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

1 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.

2 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.

3 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

4 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.

5 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:

Difference between revisions of "Development/GDB"

Latest revision as of 00:49, 9 December 2022

Contents

1 Description

2 Basic commands

3 Branch record tracing

4 Core dumps

5 Multithreaded debugging

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@@ 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"
-<!--{|  align="right" {{Table|width=40%}}   -->
-{|{{Softwarebox}}
 |-
+! Description !! Content
-! colspan="2"  style="text-align:center" | GDB: The GNU Project Debugger
 |-
 | module load
 | devel/gdb
-<!-- Neben CIS auch bereits über Kategorien  abgedeckt
-|-
-| Availability
-| [[bwUniCluster]] [[bwForFreiburg]],  [[bwForMannheim-Heidelberg]],  [[bwForUlm]],  [[bwForTübingen]]
--->
 |-
 | License
@@ Line 20: / Line 12: @@
 |-
 |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]
+| [http://www.gnu.org/software/gdb/ Homepage] &#124; [http://www.gnu.org/software/gdb/documentation/  Documentation] &#124; [https://sourceware.org/gdb/wiki/ Wiki] &#124; [http://www.gnu.org/software/gdb/mailing-lists/ Mailinglists]
-|
 |-
 | Graphical Interface
+| No
-| No <!-- Yes could link to some x11-forwarding/vnc instructions -->
 |-
-| Included in module
+| Included modules
+|  icc &#124; icpc &#124; ifort &#124; idb
-| <!-- mention if there is more than one software in the module, i.e. icc, ifort and debugger -->
 |}
+<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 ==
-It is possible to choose between several versions of GDB and GCC. By default both programms are installed. You can check the version which is currently used with:
-<pre>$ gdb --version</pre>
-<pre>$ gcc --version</pre>
-If you want to use another 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 check which versions are available:
-<pre>$ module avail</pre>
-How to load the desired version (e.g. GDB version 7.7):
-<pre>$ module load devel/gdb/7.7</pre>
-If you want to use IDB load the Intel compiler module:
-<pre>$ module load compiler/intel</pre>
-== 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>
-or
-<pre>$ man idb</pre>
-== Basic commands ==
-The code you want to debug should be compiled with the -g option. If the optimization flag is just not set, the GCC will still do some basic optimization. So it is recommended to turn off the optmization explicitly with the -O0 parameter. To start a debug session for a program execute GDB with the program path as parameter:
 <pre>$ gdb ./example</pre>
 Inside GDB is a prompt where you can enter commands. Important commands are listed below.
+{| width=600px class="wikitable"
-{| {{Table}}
 |-
 ! Command
@@ Line 107: / 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() {
-    begin();
-    loop();
-    end();
-    return 0;
-}
-</source>
-'''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
-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
-loop();
-(gdb) next
-Program received signal SIGSEGV, Segmentation fault.
-x0000000000000005 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
-begin();
-(gdb) next
-loop();
-(gdb) step
-loop () at bug.c:13
-for(i = 0; i < 8; i++)
-(gdb) next
-k = i/2*2;
-(gdb) next
-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
-v[k] = i;
-(gdb) # k is too big
-(gdb) print k
-$1 = 2
-(gdb) print i
-$2 = 2
-(gdb) quit
-</pre>
-== Core dumps ==
 When the program crashes, a log file (called core dump) can be created which contains the state of the program when it crashed. This is turned off by default because these core dumps can get quite large. If you want to turn it on you have to change your ulimits, for example:
 <pre>$ ulimit -c unlimited</pre>
@@ Line 211: / Line 96: @@
 <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>
-== Multithreaded debugging ==
+= 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:
-{| {{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).