STATUS_IGNORE);
MPI_Finalize();

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 15.3. A worked out example

SSC 335: demo

Victor Eijkhout

today

1 This is a section
This is a test document, used in [2]. It contains a discussion in section 2.
Exercise 1. Left to the reader.
Exercise 2. Also left to the reader, just like in exercise 1

Theorem 1 This is cool.

This is a formula: a ⇐ b.
(k)
xi ← yi j · x j (1)
R1√
Text: 0 x dx
Z 1
√
x dx
0

2 This is another section

one value
another values

Table 1: This is the only table in my demo

Figure 1: this is the only figure

As I showed in the introductory section 1, in the paper [1], it was shown that equation (1)
• There is an item.

Victor Eijkhout 185

Figure 15.2: First page of LATEX demo output

15. LaTeX for scientific documentation

• There is another item

– sub one
– sub two
1. item one
2. item two
(a) sub one
(b) sub two

Contents
1 This is a section 1
2 This is another section 1

List of Figures
1 this is the only figure 1

References
[1] Loyce M. Adams and Harry F. Jordan. Is SOR color-blind? SIAM J. Sci. Stat. Comput.,
7:490–506, 1986.
[2] Victor Eijkhout. Short LATEX demo. SSC 335, oct 1, 2008.

186 HPC Carpentry

Figure 15.3: First page of LATEX demo output

 15.3. A worked out example

} call MPI_Send( x,1,MPI_INTEGER,0,0,comm)

\end{lstlisting} ;
else
\section{Fortran examples} call MPI_Recv( y,1,MPI_INTEGER,1,1,comm,
MPI_STATUS_IGNORE)
\lstset{language=Fortran} end if
\begin{lstlisting} call MPI_Finalize()
Program myprogram End Program myprogram
Type(MPI_Comm) :: comm = MPI_COMM_WORLD \end{lstlisting}
call MPI_Init()
if (.not. x==y ) then \end{document}

See the output in figure 15.4.

15.3.2 Native graphing

You have seen how to include graphics files, but it is also possible to let LATEX do the drawing. For this,
there is the tikz package. Here we show another package pgfplots that uses tikz to draw numerical plots.

\documentclass{artikel3} symbolic x coords={Tom, Jack, Hary,

Liza, Henry},
\usepackage[pdftex]{hyperref} xtick=data,
\usepackage{pslatex} nodes near coords,
nodes near coords align={vertical},
\usepackage{wrapfig} ]
\usepackage{pgfplots} \addplot coordinates {(Tom,50) (Jack
\pgfplotsset{width=6.6cm,compat=1.7} ,90) (Hary,70) (Liza,80) (Henry,60) };
\end{axis}
\usepackage{geometry} \end{tikzpicture}
\addtolength{\textwidth}{.75in} \end{wrapfigure}
\addtolength{\textheight}{.75in} Lorem ipsum dolor sit amet, consectetur
adipiscing elit, sed do eiusmod tempor
\begin{document} incididunt ut labore et dolore magna
\title{SSC 335: barchart demo} aliqua. Pharetra massa massa ultricies
\author{Victor Eijkhout} mi quis hendrerit. Tempor nec feugiat
\date{today} nisl pretium fusce id velit ut tortor.
\maketitle Eget nulla facilisi etiam dignissim diam
quis enim. Cursus sit amet dictum sit
\section{Two graphs} amet justo donec. Tortor consequat id
porta nibh venenatis cras sed felis eget
\begin{wrapfigure}{l}{2in} . Senectus et netus et malesuada fames
\hrule width 3in height 0pt ac turpis egestas integer. Ultricies mi
\begin{tikzpicture} quis hendrerit dolor magna eget est. A
\begin{axis} iaculis at erat pellentesque adipiscing.
[ Sagittis orci a scelerisque purus.
ybar, Quisque non tellus orci ac. Nisl nunc mi
enlargelimits=0.15, ipsum faucibus. Vivamus at augue eget
ylabel={\#Average Marks}, arcu dictum varius duis. Maecenas
xlabel={\ Students Name}, ultricies mi eget mauris pharetra et
ultrices neque ornare. Pulvinar neque

Victor Eijkhout 187

15. LaTeX for scientific documentation

laoreet suspendisse interdum consectetur \addplot coordinates {(2016, 70)

. Nunc id cursus metus aliquam eleifend (2017, 63) (2018, 68)};
mi. Tristique sollicitudin nibh sit amet \addplot coordinates {(2016, 61)
commodo nulla. Massa tincidunt nunc (2017, 55) (2018, 59)};
pulvinar sapien et ligula ullamcorper \legend{Wheat, Tea, Rice}
malesuada. Justo laoreet sit amet cursus \end{axis}
sit. Laoreet id donec ultrices \end{tikzpicture}
tincidunt arcu non sodales. \end{wrapfigure}
Sem nulla pharetra diam sit amet. Vel
\begin{wrapfigure}{r}{2in} pharetra vel turpis nunc eget. Vulputate
\hrule width 3in height 0pt % kludge: dignissim suspendisse in est ante in
picture is not wide enough nibh mauris cursus. Sem viverra aliquet
\begin{tikzpicture} eget sit amet tellus cras. Rhoncus
\begin{axis} aenean vel elit scelerisque mauris
[ pellentesque pulvinar pellentesque.
ybar, Fusce ut placerat orci nulla
enlargelimits=0.15, pellentesque. Vel risus commodo viverra
legend style={at={(0.4,-0.25)}, maecenas accumsan lacus vel facilisis
anchor=north,legend columns=-1}, volutpat. Enim ut tellus elementum
ylabel={\#Annual Growth Percentage}, sagittis vitae et. In nibh mauris cursus
symbolic x coords={2016, 2017, mattis molestie. Curabitur gravida arcu
2018}, ac tortor dignissim convallis aenean et
xtick=data, tortor. Mauris commodo quis imperdiet
nodes near coords, massa.
nodes near coords align={vertical},
] \end{document}
\addplot coordinates {(2016, 75)
(2017, 78) (2018, 80)};

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 15.3. A worked out example

SSC 335: barchart demo

Victor Eijkhout

today

1 Two graphs
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed
do eiusmod tempor incididunt ut labore et dolore magna ali-
90 qua. Pharetra massa massa ultricies mi quis hendrerit. Tempor
nec feugiat nisl pretium fusce id velit ut tortor. Eget nulla fa-
#Average Marks

80
80 cilisi etiam dignissim diam quis enim. Cursus sit amet dictum
70 sit amet justo donec. Tortor consequat id porta nibh venenatis
cras sed felis eget. Senectus et netus et malesuada fames ac
60 turpis egestas integer. Ultricies mi quis hendrerit dolor magna
60 eget est. A iaculis at erat pellentesque adipiscing. Sagittis orci
50 a scelerisque purus. Quisque non tellus orci ac. Nisl nunc
mi ipsum faucibus. Vivamus at augue eget arcu dictum var-
ius duis. Maecenas ultricies mi eget mauris pharetra et ultri-
Tom Jack Hary Liza Henry ces neque ornare. Pulvinar neque laoreet suspendisse inter-
Students Name dum consectetur. Nunc id cursus metus aliquam eleifend mi.
Tristique sollicitudin nibh sit amet commodo nulla. Massa tin-
cidunt nunc pulvinar sapien et ligula ullamcorper malesuada.
Justo laoreet sit amet cursus sit. Laoreet id donec ultrices tincidunt arcu non sodales.
Sem nulla pharetra diam sit amet. Vel pharetra vel turpis nunc
eget. Vulputate dignissim suspendisse in est ante in nibh mau-
#Annual Growth Percentage

ris cursus. Sem viverra aliquet eget sit amet tellus cras. Rhon- 80
80 78
cus aenean vel elit scelerisque mauris pellentesque pulvinar 75
pellentesque. Fusce ut placerat orci nulla pellentesque. Vel
risus commodo viverra maecenas accumsan lacus vel facilisis 70
70 68
volutpat. Enim ut tellus elementum sagittis vitae et. In nibh
mauris cursus mattis molestie. Curabitur gravida arcu ac tor- 63
61
tor dignissim convallis aenean et tortor. Mauris commodo quis 60 59
imperdiet massa. 55

2016 2017 2018

Wheat Tea Rice

Victor Eijkhout 189

15. LaTeX for scientific documentation

15.4 Where to take it from here

This tutorial touched only briefly on some essentials of TEX and LATEX. You can find longer intros on-
line [18], or read a book [12, 11, 16]. Macro packages and other software can be found on the Comprehen-
sive TEX Archive http://www.ctan.org. For questions you can go to the newsgroup comp.text.tex,
but the most common ones can often already be found on web sites [21].

15.5 Review questions

Exercise 15.13. Write a one or two page document about your field of study. Show that you
have mastered the following constructs:
• formulas, including labels and referencing;
• including a figure;
• using bibliography references;
• construction of nested lists.

190 HPC Carpentry

 15.5. Review questions

SSC 335: listings demo

Victor Eijkhout
today

1 C examples
int main() {
MPI_Init();
MPI_Comm comm = MPI_COMM_WORLD;
if (x==y)
MPI_Send( &x,1,MPI_INT,0,0,comm);
else
MPI_Recv( &y,1,MPI_INT,1,1,comm,MPI_STATUS_IGNORE);
MPI_Finalize();
}

2 Fortran examples
Program myprogram
Type(MPI_Comm) :: comm = MPI_COMM_WORLD
call MPI_Init()
if (.not. x==y ) then
call MPI_Send( x,1,MPI_INTEGER,0,0,comm);
else
call MPI_Recv( y,1,MPI_INTEGER,1,1,comm,MPI_STATUS_IGNORE)
end if
call MPI_Finalize()
End Program myprogram

Victor Eijkhout Figure 15.4: Output of the listings demo 191

Chapter 16

Profiling and benchmarking

Much of the teaching in this book is geared towards enabling you to write fast code, whether this is
through the choice of the right method, or through optimal coding of a method. Consequently, you some-
times want to measure just how fast your code is. If you have a simulation that runs for many hours, you’d
think just looking on the clock would be enough measurement. However, as you wonder whether your
code could be faster than it is, you need more detailed measurements. This tutorial will teach you some
ways to measure the behavior of your code in more or less detail.
Here we will discuss
• timers: ways of measuring the execution time (and sometimes other measurements) of a particular
piece of code, and
• profiling tools: ways of measuring how much time each piece of code, typically a subroutine,
takes during a specific run.

16.1 Timers
There are various ways of timing your code, but mostly they come down to calling a timer routine twice
that tells you the clock values:
tstart = clockticks()
....
tend = clockticks()
runtime = (tend-tstart)/ticks_per_sec

Many systems have their own timers:

• MPI see section Parallel Programming book, section 15.6.1;
• OpenMP see section Parallel Programming book, section 28.2;
• PETSc see section Parallel Programming book, section 38.4.

192
 16.1. Timers

16.1.1 Fortran
For instance, in Fortran there is the system_clock routine:
implicit none
INTEGER :: rate, tstart, tstop
REAL :: time
real :: a
integer :: i

CALL SYSTEM_CLOCK(COUNT_RATE = rate)

if (rate==0) then
print *,"No clock available"
stop
else
print *,"Clock frequency:",rate
end if
CALL SYSTEM_CLOCK(COUNT = tstart)
a = 5
do i=1,1000000000
a = sqrt(a)
end do
CALL SYSTEM_CLOCK(COUNT = tstop)
time = REAL( ( tstop - tstart )/ rate )
print *,a,tstart,tstop,time
end

with output
Clock frequency: 10000
1.000000 813802544 813826097 2.000000

16.1.2 C
In C there is the clock function: with output
clock resolution: 1000000
res: 1.000000e+00
start/stop: 0.000000e+00,2.310000e+00
Time: 2.310000e+00

Do you see a difference between the Fortran and C approaches? Hint: what happens in both cases when
the execution time becomes long? At what point do you run into trouble?

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16. Profiling and benchmarking

16.1.3 C++

While C routines are available in C++, there is also a new chrono library that can do many things, including
handling different time formats.
std::chrono::system_clock::time_point start_time;
start_time = std::chrono::system_clock::now();
// ... code ...
auto duration =
std::chrono::system_clock::now()-start_time;
auto millisec_duration =
std::chrono::duration_cast<std::chrono::milliseconds>(duration);
std::cout << "Time in milli seconds: "
<< .001 * millisec_duration.count() << endl;

For more details, see Introduction to Scientific Programming book, section 24.8.

16.1.4 System utilities

There are unix system calls that can be used for timing: getrusage
#include <sys/resource.h>
double time00(void)
{
struct rusage ruse;
getrusage(RUSAGE_SELF, &ruse);
return( (double)(ruse.ru_utime.tv_sec+ruse.ru_utime.tv_usec
/ 1000000.0) );
}

and gettimeofday
#include <sys/time.h>
double time00(void)
{
struct timeval tp;
gettimeofday(&tp, NULL);
return( (double) (tp.tv_sec + tp.tv_usec/1000000.0) ); /* wall
}

These timers have the advantage that they can distinguish between user time and system time, that is,
exclusively timing program execution or giving wallclock time including all system activities.

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 16.2. Accurate counters

16.2 Accurate counters

The timers in the previous section had a resolution of at best a millisecond, which corresponds to several
thousand cycles on a modern CPU. For more accurate counting it is typically necessary to use assembly
language, such as the Intel RDTSC (ReaD Time Stamp Counter) instruction http://developer.intel.
com/drg/pentiumII/appnotes/RDTSCPM1.HTM.
static inline void microtime(unsigned *lo, unsigned *hi)
{
__asm __volatile (
".byte 0x0f; .byte 0x31 # RDTSC instruction
movl %%edx,%0 # High order 32 bits
movl %%eax,%1 # Low order 32 bits"
: "=g" (*hi), "=g" (*lo) :: "eax", "edx");
}

However, this approach of using processor-specific timers is not portable. For this reason, the PAPI pack-
age (http://icl.cs.utk.edu/papi/) provides a uniform interface to hardware counters. You can see
this package in action in the codes in appendix HPC book, section 31.
In addition to timing, hardware counters can give you information about such things as cache misses
and instruction counters. A processor typically has only a limited number of counters, but they can be
assigned to various tasks. Additionally, PAPI has the concept of derived metrics.

16.3 Parallel timers in MPI and OpenMP

Many packages have their own timers. For instance for MPI
double MPI_Wtime(void);
double MPI_Wtick(void);

See Parallel Programming book, section 15.6.1.

For OpenMP
double omp_get_wtime()
double omp_get_wtick()

See Parallel Programming book, section 28.2.

In neither of these packages are the timers likely to be synchronized over the parallel processes or threads.
This means that the timings of one code segment may be widely different on two processes/threads/tasks.
To have a synchronized timer you need to use an explicit barrier:
Barrier();
tstart = Wtime();
Barrier();
duration = Wtime()-tstart;

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16.4 Profiling tools

Profiling tools will give you the time spent in various events in the program, typically functions and
subroutines, or parts of the code that you have declared as such. The tool will then report how many time
the event occurred, total and average time spent, et cetera.
Here we discuss two simple tools:
• gprof, which requires instrumentation, and
• perf, which doesn’t.
• Intel VTune.
The TAU tool, discussed in section 17 for the purposes of tracing, also has profiling capabilities, presented
in a nice graphic way. Finally, we mention that the PETSc library allows you to define your own timers
and events.

16.4.1 gprof
The profiler of the GNU compiler, gprof requires recomplication with an extra flag:
% gcc -g -pg ./srcFile.c -o MyProgram

The program is then run by itself:

% ./MyProgram

and the results are post-processed and displayed:

% gprof ./exeFile gmon.out > profile.txt
% gprof -l ./exeFile gmon.out > profile_line.txt
% gprof -A ./exeFile gmon.out > profile_anotated.txt

16.4.2 perf
Coming with most Unix distributions, perf does not require any instrumentation.
Run:
perf record yourprogram options
perf record --call-graph fp yourprogram options

Post-process and display:

perf report
perf report --demangle ## for C++

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 16.5. Tracing

16.4.3 Intel VTune

The Intel VTune profiler also needs no instrumentation.

vtune -collect hotspots yourprogram options
## result dir something like: r001hs
vtune -report hotspots -r r001hs

16.4.4 MPI profiling

The MPI library has been designed to make it easy to profile. See Parallel Programming book, section 15.6.

16.5 Tracing
In profiling we are only concerned with aggregate information: how many times a routine was called,
and with what total/average/min/max runtime. However sometimes we want to know about the exact
timing of events. This is especially relevant in a parallel context when we care about load unbalance and
idle time.

Tools such as Vampyr can collect trace information about events and in particular messages, and render
them in displays such as figure 16.1.

Figure 16.1: A Vampyr timeline diagram of a parallel process.

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16.6 Parallel timing

Timing parallel operations is fraught with peril, as processes or threads can interact with each other. This
means that you may be measuring the wait time induced by synchronization. Sometimes that is actually
what you want, as in the case of a ping-pong operation; section Parallel Programming book, section 4.1.1.
Other times, this is not what you want. Consider the code
if (procno==0)
do_big_setup();
t = timer();
mpi_some_collective();
duration = timer() - t;

Figure 16.2: Timing a parallel code without and with barrier

Figure 16.2 illustrates this:

• in the naive scenario, processes other than zero start the collective immediately, but process zero
first does the setup;
• all processes presumably finish more or less together.
On the non-zero processes we now get a time measurement, which we intended to be just the collective
operation, that includes the setup time of process zero.
The solution is to put a barrier around the section that you want to time; see again figure 16.2.

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Chapter 17

TAU

The TAU tool [20] (see http://www.cs.uoregon.edu/research/tau/home.php for the official doc-
umentation) uses instrumentation to profile and trace your code. That is, it adds profiling and trace calls
to your code. You can then inspect the output after the run.
Profiling is the gathering and displaying of bulk statistics, for instance showing you which routines take
the most time, or whether communication takes a large portion of your runtime. When you get concerned
about performance, a good profiling tool is indispensible.
Tracing is the construction and displaying of time-dependent information on your program run, for in-
stance showing you if one process lags behind others. For understanding a program’s behaviour, and the
reasons behind profiling statistics, a tracing tool can be very insightful.

17.1 Usage modes

There are two ways to instrument your code:
• You can use dynamic instrumentation, where TAU adds the measurement facility at runtime:
# original commandline:
% mpicxx wave2d.cpp -o wave2d
# with TAU dynamic instrumentation:
% mpirun -np 12 tau_exec ./wave2d 500 500 3 4 5

• You can have the instrumentation added at compile time. For this, you need to let TAU take over
the compilation in some sense.
1. TAU has its own makefiles. The names and locations depend on your installation, but typi-
cally it will be something like
export TAU_MAKEFILE=$TAU_HOME/lib/Makefile.tau-mpi-pdt

2. Now you can invoke the TAU compilers tau_cc,sh, tau_cxx.sh, tau_f90.sh.
When you run your program you need to tell TAU what to do:

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17. TAU

export TAU_TRACE=1
export TAU_PROFILE=1
export TRACEDIR=/some/dir
export PROFILEDIR=/some/dir

In order to generate trace plots you need to convert TAU output:

cd /some/dir # where the trace and profile output went
tau_treemerge.pl
tau2slog2 tau.trc tau.edf -o yourrun.slog2

The slog2 file can be displayed with jumpshot.

17.2 Instrumentation
Unlike such tools as VTune which profile your binary as-is, TAU works by adding instrumentation to your
code: in effect it is a source-to-source translator that takes your code and turns it into one that generates
run-time statistics.
This instrumentation is largely done for you; you mostly need to recompile your code with a script that
does the source-to-source translation, and subsequently compiles that instrumented code. You could for
instance have the following in your makefile:
ifdef TACC_TAU_DIR
CC = tau_cc.sh
else
CC = mpicc
endif

% : %.c
<TAB>${CC} -o $@ $^

If TAU is to be used (which we detect here by checking for the environment variable TACC_TAU_DIR), we
define the CC variable as one of the TAU compilation scripts; otherwise we set it to a regular MPI compiler.
Fortran note. Cpp includes If your source contains
#include "something.h"

directives, add the option

-optPreProcess

to the TAU compiler.

To use TAU on TACC resources, do module load tau.

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 17.3. Running

17.3 Running
You can now run your instrumented code; trace/profile output will be written to file if environment vari-
ables TAU_PROFILE and/or TAU_TRACE are set:
export TAU_PROFILE=1
export TAU_TRACE=1

A TAU run can generate many files: typically at least one per process. It is therefore advisabe to create a
directory for your tracing and profiling information. You declare them to TAU by setting the environment
variables PROFILEDIR and TRACEDIR.
mkdir tau_trace
mkdir tau_profile
export PROFILEDIR=tau_profile
export TRACEDIR=tau_trace

The actual program invocation is then unchanged:

mpirun -np 26 myprogram

TACC note. At TACC, use ibrun without a processor count; the count is derived from the queue submis-
sion parameters.
While this example uses two separate directories, there is no harm in using the same for both.

17.4 Output
The tracing/profiling information is spread over many files, and hard to read as such. Therefore, you need
some further programs to consolidate and display the information.
You view profiling information with paraprof
paraprof tau_profile

Viewing the traces takes a few steps:

cd tau_trace
rm -f tau.trc tau.edf align.trc align.edf
tau_treemerge.pl
tau_timecorrect tau.trc tau.edf align.trc align.edf
tau2slog2 align.trc align.edf -o yourprogram.slog2

If you skip the tau_timecorrect step, you can generate the slog2 file by:
tau2slog2 tau.trc tau.edf -o yourprogram.slog2

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17. TAU

The slog2 file can be viewed with jumpshot:

jumpshot yourprogram.slog2

17.5 Without instrumentation

Event-based sampling on uninstrumented code:
tau_exec -ebs yourprogram

The resulting .trc file can be viewed with paraprof.

17.6 Examples
17.6.1 Bucket brigade
Let’s consider a bucket brigade implementation of a broadcast: each process sends its data to the next
higher rank.
int sendto =
( procno<nprocs-1 ? procno+1 : MPI_PROC_NULL )
;
int recvfrom =
( procno>0 ? procno-1 : MPI_PROC_NULL )
;

MPI_Recv( leftdata,1,MPI_DOUBLE,recvfrom,0,comm,MPI_STATUS_IGNORE);
myvalue = leftdata
MPI_Send( myvalue,1,MPI_DOUBLE,sendto,0,comm);

We implement the bucket brigade with blocking sends and receives: each process waits to receive from
its predecessor, before sending to its successor.
// bucketblock.c
if (procno>0)
MPI_Recv(leftdata, N, MPI_DOUBLE,recvfrom,0, comm, MPI_STATUS_IGNORE);
for (int i=0; i<N; i++)
myvalue[i] = (procno+1)*(procno+1) + leftdata[i];
if (procno<nprocs-1)
MPI_Send(myvalue,N, MPI_DOUBLE,sendto,0, comm);

The TAU trace of this is in figure 17.1, using 4 nodes of 4 ranks each. We see that the processes within
each node are fairly well synchronized, but there is less synchronization between the nodes. However,
the bucket brigade then imposes its own synchronization on the processes because each has to wait for
its predecessor, no matter if it posted the receive operation early.
Next, we introduce pipelining into this operation: each send is broken up into parts, and these parts are
sent and received with non-blocking calls.

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 17.6. Examples

Figure 17.1: Trace of a bucket brigade broadcast

// bucketpipenonblock.c
MPI_Request rrequests[PARTS];
for (int ipart=0; ipart<PARTS; ipart++) {
MPI_Irecv
(
leftdata+partition_starts[ipart],partition_sizes[ipart],
MPI_DOUBLE,recvfrom,ipart,comm,rrequests+ipart);
}

The TAU trace is in figure 17.2.

17.6.2 Butterfly exchange

The NAS Parallel Benchmark suite [17] contains a Conjugate Gradients (CG) implementation that spells
out its all-reduce operations as a butterfly exchange.
!! cgb.f
do i = 1, l2npcols
call mpi_irecv( d,
> 1,
> dp_type,
> reduce_exch_proc(i),
> i,
> mpi_comm_world,

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17. TAU

Figure 17.2: Trace of a pipelined bucket brigade broadcast

> request,
> ierr )
call mpi_send( sum,
> 1,
> dp_type,
> reduce_exch_proc(i),
> i,
> mpi_comm_world,
> ierr )

call mpi_wait( request, status, ierr )

sum = sum + d
enddo

We recognize this structure in the TAU trace: figure 17.3. Upon closer examination, we see how this
particular algorithm induces a lot of wait time. Figures 17.5 and 17.6 show a whole cascade of processes
waiting for each other.

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 17.6. Examples

Figure 17.3: Trace of a butterfly exchange

Figure 17.4: Trace of a butterfly exchange

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17. TAU

206 HPC Carpentry

Figure 17.5: Four stages of processes waiting caused by a single lagging process
 17.6. Examples

Figure 17.6: Four stages of processes waiting caused by a single lagging process

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Chapter 18

SLURM

Supercomputer clusters can have a large number of nodes, but not enough to let all their users run si-
multaneously, and at the scale that they want. Therefore, users are asked to submit jobs, which may start
executing immediately, or may have to wait until resources are available.
The decision when to run a job, and what resources to give it, is not done by a human operator, but by
software called a batch system. (The Stampede cluster at TACC ran close to 10 million jobs over its lifetime,
which corresponds to starting a job every 20 seconds.)
This tutorial will cover the basics of such systems, and in particular Simple Linux Utility for Resource
Management (SLURM).

18.1 Cluster structure

A supercomputer cluster usually has two types of nodes:
• login node, and
• compute node.
When you make an ssh connection to a cluster, you are connecting to a login node. The number of login
nodes is small, typically less than half a dozen.
Exercise 18.1. Connect to your favourite cluster. How many people are on that login node? If
you disconnect and reconnect, do you find yourself on the same login node?
Compute nodes are where your jobs are run. Different clusters have different structures here:
• Compute nodes can be shared between users, or they can be assigned exclusively.
– Sharing makes sense if user jobs have less parallelisn than the core count of a node.
– … on the other hand, it means that users sharing a node can interfere with each other’s jobs,
with one job using up memory or bandwidth that the other job needs.
– With exclusive nodes, a job has access to all the memory and all the bandwidth of that node.
• Clusters can homogeneous, having the same processor type on each compute node, or they can
have more than one processor type. For instance, the TACC Stampede2 cluster has Intel Knights-
landing and Intel Skylake nodes.
• Often, clusters have a number of ‘large memory’ nodes, on the order of a Terabyte of memory or
more. Because of the cost of such hardware, there is usually only a small number of these nodes.

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 18.2. Queues

18.2 Queues
Jobs often can not start immediately, because not enough resources are available, or because other jobs
may have higher priority (see section 18.7). It is thus typical for a job to be put on a queue, scheduled, and
started, by a batch system such as SLURM.
Batch systems do not put all jobs in one big pool: jobs are submitted to any of a number of queues, that
are all scheduled separately.
Queues can differ in the following ways:
• If a cluster has different processor types, those are typically in different queues. Also, there may
be separate queues for the nodes that have a Graphics Processing Unit (GPU) attched. Having
multiple queues means you have to decide what processor type you want your job to run on,
even if your executable is binary compatible with all of them.
• There can be ‘development’ queues, which have restrictive limits on runtime and node count, but
where jobs typically start faster.
• Some clusters have ‘premium’ queues, which have a higher charge rate, but offer higher priority.
• ‘Large memory nodes’ are typically also in a queue of their own.
• There can be further queues for jobs with large resource demands, such as large core counts, or
longer-than-normal runtimes.
For slurm, the sinfo command can tell you much about the queues.
# what queues are there?
sinfo -o "%P"
# what queues are there, and what is their status?
sinfo -o "%20P %.5a"

Exercise 18.2. Enter these commands. How many queues are there? Are they all operational at
the moment?

18.2.1 Queue limits

Queues have limits on
• the runtime of a job;
• the node count of a job; or
• how many jobs a user can have in that queue.

18.3 Job running

There are two main ways of starting a job on a cluster that is managed by slurm. You can start a program
run synchronously with srun, but this may hang until resources are available. In this section, therefore,
we focus on asynchronously executing your program by submitting a job with sbatch.

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18. SLURM

18.3.1 The job submission cycle

In order to run a batch job, you need to write a job script, or batch script. This script describes what program
you will run, where its inputs and outputs are located, how many processes it can use, and how long it
will run.
In its simplest form, you submit your script without further parameters:
sbatch yourscript

All options regarding the job run are contained in the script file, as we will now discuss.
As a result of your job submission you get a job id. After submission you can queury your job with squeue:
squeue -j 123456

or queury all your jobs:

squeue -u yourname

The squeue command reports various aspects of your job, such as its status (typically pending or running);
and if it is running, the queue (or ‘partition’) where it runs, its elapsed time, and the actual nodes where
it runs.
squeue -j 5807991
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
5807991 development packingt eijkhout R 0:04 2 c456-[012,034]

If you discover errors in your script after submitting it, including when it has started running, you can
cancel your job with scancel:
scancel 1234567

18.4 The script file

A job script looks like an executable shell script:
• It has an ‘interpreter’ line such as
#!/bin/bash

at the top, and

• it contains ordinary unix commands, including
• the (parallel) startup of you program:
# sequential program:
./yourprogram youroptions
# parallel program, general:
mpiexec -n 123 parallelprogram options

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 18.4. The script file

# parallel program, TACC:

ibrun parallelprogram options

• … and then it has many options specifying the parallel run.

18.4.1 sbatch options

In addition to the regular unix commands and the interpreter line, your script has a number of SLURM
directives, each starting with #SBATCH. (This makes them comments to the shell interpreter, so a batch
script is actually a legal shell script.)
Directives have the form
#SBATCH -option value

Common options are:

• -J: the jobname. This will be displayed when you call squeue.
• -o: name of the output file. This will contain all the stdout output of the script.
• -e: name of the error file. This will contain all the stderr output of the script, as well as slurm
error messages.
It can be a good idea to make the output and error file unique per job. To this purpose, the macro
%j is available, which at execution time expands to the job number. You will then get an output
file with a name such as myjob.o2384737.
• -p: the partition or queue. See above.
• -t hh:mm:ss: the maximum running time. If your job exceeds this, it will get cancelled. Two
considerations:
1. You can not specify a duration here that is longer than the queue limit.
2. The shorter your job, the more likely it is to get scheduled sooner rather than later.
• -w c452-[101-104,111-112,115] specific nodes to place the job.
• -A: the name of the account to which your job should be billed.
• --mail-user=you@where Slurm can notify you when a job starts or ends. You may for instance
want to connect to a job when it starts (to run top), or inspect the results when it’s done, but not
sit and stare at your terminal all day. The action of which you want to be notified is specified with
(among others) --mail-type=begin/end/fail/all
• --dependency=after:123467 indicates that this job is to start after jobs 1234567 finished. Use
afterok to start only if that job successfully finished. (See https://cvw.cac.cornell.edu/
slurm/submission_depend for more options.)
• --nodelist allows you to specify specific nodes. This can be good for getting reproducible tim-
ings, but it will probably increase your wait time in the queue.
• --array=0-30 is a specification for ‘array jobs’: a task that needs to be executed for a range of
parameter values.
TACC note. Arry jobs are not supported at TACC; use a launcher instead; section 18.5.3.
• --mem=10000 specifies the desired amount of memory per node. Default units are megabytes,
but can be explicitly indicated with K/M/G/T.

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18. SLURM

TACC note. This option can not be used to request arbitrary memory: jobs always have access
to all available physical memory, and use of shared memory is not allowed.
See https://slurm.schedmd.com/sbatch.html for a full list.
Exercise 18.3. Write a script that executes the date command twice, with a sleep in between.
Submit the script and investigate the output.

18.4.2 Environment
Your job script acts like any other shell script when it is executed. In particular, it inherits the calling
environment with all its environment variables. Additionally, slurm defines a number of environment
variables, such as the job ID, the hostlist, and the node and process count.

18.5 Parallelism handling

We discuss parallelism options separately.

18.5.1 MPI jobs

On most clusters there is a structure with compute nodes, that contain one or more multi-core processors.
Thus, you want to specify the node and core count. For this, there are options -N and -n respectively.
#SBATCH -N 4 # Total number of nodes
#SBATCH -n 4 # Total number of mpi tasks

It would be possible to specify only the node count or the core count, but that takes away flexibility:
• If a node has 40 cores, but your program stops scaling at 10 MPI ranks, you would use:
#SBATCH -N 1
#SBATCH -n 10

• If your processes use a large amount of memory, you may want to leave some cores unused. On
a 40-core node you would either use
#SBATCH -N 2
#SBATCH -n 40

or
#SBATCH -N 1
#SBATCH -n 20

Rather than specifying a total core count, you can also specify the core count per node with --ntasks-per-node.
Exercise 18.4. Go through the above examples and replace the -n option by an equivalent
--ntasks-per-node values.

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 18.6. Job running

Python note. Python MPI programs Python programs using mpi4py should be treated like other MPI
programs, except that instead of an executable name you specify the python executable and the
script name:
ibrun python3 mympi4py.py

18.5.2 Threaded jobs

The above discussion was mostly of relevance to MPI programs. Some other cases:
• For pure-OpenMP programs you need only one node, so the -N value is 1. Maybe surprisingly,
the -n value is also 1, since only one process needs to be created: OpenMP uses thread-level
parallelism, which is specified through the OMP_NUM_THREADS environment variable.
• A similar story holds for the Matlab parallel computing toolbox (note: note the distributed com-
puting toolbox), and the Python multiprocessing module.
Exercise 18.5. What happens if you specify an -n value greater than 1 for a pure-OpenMP
program?
For hybrid computing MPI-OpenMP programs, you use a combination of slurm options and enviroment
variables, such that, for instance, the product of the --tasks-per-node and OMP_NUM_THREADS is less
than the core count of the node.

18.5.3 Parameter sweeps / ensembles / massively parallel

So far we have focused on jobs where a single parallel executable is scheduled. However, there are use
cases where you want to run a sequential (or very modestly parallel) executable for a large number of
inputs. This is called variously a parameter sweep or an ensemble.
Slurm can support this itself with array jobs, though there are more sophisticated launcher tools for such
purposes.
TACC note. TACC clusters do not support array jobs. Instead, use the launcher or pylauncher mod-
ules.

18.6 Job running

When your job is running, its status is reported as R by squeue. That command also reports which nodes
are allocated to it.
squeue -j 5807991
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
5807991 development packingt eijkhout R 0:04 2 c456-[012,034]

You can then ssh into the compute nodes of your job; normally, compute nodes are off-limits. This is
useful if you want to run top to see how your processes are doing.

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18. SLURM

18.7 Scheduling strategies

Such a system looks at resource availability and the user’s priority to determine when a job can be run.
Of course, if a user is requesting a large number of nodes, it may never happen that that many become
available simultaneously, so the batch system will force the availability. It does so by determining a time
when that job is set to run, and then let nodes go idle so that they are available at that time.
An interesting side effect of this is that, right before the really large job starts, a ‘fairly’ large job can be
run, if it only has a short running time. This is known as backfill, and it may cause jobs to be run earlier
than their priority would warrant.

18.8 File systems

File systems come in different types:
• They can be backed-up or not;
• they can be shared or not; and
• they can be permanent or purged.
On many clusters each node has as local disc, either spinning or a RAM disc. This is usually limited in
size, and should only be used for temporary files during the job run.
Most of the file system lives on discs that are part of RAID array. These discs have a large amount of
redundancy to make them fault-tolerant, and in aggregate they form a shared file system: one unified file
system that is accessible from any node and where files can take on any size, or at least much larger than
any individual disc in the system.
TACC note. The HOME file system is limited in size, but is both permanent and backed up. Here you
put scripts and sources.
The WORK file system is permanent but not backed up. Here you can store output of your
simulations. However, currently the work file system can not immediately sustain the output of a
large parallel job.
The SCRATCH file system is purged, but it has the most bandwidth for accepting program output. This is
where you would write your data. After post-processing, you can then store on the work file system, or
write to tape.
Exercise 18.6. If you install software with cmake, you typically have
1. a script with all your cmake options;
2. the sources,
3. the installed header and binary files
4. temporary object files and such.
How would you orgnize these entities over your available file systems?

18.9 Examples
Very sketchy section.

214 HPC Carpentry

 18.10. Review questions

18.9.1 Job dependencies

JOB=`sbatch my_batchfile.sh | egrep -o -e "\b[0-9]+$"`

#!/bin/sh

# Launch first job

JOB=`sbatch job.sh | egrep -o -e "\b[0-9]+$"`

# Launch a job that should run if the first is successful

sbatch --dependency=afterok:${JOB} after_success.sh

# Launch a job that should run if the first job is unsuccessful

sbatch --dependency=afternotok:${JOB} after_fail.sh

18.9.2 Multiple runs in one script

ibrun stuff &
sleep 10
for h in hostlist ; do
ssh $h "top"
done
wait

18.10 Review questions

For all true/false questions, if you answer False, what is the right answer and why?
Exercise 18.7. T/F? When you submit a job, it starts running immediately once sufficient re-
sources are available.
Exercise 18.8. T/F? If you submit the following script:
#!/bin/bash
#SBATCH -N 10
#SBATCH -n 10
echo "hello world"

you get 10 lines of ‘hello world’ in your output.

Exercise 18.9. T/F? If you submit the following script:
#!/bin/bash
#SBATCH -N 10
#SBATCH -n 10
hostname

Victor Eijkhout 215

18. SLURM

you get the hostname of the login node from which your job was submitted.
Exercise 18.10. Which of these are shared with other users when your job is running:
• Memory;
• CPU;
• Disc space?
Exercise 18.11. What is the command for querying the status of your job?
• sinfo
• squeue
• sacct
Exercise 18.12. On 4 nodes with 40 cores each, what’s the largest program run, measured in
• MPI ranks;
• OpenMP threads?

216 HPC Carpentry

Chapter 19

SimGrid

Many readers of this book will have access to some sort of parallel machine so that they can run simu-
lations, maybe even some realistic scaling studies. However, not many people will have access to more
than one cluster type so that they can evaluate the influence of the interconnect. Even then, for didactic
purposes one would often wish for interconnect types (fully connected, linear processor array) that are
unlikely to be available.
In order to explore architectural issues pertaining to the network, we then resort to a simulation tool,
SimGrid.

Installation

Compilation You write plain MPI files, but compile them with the SimGrid compiler smpicc.

Running SimGrid has its own version of mpirun: smpirun. You need to supply this with options:
• -np 123456 for the number of (virtual) processors;
• -hostfile simgridhostfile which lists the names of these processors. You can basically
make these up, but are defined in:
• -platform arch.xml which defines the connectivity between the processors.
For instance, with a hostfile of 8 hosts, a linearly connected network would be defined as:
<?xml version='1.0'?>
<!DOCTYPE platform SYSTEM "http://simgrid.gforge.inria.fr/simgrid/simgrid.dtd">

<platform version="4">

<zone id="first zone" routing="Floyd">

<!-- the resources -->
<host id="host1" speed="1Mf"/>
<host id="host2" speed="1Mf"/>
<host id="host3" speed="1Mf"/>

217
19. SimGrid

<host id="host4" speed="1Mf"/>

<host id="host5" speed="1Mf"/>
<host id="host6" speed="1Mf"/>
<host id="host7" speed="1Mf"/>
<host id="host8" speed="1Mf"/>
<link id="link1" bandwidth="125MBps" latency="100us"/>
<!-- the routing: specify how the hosts are interconnected -->
<route src="host1" dst="host2"><link_ctn id="link1"/></route>
<route src="host2" dst="host3"><link_ctn id="link1"/></route>
<route src="host3" dst="host4"><link_ctn id="link1"/></route>
<route src="host4" dst="host5"><link_ctn id="link1"/></route>
<route src="host5" dst="host6"><link_ctn id="link1"/></route>
<route src="host6" dst="host7"><link_ctn id="link1"/></route>
<route src="host7" dst="host8"><link_ctn id="link1"/></route>
</zone>

</platform>

(such files can be generated with a short shell script).

The Floyd designation of the routing means that any route using the transitive closure of the paths given
can be used. It is also possible to use routing="Full" which requires full specification of all pairs that
can communicate.

218 HPC Carpentry

Chapter 20

Bibliography

[1] Alfred V. Aho, Brian W. Kernighan, and Peter J. Weinberger. The Awk Programming Language.
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on the frontiers of massively parallel computation (Frontiers ’92), McLean, Virginia, Oct 19–21, 1992,
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[5] Edsger W. Dijkstra. Programming as a discipline of mathematical nature. Am. Math. Monthly, 81:608–
612, 1974. [Cited on page 145.]
[6] Jack J. Dongarra, Jeremy Du Croz, Sven Hammarling, and Iain Duff. A set of level 3 basic linear
algebra subprograms. ACM Transactions on Mathematical Software, 16(1):1–17, March 1990. [Cited on
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[7] Jack J. Dongarra, Jeremy Du Croz, Sven Hammarling, and Richard J. Hanson. An extended set of
FORTRAN basic linear algebra subprograms. ACM Transactions on Mathematical Software, 14(1):1–
17, March 1988. [Cited on page 116.]
[8] Dale Dougherty and Arnold Robbins. sed & awk. O’Reilly Media, 2nd edition edition. Print ISBN:
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[9] Victor Eijkhout. The Science of TEX and LATEX. lulu.com, 2012. [Cited on page 39.]
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576–580, October 1969. [Cited on page 145.]
[11] Helmut Kopka and Patrick W. Daly. A Guide to LATEX. Addison-Wesley, first published 1992. [Cited on
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[12] L. Lamport. LATEX, a Document Preparation System. Addison-Wesley, 1986. [Cited on page 190.]
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fortran usage. ACM Trans. Math. Softw., 5(3):308–323, September 1979. [Cited on page 116.]

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[14] Robert Mecklenburg. Managing Projects with GNU Make. O’Reilly Media, 3rd edition edition, 2004.
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10445-6. [Cited on page 52.]
[15] Sandra Mendez, Sebastian L?hrs, Volker Weinberg, Dominic Sloan-Murphy, and Andrew
Turner. Best practice guide - parallel i/o. https://prace-ri.eu/training-support/
best-practice-guides/best-practice-guide-parallel-io/, 02 2019. [Cited on page 133.]
[16] Frank Mittelbach, Michel Goossens, Johannes Braams, David Carlisle, and Chris Rowley. The LATEX
Companion, 2nd edition. Addison-Wesley, 2004. [Cited on page 190.]
[17] NASA Advaned Supercomputing Division. NAS parallel benchmarks. https://www.nas.nasa.
gov/publications/npb.html. [Cited on page 203.]
[18] Tobi Oetiker. The not so short introduction to LATEX. http://tobi.oetiker.ch/lshort/. [Cited on
pages 177 and 190.]

[19] Jack Poulson, Bryan Marker, Jeff R. Hammond, and Robert van de Geijn. Elemental: a new framework
for distributed memory dense matrix computations. ACM Transactions on Mathematical Software.
submitted. [Cited on page 116.]
[20] S. Shende and A. D. Malony. International Journal of High Performance Computing Applications,
20:287–331, 2006. [Cited on page 199.]
[21] TEX frequently asked questions. [Cited on page 190.]
[22] R. van de Geijn, Philip Alpatov, Greg Baker, Almadena Chtchelkanova, Joe Eaton, Carter Edwards,
Murthy Guddati, John Gunnels, Sam Guyer, Ken Klimkowski, Calvin Lin, Greg Morrow, Peter Nagel,
James Overfelt, and Michelle Pal. Parallel linear algebra package (PLAPACK): Release r0.1 (beta)
users’ guide. 1996. [Cited on page 116.]
[23] Robert A. van de Geijn. Using PLAPACK: Parallel Linear Algebra Package. The MIT Press, 1997. [Cited
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[24] Greg Wilson, D. A. Aruliah, C. Titus Brown, Neil P. Chue Hong, Matt Davis, Richard T. Guy, Steven
H. D. Haddock, Kathryn D. Huff, Ian M. Mitchell, Mark D. Plumbley, Ben Waugh, Ethan P. White,
and Paul Wilson. Best practices for scientific computing. PLOS Biology, 12(1):1–7, 01 2014. [Cited on
page 6.]

220 HPC Carpentry

Chapter 21

List of acronyms

AMR Adaptive Mesh Refinement FPGA Field-Programmable Gate Array

AOS Array-Of-Structures GMRES Generalized Minimum Residual
API Application Programmer Interface GPU Graphics Processing Unit
AVX Advanced Vector Extensions GPGPU General Purpose Graphics Processing
BEM Boundary Element Method Unit
BFS Breadth-First Search GS Gram-Schmidt
BLAS Basic Linear Algebra Subprograms GUI Graphical User Interface
BSP Bulk Synchronous Parallel HDFS Hadoop File System
BVP Boundary Value Problem HPC High-Performance Computing
CAF Co-array Fortran HPF High Performance Fortran
CCS Compressed Column Storage IBVP Initial Boundary Value Problem
CG Conjugate Gradients IDE Integrated Development Environment
CGS Classical Gram-Schmidt ILP Instruction Level Parallelism
COO Coordinate Storage ILU Incomplete LU
CPU Central Processing Unit IMP Integrative Model for Parallelism
CRS Compressed Row Storage IVP Initial Value Problem
CUDA Compute-Unified Device Architecture LAPACK Linear Algebra Package
DAG Directed Acyclic Graph LAN Local Area Network
DL Deep Learning LBM Lattice Boltzmann Method
DRAM Dynamic Random-Access Memory LRU Least Recently Used
DSP Digital Signal Processing MIC Many Integrated Cores
FD Finite Difference MIMD Multiple Instruction Multiple Data
FMA Fused Multiply-Add MGS Modified Gram-Schmidt
FDM Finite Difference Method ML Machine Learning
FEM Finite Element Method MPI Message Passing Interface
FMM Fast Multipole Method MSI Modified-Shared-Invalid
FOM Full Orthogonalization Method MTA Multi-Threaded Architecture
FPU Floating Point Unit NUMA Non-Uniform Memory Access
FFT Fast Fourier Transform ODE Ordinary Diffential Equation
FSA Finite State Automaton OS Operating System
FSB Front-Side Bus PGAS Partitioned Global Address Space

221
21. List of acronyms

PDE Partial Diffential Equation SOA Structure-Of-Arrays

PRAM Parallel Random Access Machine SOR Successive Over-Relaxation
RDMA Remote Direct Memory Access SSOR Symmetric Successive Over-Relaxation
RNG Random Number Generator SP Streaming Processor
SAN Storage Area Network SPMD Single Program Multiple Data
SAS Software As a Service SPD symmetric positive definite
SFC Space-Filling Curve
SRAM Static Random-Access Memory
SGD Stochastic Gradient Descent
SSE SIMD Streaming Extensions
SIMD Single Instruction Multiple Data
SIMT Single Instruction Multiple Thread STL Standard Template Library
SLURM Simple Linux Utility for Resource Man- TDD Test-Drive Development
agement TLB Translation Look-aside Buffer
SM Streaming Multiprocessor UMA Uniform Memory Access
SMP Symmetric Multi Processing UPC Unified Parallel C
SMT Symmetric Multi Threading WAN Wide Area Network

222 HPC Carpentry

Chapter 22

Index

.bashrc, see shell, startup files backtick, see backquote, 28

.pc (unix command), 85 bash (unix command), 7, 66
.profile, see shell, startup files Basic, 39
Basic Linear Algebra Subprograms (BLAS), 116
add_compile_options (cmake command), 88 batch
add_definitions (cmake command), 92 job, 210
add_library (cmake command), 75, 76 script, 210
add_subdirectory (cmake command), 79 system, 208
alias (unix command), 32 BEM, see Boundary Element Method
AMR, see Adaptive Mesh Refinement BFS, see Breadth-First Search
AOS, see Array-Of-Structures big-endian, 123, 130
API, see Application Programmer Interface binary
Apple stripped, 45
Mac OS, 7, 81 Bitkeeper, 93
OS Ventura, 51 Bjam, 52
ar (unix command), 17, 47, 48 BLAS, see Basic Linear Algebra Subprograms
archive (git command), 115 data format, 118–119
archive utility, 47 blis, 120
ascii, 39 Boost, 172
assembly branch, 94, 111
listing, 43 break (unix command), 28
assertion, 139 breakpoint, 154, 155–157
assertions, 138–140 BSD, 7
AUTHOR_WARNING (cmake command), 90 BSP, see Bulk Synchronous Parallel
AVX, see Advanced Vector Extensions bucket brigade, 202
awk buffer
(unix command), 36 overflow, 158
bug, 138
backfill, 214 bus error, 157
background process, 22 butterfly exchange, 203
backquote, 20 BVP, see Boundary Value Problem

223
INDEX

by reference, 171 CMAKE_MODULE_PATH (cmake command), 82

CMAKE_POSITION_INDEPENDENT_CODE (cmake
C, 39 command), 76
C++ CMAKE_PREFIX_PATH (cmake command), 82
exception, 156 CMAKE_SOURCE_DIR (cmake command), 77
linking to, 168–170 CMakeLists.txt, 73
name mangling, 168 column-major, 119
c++filt (unix command), 169 commit, 93
CAF, see Co-array Fortran compiler, 39, 41
call stack, 151 optimization, 45
cat (unix command), 8, 9 optimization level, 149
Catch2, 146 options, 45
Catch2 (unix command), 81 complex numbers
catchpoint, 156 C and Fortran, 167
Cblas, 84 compute
CC (unix command), 88 node, 208
CCS, see Compressed Column Storage COO, see Coordinate Storage
cd (unix command), 11 core dump, 149
CG, see Conjugate Gradients coverage, 145
CGS, see Classical Gram-Schmidt cp (unix command), 9
chgrp (unix command), 34 CPU, see Central Processing Unit
chmod (unix command), 14, 15 CRS, see Compressed Row Storage
chown (unix command), 34 csh (unix command), 7, 66
chown ctypes (python module), 172
(unix command), 35 CUDA, see Compute-Unified Device Architecture
clang, 41, 147 cut (unix command), 17
cluster, 208 CVS, 93
CMake, 70, 72–76, 78, 79, 81, 84–86, 88–91 CXX (unix command), 88
Fortran support, 72 cxxopts, 86
version 3.15, 90 cmake integration, 86
cmake, 214
CMAKE_BUILD_TYPE (cmake command), 89 DAG, see Directed Acyclic Graph
CMAKE_C_COMPILER (cmake command), 88 date (unix command), 212
CMAKE_C_FLAGS (cmake command), 89 ddd, 147, 161
CMAKE_CURRENT_SOURCE_DIR (cmake command), DDT, 147, 161, 162, 163, 164–165
77 reverse connect, 165
CMAKE_CXX_COMPILE_FEATURES (cmake com- deadlock, 161, 162
mand), 89 DEBUG (cmake command), 90
CMAKE_CXX_COMPILER (cmake command), 88 Debug (cmake command), 89
CMAKE_CXX_FLAGS (cmake command), 89 debug flag, 150
CMAKE_Fortran_COMPILER (cmake command), 72, debugger, 147, 161
88 debugging, 147–165
CMAKE_LINKER (cmake command), 88 parallel, 165
CMAKE_LINKER_FLAGS (cmake command), 89 defensive programming, 138

224 HPC Carpentry

 INDEX

demangling, 48 shared, 214

DEPRECATION (cmake command), 90 text, 39
DESTINATION (cmake command), 74 file (unix command), 10, 38, 39
DESTINATION foo (cmake command), 74 files, 7
device find_library (cmake command), 82
null, 24 find_package (cmake command), 82
diff (unix command), 37 finger (unix command), 34
directories, 7 FMA, see Fused Multiply-Add
DL, see Deep Learning FMM, see Fast Multipole Method
DRAM, see Dynamic Random-Access Memory fmtlib, 86, 87
DSP, see Digital Signal Processing cmake integration, 87
cmke integration, 86
Eclipse, 162 fmtlib (unix command), 81
PTP, 162 FOM, see Full Orthogonalization Method
editor, 10 for (unix command), 25, 28
Eigen
foreground process, 22
cake integration, 85–86
fork, 110
eigen, 85
format specifier, 174
Eispack, 116
Fortran, 39, 119
electric fence, 159
iso C bindings, 168
elif (unix command), 27
module, 61
else (unix command), 27
submodule, 61
emacs, 10
Fortran2008, 61
ensemble, 213
FPGA, see Field-Programmable Gate Array
ENV (cmake command), 91
FPU, see Floating Point Unit
env
FSA, see Finite State Automaton
(unix command), 25
FSB, see Front-Side Bus
environment
of batch job, 212
environment variable, 18, 25–27 gcc, 41
in Cmake, 91 memory checking, 144
escape, 16, 33 gdb, 147–157
executable, 7 in parallel, 163
exit status, 21 gfortran, 143
export (unix command), 25, 26 git, 93
github, 97
FATAL_ERROR (cmake command), 90 gitlab, 97
FC (unix command), 88 Given’s rotations, 46
FD, see Finite Difference GMRES, see Generalized Minimum Residual
FDM, see Finite Difference Method GNU, 147, 161, 196
FEM, see Finite Element Method gdb, see gdb, see gdb
FFT, see Fast Fourier Transform gnuplot, see gnuplot
file Make, see Make
system gnuplot, 135

Victor Eijkhout 225

INDEX

GPGPU, see General Purpose Graphics Processing Skylake, 208

Unit VTune, 197
gprof (unix command), 196 interconnect, 217
gprof INTERFACE (cmake command), 81
(unix command), 196 interoperability
GPU, see Graphics Processing Unit C to Fortran, 166–168
grep (unix command), 15 C to python, 172–173
groups (unix command), 34 IVP, see Initial Value Problem
GS, see Gram-Schmidt
GUI, see Graphical User Interface job, 208
gzip (unix command), 18 array, 213
cancel, 211
hardware counters, 195 job (unix), 22
HDF5, 134 job script, 210
hdf5, 40, 133 jumpshot, 200
HDFS, see Hadoop File System
head (unix command), 10 kill (unix command), 22
hexdump (unix command), 40
HPC, see High-Performance Computing LAN, see Local Area Network
HPF, see High Performance Fortran language
hybrid compiled, 39
computing, 213 interpreted, 39
language interoperability, see interoperability
IBM, 130 LAPACK, see Linear Algebra Package
compiler, 41 Lapack, 116
IBVP, see Initial Boundary Value Problem routines, 117–118
IDE, see Integrated Development Environment LATEX, see also TEX, 176–190
idev (unix command), 165 launcher (unix command), 213
idle, 214 LBM, see Lattice Boltzmann Method
idle time, 197 LD_LIBRARY_PATH (unix command), 49, 51, 81
if (unix command), 27 ldd
if (unix command), 51
(unix command), 27 less (unix command), 9
ILP, see Instruction Level Parallelism libraries
ILU, see Incomplete LU creating and using, 46–51
IMP, see Integrative Model for Parallelism library
include_directories (cmake command), 92 dynamic, 173
input redirection, see redirection shared, 48
instrumentation, 199, 200 static, 47
dynamic, 199 link_libraries (cmake command), 92
Intel linker, 44, 81
C++ compiler, 53 Linpack, 116
compiler, 41 benchmark, 116
Knightslanding, 208 Linux

226 HPC Carpentry

 INDEX

distributions, 7 cmake integration, 82–83

Lisp, 39 I/O, 133
little-endian, 123, 130, 134 timer, 195
lldb, 147 MSI, see Modified-Shared-Invalid
load MTA, see Multi-Threaded Architecture
unbalance, 197 mv (unix command), 9
login
node, 208 name mangling, 45
LRU, see Least Recently Used NetCDF, 134
ls (unix command), 8 netlib, 119
Lustre, 133 ninja, 70
nm, 167
Make, 52–70 nm (unix command), 43, 45, 48, 169
and LATEX, 68–69 nm
automatic variables, 59 (unix command), 45
debugging, 67 node, 208
template rules, 59, 60 NOTICE (cmake command), 90
man (unix command), 9 null termination, 170
man NUMA, see Non-Uniform Memory Access
(unix command), 9
manual page, 9 object file, 44, 167
Matlab, 39 ODE, see Ordinary Diffential Equation
parallel computing toolbox, 213 OpenMP
matrix-matrix product cake integration, 83–84
Goto implementation, 120 timer, 195
memory Operating System (OS), 7
leak, 143, 159 option (cmake command), 91
violations, 142 OS, see Operating System
memory leak, 157 output redirection, see redirection
Mercurial, 93 overflow, 138
message (cmake command), 90
MGS, see Modified Gram-Schmidt PAPI, 195
MIC, see Many Integrated Cores parameter sweep, 213
Microsoft partition, 211
Sharepoint, 93 PATH (unix command), 29
MIMD, see Multiple Instruction Multiple Data PATH
MinSizeRel (cmake command), 89 (unix command), 18
mkdir (unix command), 11 PDE, see Partial Diffential Equation
MKL, 116, 120 perf (unix command), 196
cake integration, 84 perf
ML, see Machine Learning (unix command), 196
module, see Fortran, module PETSc, 196
more (unix command), 9, 10 cmake integration, 85
MPI, see Message Passing Interface PGAS, see Partitioned Global Address Space

Victor Eijkhout 227

INDEX

pgfplots, 187 remote, 104

ping-pong, 198 revision control, see version control
PKG_CONFIG_PATH (unix command), 85 RNG, see Random Number Generator
pkgconfig (unix command), 85, 86 root
PLapack, 116 privileges, 15, 34
POSIX, 7 row-major, 119
PRAM, see Parallel Random Access Machine rpath
prerequisite in CMake, 79
order-only, 64 rpath (unix command), 81
PRIVATE (cmake command), 75 rsh
process (unix command), 35
numbers, 22
PROJECT_NAME (cmake command), 91 SAN, see Storage Area Network
PROJECT_SOURCE_DIR (cmake command), 77 SAS, see Software As a Service
PROJECT_VERSION (cmake command), 91 Scalapack, 116
prompt, 32 scancel (unix command), 210
ps (unix command), 22 SCCS, 93
PUBLIC (cmake command), 75 Scons, 52
pull request, 110 scp
pwd (unix command), 11 (unix command), 35
pylauncher (unix command), 213 search path, 18, 29
Python, 39 sed (unix command), 36, 109
multiprocessing, 213 segmentation fault, 151
segmentation violation, 142, 157
queue, 209 SEND_ERROR (cmake command), 90
seq (unix command), 32
RAID seq
array, 214 (unix command), 28
RAM setuid (unix command), 14
disc, 214 SFC, see Space-Filling Curve
rcp SGD, see Stochastic Gradient Descent
(unix command), 35 sh (unix command), 7
RDMA, see Remote Direct Memory Access shared library, see library, shared
RDTSC, 195 Sharepoint, see Microsoft, Sharepoint
record, 40 shell, 7
Red Hat, 7 command history, 67
redirection, 23–25, 36 startup files, 32–33
Release (cmake command), 89 shift
release, 93 (unix command), 30
RelWithDebInfo (cmake command), 89 side-effects, 139
remote, 93 SIMD, see Single Instruction Multiple Data
repository, 93 SimGrid, 217–218
central, 93 compiler, 217
local, 93, 104 SIMT, see Single Instruction Multiple Thread

228 HPC Carpentry

 INDEX

single-responsibility, 146 target_include_directories (cmake com-

sleep (unix command), 212 mand), 77, 85, 92
slog2 file format, 200 target_link_directories (cmake command),
SLURM, see Simple Linux Utility for Resource Man- 81, 85
agement target_link_libraries (cmake command), 76,
SM, see Streaming Multiprocessor 85
SMP, see Symmetric Multi Processing target_sources (cmake command), 77
SMT, see Symmetric Multi Threading TAU, 199–204
SOA, see Structure-Of-Arrays on TACC resources, 200
SOR, see Successive Over-Relaxation tcsh (unix command), 7
source (unix command), 32 TDD, see Test-Drive Development
SP, see Streaming Processor template rule, see Make, template rule
SPD, see symmetric positive definite TEX, 176
SPMD, see Single Program Multiple Data environment variables, 183
squeue (unix command), 210, 213 then (unix command), 27
SRAM, see Static Random-Access Memory tikz, 187
SSE, see SIMD Streaming Extensions timer, 192–194
ssh MPI, 195
connection, 208 OpenMP, 195
ssh (unix command), 213 routines, C, 193
ssh routines, C++, 194
(unix command), 35 routines, Fortran, 193
SSOR, see Symmetric Successive Over-Relaxation TLB, see Translation Look-aside Buffer
staging area, 98 top (unix command), 34, 213
Stampede, 208 TotalView, 147, 161, 162
Stampede2, 208 touch (unix command), 9, 12
stat (unix command), 8 tr (unix command), 37
static library, see library, static TRACE (cmake command), 90
STATUS (cmake command), 90 type
STL, see Standard Template Library (unix command), 19
Subversion, 93
sudo Ubuntu, 7
(unix command), 34 UMA, see Uniform Memory Access
symbol table, 45, 147, 150 unicode, 39
System V, 7 Unix
system_clock, 193 user account, 33
unset (unix command), 27
TACC, 165, 208 UPC, see Unified Parallel C
tag, 93 upstream, 104
tag (git command), 115 uptime (unix command), 34
tail (unix command), 10 user
tar (unix command), 17 super, 34, 34
target_compile_features (cmake command),
88 Valgrind, 143

Victor Eijkhout 229

INDEX

valgrind, 158 WAN, see Wide Area Network

verbatim mode, 181 WARNING (cmake command), 90
VERBOSE (cmake command), 90 wc (unix command), 10
version control, 93 which (unix command), 18, 19
distributed, 93 who (unix command), 33
vi, 10 whoami (unix command), 33
Visual Studio, 70 wildcard, 15
VTune, 200
XCode, 70

wallclock time, 194 zsh (unix command), 7, 27

ISBN 978-1-257-99254-6
90000

9 781257 992546

230 HPC Carpentry