Debugging Numerical Programs¶
This chapter describes some tips and tricks for debugging numerical programs which use GSL.
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:
.gdbinit file in the directory where your program is
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 variables at that point. Here is an example
from the program
fft/test_trap, which contains the following
status = gsl_fft_complex_wavetable_alloc (0, &complex_wavetable);
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
$ 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
n = 0. The original call came from line 94 in the
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
Examining floating point registers¶
The contents of floating point registers can be examined using the
info float (on supported 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 is the register name:
(gdb) p $st1 $1 = 0.02859464454261210347719
Handling floating point exceptions¶
It is possible to stop the program whenever a
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 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 -Wconversion -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wnested-externs -fshort-enums -fno-common -Dinline= -g -O2
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.
Use ANSI C, and reject any non-ANSI extensions. These flags help in writing portable programs that will compile on other systems.
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.
This turns on a set of warnings for common programming problems. You need
-Wall, but it is not enough on its own.
Turn on optimization. The warnings for uninitialized variables in
-Wallrely on the optimizer to analyze the code. If there is no optimization then these warnings aren’t generated.
This turns on some extra warnings not included in
-Wall, such as missing return values and comparisons between signed and unsigned integers.
Warn if there are any missing or inconsistent prototypes. Without prototypes it is harder to detect problems with incorrect arguments.
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.
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
constcast from a pointer, or if you cast a pointer to a type which has a different size, causing an invalid alignment.
This option gives string constants a
constqualifier so that it will be a compile-time error to attempt to overwrite them.
This option makes the type of
enumas short as possible. Normally this makes an
enumdifferent from an
int. Consequently any attempts to assign a pointer-to-int to a pointer-to-enum will generate a cast-alignment warning.
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
This warns if an
externdeclaration is encountered within a function.
inlinekeyword is not part of ANSI C. Thus if you want to use
-ansiwith a program which uses inline functions you can use this preprocessor definition to remove the
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
stripcommand to remove them later if necessary.
References and Further Reading¶
The following books are essential reading for anyone writing and
debugging numerical programs with
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
For a tutorial introduction to the GNU C Compiler and related programs, see
B.J. Gough, http://www.network-theory.co.uk/gcc/intro/,’ An Introduction to GCC, Network Theory Ltd, ISBN 0954161793