Migrate from innodb_file_per_table to off in MySQL We have a large number (2,500+) of databases and users in MySQL 5.6 on a single virtualized server (4 cpus and 8GB of memory). All the tables are using InnoDB. The actual data size is not very large (~5GB), and queries per second is low, just lots of small databases and users. Each account created for our application get's their own database and user (this architecture cannot change unfortunately). 

We are seeing very poor performance, especially when trying to stop mysqld (often times it just times-out). Starting mysqld and spawning (ready for connections) takes over 3+ minutes. Running mysqldump brings the entire server to its knees. Load, CPU usage, and iowait, all skyrocket during mysqldump, and cause other queries to timeout and fail. 

It was recommend that we transition off of using innodb_file_per_table because of the excessive number of open file descriptors, shear number of directories and files, and i/o operations.

Changing innodb_file_per_table to off does this, but how can we convert all existing databases and tables to utilize this?

Below is our current /etc/my.conf just for reference, in-case there are further optimizations we can make to optimize for lots of small databases.

[mysqld]
datadir=/mysql/data
socket=/mysql/mysqld.sock
symbolic-links=0
default-storage-engine=InnoDB
slow_query_log=1
long_query_time=2
slow_query_log_file=/var/log/mysql_slow.log
expire_logs_days=30
max_connections=50

bind-address=192.241.X.X
port=3306
max_allowed_packet=4M
net_retry_count=5
max_connect_errors=100
wait_timeout=14400
connect_timeout=10

open_files_limit=65535
innodb_open_files=65535
key_buffer_size=256M
innodb_buffer_pool_size=4096M
innodb_log_buffer_size=4M
group_concat_max_len=16k
max_sort_length=16k
max_length_for_sort_data=16k
query_cache_type=1
query_cache_limit=1M
query_cache_size=64M
innodb_thread_concurrency=8
thread_concurrency=8
thread_cache_size=128
thread_stack=1M
read_buffer_size=1M
join_buffer_size=1M
sort_buffer_size=1M
read_rnd_buffer_size=1M
table_open_cache=32768
table_definition_cache=65535
tmp_table_size=33554432
max_heap_table_size=33554432
innodb_log_file_size=1024M
innodb_flush_log_at_trx_commit=2
innodb_file_per_table
log-warnings
innodb_flush_neighbors=0

user=mysql
old_passwords=0

[mysqld_safe]
syslog
pid-file=/var/run/mysqld/mysqld.pid
STEP #1

Set innodb_file_per_table to 0 in /etc/my.cnf

[mysqld]
innodb_file_per_table = 0


STEP #2

service mysql restart


STEP #3

Convert every InnoDB table to InnoDB again

echo "SET SQL_LOG_BIN = 0;" &gt; /root/ConvertInnoDBToInnoDB.sql
MYSQL_CONN="-u... -p..."
SQL="SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=InnoDB;')"
SQL="${SQL} FROM information_schema.tables WHERE engine='InnoDB'"
mysql ${MYSQL_CONN} -AN -e"${SQL}" &gt;&gt; /root/ConvertInnoDBToInnoDB.sql
less /root/ConvertInnoDBToInnoDB.sql


Once you view he script and are satisfied, login to mysql and run this

mysql&gt; source /root/ConvertInnoDBToInnoDB.sql


EPILOGUE

All .ibd files will vanish and all InnoDB tables and indexes will exist inside ibdata1

Give it a Try !!!