scientificComputing/debugging/lecture/debugging.tex

\chapter{Debugging}

\centerline{\includegraphics[width=0.7\textwidth]{xkcd_debugger}\rotatebox{90}{\footnotesize\url{www.xkcd.com}}}\vspace{4ex}


When writing a program from scratch we almost always make
mistakes. Accordingly, a quite substantial amount of time is invested
into finding and fixing errors. This process is called
\codeterm{debugging}. Don't be frustrated that a self-written program
does not work as intended and produces errors. It is quite exceptional
if a program appears to be working on the first try and, in fact,
should leave you suspicious.

In this chapter we will talk about typical mistakes, how to read and
understand error messages, how to actually debug your program code and
some hints that help to minimize errors.

\section{Types of errors and error messages}

There are a number of different classes of programming errors and it
is good to know the common ones. Some of your programming errors will
will lead to violations of the syntax or to invalid operations that
will cause \matlab{} to \codeterm{throw} an error. Throwing an error
ends the execution of a program and there will be an error messages
shown in the command window. With such messages \matlab{} tries to
explain what went wrong and to provide a hint on the possible cause.

Bugs that lead to the termination of the execution may be annoying but
are generally easier to find and to fix than logical errors that stay
hidden and the results of, e.g. an analysis, are seemingly correct.

\begin{important}[Try --- catch]
  There are ways to \codeterm{catch} errors during \codeterm{runtime}
  (i.e. when the program is executed) and handle them in the program.

\begin{lstlisting}[label=trycatch, caption={Try catch clause}]
  try
     y = function_that_throws_an_error(x);
  catch
     y = 0;
  end
\end{lstlisting}

This way of solving errors may seem rather convenient but is
risky. Having a function throwing an error and catching it in the
\codeterm{catch} clause will keep your command line clean but may
obscure logical errors! Take care when using the \codeterm{try-catch
  clause}.
\end{important}


\subsection{\codeterm{Syntax errors}}\label{syntax_error}
The most common and easiest to fix type of error. A syntax error
violates the rules (spelling and grammar) of the programming
language. For example every opening parenthesis must be matched by a
closing one or every \code{for} loop has to be closed by an
\code{end}. Usually, the respective error messages are clear and
the editor will point out and highlight most \codeterm{syntax error}s.

\begin{lstlisting}[label=syntaxerror, caption={Unbalanced parenthesis error.}]
>> mean(random_numbers
                      |
Error: Expression or statement is incorrect--possibly unbalanced (, {, or [.

Did you mean:
>>   mean(random_numbers)
\end{lstlisting}

\subsection{\codeterm{Indexing error}}\label{index_error}
Second on the list of common errors are the indexing errors. Usually
\matlab{} gives rather precise infromation about the cause, once you
know what they mean. Consider the following code.

\begin{lstlisting}[label=indexerror, caption={Indexing errors.}]
>> my_array = (1:100);
>> % first try: index 0
>> my_array(0)
Subscript indices must either be real positive integers or logicals.

>> % second try: negative index
>> my_array(-1)
Subscript indices must either be real positive integers or logicals.

>> % third try: a floating point number
>> my_array(5.7)
Subscript indices must either be real positive integers or logicals.

>> % fourth try: a character
>> my_array('z')
Index exceeds matrix dimensions.

>> % fifth try: another character
>> my_array('A')
ans =
     65 % wtf ?!?
\end{lstlisting}

The first two indexing attempts in listing \ref{indexerror} are rather
clear. We are trying to access elements with indices that are
invalid. Remember, indices in \matlab{} start with 1. Negative numbers
and zero are not permitted.  In the third attemp we index using a
floating point number. This fails because indices have to be 'integer'
values.  Using a character as an index (fourth attempt) leads to a
different error message that says that the index exceeds the matrix
dimensions. This indicates that we are trying to read data behind the
length of our variable \varcode{my\_array} which has 100 elements.
One could have expected that the character is an invalid index, but
apparently it is valid but simply too large. The fith attempt finally
succeeds. But why? \matlab{} implicitely converts the \codeterm{char}
to a number and uses this number to address the element in
\varcode{my\_array}. The \codeterm{char} has the ASCII code 65 and
thus the 65th element of \varcode{my\_array} is returned.

\subsection{\codeterm{Assignment error}}
Related to the Indexing error this error occurs when we want to write
data into a variable, that does not fit into it. Listing
\ref{assignmenterror} shows the simple case for 1-d data but, of
course, it extents to n-dimensional data. The data that is to be
filled into a matrix hat to fit in all dimensions. The command in line
7 works due to the fact, that matlab automatically extends the matrix,
if you assign values to a range outside its bounds.

\begin{lstlisting}[label=assignmenterror, caption={Assignment errors.}]
>> a = zeros(1, 100);
>> b = 0:10;

>> a(1:10) = b;
     In an assignment  A(:) = B, the number of elements in A and B must be the same.

>> a(100:110) = b;
>> size(a)
ans =
     110    1
\end{lstlisting}

\subsection{\codeterm{Dimension mismatch error}}
Similarly, some arithmetic operations are only valid if the variables
fulfill some size constraints. Consider the following commands
(listing\,\ref{dimensionmismatch}). The first one (line 3) fails
because we are trying to do al elementwise add on two vectors that
have different lengths, respectively sizes. The matrix multiplication
in line 6 also fails since for this operations to succeed the inner
matrix dimensions must agree (for more information on the
matrixmultiplication see box\,\ref{matrixmultiplication} in
chapter\,\ref{programming}). The elementwise multiplication issued in
line 10 fails for the same reason as the addition we tried
earlier. Sometimes, however, things apparently work but the result may
be surprising. The last operation in listing\,\ref{dimensionmismatch}
does not throw an error but the result is something else than the
expected elementwise multiplication.

\begin{lstlisting}[label=dimensionmismatch, caption={Some arithmetic operations make size constraints, violating them leads to dimension mismatch errors.}]
  >> a = randn(100, 1);
  >> b = randn(10, 1);
  >> a + b
  Matrix dimensions must agree.

  >> a * b      % The matrix multiplication!
  Error using  *
  Inner matrix dimensions must agree.

  >> a .* b
  Matrix dimensions must agree.

  >> c = a .* b';  % works but the result may not be what you expected!
  >> size(c)
  ans =
       100    10
\end{lstlisting}



\section{Logical error}
Sometimes a program runs smoothly and terminates without any
error. This, however, does not necessarily mean that the program is
correct. We may have made a \codeterm{logical error}. Logical errors
are hard to find, \matlab{} has no chance to find this error and can
not help us fixing bugs origination from these. We are on our own but
there are a few strategies that should help us.

\begin{enumerate}
\item Be sceptical: especially when a program executes without any
  complaint on the first try.
\item Clean code: Structure your code that you can easily read
  it. Comment, but only where necessary. Correctly indent your
  code. Use descriptive variable and function names.
\item Keep it simple.
\item Use scripts and functions and call them from the command
  line. \matlab{} can then provide you with more information. It will
  then point to the line where the error happens.
\item If you still find yourself in trouble: Apply debugging
  strategies to find and fix bugs (below).
\end{enumerate}


\subsection{Avoiding errors --- Keep it small and simple}

It would be great if we could just sit down write a program, run it
and be done. Most likely this will not happen. Rather, we will make
mistakes and have to bebug the code. There are a few guidelines that
help to reduce the number of errors.

\shortquote{Debugging time increases as a square of the program's
  size.}{Chris Wenham}

\shortquote{Everyone knows that debugging is twice as hard as writing
  a program in the first place. So if you're as clever as you can be
  when you write it, how will you ever debug it?}{Brian Kernighan}

Break down your programming problems into small parts (functions) that
do exactly one thing. This has already been discussed in the context
of writing scripts and functions. In parts this is just a matter of
feeling overwhelmed by 1000 lines of code. Further, with each task
that you incorporate into the same script the probability of naming
conflicts (same or similar names for variables) increases. Remembering
the meaning of a certain variable that was defined in the beginning of
the script is just hard.

Many tasks within an analysis can be squashed into a single line of
code. This saves some space in the file, reduces the effort of coming
up with variable names and simply looks so much more competent than a
collection of very simple lines. Consider the following listing
(listing~\ref{easyvscomplicated}). Both parts of the listing solve the
same problem but the second one breaks the task down to a sequence of
easy-to-understand commands. Finding logical and also syntactic errors
is much easier in the second case. The first version is perfectly fine
but it requires a deep understanding of the applied functions and also
the task at hand.

\begin{lstlisting}[label=easyvscomplicated, caption={Converting a series of spike times into the firing rate as a function of time. Many tasks can be solved with a single line of code. But is this readable?}]
% the one-liner
rate = conv(full(sparse(1, round(spike_times/dt), 1, 1, length(time))), kernel, 'same');

% easier to read
rate = zeros(size(time));
spike_indices = round(spike_times/dt);
rate(spike_indices) = 1;
rate = conv(rate, kernel, 'same');
\end{lstlisting}

The preferred way depends on several considerations. (i) How deep is
your personal understanding of the programming language?  (ii) What
about the programming skills of your target audience or other people
that may depend on your code? (iii) Is one solution faster or uses
less resources than the other? (iv) How much do you have to invest
into the development of the most elegant solution relative to its
importance in the project? The decision is up to you.


\section{Debugging strategies}

If you find yourself in trouble you can apply a few strategies to
solve the problem.

\begin{enumerate}
\item Lean back and take a breath.
\item Read the error messages and identify the position in the code
  where the error happens. Unfortunately this is not always the line
  or command that really introduced the bug. In some instances the
  actual error hides a few lines above.
\item No idea what the error message is trying to say? Google it!
\item Read the program line by line and understand what each line is
  doing.
\item Use \code{disp} to print out relevant information on the command
  line and compare the output with your expectations.  Do this step by
  step and start at the beginning.
\item Use the \matlab{} debugger to stop execution of the code at a
  specific line and proceed step by step. Be sceptical and test all
  steps for correctness.
\item Call for help and explain the program to someone else. When you
  do this start at the beginning and walk thorough the code line by
  line. Often it is not necessary that the other person is a
  programmer or exactly understands what is going on. Often it is the
  own refelction on the probelem and the chosen approach that helps
  finding the bug. (This is strategy is also known as \codeterm{Rubber
    duck debugging}.
\end{enumerate}


\subsection{Debugger}

The \matlab{} editor (figure\,\ref{editor_debugger}) supports
interactive debugging. Once you save a m-file in the editor and it
passes the syntax check, i.e. the little box in the upper right corner
of the editor window is green or orange, you can set on or several
\codeterm{break point}s. When the porgram is executed by calling it
from the command line it will be stopped at the line with the
breakpoint. In the editor this is indicated by a green arrow. The
command line will change too to indicate that we are now stopped in
debug mode (listing\,\ref{debuggerlisting}).

\begin{figure}
  \centering
  \includegraphics[width=0.9\linewidth]{editor_debugger.png}
  \caption{Screenshot of the \matlab{} m-file editor. Once a file is
    saved and passes the syntax check the green indicator (top-right
    corner of the editor window), a breakpoint can be set. Breakpoints
    can bes set either using the dropdown menu on top or by clicking
    the line number on the left margin. An active breakpoint is
    indicated by a red dot.}\label{editor_debugger}
\end{figure}


\begin{lstlisting}[label=debuggerlisting, caption={Command line when the program execution was stopped in the debugger.}]
>> simplerandomwalk
6   for run = 1:num_runs
K>>
\end{lstlisting}

When stopped in the debugger we can view and change the state of the
program at this step and try the next steps etc. Beware, however that
the state of a variable can be altered or even deleted which might
affect the execution of the remaining code.

The toolbar of the editor offers now a new set of tools for debugging:
\begin{enumerate}
\item \textbf{Continue} --- simply move on until the program terminates or the
  execution reaches the next breakpoint.
\item \textbf{Step} --- Execute the next command and stop.
\item \textbf{Step in} --- If the next command is the execution of a
  function step into it and stop at the first command.
\item \textbf{Step out} --- If the next command is a function call,
  proceed until the called function returns, then stop.
\item \textbf{Run to cursor} --- Execute all statements up to the
  current cursor position.
\item \textbf{Quit debugging} --- Immediately stop the debugging
  session and stop the further code execution.
\end{enumerate}

The debugger offers some more (advanced) features but the
functionality offered by the basic tools is often enough to debug the
code.