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Please help.

I know nothing about MySQL server's or apache and I need a place to start. why is it so high?

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND            
 4991 mysql     20   0  207m  53m 4056 S  150  0.7   9:44.23 mysqld             
 9386 apache    20   0 41648  16m 3964 R   20  0.2   0:01.56 apache2            
 9370 apache    20   0 42460  17m 3972 R   16  0.2   0:01.46 apache2

there are about 25 apaches too. If I turn off Apache the CPU usage for Mysql doesn't reduce either.

And ofc I've turned it off and on again.

Please assist

This MySQL server has been running for 0 days, 0 hours, 3 minutes and 30 seconds. It started up on Sep 29, 2009 at 03:46 PM

Server traffic: These tables show the network traffic statistics of this MySQL server since its startup.
Traffic Tip     ø per hour
Received    6,313 KiB 	106 MiB
Sent    35 MiB 	607 MiB
Total   42 MiB 	712 MiB
Connections     ø per hour 	%
max. concurrent connections     99 	--- 	---
Failed attempts     0 	0.00 	0.00%
Aborted     0 	0.00 	0.00%
Total   31 k 	529.08 k 	100.00%

Query statistics: Since its startup, 95,049 queries have been sent to the server.
Total   ø per hour 	ø per minute 	ø per second
95 k    1.63 M 	27.16 k 	452.61
Query type  ø per hour 	%
admin commands  0 	0.00 	0.00%
alter db    0 	0.00 	0.00%
alter table     0 	0.00 	0.00%
analyze     0 	0.00 	0.00%
backup table    0 	0.00 	0.00%
begin   0 	0.00 	0.00%
change db   37 k 	633.33 k 	57.56%
change master   0 	0.00 	0.00%
check   0 	0.00 	0.00%
checksum    0 	0.00 	0.00%
commit  0 	0.00 	0.00%
create db   0 	0.00 	0.00%
create function     0 	0.00 	0.00%
create index    0 	0.00 	0.00%
create table    0 	0.00 	0.00%
delete  0 	0.00 	0.00%
delete multi    0 	0.00 	0.00%
do  0 	0.00 	0.00%
drop db     0 	0.00 	0.00%
drop function   0 	0.00 	0.00%
drop index  0 	0.00 	0.00%
drop table  0 	0.00 	0.00%
drop user   0 	0.00 	0.00%
flush   0 	0.00 	0.00%
grant   0 	0.00 	0.00%
ha close    0 	0.00 	0.00%
ha open     0 	0.00 	0.00%
ha read     0 	0.00 	0.00%
help    0 	0.00 	0.00%
insert  204 	3,497.14 	0.32%
insert select   0 	0.00 	0.00%
kill    0 	0.00 	0.00%
load    0 	0.00 	0.00%
load master data    0 	0.00 	0.00%
load master table   0 	0.00 	0.00%
lock tables     0 	0.00 	0.00%
optimize    0 	0.00 	0.00%
preload keys    0 	0.00 	0.00%
purge   0 	0.00 	0.00%
purge before date   0 	0.00 	0.00%
rename table    0 	0.00 	0.00%
repair  0 	0.00 	0.00%
replace     1 	17.14 	0.00%
replace select  0 	0.00 	0.00%
reset   0 	0.00 	0.00%
Query type  ø per hour 	%
restore table   0 	0.00 	0.00%
revoke  0 	0.00 	0.00%
revoke all  0 	0.00 	0.00%
rollback    0 	0.00 	0.00%
savepoint   0 	0.00 	0.00%
select  5,975 	102.43 k 	9.31%
set option  493 	8,451.43 	0.77%
show binlog events  0 	0.00 	0.00%
show binlogs    12 	205.71 	0.02%
show charsets   12 	205.71 	0.02%
show collations     12 	205.71 	0.02%
show column types   0 	0.00 	0.00%
show create db  0 	0.00 	0.00%
show create table   0 	0.00 	0.00%
show databases  12 	205.71 	0.02%
show errors     0 	0.00 	0.00%
show fields     80 	1,371.43 	0.12%
show grants     1 	17.14 	0.00%
show innodb status  0 	0.00 	0.00%
show keys   45 	771.43 	0.07%
show logs   0 	0.00 	0.00%
show master status  0 	0.00 	0.00%
show ndb status     0 	0.00 	0.00%
show new master     0 	0.00 	0.00%
show open tables    1 	17.14 	0.00%
show privileges     0 	0.00 	0.00%
show processlist    3 	51.43 	0.00%
show slave hosts    0 	0.00 	0.00%
show slave status   0 	0.00 	0.00%
show status     8 	137.14 	0.01%
show storage engines    0 	0.00 	0.00%
show tables     0 	0.00 	0.00%
show variables  31 	531.43 	0.05%
show warnings   0 	0.00 	0.00%
slave start     0 	0.00 	0.00%
slave stop  0 	0.00 	0.00%
stmt close  0 	0.00 	0.00%
stmt execute    0 	0.00 	0.00%
stmt prepare    0 	0.00 	0.00%
stmt reset  0 	0.00 	0.00%
stmt send long data     0 	0.00 	0.00%
truncate    0 	0.00 	0.00%
unlock tables   0 	0.00 	0.00%
update  469 	8,040.00 	0.73%
update multi    0 	0.00 	0.00%

Flush_commands      1  	 The number of executed FLUSH statements.
Slow_queries    4 	The number of queries that have taken more than long_query_time seconds.Documentation
Begin SSL Variable  Value 	Description
Ssl_accept_renegotiates     0 	
Ssl_accepts     0 	
Ssl_callback_cache_hits     0 	
Ssl_client_connects     0 	
Ssl_connect_renegotiates    0 	
Ssl_ctx_verify_depth    0 	
Ssl_ctx_verify_mode     0 	
Ssl_default_timeout     0 	
Ssl_finished_accepts    0 	
Ssl_finished_connects   0 	
Ssl_session_cache_hits  0 	
Ssl_session_cache_misses    0 	
Ssl_session_cache_mode  NONE 	
Ssl_session_cache_overflows     0 	
Ssl_session_cache_size  0 	
Ssl_session_cache_timeouts  0 	
Ssl_sessions_reused     0 	
Ssl_used_session_cache_entries  0 	
Ssl_verify_depth    0 	
Ssl_verify_mode     0 	
Begin Handler Variable  Value 	Description
Handler_commit  0 	The number of internal COMMIT statements.
Handler_delete  0 	The number of times a row was deleted from a table.
Handler_discover    0 	The MySQL server can ask the NDB Cluster storage engine if it knows about a table with a given name. This is called discovery. Handler_discover indicates the number of time tables have been discovered.
Handler_read_first  43 	The number of times the first entry was read from an index. If this is high, it suggests that the server is doing a lot of full index scans; for example, SELECT col1 FROM foo, assuming that col1 is indexed.
Handler_read_key    14 M 	The number of requests to read a row based on a key. If this is high, it is a good indication that your queries and tables are properly indexed.
Handler_read_next   20 M 	The number of requests to read the next row in key order. This is incremented if you are querying an index column with a range constraint or if you are doing an index scan.
Handler_read_prev   619 	The number of requests to read the previous row in key order. This read method is mainly used to optimize ORDER BY ... DESC.
Handler_read_rnd    21 k 	The number of requests to read a row based on a fixed position. This is high if you are doing a lot of queries that require sorting of the result. You probably have a lot of queries that require MySQL to scan whole tables or you have joins that don't use keys properly.
Handler_read_rnd_next   32 M 	The number of requests to read the next row in the data file. This is high if you are doing a lot of table scans. Generally this suggests that your tables are not properly indexed or that your queries are not written to take advantage of the indexes you have.
Handler_rollback    0 	The number of internal ROLLBACK statements.
Handler_update  4,781 k 	The number of requests to update a row in a table.
Handler_write   4,073 k 	The number of requests to insert a row in a table.
Begin Query cache Variable  Value 	Description
Flush query cache Documentation
Qcache_free_blocks  66 	The number of free memory blocks in query cache.
Qcache_free_memory  30 M 	The amount of free memory for query cache.
Qcache_hits     20 k 	The number of cache hits.
Qcache_inserts  1,478 	The number of queries added to the cache.
Qcache_lowmem_prunes    0 	The number of queries that have been removed from the cache to free up memory for caching new queries. This information can help you tune the query cache size. The query cache uses a least recently used (LRU) strategy to decide which queries to remove from the cache.
Qcache_not_cached   4,498 	The number of non-cached queries (not cachable, or not cached due to the query_cache_type setting).
Qcache_queries_in_cache     953 	The number of queries registered in the cache.
Qcache_total_blocks     2,052 	The total number of blocks in the query cache.
Begin Threads Variable  Value 	Description
Show processes Documentation
Slow_launch_threads     0 	The number of threads that have taken more than slow_launch_time seconds to create.
Threads_cached  46 	The number of threads in the thread cache. The cache hit rate can be calculated as Threads_created/Connections. If this value is red you should raise your thread_cache_size.
Threads_connected   53 	The number of currently open connections.
Threads_created     99 	The number of threads created to handle connections. If Threads_created is big, you may want to increase the thread_cache_size value. (Normally this doesn't give a notable performance improvement if you have a good thread implementation.)
Threads_running     33 	The number of threads that are not sleeping.
Threads_cache_hitrate_%     99.68 % 	
Begin Binary log Variable   Value 	Description
Binlog_cache_disk_use   0 	The number of transactions that used the temporary binary log cache but that exceeded the value of binlog_cache_size and used a temporary file to store statements from the transaction.
Binlog_cache_use    0 	The number of transactions that used the temporary binary log cache.
Begin Temporary data Variable   Value 	Description
Created_tmp_disk_tables     3,337 	The number of temporary tables on disk created automatically by the server while executing statements. If Created_tmp_disk_tables is big, you may want to increase the tmp_table_size value to cause temporary tables to be memory-based instead of disk-based.
Created_tmp_files   0 	How many temporary files mysqld has created.
Created_tmp_tables  4,880 	The number of in-memory temporary tables created automatically by the server while executing statements.
Begin Delayed inserts Variable  Value 	Description
Delayed_errors  0 	The number of rows written with INSERT DELAYED for which some error occurred (probably duplicate key).
Delayed_insert_threads  0 	The number of INSERT DELAYED handler threads in use. Every different table on which one uses INSERT DELAYED gets its own thread.
Delayed_writes  0 	The number of INSERT DELAYED rows written.
Not_flushed_delayed_rows    0 	The number of rows waiting to be written in INSERT DELAYED queues.
Begin Key cache Variable    Value 	Description
Key_blocks_not_flushed  0 	The number of key blocks in the key cache that have changed but haven't yet been flushed to disk. It used to be known as Not_flushed_key_blocks.
Key_blocks_unused   13 k 	The number of unused blocks in the key cache. You can use this value to determine how much of the key cache is in use.
Key_blocks_used     1,541 	The number of used blocks in the key cache. This value is a high-water mark that indicates the maximum number of blocks that have ever been in use at one time.
Key_read_requests   27 M 	The number of requests to read a key block from the cache.
Key_reads   2,413 	The number of physical reads of a key block from disk. If Key_reads is big, then your key_buffer_size value is probably too small. The cache miss rate can be calculated as Key_reads/Key_read_requests.
Key_write_requests  43 k 	The number of requests to write a key block to the cache.
Key_writes  193 	The number of physical writes of a key block to disk.
Key_buffer_fraction_%   20.88 % 	
Key_write_ratio_%   0.45 % 	
Key_read_ratio_%    0.01 % 	
Begin Joins Variable    Value 	Description
Select_full_join    9 	The number of joins that do not use indexes. If this value is not 0, you should carefully check the indexes of your tables.
Select_full_range_join  0 	The number of joins that used a range search on a reference table.
Select_range    805 	The number of joins that used ranges on the first table. (It's normally not critical even if this is big.)
Select_range_check  0 	The number of joins without keys that check for key usage after each row. (If this is not 0, you should carefully check the indexes of your tables.)
Select_scan     4,115 	The number of joins that did a full scan of the first table.
Begin Replication Variable  Value 	Description
Show slave hosts Show slave status Documentation
Rpl_status  NULL 	The status of failsafe replication (not yet implemented).
Slave_open_temp_tables  0 	The number of temporary tables currently open by the slave SQL thread.
Slave_retried_transactions  0 	Total (since startup) number of times the replication slave SQL thread has retried transactions.
Slave_running   OFF 	This is ON if this server is a slave that is connected to a master.
Begin Sorting Variable  Value 	Description
Sort_merge_passes   0 	The number of merge passes the sort algorithm has had to do. If this value is large, you should consider increasing the value of the sort_buffer_size system variable.
Sort_range  47 	The number of sorts that were done with ranges.
Sort_rows   21 k 	The number of sorted rows.
Sort_scan   4,982 	The number of sorts that were done by scanning the table.
Begin Tables Variable   Value 	Description
Flush (close) all tables Show open tables
Open_tables     276 	The number of tables that are open.
Opened_tables   282 	The number of tables that have been opened. If opened tables is big, your table cache value is probably too small.
Table_locks_immediate   9,116 	The number of times that a table lock was acquired immediately.
Table_locks_waited  56 	The number of times that a table lock could not be acquired immediately and a wait was needed. If this is high, and you have performance problems, you should first optimize your queries, and then either split your table or tables or use replication.
Begin Variable  Value 	Description
Open_files  368 	The number of files that are open.
Open_streams    0 	The number of streams that are open (used mainly for logging).
share|improve this question
@Dorjan - dataset - just estimate what is the size of data mysql works on. depends very much on what you have in db and what is the usage patter. start with telling what is the total size of database in MB/GB. relativly low cpu usage compared with high load tells me that you are IO bound.. too many writes to disk most probably. – pQd Sep 29 '09 at 17:20
50MiB is the size :S – Dorjan Sep 30 '09 at 9:35

Since its startup, 95,049 queries have been sent to the server.

Pretty impressive for 3 minutes of uptime. Were things running fine and dandy before? If you shut down apache and waited, and mysqld CPU usage doesn't go down, and both services are on the same box, I would guess that someone else is querying your server. If that is so you may want to close that mysql port from the internet.

If you can post the output of "show processlist;" to your sql server while apache is shut off (assuming this is a non-critical machine), that might help shed some light on what is being queried to mysql.

$ mysql -u root -p
mysql> show processlist;

I know i'm making a lot of assumptions but under normal conditions with both services running, it would seem to me that your website is bogged down and is either popular or there is some major spamming going on.

share|improve this answer
It could just be badly designed tbh. 150 queries per page load. – Dorjan Sep 29 '09 at 16:09
atm there are only 4-3 processes ever going, so I don't know why MySQL needs 180% CPU when there is nothing going on... – Dorjan Sep 29 '09 at 16:10

What is mysql doing? Do you have mytop installed or can you check the output of show processlist in mysql?

share|improve this answer
Updated question with logs – Dorjan Sep 29 '09 at 14:53

Most probably you're being killed by disk IO - mainly writes, probably caused by excessive creation of temporary tables.

If the problem is with temporary tables:

Try to optimize [if you can] queries to avoid temporary tables [you get them for instance when you run select something from table group by column].

If you cannot change SQL code, your dataset is small and you can afford giving more memory to MySQL - try to fiddle with max_heap_table_size and tmp_table_size in my.cnf, look here.

What's your value for long_query_time? It seems you have very few slow queries - either because long_query_time is high or because you receive tons of queries that execute in under a few seconds.

What's the size of your dataset?

share|improve this answer
How do i find the size of the dataset> Value for long_query_time? – Dorjan Sep 29 '09 at 16:08
Not sure what the long_query_time is but there are several queries that are exceeding it. However according the the documentation this can be misleading if the server is under heavy load (which it is / isn't). 180% CPU yet no processes running :S – Dorjan Sep 29 '09 at 16:36

tail -f /var/log/mysql.log will let you follow whats going on in the log file. With that load there might be extreme amounts of logging data though to go through.

Something thats common: Do you have comment sections, a forum, a guestbook or similiar that spammers might utilize?

netstat -lapute | grep mysql will show active connections to mysql

share|improve this answer
logging is off. – Dorjan Sep 29 '09 at 14:51
up vote 0 down vote accepted

the answer was a corrupted index or some-such. I recreated the db then copied over the data and it worked.

Weird but I guess it is one of those things that happen.

Thanks for all the help! You really did :)

share|improve this answer

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