The 'order by' clause is forcing MySQL to use a temporary table; as a test could you try running the query without the order by clause? Does it run quicker? MySQL must use a temporary table if you 'group by' or 'order by' a column not contained in the first table of the select, sometimes you can get around this limitation just by rewriting the select. Give it a try, it can make a huge difference. Do the tables have a lot of insert,update, delete operations? If so it may be worth you running OPTIMIZE TABLE to rebuild indexes. Be warned it can take some time to complete and tables are locked whilst it runs. If you have slaves running you may want to add LOCAL to the OPTIMIZE TABLE statement so the operation does not run on your slaves. I'm stuck doing some other stuff at the mo but I will try and have a proper look at this later and will get back to you. Regards
John Daisley Business Intelligence Developer - MySQL Database Administrator Inspired Gaming Group Plc Direct Dial +44 (0)1283 519244 Telephone +44 (0)1283 512777 ext 2244 Mobile +44 (0)7812 451238 ________________________________ From: jingtian.seu...@gmail.com [mailto:jingtian.seu...@gmail.com] On Behalf Of TianJing Sent: 15 December 2009 12:43 To: Daisley, John (Burton) Cc: mysql@lists.mysql.com Subject: Re: mysql server optimization yes,you are right,the longblob is already move to a separate table fdna,it is about 10Gb/database the fdata is about 30Gb/database ,the fgroup is about 10Gb/database.the MYI file is almost the same or much bigger than the MYD file. show create table for fdna is: | fdna | CREATE TABLE `fdna` ( `fref` varchar(100) NOT NULL, `foffset` int(10) unsigned NOT NULL, `fdna` longblob, PRIMARY KEY (`fref`,`foffset`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1 | show create table for fdata is: | fdata | CREATE TABLE `fdata` ( `fid` int(11) NOT NULL AUTO_INCREMENT, `fref` varchar(100) NOT NULL, `fstart` int(10) unsigned NOT NULL, `fstop` int(10) unsigned NOT NULL, `fbin` double(20,6) NOT NULL, `ftypeid` int(11) NOT NULL, `fscore` float DEFAULT NULL, `fstrand` enum('+','-') DEFAULT NULL, `fphase` enum('0','1','2') DEFAULT NULL, `gid` int(11) NOT NULL, `ftarget_start` int(10) unsigned DEFAULT NULL, `ftarget_stop` int(10) unsigned DEFAULT NULL, PRIMARY KEY (`fid`), UNIQUE KEY `fref` (`fref`,`fbin`,`fstart`,`fstop`,`ftypeid`,`gid`), KEY `ftypeid` (`ftypeid`), KEY `gid` (`gid`) ) ENGINE=MyISAM AUTO_INCREMENT=381002371 DEFAULT CHARSET=latin1 | show create for fgroup is: -----------------------------+ | fgroup | CREATE TABLE `fgroup` ( `gid` int(11) NOT NULL AUTO_INCREMENT, `gclass` varchar(100) DEFAULT NULL, `gname` varchar(100) DEFAULT NULL, PRIMARY KEY (`gid`), UNIQUE KEY `gclass` (`gclass`,`gname`) ) ENGINE=MyISAM AUTO_INCREMENT=240501186 DEFAULT CHARSET=latin1 | show create for ftype is: | ftype | CREATE TABLE `ftype` ( `ftypeid` int(11) NOT NULL AUTO_INCREMENT, `fmethod` varchar(100) NOT NULL, `fsource` varchar(100) DEFAULT NULL, PRIMARY KEY (`ftypeid`), UNIQUE KEY `ftype` (`fmethod`,`fsource`), KEY `fmethod` (`fmethod`), KEY `fsource` (`fsource`) ) ENGINE=MyISAM AUTO_INCREMENT=16 DEFAULT CHARSET=latin1 | the index on fdata is : --+---------+ | Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | +-------+------------+----------+--------------+-------------+---------- -+-------------+----------+--------+------+------------+---------+ | fdata | 0 | PRIMARY | 1 | fid | A | 463619315 | NULL | NULL | | BTREE | | | fdata | 0 | fref | 1 | fref | A | 1 | NULL | NULL | | BTREE | | | fdata | 0 | fref | 2 | fbin | A | 229060 | NULL | NULL | | BTREE | | | fdata | 0 | fref | 3 | fstart | A | 231809657 | NULL | NULL | | BTREE | | | fdata | 0 | fref | 4 | fstop | A | 463619315 | NULL | NULL | | BTREE | | | fdata | 0 | fref | 5 | ftypeid | A | 463619315 | NULL | NULL | | BTREE | | | fdata | 0 | fref | 6 | gid | A | 463619315 | NULL | NULL | | BTREE | | | fdata | 1 | ftypeid | 1 | ftypeid | A | 15 | NULL | NULL | | BTREE | | | fdata | 1 | gid | 1 | gid | A | 231809657 | NULL | NULL | | BTREE | | index for fgroup is: +--------+------------+----------+--------------+-------------+--------- --+-------------+----------+--------+------+------------+---------+ | Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | +--------+------------+----------+--------------+-------------+--------- --+-------------+----------+--------+------+------------+---------+ | fgroup | 0 | PRIMARY | 1 | gid | A | 232212341 | NULL | NULL | | BTREE | | | fgroup | 0 | gclass | 1 | gclass | A | 5 | NULL | NULL | YES | BTREE | | | fgroup | 0 | gclass | 2 | gname | A | 232212341 | NULL | NULL | YES | BTREE | | the EXPLAIN EXTENDED for the query is : +----+-------------+--------+--------+-------------------------------+-- -------+---------+----------------------+------+----------+------------- ---------------------------------+ | id | select_type | table | type | possible_keys | key | key_len | ref | rows | filtered | Extra | +----+-------------+--------+--------+-------------------------------+-- -------+---------+----------------------+------+----------+------------- ---------------------------------+ | 1 | SIMPLE | fdata | range | fref,ftypeid,gid | fref | 114 | NULL | 8 | 75.00 | Using where; Using temporary; Using filesort | | 1 | SIMPLE | ftype | eq_ref | PRIMARY,ftype,fmethod,fsource | PRIMARY | 4 | yhchr1.fdata.ftypeid | 1 | 100.00 | Using where | | 1 | SIMPLE | fgroup | eq_ref | PRIMARY | PRIMARY | 4 | yhchr1.fdata.gid | 1 | 100.00 | | +----+-------------+--------+--------+-------------------------------+-- -------+---------+----------------------+------+----------+------------- ---------------------------------+ On Tue, Dec 15, 2009 at 6:54 PM, Daisley, John (Burton) <john.dais...@llg.co.uk> wrote: I'm fairly sure that the longblob column will prevent MySQL from being able to use 'in memory temp tables' regardless of whether it is included in the SELECT. In an ideal world I would move that longblob to a separate table. How big are the tables fdata,ftype,fgroup? Can you post the results of EXPLAIN EXTENDED for the query you posted? Can you also post the output of 'SHOW CREATE TABLE' for the tables fdata,ftype,fgroup? John Daisley Business Intelligence Developer - MySQL Database Administrator Inspired Gaming Group Plc Direct Dial +44 (0)1283 519244 Telephone +44 (0)1283 512777 ext 2244 Mobile +44 (0)7812 451238 Email john.dais...@llg.co.uk www.inspiredgaminggroup.com -----Original Message----- From: TianJing <tianj...@genomics.org.cn> Sent: 15 December 2009 10:28 To: mg_s...@hotmail.com Cc: mysql@lists.mysql.com Subject: Re: mysql server optimization i use MyISAM storage,the MYI file is more than 500Gb. most of the sql is select with many 'and','or','order by',for example: SELECT fref,fstart,fstop,fsource,fmethod,fscore,fstrand,fphase,gclass,gname,fta rget_start,ftarget_stop,fdata.fid,fdata.gid FROM fdata,ftype,fgroup WHERE fgroup.gid = fdata.gid AND ftype.ftypeid = fdata.ftypeid AND fdata.fref='chr18' AND (fbin='10000000000' OR fbin between '1000000000' and '1000000000' OR fbin between '99999999.9999999' and '100000000' OR fbin between '10000000.0000049' and '10000000.0000051' OR fbin between '1000000.0000549' and '1000000.0000551' OR fbin between '100000.0005529' and '100000.0005531' OR fbin between '10000.0055379' and '10000.0055381' OR fbin between '1000.0553839' and '1000.0553841') AND fdata.fstop>='55384910' AND fdata.fstart<='55384989' AND ((fmethod = 'genotype' AND fsource = 'SoapSNP') OR (fmethod = 'gt_novel' AND fsource = 'SoapSNP') OR (fmethod = 'SNP' AND fsource = 'MutaGeneSys_06JUNE07') OR (fmethod = 'snp' AND fsource = 'HapMap_gt') OR (fmethod = 'similarity') OR (fmethod = 'HSP') OR (fmethod = 'match') OR (fmethod = 'CDS' AND fsource = 'UCSC_1') OR (fmethod = '5\'-UTR' AND fsource = 'UCSC_1') OR (fmethod = '3\'-UTR' AND fsource = 'UCSC_1') OR (fmethod = 'transcription_start_site' AND fsource = 'UCSC_1') OR (fmethod = 'polyA_site' AND fsource = 'UCSC_1') OR (fmethod = 'UTR' AND fsource = 'UCSC_1') OR (fmethod = 'five_prime_untranslated_region' AND fsource = 'UCSC_1') OR (fmethod = 'three_prime_untranslated_region' AND fsource = 'UCSC_1') OR (fmethod = 'five_prime_UTR' AND fsource = 'UCSC_1') OR (fmethod = 'three_prime_UTR' AND fsource = 'UCSC_1') OR (fmethod = 'exon' AND fsource = 'UCSC_1') OR (fmethod = 'mRNA' AND fsource = 'UCSC_1')) ORDER BY fgroup.gname; there is a longblob column in the table, but even i do not select this blob column, the i/o is still higher. i have 16G memery in total, the oracle database take 1/4 of them, i try to increasing the key_buffer_size to 2048M and tmp_table_size to 1024M,but the machine crashed out of memery in one day,the mysqld takes over 18G memery! i use show profiles find that 'sending data' and 'copying to tmp table' takes lots of time. On Tue, Dec 15, 2009 at 5:36 PM, John Daisley <mg_s...@hotmail.com> wrote: > What kind of queries are being run and what type of data is stored? > > There are a number of factors which causes MySQL to use on disk temporary > tables instead of in memory tables. (If there a BLOB or TEXT columns in the > table for example). > > As a starting point you could (if you have the memory in your box) try > increasing the values for tmp_table_size and max_heap_size, these control > how large an in-memory temp table can grow before it is converted to an on > disk temp table. > > Regards > John > > =================== > > John Daisley > > MySQL 5.0 Certified Database Administrator (CMDBA) > MySQL 5.0 Certified Developer > Cognos BI Developer > > Telephone: +44(0)1283 537111 > Mobile: +44(0)7812 451238 > Email: john.dais...@butterflysystems.co.uk > > =================== > > Sent via HP IPAQ mobile device > > -----Original Message----- > From: TianJing <jingtian.seu...@gmail.com> > Sent: 15 December 2009 03:08 > To: mysql@lists.mysql.com > Subject: mysql server optimization > > Dear all, > > i am nowing having a problem with the mysql server optimization, i have 20 > database on a server,each database is about 80Gb,the sql seems very > slow,almost > 5s.and the server i/o is so high,when i check the > processlist,the 'copying to tmp table' state takes a long time. > > i have already use index,but the sql use lots of 'and','or','order by', > and > for some reason i can not optimization the sql,i hope to do some > optimization on mysql server to mitigate this phenomenon,could any one > give > me some suggestion? > > thanks. > > my server is linux,8CPU and 4G memery,the my.cnf is: > > [mysqld] > port = 3306 > skip-locking > skip-name-resolve > key_buffer_size = 16M > max_allowed_packet = 1M > table_open_cache = 64 > sort_buffer_size = 512M > net_buffer_length = 8K > read_buffer_size = 512K > read_rnd_buffer_size = 512M > myisam_sort_buffer_size = 8M > table_cache = 1024 > log-bin=mysql-bin > binlog_format=mixed > > > -- > Tianjing > > -- Tianjing Tel:0755-2527-3851 MSN:tianjing...@hotmail.com <mailto:msn%3atianjing...@hotmail.com> <msn%3atianjing...@hotmail.com <mailto:msn%253atianjing...@hotmail.com> > _____________________________________________________________________ This e-mail has been scanned for viruses by MessageLabs. -- Tianjing Tel:0755-2527-3851 MSN:tianjing...@hotmail.com <mailto:msn%3atianjing...@hotmail.com> _____________________________________________________________________ This e-mail has been scanned for viruses by MessageLabs.
