General Advice About Matlab Hacking

• You want to have the graphics windows from Matlab opening up on your local machine, even when you are running Matlab remotely. Use ssh-agent for this - it's availabe through putty, openssh, ....
• Start up matlab without all of the Java GUI windows. My personal alias (using tcsh) is

          alias matlab '/usr/local/bin/matlab  -nojvm -nosplash'
  

  for pre-2009a versions, and

          alias matlab '/usr/local/bin/matlab  -nodesktop -nosplash'
  

  for the newer ones. Nosplash prevents the advertisement screen on startup.
• Avoid using loops whenever possible. Array operations are essential to decent performance. Example: matrix-matrix multiply of 200x200 matrices is over 1000 times faster using A*B instead of the usual triply nested loops. "Think vector" is a rule for Matlab, and it also applies to high performance computing (HPC) in general. The reason vectorization helps in HPC is that it generally maps well to hardware pipelines, or allows expressing the operations in terms of optimized BLAS libraries.
• Use script files; interactive operations should be for examining variables, debugging, experimenting with graphics options, making small changes.
• Use the diary function to keep track of session and to avoid having to retype in useful commands later. Beware, however: the diary file will be appended with each new Matlab session.
• Useful settings to put in your startup.m file, or at top of every Matlab script file:
  • !rm session Removes the file "session" from the current directory
  • diary session Creates a new file named "session" to store commands, results
  • format short e Makes Matlab print all variables using exponential notation. Otherwise, a single entry large in absolute value in an array can cause all the other entries to be printed as 0.0000. Try the commands

    format short; y = -10:12 ; z = y.^10

    to see what happens
  • format compact You may have noticed that Matlab prints a blank line before and after every command/result. This supresses those blank lines.
  • dbstop if error causes Matlab to stop inside any function that causes an error, so that you can examine local variables inside that function. Otherwise, when an error occurs, Matlab returns from the function and you cannot find out what values were held inside the function. Use "return" to go back to calling function, and "dbquit" to exit the debugger. This seems to be the default now in Matlab, to drop into the debugger when an error occurs.
  Most of these things can be done via the file "startup.m". by putting them into the scripts they will take effect wherever they are run. That is, you may ship your code around to other machines or give them to other people who not have your personalized startup.m file available.
• When creating arrays in a loop, first preallocate the space using zeros(). The loop

  for k = 1:n
      C(1:n,k) = v(1:n);
  end
  

  makes n calls for memory allocation from operating system, and it requires copying over the part of C built up so far to the newly allocated space each time. Instead use

  C = zeros(n,n);
  for k = 1:n
      C(1:n,k) = v(1:n);
  end
  

  Better yet, use: C = v(1:n)*ones(1,n);
• The manuals are out of date before being printed. The online help facility will show many useful commands not documented elsewhere. The demo command may also point out useful capabilities.
• When you use "help", pay attention to the lines near the end start with "See also". That's a good way to learn about new commands when you don't have a priori idea of what they would be named. Only in 2008 did I learn about "setdiff", and for 25 years had been doing it the hard way.
• Conformality problems:

  x = 1:n

  sets up a vector of length n, but is it a row vector or column vector? In the first case,

  y = A(1:n,1:n)*x

  gives an error message, while in the second it is valid. Handle this by converting it into a column vector: x = x(:). This makes x a column vector whether it is a row or column vector to begin with. It also converts a 2D array into a 1D array. Also see the reshape() function.
• Inquiry functions are useful for debugging: whos, length, size.
• You can use shell escape to edit a file, e.g., !emacs filename, or to do other stuff if you have only one window.
• Plotting: some graphics commands do not produce the result until the end of a script file is reached, or a command changing the view or axes occurs. Use drawnow to force drawing. Originally the behaviour was forced by Matlab using only one threaded.
• Performance evaluation: use clock or cputime. Avoid tic toc because then you cannot have nested timings. Some older Matlab scripts have a "flop" command, which gives an estimate of the number of floating point operations performed so far. However, that has been gone from Matlab from version 6.0 and higher. For that information, you'll have to count or estimate your own flops. If you need to use an older m-file, you may find it useful to write a flop() function that returns a zero value to prevent error messages.
• Sparse matrices should be used whenever reasonable. Convert to a sparse matrix by means of A = sparse(A). Note that many routines ( eig, svd, qr) require A to be dense; in that case use eig(full(A)), etc. We'll cover sparse matrices later, just keep this as a rule to bear in mind then.

• Next page: More Plotting
• Class home page: P573

• Started: Mon Feb 2 14:17:07 EST 2004
• Last Modified: Tue 22 Sep 2009, 03:37 PM