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My server keeps running out of memory for mysql. I keep getting. 150708 3:39:09 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258064 bytes)

When I looked in my.cnf I saw that innodb_buffer_pool_size was 134217728

I am assuming that is in bytes which would translate to 134MB. Should I change innodb_buffer_pool_size=134217728

to innodb_buffer_pool_size=500MB

When I ran Rolando's query I got 481M as the Recommended_InnoDB_Buffer_Pool_Size: 

SELECT CONCAT(CEILING(RIBPS/POWER(1024,pw)),SUBSTR(' KMGT',pw+1,1)) Recommended_InnoDB_Buffer_Pool_Size FROM ( SELECT RIBPS,FLOOR(LOG(RIBPS)/LOG(1024)) pw FROM ( SELECT SUM(data_length+index_length)*1.1*growth RIBPS FROM information_schema.tables AAA, (SELECT 1.25 growth) BBB WHERE ENGINE='InnoDB' ) AA ) A;

Recommended_InnoDB_Buffer_Pool_Size 481M

Below is the full copy of my.cnf

[mysqld] thread_cache_size=6 query_cache_type=2 key_buffer_size=256M open_files_limit=10000 query_cache_size=256M # safe-show-database table_cache=1024 query_cache_limit=1M default-storage-engine=MyISAM innodb_file_per_table=1 innodb_read_io_threads=8 innodb_write_io_threads=8 # Try number of cpus*2 for thread_concurrency thread_concurrency=12 max_allowed_packet=268435456 max_connections=200 query_cache_size=64M thread_cache_size=16 join_buffer_size=256K read_buffer_size=256K sort_buffer_size=256K tmp_table_size=512M max_heap_table_size=512M max_delayed_threads=0 innodb_buffer_pool_size=134217728

This is the backtrace around the time of the last crash I already fixed the thecityo_production_wp/wp_wfVulnScanners error:

I have 10 GB of ram and 180 GB Disk space along with 6 shared cores.

key_buffer_size=268435456 read_buffer_size=262144 max_used_connections=0 max_threads=200 thread_count=0 connection_count=0 It is possible that mysqld could use up to key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 366904 K bytes of memory Hope thats ok; if not, decrease some variables in the equation. Thread pointer: 0x0 Attempting backtrace. You can use the following information to find out where mysqld died. If you see no messages after this, something went terribly wrong... stack_bottom = 0 thread_stack 0x40000 /usr/sbin/mysqld(my_print_stacktrace+0x35)[0x7aabf5] /usr/sbin/mysqld(handle_fatal_signal+0x4a4)[0x686324] /lib64/libpthread.so.0(+0xf710)[0x7fdd49402710] /lib64/libc.so.6(gsignal+0x35)[0x7fdd485c9625] /lib64/libc.so.6(abort+0x175)[0x7fdd485cae05] /usr/sbin/mysqld[0x8fbd91] /usr/sbin/mysqld[0x8b9638] /usr/sbin/mysqld[0x926aa5] /usr/sbin/mysqld[0x91b362] /usr/sbin/mysqld[0x857c7a] /usr/sbin/mysqld[0x84cbc2] /lib64/libpthread.so.0(+0x79d1)[0x7fdd493fa9d1] /lib64/libc.so.6(clone+0x6d)[0x7fdd4867f8fd] The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains information that should help you find out what is causing the crash. 150708 03:31:13 mysqld_safe mysqld from pid file /var/lib/mysql/mo.serveroflight.com.pid ended 150708 03:36:35 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql 150708 3:36:35 [Warning] 'THREAD_CONCURRENCY' is deprecated and will be removed in a future release. 150708 3:36:35 [Note] Plugin 'FEDERATED' is disabled. 150708 3:36:35 InnoDB: The InnoDB memory heap is disabled 150708 3:36:35 InnoDB: Mutexes and rw_locks use GCC atomic builtins 150708 3:36:35 InnoDB: Compressed tables use zlib 1.2.3 150708 3:36:35 InnoDB: Using Linux native AIO 150708 3:36:35 InnoDB: Initializing buffer pool, size = 128.0M 150708 3:36:35 InnoDB: Completed initialization of buffer pool 150708 3:36:35 InnoDB: highest supported file format is Barracuda. InnoDB: Log scan progressed past the checkpoint lsn 48687241371 150708 3:36:35 InnoDB: Database was not shut down normally! InnoDB: Starting crash recovery. InnoDB: Reading tablespace information from the .ibd files... InnoDB: Restoring possible half-written data pages from the doublewrite InnoDB: buffer... InnoDB: Doing recovery: scanned up to log sequence number 48687308434 150708 3:36:36 InnoDB: Starting an apply batch of log records to the database... InnoDB: Progress in percents: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 InnoDB: Apply batch completed 150708 3:36:36 InnoDB: Error: table 'thecityo_production_wp/wp_wfNet404s' InnoDB: in InnoDB data dictionary has tablespace id 20744, InnoDB: but tablespace with that id or name does not exist. Have InnoDB: you deleted or moved .ibd files? InnoDB: This may also be a table created with CREATE TEMPORARY TABLE InnoDB: whose .ibd and .frm files MySQL automatically removed, but the InnoDB: table still exists in the InnoDB internal data dictionary. InnoDB: Please refer to InnoDB: http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting-datadict.html InnoDB: for how to resolve the issue. 150708 3:36:36 InnoDB: Error: table 'thecityo_production_wp/wp_wfVulnScanners' InnoDB: in InnoDB data dictionary has tablespace id 20745, InnoDB: but tablespace with that id or name does not exist. Have InnoDB: you deleted or moved .ibd files? InnoDB: This may also be a table created with CREATE TEMPORARY TABLE InnoDB: whose .ibd and .frm files MySQL automatically removed, but the InnoDB: table still exists in the InnoDB internal data dictionary. InnoDB: Please refer to InnoDB: http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting-datadict.html InnoDB: for how to resolve the issue. 150708 3:36:36 InnoDB: Waiting for the background threads to start 150708 3:36:37 InnoDB: 5.5.42 started; log sequence number 48687308434 150708 3:36:37 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306 150708 3:36:37 [Note] - '0.0.0.0' resolves to '0.0.0.0'; 150708 3:36:37 [Note] Server socket created on IP: '0.0.0.0'. 150708 3:36:37 [Note] Event Scheduler: Loaded 0 events 150708 3:36:37 [Note] /usr/sbin/mysqld: ready for connections. Version: '5.5.42-cll' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL) 150708 3:38:40 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258640 bytes) 150708 3:38:43 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258104 bytes) 150708 3:38:48 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258640 bytes) 150708 3:38:48 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258640 bytes) 150708 3:38:48 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258640 bytes) 150708 3:38:48 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258640 bytes) 150708 3:38:48 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258640 bytes) 150708 3:38:48 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258640 bytes) 150708 3:38:48 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258640 bytes) 150708 3:38:48 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258640 bytes) 150708 3:38:48 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258640 bytes) 150708 3:38:48 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258104 bytes) 150708 3:38:49 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258104 bytes) 150708 3:38:49 InnoDB: Unable to allocate memory of size 289800. 150708 3:38:51 InnoDB: Assertion failure in thread 139869977511680 in file mem0mem.c line 361 InnoDB: We intentionally generate a memory trap. InnoDB: Submit a detailed bug report to http://bugs.mysql.com. InnoDB: If you get repeated assertion failures or crashes, even InnoDB: immediately after the mysqld startup, there may be InnoDB: corruption in the InnoDB tablespace. Please refer to InnoDB: http://dev.mysql.com/doc/refman/5.5/en/forcing-innodb-recovery.html InnoDB: about forcing recovery. 07:38:51 UTC - mysqld got signal 6 ; This could be because you hit a bug. It is also possible that this binary or one of the libraries it was linked against is corrupt, improperly built, or misconfigured. This error can also be caused by malfunctioning hardware. We will try our best to scrape up some info that will hopefully help diagnose the problem, but since we have already crashed, something is definitely wrong and this may fail. key_buffer_size=268435456 read_buffer_size=262144 max_used_connections=181 max_threads=200 thread_count=164 connection_count=164 It is possible that mysqld could use up to key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 366904 K bytes of memory Hope thats ok; if not, decrease some variables in the equation. Thread pointer: 0x3aef460 Attempting backtrace. You can use the following information to find out where mysqld died. If you see no messages after this, something went terribly wrong... stack_bottom = 7f70e2625e58 thread_stack 0x40000 /usr/sbin/mysqld(my_print_stacktrace+0x35)[0x7aabf5] /usr/sbin/mysqld(handle_fatal_signal+0x4a4)[0x686324] /lib64/libpthread.so.0(+0xf710)[0x7f7120768710] /lib64/libc.so.6(gsignal+0x35)[0x7f711f92f625] /lib64/libc.so.6(abort+0x175)[0x7f711f930e05] /usr/sbin/mysqld[0x8fbd91] /usr/sbin/mysqld[0x8fbdee] /usr/sbin/mysqld[0x881fc7] /usr/sbin/mysqld[0x83c104] /usr/sbin/mysqld[0x83efa5] /usr/sbin/mysqld[0x81819b] /usr/sbin/mysqld(_Z13rr_sequentialP11READ_RECORD+0x1f)[0x74de7f] /usr/sbin/mysqld(_Z10sub_selectP4JOINP13st_join_tableb+0x79)[0x5ace99] /usr/sbin/mysqld[0x5b16c7] /usr/sbin/mysqld(_ZN4JOIN4execEv+0xc81)[0x5c6f41] /usr/sbin/mysqld(_Z12mysql_selectP3THDPPP4ItemP10TABLE_LISTjR4ListIS1_ES2_jP8st_orderSB_S2_SB_yP13select_resultP18st_select_lex_unitP13st_select_lex+0x12c)[0x5c873c] /usr/sbin/mysqld(_Z13handle_selectP3THDP3LEXP13select_resultm+0x165)[0x5c9175] /usr/sbin/mysqld[0x584392] /usr/sbin/mysqld(_Z21mysql_execute_commandP3THD+0x144d)[0x5894cd] 150708 3:39:09 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258064 bytes) /usr/sbin/mysqld(_Z11mysql_parseP3THDPcjP12Parser_state+0x330)[0x58ce20] /usr/sbin/mysqld(_Z16dispatch_command19enum_server_commandP3THDPcj+0x1af3)[0x58f1e3] /usr/sbin/mysqld(_Z24do_handle_one_connectionP3THD+0xd7)[0x629297] /usr/sbin/mysqld(handle_one_connection+0x51)[0x6293d1] /lib64/libpthread.so.0(+0x79d1)[0x7f71207609d1] /lib64/libc.so.6(clone+0x6d)[0x7f711f9e58fd] Trying to get some variables. Some pointers may be invalid and cause the dump to abort. Query (7f70e40187c0): is an invalid pointer Connection ID (thread ID): 234 Status: NOT_KILLED The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains information that should help you find out what is causing the crash. 150708 03:39:11 mysqld_safe Number of processes running now: 0 150708 03:39:11 mysqld_safe mysqld restarted 150708 3:39:11 [Warning] 'THREAD_CONCURRENCY' is deprecated and will be removed in a future release. 150708 3:39:12 [Note] Plugin 'FEDERATED' is disabled. 150708 3:39:12 InnoDB: The InnoDB memory heap is disabled 150708 3:39:12 InnoDB: Mutexes and rw_locks use GCC atomic builtins 150708 3:39:12 InnoDB: Compressed tables use zlib 1.2.3 150708 3:39:12 InnoDB: Using Linux native AIO 150708 3:39:12 InnoDB: Initializing buffer pool, size = 128.0M 150708 3:39:12 InnoDB: Completed initialization of buffer pool 150708 3:39:12 InnoDB: highest supported file format is Barracuda. InnoDB: Log scan progressed past the checkpoint lsn 48687567559 150708 3:39:12 InnoDB: Database was not shut down n
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2 Answers 2

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I am not totally convinced MySQL is running out of memory. Here is why:

ASPECT #1

When you use mysqltuner.pl, it calculates the total usage in the worst case scenario. It does it by adding 3 figures together

  • key_buffer_size
  • innodb_buffer_pool_size
  • thread_memory : max_connections * the sum of
    • sort_buffer_size
    • join_buffer_size
    • read_buffer_size
    • read_rnd_buffer_size

In your case, given your current settings, that would be the sum of

  • key_buffer_size (256M)
  • innodb_buffer_pool_size (128M)

  • thread_memory (200M) : max_connections (200) * the sum of

    • sort_buffer_size (256K)
    • join_buffer_size (256K)
    • read_buffer_size (256K)
    • read_rnd_buffer_size (256K is default)

  • With given settings, your absolute worst case memory consumption for MySQL is 584M (256M + 128M + 200M).

  • If you use RIBPS, your absolute worst case memory consumption for MySQL would become 939M (256M + 481M + 200M).
  • If you use 500M, your absolute worst case memory consumption for MySQL would become 958M (256M + 481M + 200M).

Therefore, at its very worst, MySQL would consume only 9.58% of RAM.

ASPECT #2

You did not mention if the Server is a dedicated DB Server or if you are running a full stack. If you are running a full stack, please lower any memory-sensitive settings in the other parts of the stack (Varnish (more like Vanish), PHP, Munin, Nagios, Tomcat, Hibernate, etc).

ASPECT #3

Looking at the first crash around 3:36 AM I see

150708 3:36:36 InnoDB: Error: table 'thecityo_production_wp/wp_wfNet404s' InnoDB: in InnoDB data dictionary has tablespace id 20744, InnoDB: but tablespace with that id or name does not exist. Have InnoDB: you deleted or moved .ibd files? InnoDB: This may also be a table created with CREATE TEMPORARY TABLE InnoDB: whose .ibd and .frm files MySQL automatically removed, but the InnoDB: table still exists in the InnoDB internal data dictionary.

At that point, MySQL is complaining that the data dictionary entry for the table wp_wfNet404s in the thecityo_production_wp database is still inside the system tablespace.

Next, mysqld restarted and was ready for new connections

150708 3:36:37 [Note] /usr/sbin/mysqld: ready for connections. Version: '5.5.42-cll' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

One minute later, it crashed again. What was in the stack trace of the second crash ?

stack_bottom = 7f70e2625e58 thread_stack 0x40000 /usr/sbin/mysqld(my_print_stacktrace+0x35)[0x7aabf5] /usr/sbin/mysqld(handle_fatal_signal+0x4a4)[0x686324] /lib64/libpthread.so.0(+0xf710)[0x7f7120768710] /lib64/libc.so.6(gsignal+0x35)[0x7f711f92f625] /lib64/libc.so.6(abort+0x175)[0x7f711f930e05] /usr/sbin/mysqld[0x8fbd91] /usr/sbin/mysqld[0x8fbdee] /usr/sbin/mysqld[0x881fc7] /usr/sbin/mysqld[0x83c104] /usr/sbin/mysqld[0x83efa5] /usr/sbin/mysqld[0x81819b] /usr/sbin/mysqld(_Z13rr_sequentialP11READ_RECORD+0x1f)[0x74de7f] /usr/sbin/mysqld(_Z10sub_selectP4JOINP13st_join_tableb+0x79)[0x5ace99] /usr/sbin/mysqld[0x5b16c7] /usr/sbin/mysqld(_ZN4JOIN4execEv+0xc81)[0x5c6f41] /usr/sbin/mysqld(_Z12mysql_selectP3THDPPP4ItemP10TABLE_LISTjR4ListIS1_ES2_jP8st_orderSB_S2_SB_yP13select_resultP18st_select_lex_unitP13st_select_lex+0x12c)[0x5c873c] /usr/sbin/mysqld(_Z13handle_selectP3THDP3LEXP13select_resultm+0x165)[0x5c9175] /usr/sbin/mysqld[0x584392] /usr/sbin/mysqld(_Z21mysql_execute_commandP3THD+0x144d)[0x5894cd] 150708 3:39:09 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258064 bytes) /usr/sbin/mysqld(_Z11mysql_parseP3THDPcjP12Parser_state+0x330)[0x58ce20] /usr/sbin/mysqld(_Z16dispatch_command19enum_server_commandP3THDPcj+0x1af3)[0x58f1e3] /usr/sbin/mysqld(_Z24do_handle_one_connectionP3THD+0xd7)[0x629297] /usr/sbin/mysqld(handle_one_connection+0x51)[0x6293d1] /lib64/libpthread.so.0(+0x79d1)[0x7f71207609d1] /lib64/libc.so.6(clone+0x6d)[0x7f711f9e58fd]

It looks like you were doing some kind of SELECT ... JOIN query. My guess would be you were accessing the corrupt table in the SELECT ... JOIN because of this line 

/usr/sbin/mysqld(_Z13rr_sequentialP11READ_RECORD+0x1f)[0x74de7f]

which might by some kind of sequential read.

If you keep seeing

150708 3:36:36 InnoDB: Error: table 'thecityo_production_wp/wp_wfNet404s'

upon every crash and restart of mysqld, you need to clean that entry out of ibdata1.

I would not be fooled by

150708 3:39:09 [ERROR] /usr/sbin/mysqld: Out of memory (Needed 258064 bytes)

It is complaining about not allocating 252K. That's just a side affect of the error because it could allocate needed memory for an operation that cannot read from a table.

EPILOGUE

Please look into removing the pidgeon hole in the data dictionary. Also, look for other memory consuming components in the DB Server.

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  • Thank you Rolando, I cleaned up the corrupted databases of 'thecityo_production_wp/wp_wfNet404s' and thecityo_production_wp/wp_wfVulnScanners after I posted this message. So I think the Data Dictionary is not corrupt anymore. If that seemed to solve the problem I will vote yours as the answer. Thank you for the response. Commented Jul 10, 2015 at 12:18
  • Good point on running a full stack. The database is not running on a dedicated server, although it would be good to do that. I am going to check on php and the other processes running. Thanks! Commented Jul 10, 2015 at 12:27
  • Cleaning up the database seemed to solve the problem. I had to use a special drop command to get the table to drop. I am having trouble finding the command I ran, but it was something like drop table '#mysql5.3#tablename'. If anyone can add the command to this forum that would be great. Commented Jul 13, 2015 at 16:11
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10 GB of ram -- nothing is threatening to hit this.
open_files_limit=10000 -- Try 2000
query_cache_size=256M -- No more than 50M
default-storage-engine=MyISAM -- Unless you already have some InnoDB tables, this means that innodb_buffer_pool_size may as well be 0 -- you aren't using it.

So, I will guess one of this is the case:

  • 32-bit OS
  • 32-bit build of MySQL
  • The OS is limiting how much memory each process can have.

What OS?

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