pt-query-digest Alternatives - MySQL Query Management & Monitoring with ClusterControl

Agus Syafaat

When your database workload is over stressed, you first want to look at what queries are running in an attempt to see the pattern of the query. Is it write heavy? Read heavy? Where is the bottleneck? 

Identifying Query Issues

To figure it out you can enable the general log or the slow log to try to capture the queries which are running  and writing to the file. You also can read from the binary log (as binary log captures all the changes in the database) and look at reads directly from the running processlist in the database. You can even capture the query from the network perspective by looking through tcpdump.

What to do next? You can analyze the query that is written to general log file, slow log file, binary log to check if there is something interesting going on (eg. bottleneck in the query). 

Percona has a tool to analyze these type queries, named pt-query-digest.  It is included when you install the Percona Toolkit, a collection of utilities tools that help DBA to manage their databases. In this blog we will take a look at this tool and how it compares to the Query Management features of ClusterControl.

Installation Procedure

Percona repositories support two packages Linux Distribution for setup, which is Debian-based and RPM-based package distribution. The installation are just simple as shown below :

Debian-based package (Ubuntu, Debian)

Configure Percona package repositories by download the package

wget https://repo.percona.com/apt/percona-release_latest.generic_all.deb

And then install the downloaded package using dpkg

sudo dpkg -i percona-release_latest.generic_all.deb

After that, just run the installation from package manager

sudo apt-get install percona-toolkit

RPM-based package (RHEL, CentOS, Oracle Enterprise Linux, Amazon AMI)

Configure Percona package repositories by installing the rpm package directly.

sudo yum install https://repo.percona.com/yum/percona-release-latest.noarch.rpm 

After that, just run the installation from package manager

sudo apt-get install percona-toolkit

Percona utilities will be installed in your machine, and you just need to use it.

Query Workload Analyze

There are several ways to generate the statistics from the query workload using pt-query-digest, below is the command how to do it using a slow query file, general file, show processlist in database, and read through binary log.

Generate from show processlist database

pt-query-digest --processlist h=localhost,D=sbt,u=sbtest,p=12qwaszx --output slowlog > /tmp/slow_query.log

Generate from the slow query files / general query file

pt-query-digest mysql-slow.log > /tmp/slow_query.log

Generate from binary log. Before you run the pt-query-digest, you need to extract the binary log into readable format using mysqlbinlog. Don’t forget to add --type option and type binlog as the source.

pt-query-digest --type binlog mysql-bin.000001.txt > slow_query.log

After finish generating the file, you will see the report as shown below :

# 12s user time, 170ms system time, 27.44M rss, 221.79M vsz

# Current date: Sun May 10 21:40:47 2020

# Hostname: n2

# Files: mysql-1

# Overall: 94.92k total, 47 unique, 2.79k QPS, 27.90x concurrency ________

# Time range: 2020-05-10 21:39:37 to 21:40:11

# Attribute          total     min     max     avg     95%  stddev  median

# ============     ======= ======= ======= ======= ======= ======= =======

# Exec time           949s     6us      1s    10ms    42ms    42ms     2ms

# Lock time            31s       0      1s   327us    80us    11ms    22us

# Rows sent         69.36k       0     490    0.75    0.99   11.30       0

# Rows examine     196.34k       0     490    2.12    0.99   21.03    0.99

# Rows affecte      55.28k       0      15    0.60    0.99    1.26       0

# Bytes sent        13.12M      11   6.08k  144.93  299.03  219.02   51.63

# Query size        15.11M       5     922  166.86  258.32   83.13  174.84



# Profile

# Rank Query ID                      Response time  Calls R/Call V/M   Ite

# ==== ============================= ============== ===== ====== ===== ===

#    1 0xCE367F5CFFCAF46E816F682E... 162.6485 17.1%   199 0.8173  0.03 SELECT order_line? stock?

#    2 0x360F872745C81781F8F75EDE... 107.4898 11.3% 14837 0.0072  0.02 SELECT stock?

#    3 0xE0CE1933D0392DA3A42FAA7C... 102.2281 10.8% 14866 0.0069  0.03 SELECT item?

#    4 0x492B86BCB2B1AE1278147F95...  98.7658 10.4% 14854 0.0066  0.04 INSERT order_line?

#    5 0x9D086C2B787DC3A308043A0F...  93.8240  9.9% 14865 0.0063  0.02 UPDATE stock?

#    6 0x5812BF2C6ED2B9DAACA5D21B...  53.9681  5.7%  1289 0.0419  0.05 UPDATE customer?

#    7 0x51C0DD7AF0A6D908579C28C0...  44.3869  4.7%   864 0.0514  0.03 SELECT customer?

#    8 0xFFFCA4D67EA0A788813031B8...  41.2123  4.3%  3250 0.0127  0.01 COMMIT

#    9 0xFDDEE3813C59881488D9C47F...  36.0707  3.8%  1180 0.0306  0.02 UPDATE customer?

#   10 0x8FBBE0AFA061755CCC1C27AB...  31.6417  3.3%  1305 0.0242  0.03 UPDATE orders?

#   11 0x8AA6EB56551923DB9A49E40A...  23.3281  2.5%  1522 0.0153  0.04 SELECT customer? warehouse?

#   12 0xF34C10B3DA8DB048A630D4C7...  21.1662  2.2%  1305 0.0162  0.03 UPDATE order_line?

#   13 0x59DBA67188951C532AFC2598...  20.8006  2.2%  1503 0.0138  0.33 INSERT new_orders?

#   14 0xDADBEB0FBFA537F5D8722F42...  17.2802  1.8%  1290 0.0134  0.03 SELECT customer?

#   15 0x597A805ADA793440507F3334...  16.4394  1.7%  1516 0.0108  0.03 INSERT orders?

#   16 0x1B1EA568857A6AAC6544B44A...  13.9560  1.5%  1309 0.0107  0.05 SELECT new_orders?

#   17 0xCE3EDD98779478DE17154DCE...  12.1470  1.3%  1322 0.0092  0.05 INSERT history?

#   18 0x9DFD75E88091AA333A777668...  11.6842  1.2%  1311 0.0089  0.05 SELECT orders?

# MISC 0xMISC                         39.6393  4.2% 16334 0.0024   0.0 <29 ITEMS>



# Query 1: 6.03 QPS, 4.93x concurrency, ID 0xCE367F5CFFCAF46E816F682E53C0CF03 at byte 30449473

# This item is included in the report because it matches --limit.

# Scores: V/M = 0.03

# Time range: 2020-05-10 21:39:37 to 21:40:10

# Attribute    pct   total     min     max     avg     95%  stddev  median

# ============ === ======= ======= ======= ======= ======= ======= =======

# Count          0     199

# Exec time     17    163s   302ms      1s   817ms   992ms   164ms   816ms

# Lock time      0     9ms    30us   114us    44us    84us    18us    36us

# Rows sent      0     199       1       1       1       1       0       1

# Rows examine  39  76.91k     306     468  395.75  441.81   27.41  381.65

# Rows affecte   0       0       0       0       0       0       0       0

# Bytes sent     0  15.54k      79      80   79.96   76.28       0   76.28

# Query size     0  74.30k     382     384  382.35  381.65       0  381.65

# String:

# Databases    sbt

# Hosts        localhost

# Last errno   0

# Users        sbtest

# Query_time distribution

#   1us

#  10us

# 100us

#   1ms

#  10ms

# 100ms  ################################################################

#    1s  ####

#  10s+

# Tables

#    SHOW TABLE STATUS FROM `sbt` LIKE 'order_line6'\G

#    SHOW CREATE TABLE `sbt`.`order_line6`\G

#    SHOW TABLE STATUS FROM `sbt` LIKE 'stock6'\G

#    SHOW CREATE TABLE `sbt`.`stock6`\G

# EXPLAIN /*!50100 PARTITIONS*/

SELECT COUNT(DISTINCT (s_i_id))

                        FROM order_line6, stock6

                       WHERE ol_w_id = 1

                         AND ol_d_id = 1

                         AND ol_o_id < 3050

                         AND ol_o_id >= 3030

                         AND s_w_id= 1

                         AND s_i_id=ol_i_id

                         AND s_quantity < 18\G



# Query 2: 436.38 QPS, 3.16x concurrency, ID 0x360F872745C81781F8F75EDE9DD44246 at byte 30021546

# This item is included in the report because it matches --limit.

# Scores: V/M = 0.02

# Time range: 2020-05-10 21:39:37 to 21:40:11

# Attribute    pct   total     min     max     avg     95%  stddev  median

# ============ === ======= ======= ======= ======= ======= ======= =======

# Count         15   14837

# Exec time     11    107s    44us   233ms     7ms    33ms    13ms     3ms

# Lock time      1   522ms    15us   496us    35us    84us    28us    23us

# Rows sent     20  14.49k       1       1       1       1       0       1

# Rows examine   7  14.49k       1       1       1       1       0       1

# Rows affecte   0       0       0       0       0       0       0       0

# Bytes sent    28   3.74M     252     282  264.46  271.23    8.65  258.32

# Query size    19   3.01M     209     215  213.05  212.52    2.85  212.52

# String:

# Databases    sbt

# Hosts        localhost

# Last errno   0

# Users        sbtest

# Query_time distribution

#   1us

#  10us  #

# 100us  ##

#   1ms  ################################################################

#  10ms  #############

# 100ms  #

#    1s

#  10s+

# Tables

#    SHOW TABLE STATUS FROM `sbt` LIKE 'stock9'\G

#    SHOW CREATE TABLE `sbt`.`stock9`\G

# EXPLAIN /*!50100 PARTITIONS*/

SELECT s_quantity, s_data, s_dist_01 s_dist

                                                      FROM stock9

                                                    WHERE s_i_id = 60407 AND s_w_id= 2 FOR UPDATE\G

As you can see on the above pt-query-digest report result, we can divided into 3 parts.

Summary Report 

There is much information you can find in the summary report, starting from the hostname server, the date you execute the command, information related to  the query were logged, QPS, and time frame capture. Beside that, you also can see statistics of timing on each Attribute. 

# 12s user time, 170ms system time, 27.44M rss, 221.79M vsz

# Current date: Sun May 10 21:40:47 2020

# Hostname: n2

# Files: mysql-1

# Overall: 94.92k total, 47 unique, 2.79k QPS, 27.90x concurrency ________

# Time range: 2020-05-10 21:39:37 to 21:40:11

# Attribute          total     min     max     avg     95%  stddev  median

# ============     ======= ======= ======= ======= ======= ======= =======

# Exec time           949s     6us      1s    10ms    42ms    42ms     2ms

# Lock time            31s       0      1s   327us    80us    11ms    22us

# Rows sent         69.36k       0     490    0.75    0.99   11.30       0

# Rows examine     196.34k       0     490    2.12    0.99   21.03    0.99

# Rows affecte      55.28k       0      15    0.60    0.99    1.26       0

# Bytes sent        13.12M      11   6.08k  144.93  299.03  219.02   51.63

# Query size        15.11M       5     922  166.86  258.32   83.13  174.84

Query Profiling Based on Rank 

You can see useful information in the profiling query.

# Profile

# Rank Query ID                      Response time  Calls R/Call V/M   Ite

# ==== ============================= ============== ===== ====== ===== ===

#    1 0xCE367F5CFFCAF46E816F682E... 162.6485 17.1%   199 0.8173  0.03 SELECT order_line? stock?

#    2 0x360F872745C81781F8F75EDE... 107.4898 11.3% 14837 0.0072  0.02 SELECT stock?

There is a lot of information such as the queries running, response time of the query (including the percentage calculation), how many calls the query is making, and reads per call.

Query Distribution

Query distribution statistics describe detailed information based on query profiling rank, you can see the QPS concurrency, statistics information related to the query Attribute. 

# Query 1: 6.03 QPS, 4.93x concurrency, ID 0xCE367F5CFFCAF46E816F682E53C0CF03 at byte 30449473

# This item is included in the report because it matches --limit.

# Scores: V/M = 0.03

# Time range: 2020-05-10 21:39:37 to 21:40:10

# Attribute    pct   total     min     max     avg     95%  stddev  median

# ============ === ======= ======= ======= ======= ======= ======= =======

# Count          0     199

# Exec time     17    163s   302ms      1s   817ms   992ms   164ms   816ms

# Lock time      0     9ms    30us   114us    44us    84us    18us    36us

# Rows sent      0     199       1       1       1       1       0       1

# Rows examine  39  76.91k     306     468  395.75  441.81   27.41  381.65

# Rows affecte   0       0       0       0       0       0       0       0

# Bytes sent     0  15.54k      79      80   79.96   76.28       0   76.28

# Query size     0  74.30k     382     384  382.35  381.65       0  381.65

# String:

# Databases    sbt

# Hosts        localhost

# Last errno   0

# Users        sbtest

# Query_time distribution

#   1us

#  10us

# 100us

#   1ms

#  10ms

# 100ms  ################################################################

#    1s  ####

#  10s+

# Tables

#    SHOW TABLE STATUS FROM `sbt` LIKE 'order_line6'\G

#    SHOW CREATE TABLE `sbt`.`order_line6`\G

#    SHOW TABLE STATUS FROM `sbt` LIKE 'stock6'\G

#    SHOW CREATE TABLE `sbt`.`stock6`\G

# EXPLAIN /*!50100 PARTITIONS*/

SELECT COUNT(DISTINCT (s_i_id))

                        FROM order_line6, stock6

                       WHERE ol_w_id = 1

                         AND ol_d_id = 1

                         AND ol_o_id < 3050

                         AND ol_o_id >= 3030

                         AND s_w_id= 1

                         AND s_i_id=ol_i_id

                         AND s_quantity < 18\G

There is also information regarding query time distribution, host, user, and database.

Query Monitoring with ClusterControl

ClusterControl has a Query Monitoring feature you can find in the Query Monitor tab as shown below.

You can see information related to the query that is executed in the database, including statistical information and execution time. You can also configure the Query Monitor Setting which is still on the same page. There is an option to enable the slow query and queries not using index by clicking on Settings

You just need to set the Long Query Time, which is the threshold of the query that categorizes for long based on execution time. Also there is an option to enable the query that is not using indexes.

Conclusion

Monitoring and analyzing the query workload can be beneficial so you know and understand your database workload, both pt-query-digest and the ClusterControl Query Monitor provide information related to the query running in the database to help you achieve that understanding.

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