Development/GDB: Difference between revisions

From bwHPC Wiki
Jump to navigation Jump to search
 
(43 intermediate revisions by 7 users not shown)
Line 1: Line 1:
{{Softwarepage|devel/gdb}}
{| style="border-style: solid; border-width: 1px"

! Navigation: [[BwHPC_Best_Practices_Repository|bwHPC BPR]]
{| width=600px class="wikitable"
|-
! Description !! Content
|-
| module load
| devel/gdb
|-
| License
| [http://www.gnu.org/licenses/ GPL]
|-
|Citing
| n/a
|-
| Links
| [http://www.gnu.org/software/gdb/ Homepage] | [http://www.gnu.org/software/gdb/documentation/ Documentation] | [https://sourceware.org/gdb/wiki/ Wiki] | [http://www.gnu.org/software/gdb/mailing-lists/ Mailinglists]
|-
| Graphical Interface
| No
|-
| Included modules
| icc | icpc | ifort | idb
|}
|}
<br>
= 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>.
<br>


= Debugging =
= Basic commands =
The code you want to debug should be compiled with the <kbd><font color=green>-g</font></kbd> 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 <font color=green>-O0</font> parameter for debugging. To start a debug session for a program execute GDB with the program path as parameter:

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.

== Loading ==
There is no need for loading GDB because it is available by default. If you want to use IDB load the Intel compiler module:
<pre>$ module load compiler/intel</pre>

== Documentation ==
'''Online documentation:''' [http://www.gnu.org/software/gdb/documentation/ GDB documentation] and [http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/debugger/user_guide/index.htm IDB Documentation]

'''Local documentation:'''
For detailed lists of the different program options consult the man page:
<pre>$ man gdb</pre>
or
<pre>$ man idb</pre>

== Basic commands ==
The code you want to debug should be compiled with the -g option and it is recommended that optimization flags are not set. To start a debug session for a program execute GDB with the program path as parameter:
<pre>$ gdb ./example</pre>
<pre>$ gdb ./example</pre>


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


{| width=600px class="wikitable"
{| {{Table}}
|-
|-
! Command
! Command
Line 68: Line 76:
|}
|}


'''Example:'''
We debug the following program called bug.c which crashes on execution.
<source lang="c">
#include <stdio.h>


int global = 0;


= Branch record tracing =
void begin() {
Starting with GBD-10.1, the debugger has been installed with Intel Processor Trace [https://github.com/intel/libipt libipt], allowing recording and replaying of process state.
global = 1;
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,
void loop() {
<kbd>valgrind</kbd> would ''not'' have helped: this loops overwrites <kbd>v</kbd> an
int v[2];
array of 2 ints on the stack and the return address leading to the execution of IP <kbd>0x07</kbd>.
int i, k;


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


<br>
void end() {
global = 2;
}


= Core dumps =
int main() {
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:
begin();
<pre>$ ulimit -c unlimited</pre>
loop();
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):
end();
<pre>$ gdb ./ex core.xxx</pre>
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.
<br>


return 0;
}
</source>


= Multithreaded debugging =
'''Sample GDB session:'''
<pre>
$ 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
</pre>

== 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.
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:

{| {{Table}}
|-
! Command
! Description
|-
| info threads
| Shows the status of all existing threads.
|-
| thread ''num''
| Switches to the thread with the number ''num''
|}

= Valgrind =

Valgrind can be used for debugging and profiling programs. It ships with various tools, some of them are described in the following table.

{| {{Table}}
|-
! Tool
! Description
|-
| memcheck
| Detects heap array overruns, memory leaks and incorrect freeing of heap memory.
|-
| exp-sgcheck
| Detects stack and global array overruns.
|-
| callgrind
| Profiler. Helps finding bottlenecks.
|-
| helgrind
| Detects race conditions and deadlocks.
|-
| drd
| Detects race conditions. Does not detect deadlocks but needs less memory than helgrind.
|}

'''Loading:''' There is no need for loading valgrind because it is available by default.

'''Online documentation:''' http://valgrind.org/docs/
'''Local documentation:''' <pre>man valgrind</pre>

'''Usage:'''
To simulate your program and gather information about it using a specific tool, valgrind can be called like this
<pre>$ valgrind --tool=<tool> --log-file=<logfile> ./example</pre>
For example to check for race conditions the command would look like this:
<pre>$ valgrind --tool=drd --log-file=log.mem ./example</pre>

Beware that the simulation via valgrind can take much longer and can consume much more memory compared to a normal execution.
Furthermore the tools can give false positives, i.e. they report errors even though the are none.

'''Example for helgrind and drd:'''

This small program demonstrates how to detect data races in parallel programs. Both helgrind and drd support POSIX Threads (Pthreads) but not OpenMP so prepare to get many false positives when using these tools with OpenMP.

<source lang=c>
/* pthreads.c */
#include <pthread.h>
#include <stdio.h>
#include <unistd.h>
#include <math.h>

#define NUM_THREADS 2

int v = 0;

void* f(void* x)
{
int j = 0;
int k = *(int*)x;
for(j = 0; j < 100; j++)
v += sin(j) + 1 + k;

return NULL;
}

int main(int argc, char *argv[])
{
pthread_t threads[NUM_THREADS];
int idx[NUM_THREADS];
int t;
for(t=0; t<NUM_THREADS; t++) {
idx[t] = t;
pthread_create(&threads[t], NULL, f, (void*)&idx[t]);
}
for(t=0; t<NUM_THREADS; t++)
pthread_join(threads[t], NULL);

printf("%i\n", v);

pthread_exit(NULL);

return 0;
}
</source>
The program can be compiled with
<pre>$ gcc -Wall pthreads.c -o pthreads -pthread -lm -O2</pre>
where -pthread tells the compiler to link against the Pthreads library and -lm is needed for linking against the math library.
This program has a race condition, consecutive executions can give different outputs. Such errors are hard to find because they can show up very rarely.
Helgrind can tell you the problematic part of your code:
<pre>
$ valgrind --tool=helgrind ./pthreads
...
==29237== ----------------------------------------------------------------
==29237==
==29237== Possible data race during read of size 4 at 0x600C78 by thread #3
==29237== Locks held: none
==29237== at 0x4007BC: f(void*) (in /pfs/data2/home/xx/xxxx/xxxx/pthreads)
==29237== by 0x4A0C0D4: mythread_wrapper (hg_intercepts.c:219)
==29237== by 0x3EDA6079D0: start_thread (in /lib64/libpthread-2.12.so)
==29237== by 0x3ED9AE8B6C: clone (in /lib64/libc-2.12.so)
==29237==
==29237== This conflicts with a previous write of size 4 by thread #2
==29237== Locks held: none
==29237== at 0x4007FB: f(void*) (in /pfs/data2/home/xx/xxxx/xxxx/pthreads)
==29237== by 0x4A0C0D4: mythread_wrapper (hg_intercepts.c:219)
==29237== by 0x3EDA6079D0: start_thread (in /lib64/libpthread-2.12.so)
==29237== by 0x3ED9AE8B6C: clone (in /lib64/libc-2.12.so)
==29237==
==29237== ----------------------------------------------------------------
...
</pre>
Now we know that we have to check the function f for a possible data race. A similar output can be achieved using drd with the following command:
<pre>$ valgrind --tool=drd ./pthreads</pre>

Valgrind can give even better hints when compiled with debug information (helgrind produces similar output):
<pre>
$ gcc -g -Wall pthreads.c -o pthreads -pthread -lm
$ valgrind --tool=drd ./pthreads
...
==604== Thread 3:
==604== Conflicting load by thread 3 at 0x00600cc0 size 4
==604== at 0x400749: f(void*) (pthreads.c:17)
==604== by 0x4A128B4: vgDrd_thread_wrapper (drd_pthread_intercepts.c:355)
==604== by 0x3EDA6079D0: start_thread (in /lib64/libpthread-2.12.so)
==604== by 0x3ED9AE8B6C: clone (in /lib64/libc-2.12.so)
==604== Allocation context: BSS section of fs/data2/home/xx/xxxx/xxxx/pthreads
==604== Other segment start (thread 2)
==604== (thread finished, call stack no longer available)
==604== Other segment end (thread 2)
==604== (thread finished, call stack no longer available)
...
</pre>
The execution can take longer but now we know that the problem is most likely in line 17 (which is correct).

= Parallel Debugger ddt =

{| style="width:100%; vertical-align:top; background:#f5fffa;border:1px solid #e7aa01;"
| style="padding:2px;" | <div style="margin:3px; background:#cef2e0; font-size:120%; font-weight:bold; border:1px solid #e7aa01; text-align:left; color:#000; padding:0.2em 0.4em;">Currently only for employees of KIT</div>
|-
| style="color:#000;" | <div style="padding:2px 5px">On bwUniCluster the GUI based distributed debugging tool (ddt) may be used to debug serial as
well as parallel applications. For serial applications also the GNU gdb or Intel idb debugger
may be used. The Intel idb comes with the compiler and information on this tool is available
together with the compiler documentation. In order to debug your program it must be
compiled and linked using the -g compiler option. This will force the compiler to add additional information to the object code which is used by the debugger at runtime.
</div>
|}



ddt consists of a graphical frontend and a backend serial debugger which controls the
application program. One instance of the serial debugger controls one MPI process. Via the
frontend the user interacts with the debugger to select the program that will be debugged,
to specify different options and to monitor the execution of the program. Debugging
commands may be sent to one, all or a subset of the MPI processes.

Before the parallel debugger ddt can be used, it is necessary to load the corresponding
module file:
<pre>
$ module use /opt/bwhpc/ka/modulefiles (only available for employees of KIT)
$ module add debugger/ddt
</pre>

Now ddt may be started with the command
<pre>
$ ddt program
</pre>

where program is the name of your program that you want to debug.

[[File:ddt1_750.jpg]]

Figure: DDT startup window

The above figure shows ddt’s startup window. Before actually starting the debugging session
you should check the contents of several fields in this window:

1. The top line shows the executable file that will be run under control of the debugger. In
the following lines you may input some options that are passed to your program or to the
MPI environment.

2. If your program reads data from stdin you can specify an input file in the startup window.

3. Before starting an MPI program you should check that "Open MPI (Compatability)" or
"Intel MPI" is the MPI implementation that has been selected. If this is not the case, you
have to change this. Otherwise ddt may not be able to run your program. In order to debug
serial programs, the selected MPI implementation should be "none". You may also change
the underlying serial debugger using the "change" button. By default ddt uses its own serial debugger, but it may also use the Intel idb debugger.

4. Select the number of MPI processes that will be started by ddt. If you are using ddt within
a batch job, replace mpirun by ddt in the command line of ????? and make sure that the
chosen number of MPI processes is identical to the number of MPI tasks (-p option ???) that
you selected with the ?????? command. When you debug a serial program, select 1.

5. After you have checked all inputs in the ddt startup window, you can start the debugging
session by pressing the "run" button.


The ddt window now shows the source code of the program that is being debugged and breakpoints can be set by just pointing to the corresponding line and pressing the right
mouse button. So you may step through your program, display the values of variables
and arrays and look at the message queues.

[[File:ddt2_750.jpg]]

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"