Gdb basics for my sql db as (percona live europe 2019)

GDB Basics for MySQL DBAs
Valerii Kravchuk, Principal Support Engineer, MariaDB
vkravchuk@gmail.com
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Who am I?
Valerii (aka Valeriy) Kravchuk:
● MySQL Support Engineer in MySQL AB, Sun and Oracle, 2005-2012
● Principal Support Engineer in Percona, 2012-2016
● Principal Support Engineer in MariaDB Corporation since March 2016
● http://mysqlentomologist.blogspot.com - my blog about MySQL (a lot about
MySQL bugs, but some HowTos as well)
● https://www.facebook.com/valerii.kravchuk - my Facebook page, a lot about
MySQL (mostly bugs…)
● http://bugs.mysql.com - my personal playground
● @mysqlbugs #bugoftheday
● Community Contributor of the Year 2019
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GDB for DBAs?
GDB, gdb, GNU Debugger
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Usually gdb is used by developers, to study core
dumps...
● Mostly like this:
gdb /path/to/mysqld /path/to/coredump
● Bug #76432 - “handle_fatal_signal (sig=11) in __strlen_sse2_pminub on
CHANGE MASTER”
● Bug #69898 - “change_master() invokes ha_innobase::truncate() in a
DML transaction” - a lot of useful gdb-related reading inside (check how
Marko uses call rec_print_old(stderr,$8.frame+0x16e) etc)
See also related Bug #69825 and how bug reporter attached full backtrace
in related Bug #73155
● Bug #96224 - “The MTR case innodb.innodb_corrupt_bit get a randomly
coredump” for a more recent example (fixed in upcoming 8.0.18).
Developers and users with QA mindset often use debug builds, hit debug
assertions etc, for MySQL DBAs to never hit the problems :)
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...or (surprise!) to debug their code
● Running “under gdb”:
gdb --args bin/mysqlcheck -u root -p -S/tmp/mysql.sock
--all-databases --optimize
(gdb) thread apply all bt
● Attaching gdb to the process already running:
gdb -p `pidof mysqld`
● Some examples:
○ Percona Server Bug #1483251 - “savepoints and replication”. Check
how Vlad Lesin uses backtrace to understand the reason of the bug
○ Percona Server Bug #1426345 - “Prepared statements in stored
procedures crash query response time plugin”. Check how Nickolay
Ihalainen pinpoint the root cause of the bug by comparing values of
various variables in gdb
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More examples here on how MariaDB
developers use gdb
● MDEV-13797 - InnoDB may hang if shutdown is initiated
soon after startup, while rolling back recovered
incomplete transactions
● MDEV-12052 - our buildbot tries to get backtrace for all
threads for crash
● MDEV-12413 - be ready to run some gdb commands
when you report bugs
● MDEV-14051 - this is how developers use “advanced”
gdb. See Bug #88150
● MDEV-13787 - real crash (fixed)
● MDEV-11044 - dumping pages etc, can't repeat, but still
some useful details
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But production DBAs also may benefit from gdb!
● First of all, gdb allows to inspect the values of variables
in the mysqld process memory, and thus you can check
some details about user threads and statements
executed that may not be easily available via SQL
(missing feature, can’t connect, hangs, bugs)
● Also gdb allows to change the values of variables, both
global and session ones (missing feature, read only
ones) directly or indirectly (by calling functions in the
code)
● Finally, attaching gdb allows to get a backtrace for further
study of the root cause of the problem
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GDB for DBAs?
● So, eventually DBAs I work with agree to install gdb (and
-debuginfo, -dbg etc packages to get symbolic information
for their binaries), and even enable coredumps on their
production servers
● They try to use gdb to get backtraces and more in
testing/staging environment
● Sending gdb outputs (backtraces of all threads in case of
any coredump) becomes a part of their SOP…
● And these help A LOT!
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Domas is famous for these tricks...
● http://dom.as/2009/02/15/poor-mans-contention-profiling/ -
this is what ended up as http://poormansprofiler.org/ and
pt-pmp
● http://dom.as/2009/07/30/evil-replication-management/ -
mysql> system gdb -p $(pidof mysqld) -ex "set
opt_log_slave_updates=1" -batch
● http://dom.as/2010/01/02/read-ahead/ -
gdb -ex "set srv_startup_is_before_trx_rollback_phase=1"
-batch -p $(pidof mysqld)
● http://dom.as/2009/12/29/when-bad-things-happen/
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More examples of gdb use for MySQL DBAs
● Remember the names:
Domas Mituzas, Shane Bester, Roel Van De Paar, Mark Callaghan,
Aurimas Mikalauskas, Zhai Weixiang, ...
● http://www.percona.com/blog/2012/09/09/obtain-last-executed-statement-from-
optimized-core-dump/
● http://www.percona.com/blog/2013/11/11/how-to-extract-all-running-queries-inc
luding-the-last-executed-statement-from-a-core-file/
● http://mysqlbugs.blogspot.com.au/2012/09/how-to-obtain-all-executing-queries.
html
● http://www.percona.com/blog/2010/03/23/too-many-connections-no-problem/
● All the above (or examples from any links shared here) are not recipes for
current/your exact version - more like inspiration for checks. They may
not apply literally to your version of MySQL!
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What MySQL DBA can do with gdb?
● Check stack traces (and variables), per thread:
thread apply all bt [full]
● Print variables, up to complex one (MySQL 5.6 times):
thread 1
print do_command::thd->query_string.string.str
In MySQL 5.7: (gdb) p dispatch_command::com_data->com_query.query
● Set new values for variables (global and per thread, even those formally
read-only in MySQL while it’s running):
set max_connections=5000
set opt_log_slave_updates=1
● Call functions (that may do complex changes):
call rpl_filter->add_do_db(strdup("hehehe"))
● Set breakpoints and watchpoints and get information when shit happens
● Use gdb as a command line utility (-batch), use Python scripting & more…
● All these may not work, fail, hang, crash, produce obscure errors…
● For this to work well DBA has to read and understand the source code
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pt-pmp (Poor Man’s Profiler)
● https://www.percona.com/doc/percona-toolkit/LATEST/pt-pmp.html
pt-pmp [-i 1] [-s 0] [-b mysqld] [-p pidofmysqld] [-l 0] [-k file] [--version]
● It is based on original idea by Domas, http://poormansprofiler.org/. I use
the awk code from the above to analyse backtraces of all threads.
● When mysqld hangs or is slow, you can get some insight quickly - use
pt-pmp to find out why (or what threads mostly do at the moment). For
example, see Bug #92108 (fixed in 5.7.25+, binlog access vs P_S query),
● Yet another example of how it is used: Bug #78277 - InnoDB deadlock,
thread stuck on kernel calls from transparent page compression, “Open”
● Use in production as a last resort (may hang mysqld, --SIGCONT)
● pt-pmp surely slows server down :) Hints:
○ https://bugs.launchpad.net/percona-toolkit/+bug/1320168 - partial
workaround
○ Use quickstack instead of gdb (check this discussion and this post)
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Multi-threaded mysqld process and gdb
● process/thread/frame concepts:
(gdb) thread 2
[Switching to thread 2 (Thread 0x7fe771550700 (LWP 2544))]
#0 0x0000000000605774 in Item_func_numhybrid::val_int (
this=<value optimized out>)
at /home/openxs/bzr2/percona-5.6/sql/item_func.cc:1013
1013 }
(gdb) bt
...
#12 0x00000000006f8a45 in dispatch_command (command=COM_QUERY,
thd=0x7fe760f94000, packet=0x7fe77154fac0 "", packet_length=0)
at /home/openxs/bzr2/percona-5.6/sql/sql_parse.cc:1434
...
(gdb) frame 12
#12 0x00000000006f8a45 in dispatch_command (command=COM_QUERY,
thd=0x7fe760f94000, packet=0x7fe77154fac0 "", packet_length=0)
at /home/openxs/bzr2/percona-5.6/sql/sql_parse.cc:1434
warning: Source file is more recent than executable.
1434 mysql_parse(thd, thd->query(), thd->query_length(), &parser_state);
(gdb) p thd->query_string.string.str
$2 = 0x7fe75301d010 "select benchmark(5", '0' <repeats 13 times>, ", 2*2)"
● https://sourceware.org/gdb/onlinedocs/gdb/Variables.html
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THD structure
grep -rn THD sql/sql_class.h
class THD :public MDL_context_owner,
public Statement,
public Open_tables_state
HASH user_vars; // hash for user vars
struct system_variables variables; // Changeable local
vars
struct system_status_var status_var;// Per thread stat
vars
struct system_status_var *initial_status_var; /* used by
show status */
Security_context main_security_ctx;
...
CSET_STRING query_string; // inherited from Statement…
... 14

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Checking core dump
● Make sure you know how to run gdb commands on core
file:
gdb -ex "set pagination 0"
-ex "thread apply all bt"
...
-batch `which mysqld` core.<pid> > backtrace.txt
● Make sure you know how to get core when mysqld
crashes:
http://www.percona.com/blog/2011/08/26/getting-mysql-core-file-on-linux/
● In case of troubles with SELinux, systemd etc read this
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Attaching to alive mysqld
This is how it goes:
[root@centos openxs]# mysql -uroot -e "show variables like
'innodb_autoinc_lock_mode'"
+--------------------------+-------+
| Variable_name | Value |
+--------------------------+-------+
| innodb_autoinc_lock_mode | 0 |
+--------------------------+-------+
[root@centos openxs]# mysql -uroot -e "set global
innodb_autoinc_lock_mode=1"
ERROR 1238 (HY000) at line 1: Variable 'innodb_autoinc_lock_mode' is a
read only variable
[root@centos openxs]# gdb -ex "set innobase_autoinc_lock_mode=1" -batch -p
`pidof mysqld`
…
[Thread debugging using libthread_db enabled]
0x00007ff31d6830d3 in poll () from /lib64/libc.so.6
… check the variable value again now
[root@centos openxs]# ps aux | grep mysqld
[root@centos openxs]# kill -SIGCONT `pidof mysqld`
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Finding processlist thread id with gdb
http://mysqlentomologist.blogspot.fi/2017/07/how-to-find-pro
cesslist-thread-id-in-gdb.html
● It may depend on MySQL version (changes in 5.7+)
● Basic idea - check threads one by one, find frame where
thd is defined, print:
(gdb) thread 2
(gdb) p do_command::thd->thread_id
● In 5.7+ there is some difference:
(gdb) thread 7
(gdb) p do_command::thd->m_thread_id
(gdb) p do_command::thd->m_main_security_ctx
● Even more difference if you want to automate looping
through threads… (more C++, singletons vs variables)
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Checking session variables with gdb
http://mysqlentomologist.blogspot.fi/2017/08/how-to-find-valu
es-of-session-variables.html
● It started with a “simple” question: how to find out from
the core dump if the session behind the crashing thread
had mrr=ON in the optimizer_switch?
● Basic idea is simple, it’s in thd->variables, somehow:
(gdb) p do_command::thd->variables->optimizer_switch
(gdb) p global_system_variables->optimizer_switch
● Then see defines in sql/sql_const.h:
#define OPTIMIZER_SWITCH_MRR (1ULL << 6)
● Then we can print it better:
p do_command::thd->variables->optimizer_switch & (1<<6)
p /t do_command::thd->variables->optimizer_switch
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Checking user variables with gdb
http://mysqlentomologist.blogspot.com/2017/08/how-to-find-v
alues-of-user-variables.html
● Basically it’s somewhere there, in thd:
p do_command::thd->user_vars
● But it’s not a simple array, it’s a HASH:
(gdb) p my_hash_element(&(do_command::thd->user_vars),
1)
(gdb) set $uvar = (user_var_entry
*)(my_hash_element(&(do_command::thd->user_vars), 1))
(gdb) p $uvar
(gdb) p *$uvar
● We can also get element by name:
(gdb) set $uvar=(user_var_entry
*)(my_hash_search(&(do_command::thd->user_vars), "e",
strlen("e")))
(gdb) p *((my_decimal *)$uvar->m_ptr)
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HASH structures in MySQL
http://mysqlentomologist.blogspot.com/2017/08/more-on-stu
dying-mysql-hashes-in-gdb.html
● HASH structure is used everywhere in MySQL, from keyring to UDFs and
table cache, to replication and NDB Cluster, with everything in between
● Check include/hash.h:
typedef struct st_hash {
...
ulong records;
DYNAMIC_ARRAY array;
...
} HASH;
● This gives us a way eventually to dump data without calling functions:
(gdb) set $uvars=&(do_command::thd->user_vars)
...
(gdb) p *(user_var_entry *)
(((HASH_LINK*)((&($uvars->array))->buffer) + (0))->data)
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Some gdb versions have Python, and this helps
● If you like and know Python and have gdb linked with it (try py print(1+1))...
● Use ~/.gdbinit file for complex Python macros
● http://mysqlbugs.blogspot.com/2012/09/how-to-obtain-all-executing-queries.
html - Shane Bester on simplified navigation over threads, nice printing of
selected values etc,
● https://mariadb.org/duel-gdb-vs-linked-lists-trees-hash-tables/ - “Duel: gdb
vs. linked lists, trees, and hash tables”. Sergei Golubchik on simplified
way to apply “something” (like print) to all/selected items of arrays, linked
lists etc. Check https://github.com/vuvova/gdb-tools
● https://mariadb.org/making-life-prettier-gdb-prettyprinting-api/ - “Making life
prettier with gdb PrettyPrinting API”. Sergei Golubchik on how to use
Python classes to pretty print almost anything inside MySQL code in gdb
● Make sure to check if you have Python 2 or 3 in gdb! (pip vs pip3 etc):
[openxs@fc23 ~]$ ldd `which gdb` | grep pyt
libpython3.5m.so.1.0 => /lib64/libpython3.5m.so.1.0
(0x00007fee3957d000)
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Some things to check before relying on gdb
● Check that gdb is installed and works
● Check that MySQL/Percona/MariaDB server you use has
symbolic information for gdb
● DBA may need to get sudo/root access
● Make sure you know how to enable core dumps on your
Linux, and know where they are located (it may become
complicated)
● Install pt-pmp (or entire Percona Toolkit) -
https://www.percona.com/get/pt-pmp - and check it
● Check all “recipes” at staging environment first!
● It’s probably a good idea to create useful ~/.gdbinit
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Results of using gdb to study MySQL internals
● Immediate DBA problems solved without restart etc
● Better understanding of how MySQL works!
● Blog posts, talks, presentations:
○ http://mysqlentomologist.blogspot.com/2016/01/exploring-metadata-locks-with-gdb-first.html
○ http://mysqlentomologist.blogspot.com/2016/01/exploring-metadata-locks-with-gdb.html
○ http://mysqlentomologist.blogspot.com/2016/01/exploring-metadata-locks-with-gdb-how.html
○ http://mysqlentomologist.blogspot.com/2015/03/using-gdb-to-understand-what-locks-and_31.html
○ http://mysqlentomologist.blogspot.com/2015/04/using-gdb-to-understand-what-locks-and.html
○ http://www.slideshare.net/valeriikravchuk1/understanding-innodb-locks-and-deadlocks
● Bug reports and documentation requests to make MySQL
and its manual better:
○ Bug #79665 - Manual does NOT explain locks set by INSERT ... ON DUPLICATE KEY UPDATE
properly
○ Bug #77390 - Manual does not explain a "deadlock" case of online ALTER
○ Bug #76588 - Metadata lock is NOT released when SELECT completes in case of autocommit=0
○ Bug #76563 - Manual does NOT explain when exactly AUTO-INC lock is set for "bulk inserts"
○ Bug #76533 - AUTO_INC lock seems to be NOT set for INSERT INTO t(val) SELECT val FROM t
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Is gdb an ultimate answer for MySQL DBA?
No, usually it is a temporary, one time solution or last
resort
Instead you may (or should, whenever possible):
● Use real profilers at OS level (like perf)
● Use troubleshooting tools at MySQL level (like P_S)
● Implement missing feature (like setting some variable
dynamically) or request it from developers
● Consider upgrade to version or fork that already has a
feature you miss
● Plan your work and do maintenance properly
● Read the manual and source code
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Thank you!
Questions and Answers?
Please, report bugs at:
http://bugs.mysql.com
https://jira.mariadb.org
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Gdb basics for my sql db as (percona live europe 2019)

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