Hi, we are having the following problem:

Our OpenProject server takes an abnormaly long time to create workpackages with relations (up to 40 seconds).

We are running OpenProject (8.2.0) and MySQL (5.5.59) on a virtualized Ubuntu 14.04.5 LTS Server (Intel Xeon 6x 2.93GHz | 16GB Ram)

When creating a workpackage with relations the CPU load goes up to 100%, Memory stays at around 5%.

We were able to narrow the problem down to our MySQL server with the following SQL requests (long query_time):

# Time: 190117 16:12:34
# User@Host: openproject[openproject] @ localhost [127.0.0.1]
# Query_time: 6.053698  Lock_time: 0.000148 Rows_sent: 7  Rows_examined: 111088
SET timestamp=1547737954;
SELECT `work_packages`.* FROM `work_packages` WHERE (id IN (SELECT common_id FROM (SELECT to_id common_id FROM `relations` WHERE (`relations`.`hierarchy` != 0) AND `relations`.`relates` = 0 AND `relations`
.`duplicates` = 0 AND `relations`.`follows` = 0 AND `relations`.`blocks` = 0 AND `relations`.`includes` = 0 AND `relations`.`requires` = 0 AND `relations`.`from_id` IN (SELECT `relations`.`from_id` FROM `r
elations` WHERE `relations`.`to_id` IN (13794, 13795) AND `relations`.`relates` = 0 AND `relations`.`duplicates` = 0 AND `relations`.`blocks` = 0 AND `relations`.`includes` = 0 AND `relations`.`requires` =
 0 AND (hierarchy + relates + duplicates + follows + blocks + includes + requires > 0)) UNION SELECT from_id common_id FROM `relations` WHERE `relations`.`to_id` IN (13794, 13795) AND `relations`.`relates`
 = 0 AND `relations`.`duplicates` = 0 AND `relations`.`blocks` = 0 AND `relations`.`includes` = 0 AND `relations`.`requires` = 0 AND (hierarchy + relates + duplicates + follows + blocks + includes + requir
es > 0)) following_relations));
# User@Host: openproject[openproject] @ localhost [127.0.0.1]
# Query_time: 5.471664  Lock_time: 5.471491 Rows_sent: 0  Rows_examined: 1
SET timestamp=1547737954;
UPDATE `delayed_jobs` SET `delayed_jobs`.`locked_at` = '2019-01-17 15:12:29', `delayed_jobs`.`locked_by` = 'host:xxxOPENPROJECT03 pid:937' WHERE ((run_at <= '2019-01-17 15:12:29' AND (locked_at IS NULL OR
 locked_at < '2019-01-17 11:12:29') OR locked_by = 'host:xxxOPENPROJECT03 pid:937') AND failed_at IS NULL) ORDER BY priority ASC, run_at ASC LIMIT 1;

Since then we made a few changes to the my.cnf to use more memory and processing power.

my.cnf:

#
# 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
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
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address		= 0.0.0.0
#
# * 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	= 16M
query_cache_size    = 0
query_cache_type    = 0
#
# * 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!
#

innodb_buffer_pool_size=8G
innodb_buffer_pool_instances=8

# * 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

#custom options
join_buffer_size = 256K
tmp_table_size = 32M
max_heap_table_size = 32M

innodb_file_per_table = ON
innodb_log_file_size = 1G

[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/

If you have any suggestions on how to fix this issue I'd greatly appreciate the input.

Thank you,

Stuart