1

I recently moved from standard shared hosting to Digital Ocean.

While I've thoroughly enjoyed the experience - especially learning to manage some (relatively) large DB's - I've run into one major issue.

My Droplet on Digital Ocean has 2GB RAM and 2 CPU's. The only thing I'm running on the server is a fairly low-profile PHP app. However, one page in this app contains a rather extensive query that, at the moment, returns around 10k rows. There are a few joins involved (not all of them indexed).

Whenever I hit this page, it takes a good 60 seconds to load. Mysql's CPU usage shoots up to the server max: enter image description here

I've used SQL Tuner, converted the tables to InnoDB (per a recommendation I read, though I have at most 25 concurrent users), made and tested a huge number of changes to my.cnf, and spent a significant number of hours trying to decipher this issue. However, I'm still getting the same results (and some frustrated users).

Is this problem 100% the fault of the query? Or, are there further changes I could make to my.cnf (or anywher else) that could help decrease the CPU load and increase the loading speed?

Thanks for any assistance!

MySQL Version information: enter image description here

The my.cnf, including portions generated by Percona and recommendations made by SQL Tuner:

#
# The MySQL database server configuration file.
#
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
# 
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
[client]
port        = 3306
socket      = /var/run/mysqld/mysqld.sock

# Here is entries for some specific programs
# The following values assume you have at least 32M ram

# This was formally known as [safe_mysqld]. Both versions are currently parsed.
[mysqld_safe]
socket      = /var/run/mysqld/mysqld.sock
nice        = 0

[mysqld]
#
# * Basic Settings
#
user        = mysql
default_storage_engine         = InnoDB
pid-file    = /var/run/mysqld/mysqld.pid
socket      = /var/run/mysqld/mysqld.sock
port        = 3306
basedir     = /usr
datadir     = /var/lib/mysql
tmpdir      = /tmp
lc-messages-dir = /usr/share/mysql
skip-external-locking

# CACHES AND LIMITS #
tmp_table_size                 = 32M
max_heap_table_size            = 32M
query_cache_type               = 0
query_cache_size               = 0
max_connections                = 50
thread_cache_size              = 50
open_files_limit               = 65535
table_definition_cache         = 1024
table_open_cache               = 2048

# INNODB #
innodb_flush_method            = O_DIRECT
innodb_log_files_in_group      = 2
innodb_log_file_size           = 250M
innodb_flush_log_at_trx_commit = 1
innodb_file_per_table          = 1
innodb_buffer_pool_size        = 1000M
join_buffer_size = 250M

# LOGGING #
log_error                      = /var/log/mysql/error.log
log_queries_not_using_indexes  = 1
slow_query_log                 = 1
slow_query_log_file            = /var/log/mysql/mysql-slow.log
long_query_time                = 1


#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address        = 127.0.0.1
#
# * Fine Tuning
#
key_buffer      = 16M
max_allowed_packet  = 16M
thread_stack        = 192K
thread_cache_size       = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover         = BACKUP
#max_connections        = 100
#table_cache            = 64
#thread_concurrency     = 10
#
# * Query Cache Configuration
#
query_cache_limit   = 1M
query_cache_size        = 16M
#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1
#
# Error log - should be very few entries.
#
log_error = /var/log/mysql/error.log
#
# Here you can see queries with especially long duration
#log_slow_queries   = /var/log/mysql/mysql-slow.log
#long_query_time = 2
#log-queries-not-using-indexes
#
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
#       other settings you may need to change.
#server-id      = 1
#log_bin            = /var/log/mysql/mysql-bin.log
expire_logs_days    = 10
max_binlog_size         = 100M
#binlog_do_db       = include_database_name
#binlog_ignore_db   = include_database_name
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
#
# * Security Features
#
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
#
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
#
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem



[mysqldump]
quick
quote-names
max_allowed_packet  = 16M

[mysql]
#no-auto-rehash # faster start of mysql but no tab completition

[isamchk]
key_buffer      = 16M

#
# * IMPORTANT: Additional settings that can override those from this file!
#   The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/

Edit - In hindsight... I'm assuming it's this generated query. It takes 42s to run in PHPMyAdmin.

SELECT  x.*,
if(fielding_rating_pos2=0,'-',if(TRUNCATE((fielding_rating_pos2+40)/40,
                        0)<1,1,
                                        0)))) as fielding_rating_pos2, if(TRUNCATE((fielding_rating_pos2+40
  )/40,
                0)>5, 5,TRUNCATE((fielding_rating_pos2+40)/40,
if(fielding_rating_pos3=0,'-',if(TRUNCATE((fielding_rating_pos3+40)/40,
                        0)<1,1,
                                        0)))) as fielding_rating_pos3, if(fielding_rating_pos4=0,
'-',
if(TRUNCATE((fielding_rating_pos3+40)/40,0)>5, 5,TRUNCATE((fielding_rating_pos3+40)/40,
        0
  )<1,1,
        0)))) as fielding_rating_pos4, if(TRUNCATE((fielding_rating_pos4+40)/40,
if(fielding_rating_pos5=0,'-',if(TRUNCATE((fielding_rating_pos5+40)/40,
        0)<1,1,
0
  )>5, 5,
0)))) as fielding_rating_pos5, if(fielding_rating_pos6=0,'-',
if(TRUNCATE((fielding_rating_pos6+40)/40, 0)<1,1,if(TRUNCATE((fielding_rating_pos6+40)/40,
0
  )>5,
5,TRUNCATE((fielding_rating_pos6+40)/40,0)))) as fielding_rating_pos6,
TRUNCATE((fielding_rating_pos4+40)/40, 5,TRUNCATE((fielding_rating_pos5+40)/40,
if(fielding_rating_pos7=0,'-',if(TRUNCATE((fielding_rating_pos7+40)/40,
0)<1,1,
0)))) as fielding_rating_pos7, if(TRUNCATE((fielding_rating_pos5+40
  )/40,
0
  )>5,
'-',
0)>5, 5,TRUNCATE((fielding_rating_pos8+40)/40,0)))) as fielding_rating_pos8,
if(fielding_rating_pos9=0,'-',if(TRUNCATE((fielding_rating_pos9+40)/40,
if(TRUNCATE((fielding_rating_pos7+40)/40,0)>5, 5,TRUNCATE((fielding_rating_pos7+40)/40,
0)<1,1,
0)))) as fielding_rating_pos9, if(TRUNCATE((fielding_rating_pos4+40)/40,
if(fielding_rating_pos8=0, if(fielding_ratings_catcher_arm=0,
'-',
0
  )<1,1,
0)>5,5,TRUNCATE((fielding_ratings_catcher_arm+40)/40, 0)))) as fielding_ratings_catcher_arm,
if(fielding_ratings_infield_arm=0, '-',if(TRUNCATE((fielding_ratings_infield_arm+40)/40,
if(TRUNCATE((fielding_rating_pos9+40)/40,0)>5, 5,TRUNCATE((fielding_rating_pos9+40)/40,
0)<1,1,if(TRUNCATE((fielding_ratings_infield_arm+40)/40, 0)>5,
5,TRUNCATE((fielding_ratings_infield_arm+40)/40,0)))) as fielding_ratings_infield_arm,
if(fielding_ratings_outfield_arm=0,'-',if(TRUNCATE((fielding_ratings_outfield_arm+40)/40,
0)<1,1,if(TRUNCATE((fielding_ratings_outfield_arm+40)/40,0)>5,
5,TRUNCATE((fielding_ratings_outfield_arm+40)/40,0)))
  ) as fielding_ratings_outfield_arm FROM  players_fielding as pf,
if(TRUNCATE((fielding_ratings_catcher_arm+40)/40, if(TRUNCATE((fielding_rating_pos8+40)/40,
    ( if(TRUNCATE((fielding_rating_pos8+40)/40, 0)<1,1,if(TRUNCATE((fielding_ratings_catcher_arm+40)/40,
        SELECT  px.player_id,first_name,last_name,position,role,age,porder,
                slot,batting_ratings_talent_contact,batting_ratings_talent_gap,
                batting_ratings_talent_power,batting_ratings_talent_eye,
                batting_ratings_talent_strikeouts,running_ratings_speed,
        running_ratings_stealing,
                if(TRUNCATE((batting_ratings_talent_contact+40)/40, 0)<1,
                1,
                                0)>5,5,TRUNCATE((batting_ratings_talent_contact+40)/40,
                                0))) as batting_ratings_talent_contact,if(TRUNCATE((batting_ratings_talent_gap+40
                  )/40,
        0)<1,1,
        0)>5,5,TRUNCATE((batting_ratings_talent_gap+40)/40,0))
    ) as batting_ratings_talent_gap,
if(TRUNCATE((batting_ratings_talent_power+40)/40,0)<1, 1,if(TRUNCATE((batting_ratings_talent_power+40)/40,
0)>5, running_ratings_baserunning FROM ( SELECT  player_id, 5,
TRUNCATE((batting_ratings_talent_power+40)/40,0))) as batting_ratings_talent_power,
if(TRUNCATE((batting_ratings_talent_eye+40)/40,0)<1,1, if(TRUNCATE((batting_ratings_talent_contact+40)/40,
        if(TRUNCATE((batting_ratings_talent_eye+40)/40,0)>5,5, TRUNCATE((batting_ratings_talent_eye+40)/40,
                                0))) as batting_ratings_talent_eye, if(TRUNCATE((batting_ratings_talent_strikeouts+40)/40,
                                        if(TRUNCATE((batting_ratings_talent_gap+40)/40,
                                0)<1,1,
                                                        0)>5,5,TRUNCATE((batting_ratings_talent_strikeouts+40)/40,
                                                0))) as batting_ratings_talent_strikeouts FROM  players_batting) as ps RIGHT JOIN ( SELECT  first_name,
last_name,position,role,age,
0)<1,1,
0))) as running_ratings_speed, if(TRUNCATE((batting_ratings_talent_strikeouts+40
  )/40,
if(TRUNCATE((running_ratings_stealing+40)/40,0)<1,1,if(TRUNCATE((running_ratings_stealing+40)/40,
        0)>5,5,TRUNCATE((running_ratings_stealing+40)/40,0))
  ) as running_ratings_stealing,
        if(TRUNCATE((running_ratings_baserunning+40)/40,0)<1,
if(TRUNCATE((running_ratings_speed+40)/40, 1,if(TRUNCATE((running_ratings_baserunning+40)/40,
                        0
                          )>5,
                5,
                                0))
  ) as running_ratings_baserunning, pp.* FROM  players as p,
                    ( SELECT  dp2.* FROM if(TRUNCATE((running_ratings_speed+40)/40,
                0
          )>5, 5,
        SELECT  dp1.player_id,
                porder) as porder, slot FROM TRUNCATE((running_ratings_speed+40)/40,
                    ( TRUNCATE((running_ratings_baserunning+40)/40, ( if(porder IS NULL,
                                                999999, SELECT  dp.player_id,slot FROM  ootp_sql_draft_pool as dp LEFT JOIN  amateur_draft as ad  ON dp.player_id=ad.player_id
                                            WHERE  dp.league_id=101
                                              AND  ad.player_id IS NULL) as dp1
                                    LEFT JOIN  ootp_sql_draft_list as dl  ON dp1.player_id=dl.player_id
                                    WHERE  human_manager_id IN (3,-999,NULL)
                                    ORDER BY  porder) as dp2
                            GROUP BY  player_id) as pp
                    WHERE  p.player_id=pp.player_id
                      AND  position!=1) as px  ON ps.player_id=px.player_id
                          ) as x
    WHERE  pf.player_id=x.player_id
    ORDER BY  batting_ratings_talent_contact DESC,batting_ratings_talent_power DESC,
        batting_ratings_talent_eye DESC,last_name,first_name
    LIMIT  0,100 
  • I just indexed several of the tables. I didn't write this app, so I'm concerned that my indexes might break something. However, I checked for nulls and duplicates first, and it appears I didn't break anything. Now, the query is down to 13s, which is a completely incredible amount of progress. Do you think it's likely that my addition of indexes will break anything? These tables have already been in heavy use, so I would think I couldn't index something I shouldn't at this point. However, I suppose it might break something down the road. – Kiel Oct 31 '16 at 18:25
  • 1
    That was my concern - I just forced uniqueness on a couple of columns. However, they are values that SHOULD be unique, even though they hadn't been forced. I'll just have to monitor it over time. Thanks so much for your help. I knew to try this, but I was nervous. Looks like it's okay so far. – Kiel Oct 31 '16 at 18:30
3

I would recommend adding indexes on the columns participating in the JOIN conditions and the WHERE clauses.

Indexes are designed to help the query optimizer make better choices. Unless you enforce uniqueness on a column that isn't meant to be unique, your indexes will only help.

That said, you may want to enforce uniqueness in the index for columns that should be unique, which helps the optimizer even more.

Keep in mind that indexes (and the statistics using these indexes) need regular maintenance, and they will add additional writes when the table is updated (a small overhead). This is generally far less overhead than the time taken to run queries.

  • 1
    Down to 5 second queries and 8 second page loads. Thank you SO much. I set all proper indexes, some unique and others not, and I simply can't believe the difference. Now, time to do some more research - thanks so much! – Kiel Oct 31 '16 at 20:02
  • 2
    @Kiel That's a horrendous query to begin with, so I'm glad you got some benefit from indexing. Next step (if you're able) is to try rewriting it if you can. – Randolph West Oct 31 '16 at 20:28
1

For only 2GB of RAM, innodb_buffer_pool_size = 1000M is dangerously high; recommend only 400M. The risk is that mysqld will run out of RAM and swapping will ensue. Swapping is deadly for MySQL performance.

Also decrease these:

join_buffer_size = 16M
tmp_table_size                 = 16M
max_heap_table_size            = 16M

5 seconds is still terribly long for a query. If the above changes don't cure that, let's see the query. Also:

SHOW CREATE TABLE
EXPLAIN SELECT ...

High CPU means (almost always) lack of optimal index (usually 'composite') and/or poorly written SELECT.

  • Hi Rick! The Select most certainly is terrible - it's a huge concatenation of of options. I'll change these other configurations and see if things are improved at all. Thanks for your suggestions! – Kiel Nov 1 '16 at 13:28

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