MySQL runs out of memory when importing innodb database

innodbmemoryMySQLmysql-5.5Ubuntu

I have a small VPS with 512MB RAM and no swap (can't have any).

I am importing a 1.5GB innodb database with

mysql -u -p < database.sql

Before the operation can finish it says : Lost connection to MySQL server. That is because the mysqld crashed trying to get more than 480MB of RAM.

This is my my.cnf

[client]
port            = 3306
socket          = /var/run/mysqld/mysqld.sock

[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       = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover         = BACKUP
max_connections        = 4
#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!
#
innodb_buffer_pool_size=80M
innodb_additional_mem_pool_size=20M

innodb_flush_log_at_trx_commit=0
innodb_log_buffer_size = 8M

[mysqldump]
quick
quote-names
max_allowed_packet      = 16M

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

[isamchk]
key_buffer              = 16M

More info:
* There are lots of tables : 30k tables
* I am running mysql 5.5 on ubuntu 12.04
* I've read a lot of stuff on mysql innodb memory usage… I must be missing something because the formula they present are not working

This script

mysql -u admin -p -e "show variables; show status" | awk '
{
VAR[$1]=$2
}
END {
MAX_CONN = VAR["max_connections"]
MAX_USED_CONN = VAR["Max_used_connections"]
BASE_MEM=VAR["key_buffer_size"] + VAR["query_cache_size"] + VAR["innodb_buffer_pool_size"] + VAR["innodb_additional_mem_pool_size"] + VAR["innodb_log_buffer_size"]
MEM_PER_CONN=VAR["read_buffer_size"] + VAR["read_rnd_buffer_size"] + VAR["sort_buffer_size"] + VAR["join_buffer_size"] + VAR["binlog_cache_size"] + VAR["thread_stack"] + VAR["tmp_table_size"]
MEM_TOTAL_MIN=BASE_MEM + MEM_PER_CONN*MAX_USED_CONN
MEM_TOTAL_MAX=BASE_MEM + MEM_PER_CONN*MAX_CONN

printf "+------------------------------------------+--------------------+\n"
printf "| %40s | %15.3f MB |\n", "key_buffer_size", VAR["key_buffer_size"]/1048576
printf "| %40s | %15.3f MB |\n", "query_cache_size", VAR["query_cache_size"]/1048576
printf "| %40s | %15.3f MB |\n", "innodb_buffer_pool_size", VAR["innodb_buffer_pool_size"]/1048576
printf "| %40s | %15.3f MB |\n", "innodb_additional_mem_pool_size", VAR["innodb_additional_mem_pool_size"]/1048576
printf "| %40s | %15.3f MB |\n", "innodb_log_buffer_size", VAR["innodb_log_buffer_size"]/1048576
printf "+------------------------------------------+--------------------+\n"
printf "| %40s | %15.3f MB |\n", "BASE MEMORY", BASE_MEM/1048576
printf "+------------------------------------------+--------------------+\n"
printf "| %40s | %15.3f MB |\n", "sort_buffer_size", VAR["sort_buffer_size"]/1048576
printf "| %40s | %15.3f MB |\n", "read_buffer_size", VAR["read_buffer_size"]/1048576
printf "| %40s | %15.3f MB |\n", "read_rnd_buffer_size", VAR["read_rnd_buffer_size"]/1048576
printf "| %40s | %15.3f MB |\n", "join_buffer_size", VAR["join_buffer_size"]/1048576
printf "| %40s | %15.3f MB |\n", "thread_stack", VAR["thread_stack"]/1048576
printf "| %40s | %15.3f MB |\n", "binlog_cache_size", VAR["binlog_cache_size"]/1048576
printf "| %40s | %15.3f MB |\n", "tmp_table_size", VAR["tmp_table_size"]/1048576
printf "+------------------------------------------+--------------------+\n"
printf "| %40s | %15.3f MB |\n", "MEMORY PER CONNECTION", MEM_PER_CONN/1048576
printf "+------------------------------------------+--------------------+\n"
printf "| %40s | %18d |\n", "Max_used_connections", MAX_USED_CONN
printf "| %40s | %18d |\n", "max_connections", MAX_CONN
printf "+------------------------------------------+--------------------+\n"
printf "| %40s | %15.3f MB |\n", "TOTAL (MIN)", MEM_TOTAL_MIN/1048576
printf "| %40s | %15.3f MB |\n", "TOTAL (MAX)", MEM_TOTAL_MAX/1048576
printf "+------------------------------------------+--------------------+\n"
}'

And this is the output

+------------------------------------------+--------------------+
|                          key_buffer_size |          16.000 MB |
|                         query_cache_size |          16.000 MB |
|                  innodb_buffer_pool_size |          80.000 MB |
|          innodb_additional_mem_pool_size |          20.000 MB |
|                   innodb_log_buffer_size |           8.000 MB |
+------------------------------------------+--------------------+
|                              BASE MEMORY |         140.000 MB |
+------------------------------------------+--------------------+
|                         sort_buffer_size |           2.000 MB |
|                         read_buffer_size |           0.125 MB |
|                     read_rnd_buffer_size |           0.250 MB |
|                         join_buffer_size |           0.125 MB |
|                             thread_stack |           0.188 MB |
|                        binlog_cache_size |           0.031 MB |
|                           tmp_table_size |          16.000 MB |
+------------------------------------------+--------------------+
|                    MEMORY PER CONNECTION |          18.719 MB |
+------------------------------------------+--------------------+
|                     Max_used_connections |                  1 |
|                          max_connections |                  4 |
+------------------------------------------+--------------------+
|                              TOTAL (MIN) |         158.719 MB |
|                              TOTAL (MAX) |         214.875 MB |
+------------------------------------------+--------------------+

However in top I can see mysqld memory usage going to 481m and then mysql crash.

What configuration am I missing to limit the memory usage?!
Thanks

Best Answer

Workarounds

BigDump http://www.ozerov.de/bigdump/

It executes only a small part of the huge dump and restarts itself. The next session starts where the last was stopped to keep you from running into your server’s limits. Instructions for using it are on the BigDump website. Basically you place your SQL file in a folder on your server, along with the bigdump.php file. You edit that file with your database information and then visit the page on your server and set the import to go. This is a fairly quick process and will save you a lot of time.

SQLDumpSpliter http://www.rusiczki.net/2007/01/24/sql-dump-file-splitter/

Create the splits and then upload them to a directory on your server.

If you want to restore the dump, you have to execute the yourdatabase_DataStructure.sql first because it contains the Tables structure. After that, you can execute the other .sql-files as they contain the data of the now existing tables. Using SSH, CD to your directory again and make sure to send this first:

mysql -u db_user -p db_name < yourbackup_DataStructure.sql

Then your splits:

mysql -u db_user -p db_name < yourbackup_1.sql
mysql -u db_user -p db_name < yourbackup_2.sql

Source: http://www.ontwerps.nl/methods-importing-large-sql-files

UPDATE 2013-04-15 18:04 EDT

I just noticed you have innodb_file_per_table OFF. What gives ?

You currently have all the InnoDB data and the corresponding index sitting in a single file.
Any CREATE TABLE statement must make data dictionary updates and look for space (small but annoying in this instance)
Internal Fragmentation of ibdata1
Dropping a table means scanning the table and its indexes for availability to lock. With data and index pages possibly fragmented, this takes spindles, seek time, and latency.
See Pictorial Representation of ibdata1 to see everything that goes into ibdata1

Recommendation : Remove all Data and Index Pages from ibdata1

This will give ibdata1 a breather to handle just data dictionary and MVCC management. In addition, ibdata1 will stay rather lean and mean and can be read more quickly.

You will need to perform the InnoDB Infrastructure Cleanup. I wrote out all the steps back on October 29, 2010 in StackOverflow.

UPDATE 2013-04-22 08:10 EDT

Three suggestions

SUGGESTION 1 : I just noticed something else. You are using an ancient version of MySQL (5.0.45). You should think about upgrading to MySQL 5.6.11 as it performs significantly faster that MySQL 5.5 and way faster than MySQL 5.0.

SUGGESTION 2 : You should also go ahead and implement the InnoDB Infrastructure Cleanup.

SUGGESTION 3 : You should also check the disk itself. If the data is sitting on a RAID10 set, one of the disks may have an issues. Check the disk controller's battery as well because it can slow down disk caching and affect read performance.

Best Answer

Workarounds

Related Solutions

MySQL Replication: Insert generating VERY huge temporary tables

MySQL database drop insanely slow

UPDATE 2013-04-15 18:04 EDT

Recommendation : Remove all Data and Index Pages from ibdata1

UPDATE 2013-04-22 08:10 EDT

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