Development/GDB

Description	Content
module load	devel/gdb
Availability	bwUniCluster | BwForCluster_Chemistry
License	GPL
Citing	n/a
Links	Homepage | Documentation | Wiki | Mailinglists
Graphical Interface	No
Included modules	icc | icpc | ifort | idb

Introduction

The GNU Debugger (GDB) is a standard debugger for serial programs although it can be used for parallel and even distributed programs with few processes too. The Intel Debugger (IDB) uses the same commands for basic debugging as GDB and hence can be used instead of GDB just by substituting idbc for gdb.

Versions and Availability

A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the

Cluster Information System CIS

{{#widget:Iframe |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/devel/gdb |width=99% |height=120 }} On the command line interface of any bwHPC cluster you'll get a list of available versions by using the command 'module avail devel/gdb'.

$ : bwUniCluster
$ module avail devel/gdb
------------------------ /opt/bwhpc/common/modulefiles -------------------------
devel/gdb/7.7

Attention!
The default Linux GDB may be a different version. Check the default version by: 'gdb --version' without loaded GDB-module.

$ module clear                             # clear all loaded modules
Are you sure you want to clear all loaded modules!? [n] y
$ gdb --version                            # this is the default version
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-83.el6)
[...]
$ module avail devel/gdb                   # available GDB-module
------------------------ /opt/bwhpc/common/modulefiles -------------------------
devel/gdb/7.7

It is not recommended (or impossible) the debug MPI-based binaries with GDB. You can't attach to MPI'ed jobs, too.

Loading

It is possible to choose between several versions of GDB. By default both programs are installed. You can check the version which is currently used with:

$ gdb --version

$ gcc --version

To use a different version of GCC or GDB, you have to load it through the module system. For example you need GDB 7.7 or higher for GCC version 4.8 and above. In this case load the devel/gdb module.
How to load the desired version (e.g. GDB version 7.7):

$ module load devel/gdb/7.7

If you want to use IDB load the Intel compiler module:

$ module load compiler/intel

Documentation

For online documentation see the links section in the summary table at the top of this page. For local documentation consult the man page.

$ man gdb

or

$ man idb

Basic commands

The code you want to debug should be compiled with the -g option. If the optimization flag is not set, the GCC will still do some basic optimization. Therefore, it is recommended to turn off the optmization explicitly with the -O0 parameter for debugging. To start a debug session for a program execute GDB with the program path as parameter:

$ gdb ./example

Inside GDB is a prompt where you can enter commands. Important commands are listed below.

Command	Description
help cmd	Show help for command cmd.
break func	Set a breakpoint at function func.
run	Start program.
next	Go to next program line. Do not enter functions.
step	Go to next program line. Enter functions.
list	Show the surrounding source code of the currently processed line.
print expr	Print the value of the expression expr.
display expr	Display the value of the expression expr every time the program stops.
watch expr	Stop when value of the expression expr changes.
continue	Continue execution until a breakpoint or a watchpoint appears.
backtrace	Print a list of functions that are currently active.
quit	Exit GDB.

Example: We debug the following program called bug.c which crashes on execution.

#include <stdio.h>

int global = 0;

void begin() {
    global = 1;
}

void loop() {
    int v[2];
    int i, k;

    for(i = 0; i < 8; i++) {
        k = i/2*2;	/* should have been k = i/(2*2); */
        v[k] = i;
    }
}

void end() {
    global = 2;
}

int main() {
    begin();
    loop();
    end();

    return 0;
}

Sample GDB session:

$ gcc -g bug.c -o bug
$ gdb ./bug
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-60.el6_4.1)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /pfs/data2/home/xx/xxx/xxxx/bug...done.
(gdb) break main
Breakpoint 1 at 0x4005b2: file bug.c, line 26.
(gdb) run
Starting program: /pfs/data2/home/xx/xxx/xxxx/bug

Breakpoint 1, main () at bug.c:26
26              begin();
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.132.el6.x86_64 libgcc-4.4.7-4.el6.x86_64
(gdb) next
27              loop();
(gdb) next

Program received signal SIGSEGV, Segmentation fault.
0x0000000000000005 in ?? ()
(gdb) # now we know that the bug is in loop(). start again.
(gdb) run
The program being debugged has been started already.
Start it from the beginning? (y or n) y
Starting program: /pfs/data2/home/xx/xxx/xxxx/bug

Breakpoint 1, main () at bug.c:26
26              begin();
(gdb) next
27              loop();
(gdb) step
loop () at bug.c:13
13              for(i = 0; i < 8; i++)
(gdb) next
15                      k = i/2*2;
(gdb) next
16                      v[k] = i;
(gdb) # maybe k gets too big?
(gdb) watch (k >= 2)
Hardware watchpoint 2: (k >= 2)
(gdb) continue
Continuing.
Hardware watchpoint 2: (k >= 2)

Old value = 0
New value = 1
loop () at bug.c:16
16                      v[k] = i;
(gdb) # k is too big
(gdb) print k
$1 = 2
(gdb) print i
$2 = 2
(gdb) quit

Core dumps

When the program crashes, a log file (called core dump) can be created which contains the state of the program when it crashed. This is turned off by default because these core dumps can get quite large. If you want to turn it on you have to change your ulimits, for example:

$ ulimit -c unlimited

Every time your program crashes a new file called core.xxx (where xxx is a number) will be created in the directory from which you started the executable. You can call gdb to examine your core dump using the following command (assuming your program is called ex):

$ gdb ./ex core.xxx

Now you can print a backtrace to check in which function the error happened and what values the parameters had. Additionally you can examine the values of your variables to reproduce the error.

Multithreaded debugging

GDB can also be useful for multithreaded applications for example when OpenMP was used. By going through each thread separately you can better see what is really going on and you can check the computation step by step. The following commands are useful for multithreaded debugging:

Command	Description
info threads	Shows the status of all existing threads.
thread num	Switches to the thread with the number num

Example: We debug the following program called thread_bug.c which crashes on execution.

#include <stdio.h>
#include <pthread.h>

pthread_t thread;

void* thread3 (void* d)
{
    int w[2];
    int c, l;

    for(c = 0; c < 8; c++) {
        l = c/2*2;	/* should have been l = c/(2*2); */
        w[l] = c;
    }

    return NULL;
}

void* thread2 (void* d)
{
    int v[2];
    int i, k;

    for(i = 0; i < 8; i++) {
        sleep(4);
        k = i/(2*2);    /* should have been k = i/(2*2); */
        v[k] = i;
    }

    return NULL;
}

int main (){

    pthread_create (&thread, NULL, thread2, NULL);
    pthread_create (&thread, NULL, thread3, NULL);
  
    //Thread 1
    int count1 = 0;

    while(count1 < 4000){
      printf("Thread 1: %d\n", count1++);
    }

    pthread_join(thread, NULL);
    return 0;
}

Sample GDB thread session:

$ gcc -g thread_bug.c -o thread_bug -lpthread
$ gdb ./thread_bug
[...]
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /pfs/data2/home/xx/xxx/xxxx/bug...done.
(gdb) break thread3
Breakpoint 1 at 0x40060c: file thread_bug.c, line 11.
(gdb) break thread2
Breakpoint 2 at 0x400650: file thread_bug.c, line 24.
(gdb) break main
Breakpoint 3 at 0x40069e: file thread_bug.c, line 35.
(gdb) run
Starting program: /tank/home/doros/.t/thread_bug 
[Thread debugging using libthread_db enabled]

Breakpoint 3, main () at thread_bug.c:35
35	  pthread_create (&thread, NULL, thread2, NULL);
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.132.el6.x86_64
(gdb) info threads
* 1 Thread 0x7ffff7fe5700 (LWP 28260)  main () at thread_bug.c:35
(gdb) next
[New Thread 0x7ffff7fe3700 (LWP 28303)]
36	  pthread_create (&thread, NULL, thread3, NULL);
(gdb) info threads
  2 Thread 0x7ffff7fe3700 (LWP 28303)  thread2 (d=0x0) at thread_bug.c:24
* 1 Thread 0x7ffff7fe5700 (LWP 28260)  main () at thread_bug.c:36
(gdb) next
[Switching to Thread 0x7ffff7fe3700 (LWP 28303)]

Breakpoint 2, thread2 (d=0x0) at thread_bug.c:24
24	    for(i = 0; i < 8; i++) {
(gdb) next
25		sleep(4);
(gdb) next
[New Thread 0x7ffff77e2700 (LWP 28344)]
[Switching to Thread 0x7ffff77e2700 (LWP 28344)]

Breakpoint 1, thread3 (d=0x0) at thread_bug.c:11
11	    for(c = 0; c < 8; c++) {
(gdb) info threads
* 3 Thread 0x7ffff77e2700 (LWP 28344)  thread3 (d=0x0) at thread_bug.c:11
  2 Thread 0x7ffff7fe3700 (LWP 28303)  0x000000362f8accdd in nanosleep () from /lib64/libc.so.6
  1 Thread 0x7ffff7fe5700 (LWP 28260)  0x000000362f8725db in _IO_new_file_overflow () from /lib64/libc.so.6
(gdb) thread 2
[Switching to thread 2 (Thread 0x7ffff7fe3700 (LWP 28303))]#0  0x000000362f8accdd in nanosleep () from /lib64/libc.so.6
(gdb) next
Single stepping until exit from function nanosleep,
which has no line number information.
[Switching to Thread 0x7ffff77e2700 (LWP 28344)]

Breakpoint 1, thread3 (d=0x0) at thread_bug.c:11
11	    for(c = 0; c < 8; c++) {
(gdb) thread 2
[Switching to thread 2 (Thread 0x7ffff7fe3700 (LWP 28303))]#0  0x000000362f8acce9 in nanosleep () from /lib64/libc.so.6
(gdb) next
Single stepping until exit from function nanosleep,
which has no line number information.
0x000000362f8acb50 in sleep () from /lib64/libc.so.6
(gdb) info threads
  3 Thread 0x7ffff77e2700 (LWP 28344)  thread3 (d=0x0) at thread_bug.c:11
* 2 Thread 0x7ffff7fe3700 (LWP 28303)  0x000000362f8acb50 in sleep () from /lib64/libc.so.6
  1 Thread 0x7ffff7fe5700 (LWP 28260)  0x000000362f8476f0 in vfprintf () from /lib64/libc.so.6
(gdb) thread 3
[Switching to thread 3 (Thread 0x7ffff77e2700 (LWP 28344))]#0  thread3 (d=0x0) at thread_bug.c:11
11	    for(c = 0; c < 8; c++) {
(gdb) next
12	        l = c/2*2;	/* should have been l = c/(2*2); */
(gdb) watch (k >= 2)
No symbol "k" in current context.
(gdb) watch (l >= 2)
Hardware watchpoint 4: (l >= 2)
(gdb) continue
Continuing.
Thread 1: 0
Thread 1: 1
Thread 1: 2
Thread 1: 3
Thread 1: 4
[...]
Hardware watchpoint 4: (l >= 2)

Old value = 0
New value = 1
thread3 (d=0x0) at thread_bug.c:13
13	        w[l] = c;
(gdb) print l
$1 = 2
(gdb) print c
$2 = 2
(gdb) quit

Disassembling

Command	Description
info functions	Shows names and data types of all defined functions.
info line "function"	Map source lines to memory adresses (and back).
disassemble function	Disassembles "function" (or a function fragment).

Sample GDB disassembling session:

$ gcc -g bug.c -o bug
$ gdb ./bug
[...]
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from bug...done.
(gdb) info functions
All defined functions:

File bug.c:
void begin();
void end();
void loop();
int main();

Non-debugging symbols:
0x0000000000400370  _init
0x00000000004003a0  __libc_start_main@plt
0x00000000004003b0  __gmon_start__@plt
0x00000000004003c0  _start
0x00000000004003f0  deregister_tm_clones
0x0000000000400430  register_tm_clones
0x0000000000400470  __do_global_dtors_aux
0x0000000000400490  frame_dummy
0x0000000000400540  __libc_csu_init
0x00000000004005b0  __libc_csu_fini
0x00000000004005b4  _fini

Sample GDB disassembling session:

(gdb) disassemble main
Dump of assembler code for function main:
   0x000000000040050f <+0>:     push   %rbp
   0x0000000000400510 <+1>:     mov    %rsp,%rbp
   0x0000000000400513 <+4>:     mov    $0x0,%eax
   0x0000000000400518 <+9>:     callq  0x4004b6 <begin>
   0x000000000040051d <+14>:    mov    $0x0,%eax
   0x0000000000400522 <+19>:    callq  0x4004c7 <loop>
   0x0000000000400527 <+24>:    mov    $0x0,%eax
   0x000000000040052c <+29>:    callq  0x4004fe <end>
   0x0000000000400531 <+34>:    mov    $0x0,%eax
   0x0000000000400536 <+39>:    pop    %rbp
   0x0000000000400537 <+40>:    retq
End of assembler dump.

Sample GDB disassembling session:

(gdb) disassemble /m main
Dump of assembler code for function main:
23      int main() {
   0x000000000040050f <+0>:     push   %rbp
   0x0000000000400510 <+1>:     mov    %rsp,%rbp

24          begin();
   0x0000000000400513 <+4>:     mov    $0x0,%eax
   0x0000000000400518 <+9>:     callq  0x4004b6 <begin>

25          loop();
   0x000000000040051d <+14>:    mov    $0x0,%eax
   0x0000000000400522 <+19>:    callq  0x4004c7 <loop>

26          end();
   0x0000000000400527 <+24>:    mov    $0x0,%eax
   0x000000000040052c <+29>:    callq  0x4004fe <end>

27
28          return 0;
   0x0000000000400531 <+34>:    mov    $0x0,%eax

29      }
   0x0000000000400536 <+39>:    pop    %rbp
   0x0000000000400537 <+40>:    retq

End of assembler dump.

Sample GDB disassembling session:

(gdb) disassemble /m loop
Dump of assembler code for function loop:
9       void loop() {
   0x00000000004004c7 <+0>:     push   %rbp
   0x00000000004004c8 <+1>:     mov    %rsp,%rbp

10          int v[2];
11          int i, k;
12
13          for(i = 0; i < 8; i++) {
   0x00000000004004cb <+4>:     movl   $0x0,-0x4(%rbp)
   0x00000000004004d2 <+11>:    jmp    0x4004f5 <loop+46>
   0x00000000004004f1 <+42>:    addl   $0x1,-0x4(%rbp)
   0x00000000004004f5 <+46>:    cmpl   $0x7,-0x4(%rbp)
   0x00000000004004f9 <+50>:    jle    0x4004d4 <loop+13>

14              k = i/2*2;      /* should have been k = i/(2*2); */
   0x00000000004004d4 <+13>:    mov    -0x4(%rbp),%eax
   0x00000000004004d7 <+16>:    mov    %eax,%edx
   0x00000000004004d9 <+18>:    shr    $0x1f,%edx
   0x00000000004004dc <+21>:    add    %edx,%eax
   0x00000000004004de <+23>:    sar    %eax
   0x00000000004004e0 <+25>:    add    %eax,%eax
   0x00000000004004e2 <+27>:    mov    %eax,-0x8(%rbp)

15              v[k] = i;
   0x00000000004004e5 <+30>:    mov    -0x8(%rbp),%eax
   0x00000000004004e8 <+33>:    cltq
   0x00000000004004ea <+35>:    mov    -0x4(%rbp),%edx
   0x00000000004004ed <+38>:    mov    %edx,-0x10(%rbp,%rax,4)

16          }
17      }
   0x00000000004004fb <+52>:    nop
   0x00000000004004fc <+53>:    pop    %rbp
   0x00000000004004fd <+54>:    retq

End of assembler dump.

Sample objdump disassembling session:

$ objdump -S -D bug
[...]
00000000004004c7 <loop>:

void loop() {
  4004c7:       55                      push   %rbp
  4004c8:       48 89 e5                mov    %rsp,%rbp
    int v[2];
    int i, k;

    for(i = 0; i < 8; i++) {
  4004cb:       c7 45 fc 00 00 00 00    movl   $0x0,-0x4(%rbp)
  4004d2:       eb 21                   jmp    4004f5 <loop+0x2e>
        k = i/2*2;      /* should have been k = i/(2*2); */
  4004d4:       8b 45 fc                mov    -0x4(%rbp),%eax
  4004d7:       89 c2                   mov    %eax,%edx
  4004d9:       c1 ea 1f                shr    $0x1f,%edx
  4004dc:       01 d0                   add    %edx,%eax
  4004de:       d1 f8                   sar    %eax
  4004e0:       01 c0                   add    %eax,%eax
  4004e2:       89 45 f8                mov    %eax,-0x8(%rbp)
        v[k] = i;
  4004e5:       8b 45 f8                mov    -0x8(%rbp),%eax
  4004e8:       48 98                   cltq
  4004ea:       8b 55 fc                mov    -0x4(%rbp),%edx
  4004ed:       89 54 85 f0             mov    %edx,-0x10(%rbp,%rax,4)

void loop() {
    int v[2];
    int i, k;

    for(i = 0; i < 8; i++) {
  4004f1:       83 45 fc 01             addl   $0x1,-0x4(%rbp)
  4004f5:       83 7d fc 07             cmpl   $0x7,-0x4(%rbp)
  4004f9:       7e d9                   jle    4004d4 <loop+0xd>
        k = i/2*2;      /* should have been k = i/(2*2); */
        v[k] = i;
    }
}
  4004fb:       90                      nop
  4004fc:       5d                      pop    %rbp
  4004fd:       c3                      retq
[...]