Здравствуйте красно глазики!

Столкнулся с проблемой, есть скрипт который перебирает бинарное дерево (начиная с самой вершины), ища где есть свободная ветка (то есть под какой ячейкой незанятое одно из двух мест). Когда в дереве становится около 1000 элементов, скрипт работает довольно медленно (0.5 - 1 сек), а таких запросов происходит много, и в результате скрипт выполняется очень долго, при этом процессор и ОЗУ почти не нагружается (о чем говорит htop). Как выделить mysql больше ресурсов?
Пытался настроить по этой статьи , но у меня нет большинства параметров о которых там написано, в конфигурационном файле, а если их пишу самостоятельно, то ничего не меняется.
Помогите пожалуйста.

/etc/mysql/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 = 127.0.0.1
#
# * Fine Tuning
#
key_buffer = 16M
max_allowed_packet = 16M
thread_stack = 192K
thread_cache_size = 16
# 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 logging goes TO syslog due TO /etc/mysql/conf.d/mysqld_safe_syslog.cnf.
#
# 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/