Development/GDB: Difference between revisions

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{{Softwarepage|devel/gdb}}

{| width=600px class="wikitable"
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|-
|-
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| module load
| module load
| devel/gdb
| devel/gdb
|-
| Availability
| [[bwUniCluster]] | [[BwForCluster_Chemistry]]
|-
|-
| License
| License
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<br>
<br>
= Introduction =
= Description =
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. In the past Intel supported their own '''idb''' debugger, however this has been deprecated in favor of their own port called <kbd>gdb-ia</kbd>.
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. In the past Intel supported their own '''idb''' debugger, however this has been deprecated in favor of their own port called <kbd>gdb-ia</kbd>.
<br>
<br>

= Versions and Availability =
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
<br>
<big>

[https://cis-hpc.uni-konstanz.de/prod.cis/ Cluster Information System CIS]

</big>
{{#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 <kbd>module avail devel/gdb</kbd>.
<pre>
$ : bwUniCluster 2.0
$ module avail devel/gdb
------------------------ /opt/bwhpc/common/modulefiles/Core -------------------------
devel/gdb/9.2 devel/gdb/10.1 (D)</pre>

<font color=red>Attention!</font><br>
The installed default system GDB may be a different version.
Check the <font color=green>default</font> version by: <pre>gdb --version</pre> <font color=red>without loaded GDB-module</font>.
<pre>
$ module purge # clear all loaded modules
$ gdb --version # this is the default version
GNU gdb (GDB) Red Hat Enterprise Linux 8.2-11.el8
[...]
$ module avail devel/gdb # available GDB-module
------------------------ /opt/bwhpc/common/modulefiles/Core -------------------------
devel/gdb/9.2 devel/gdb/10.1 (D)</pre>
It is ''not'' recommended to debug MPI-parallel binaries with GDB, please read [[MPI]] on how to do that.
Rather parallel debuggers like ARM Forge (formerly Allinea ddt) or Totalview ease debugging with a GUI.
<br>


= 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:
<pre>$ gcc --version</pre>
<br>
To use a different version ofGDB, you have to load it through the module system.
For example if you need GDB 10.1, load the <kbd>devel/gdb</kbd> module.
<br>
How to load the desired version (e.g. GDB version 9.2):
<pre>$ module load devel/gdb/9.2</pre>
<br>


= 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.
<pre>$ man gdb</pre>
<br>



= Basic commands =
= Basic commands =
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|}
|}


'''Example:'''
We debug the following program called <kbd>bug.c</kbd> which crashes on execution.
<source lang="c">
#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;
}
</source>

'''Sample GDB session:'''
<pre>
$ gcc -Wall -O0 -g bug.c -o bug
$ gdb ./bug
GNU gdb (GDB) Red Hat Enterprise Linux 8.2-11.el8
[...]
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();
(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
</pre>
<br>


= Branch record tracing =
= Branch record tracing =
Line 227: Line 82:
This allows disassembling previously executed instructions, checking for previously called functions and branch tracing.
This allows disassembling previously executed instructions, checking for previously called functions and branch tracing.


Honestly, Segmentation Violations are better caught using [[Development/Valgrind|Valgrind]]. However in this case,
E.g. with the previous executable <kbd>bug</kbd> we may shorten the debug cycle by turning on recording.
<kbd>valgrind</kbd> would ''not'' have helped: this loops overwrites <kbd>v</kbd> an

array of 2 ints on the stack and the return address leading to the execution of IP <kbd>0x07</kbd>.
<pre>
$ gdb bug
GNU gdb (GDB) 10.1
[...]
Reading symbols from bug...
(gdb) break main
Breakpoint 1 at 0x400593: file bug.c, line 24.
(gdb) # Before we may turn on recording state, we have to have a running context
(gdb) run
Starting program: /pfs/data5/home/es/es_es/es_rakeller/C/bug

Breakpoint 1, main () at bug.c:24
(gdb) # Now we may turn on branch tracing with Intel Process Tracing semantics.
(gdb) record btrace pt
(gdb) cont
Continuing.

Program received signal SIGSEGV, Segmentation fault.
0x0000000000000007 in ?? ()
(gdb) # Just for information check how many instructions and functions have executed.
(gdb) info record
Active record target: record-btrace
Recording format: Intel Processor Trace.
Buffer size: 16kB.
Recorded 131 instructions in 4 functions (0 gaps) for thread 1 (process 1153077).
(gdb) # The last function call history shows the control flow on function level
(gdb) record function-call-history
1 main
2 begin
3 main
4 loop
(gdb) # Even more detail with the instruction counts and line numbers included:
(gdb) record function-call-history /ilc
1 main inst 1,2 at bug.c:24
2 begin inst 3,8 at bug.c:5,7
3 main inst 9,10 at bug.c:25
4 loop inst 11,131 at bug.c:9,17
(gdb) # Disassembles the last 10 instructions executed leading to the crash.
(gdb) record instruction-history
122 0x0000000000400565 <loop+30>: mov -0x8(%rbp),%eax
123 0x0000000000400568 <loop+33>: cltq
124 0x000000000040056a <loop+35>: mov -0x4(%rbp),%edx
125 0x000000000040056d <loop+38>: mov %edx,-0x10(%rbp,%rax,4)
126 0x0000000000400571 <loop+42>: addl $0x1,-0x4(%rbp)
127 0x0000000000400575 <loop+46>: cmpl $0x7,-0x4(%rbp)
128 0x0000000000400579 <loop+50>: jle 0x400554 <loop+13>
129 0x000000000040057b <loop+52>: nop
130 0x000000000040057c <loop+53>: pop %rbp
131 0x000000000040057d <loop+54>: ret
(gdb) # And another 10 disassembled instructions, nicely showing the control flow
(gdb) record instruction-history -
112 0x0000000000400571 <loop+42>: addl $0x1,-0x4(%rbp)
113 0x0000000000400575 <loop+46>: cmpl $0x7,-0x4(%rbp)
114 0x0000000000400579 <loop+50>: jle 0x400554 <loop+13>
115 0x0000000000400554 <loop+13>: mov -0x4(%rbp),%eax
116 0x0000000000400557 <loop+16>: mov %eax,%edx
117 0x0000000000400559 <loop+18>: shr $0x1f,%edx
118 0x000000000040055c <loop+21>: add %edx,%eax
119 0x000000000040055e <loop+23>: sar %eax
120 0x0000000000400560 <loop+25>: add %eax,%eax
121 0x0000000000400562 <loop+27>: mov %eax,-0x8(%rbp)
</pre>

Honestly, above Segmentation Violation would have been caught much easier by using <kbd>valgrind</kbd>.


More information is available in [https://sourceware.org/gdb/current/onlinedocs/gdb/Process-Record-and-Replay.html#Process-Record-and-Replay gdb's feature documentation]
More information is available in [https://sourceware.org/gdb/current/onlinedocs/gdb/Process-Record-and-Replay.html#Process-Record-and-Replay gdb's feature documentation]
Line 310: Line 102:
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.
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:
The following commands are useful for multithreaded debugging:

{| width=600px class="wikitable"
|-
! 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 <kbd>thread_bug.c</kbd> which crashes on execution.
<source lang="c">
#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;
}
</source>

'''Sample GDB thread session:'''
<pre>
$ gcc -g thread_bug.c -o thread_bug -lpthread
$ gdb ./thread_bug
[...]
Reading symbols from /pfs/data2/home/xx/xxx/xxxx/thread_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
</pre>
= Disassembling =
{| width=600px class="wikitable"
|-
! 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:'''
<pre>
$ gcc -Wall -O0 -g bug.c -o bug
$ gdb ./bug
[...]
(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
</pre>
'''Sample GDB disassembling session:'''
<pre>
(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.
</pre>
'''Sample GDB disassembling session:'''
<pre>
(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.
</pre>
'''Sample GDB disassembling session:'''
<pre>
(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.
</pre>
'''Sample objdump disassembling session:'''
<pre>
$ 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
[...]
</pre>

[[Category:debugger software]][[Category:bwUniCluster]]

Latest revision as of 00:49, 9 December 2022

The main documentation is available via module help devel/gdb on the cluster. Most software modules for applications provide working example batch scripts.


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


Description

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. In the past Intel supported their own idb debugger, however this has been deprecated in favor of their own port called gdb-ia.

Basic commands

The code you want to debug should be compiled with the -g option. If the optimization flag is not set, GCC will still do some basic optimization, like dead-code elimination or reorder instruction execution obfuscating the order when debugging. Therefore, it is recommended to turn off optimization 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.


Branch record tracing

Starting with GBD-10.1, the debugger has been installed with Intel Processor Trace libipt, allowing recording and replaying of process state. This allows disassembling previously executed instructions, checking for previously called functions and branch tracing.

Honestly, Segmentation Violations are better caught using Valgrind. However in this case, valgrind would not have helped: this loops overwrites v an array of 2 ints on the stack and the return address leading to the execution of IP 0x07.

More information is available in gdb's feature documentation


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:

Retrieved from "https://wiki.bwhpc.de/wiki/index.php?title=Development/GDB&oldid=11631"