GNU Scientific Library -- Reference Manual - Debugging Numerical Programs

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# Debugging Numerical Programs

This chapter describes some tips and tricks for debugging numerical programs which use GSL.

## Using gdb

Any errors reported by the library are passed to the function `gsl_error`. By running your programs under gdb and setting a breakpoint in this function you can automatically catch any library errors. You can add a breakpoint for every session by putting

    break gsl_error

into your ``.gdbinit'` file in the directory where your program is started.

If the breakpoint catches an error then you can use a backtrace (`bt`) to see the call-tree, and the arguments which possibly caused the error. By moving up into the calling function you can investigate the values of variable at that point. Here is an example from the program `fft/test_trap`, which contains the following line,

    status = gsl_fft_complex_wavetable_alloc (0, &complex_wavetable);

The function `gsl_fft_complex_wavetable_alloc` takes the length of an FFT as its first argument. When this line is executed an error will be generated because the length of an FFT is not allowed to be zero.

To debug this problem we start `gdb`, using the file ``.gdbinit'` to define a breakpoint in `gsl_error`,

    bash$ gdb test_trap

    GDB is free software and you are welcome to distribute copies
    of it under certain conditions; type "show copying" to see
    the conditions.  There is absolutely no warranty for GDB;
    type "show warranty" for details.  GDB 4.16 (i586-debian-linux),
    Copyright 1996 Free Software Foundation, Inc.

    Breakpoint 1 at 0x8050b1e: file error.c, line 14.

When we run the program this breakpoint catches the error and shows the reason for it.

    (gdb) run
    Starting program: test_trap

    Breakpoint 1, gsl_error (reason=0x8052b0d
        "length n must be positive integer",
        file=0x8052b04 "c_init.c", line=108, gsl_errno=1)
        at error.c:14
    14        if (gsl_error_handler)

The first argument of `gsl_error` is always a string describing the error. Now we can look at the backtrace to see what caused the problem,

    (gdb) bt
    #0  gsl_error (reason=0x8052b0d
        "length n must be positive integer",
        file=0x8052b04 "c_init.c", line=108, gsl_errno=1)
        at error.c:14
    #1  0x8049376 in gsl_fft_complex_wavetable_alloc (n=0,
        wavetable=0xbffff778) at c_init.c:108
    #2  0x8048a00 in main (argc=1, argv=0xbffff9bc)
        at test_trap.c:94
    #3  0x80488be in ___crt_dummy__ ()

We can see that the error was generated in the function `gsl_fft_complex_wavetable_alloc` when it was called with an argument of n=0. The original call came from line 94 in the file ``test_trap.c'`.

By moving up to the level of the original call we can find the line that caused the error,

    (gdb) up
    #1  0x8049376 in gsl_fft_complex_wavetable_alloc (n=0,
        wavetable=0xbffff778) at c_init.c:108
    108   GSL_ERROR ("length n must be positive integer", GSL_EDOM);
    (gdb) up
    #2  0x8048a00 in main (argc=1, argv=0xbffff9bc)
        at test_trap.c:94
    94    status = gsl_fft_complex_wavetable_alloc (0,
            &complex_wavetable);

Thus we have found the line that caused the problem. From this point we could also print out the values of other variables such as `complex_wavetable`.

## Examining floating point registers

The contents of floating point registers can be examined using the command `info float` (not available on all platforms).

    (gdb) info float
         st0: 0xc4018b895aa17a945000  Valid Normal -7.838871e+308
         st1: 0x3ff9ea3f50e4d7275000  Valid Normal 0.0285946
         st2: 0x3fe790c64ce27dad4800  Valid Normal 6.7415931e-08
         st3: 0x3ffaa3ef0df6607d7800  Spec  Normal 0.0400229
         st4: 0x3c028000000000000000  Valid Normal 4.4501477e-308
         st5: 0x3ffef5412c22219d9000  Zero  Normal 0.9580257
         st6: 0x3fff8000000000000000  Valid Normal 1
         st7: 0xc4028b65a1f6d243c800  Valid Normal -1.566206e+309
       fctrl: 0x0272 53 bit; NEAR; mask DENOR UNDER LOS;
       fstat: 0xb9ba flags 0001; top 7; excep DENOR OVERF UNDER LOS
        ftag: 0x3fff
         fip: 0x08048b5c
         fcs: 0x051a0023
      fopoff: 0x08086820
      fopsel: 0x002b

Individual registers can be examined using the variables $reg, where reg is the register name.

    (gdb) p $st1
    $1 = 0.02859464454261210347719

## Handling floating point exceptions

It is possible to stop the program whenever a `SIGFPE` floating point exception occurs. This can be useful for finding the cause of an unexpected infinity or `NaN`. The current handler settings can be shown with the command `info signal SIGFPE`.

    (gdb) info signal SIGFPE
    Signal  Stop  Print  Pass to program Description
    SIGFPE  Yes   Yes    Yes             Arithmetic exception

Unless the program uses a signal handler the default setting should be changed so that SIGFPE is not passed to the program, as this would cause it to exit. The command `handle SIGFPE stop nopass` prevents this.

    (gdb) handle SIGFPE stop nopass
    Signal  Stop  Print  Pass to program Description
    SIGFPE  Yes   Yes    No              Arithmetic exception

Depending on the platform it may be necessary to instruct the kernel to generate signals for floating point exceptions. For programs using GSL this can be achieved using the `GSL_IEEE_MODE` environment variable in conjunction with the function `gsl_ieee_env_setup()` as described in see section IEEE floating-point arithmetic.

    (gdb) set env GSL_IEEE_MODE=double-precision

## GCC warning options for numerical programs

Writing reliable numerical programs in C requires great care. The following GCC warning options are recommended when compiling numerical programs:

    gcc -ansi -pedantic -Werror -Wall -W
      -Wmissing-prototypes -Wstrict-prototypes
      -Wtraditional -Wconversion -Wshadow
      -Wpointer-arith -Wcast-qual -Wcast-align
      -Wwrite-strings -Wnested-externs
      -fshort-enums -fno-common -Dinline= -g -O4

For details of each option consult the manual Using and Porting GCC. The following table gives a brief explanation of what types of errors these options catch.

`-ansi -pedantic`
  Use ANSI C, and reject any non-ANSI extensions. These flags help in writing portable programs that will compile on other systems.
`-Werror`
  Consider warnings to be errors, so that compilation stops. This prevents warnings from scrolling off the top of the screen and being lost. You won't be able to compile the program until it is completely warning-free.
`-Wall`
  This turns on a set of warnings for common programming problems. You need `-Wall`, but it is not enough on its own.
`-O4`
  Turn on optimization. The warnings for uninitialized variables in `-Wall` rely on the optimizer to analyze the code. If there is no optimization then the warnings aren't generated.
`-W`
  This turns on some extra warnings not included in `-Wall`, such as missing return values and comparisons between signed and unsigned integers.
`-Wmissing-prototypes -Wstrict-prototypes`
  Warn if there are any missing or inconsistent prototypes. Without prototypes it is harder to detect problems with incorrect arguments.
`-Wtraditional`
  This warns about certain constructs that behave differently in traditional and ANSI C. Whether the traditional or ANSI interpretation is used might be unpredictable on other compilers.
`-Wconversion`
  The main use of this option is to warn about conversions from signed to unsigned integers. For example, `unsigned int x = -1`. If you need to perform such a conversion you can use an explicit cast.
`-Wshadow`
  This warns whenever a local variable shadows another local variable. If two variables have the same name then it is a potential source of confusion.
`-Wpointer-arith -Wcast-qual -Wcast-align`
  These options warn if you try to do pointer arithmetic for types which don't have a size, such as `void`, if you remove a `const` cast from a pointer, or if you cast a pointer to a type which has a different size, causing an invalid alignment.
`-Wwrite-strings`
  This option gives string constants a `const` qualifier so that it will be a compile-time error to attempt to overwrite them.
`-fshort-enums`
  This option makes the type of `enum` as short as possible. Normally this makes an `enum` different from an `int`. Consequently any attempts to assign a pointer-to-int to a pointer-to-enum will generate a cast-alignment warning.
`-fno-common`
  This option prevents global variables being simultaneously defined in different object files (you get an error at link time). Such a variable should be defined in one file and referred to in other files with an `extern` declaration.
`-Wnested-externs`
  This warns if an `extern` declaration is encountered within an function.
`-Dinline=`
  The `inline` keyword is not part of ANSI C. Thus if you want to use `-ansi` with a program which uses inline functions you can use this preprocessor definition to remove the `inline` keywords.
`-g`
  It always makes sense to put debugging symbols in the executable so that you can debug it using `gdb`. The only effect of debugging symbols is to increase the size of the file, and you can use the `strip` command to remove them later if necessary.

## References and Further Reading

The following books are essential reading for anyone writing and debugging numerical programs with GCC and GDB.

- R.M. Stallman, Using and Porting GNU CC, Free Software Foundation, ISBN 1882114388
- R.M. Stallman, R.H. Pesch, Debugging with GDB: The GNU Source-Level Debugger, Free Software Foundation, ISBN 1882114779

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