We are going to move from myisam to innodb. Penguin2 has been happily running innodb for some time.
Main problem are fulltext columns, the text from Trello is captured below. This is for the following tables
Initial good candidates are (from issues/database-not-responding):
+ 2.1G Dec 4 22:15 ProbeSetXRef.MYD (done!) + 2.3G Dec 18 14:56 ProbeSet.MYD - with fulltext column + 2.6G Aug 27 2019 ProbeSE.MYD (used?) + 7.1G Nov 2 05:07 ProbeSetSE.MYD (done!) + 11G Aug 27 2019 ProbeData.MYD (used?) + 63G Dec 4 22:15 ProbeSetData.MYD
I am starting with the two SE tables first - because they are small.
Actually ProbeData and ProbeSE (containing the Affy data) are not referenced in GN2. I need to check that.
For every table
With the SQL database we need to move from myisam to innodb format, mostly to stop the problem of full table locks. Also I expect the occasional crashes we see to go away.
Today, as a start, I moved the ProbeSetSE table to innodb. The result is that the disk representation is 3x the size and a full table scan takes 3x the time (somewhat unsurprising). This may impact correlation, i.e. those routines that go through all the data. We'll have to test that carefully. For the SE I don't think we do that, so it is no biggie.
There are no real performance gains that I can tell, though for the mapping page I see no slowing down either.
I'll need to free up space on the NVME storage to do the larger tables.
I also took the opportunity to add a primary key because InnoDB requires it and I changed the *table* language from latin1-sweden to utf8. These are major upgrades.
There are no real performance gains that I can tell, though for the mapping page I see no slowing down either.
I'll need to free up space on the NVME storage to do the larger tables.
I also took the opportunity to add a primary key because InnoDB requires it and I changed the *table* language from latin1-sweden to utf8mb4. These are major upgrades.
In the coming week I'll have to reboot the server to add a disk, move stuff across to free up space on the NVME, and convert a few more tables. I aim to get the largest tables done - because these are the one that hurt when locked:
+ 2.1G Dec 4 22:15 ProbeSetXRef.MYD + 2.3G Dec 18 14:56 ProbeSet.MYD - with fulltext column + 2.6G Aug 27 2019 ProbeSE.MYD + 7.1G Nov 2 05:07 ProbeSetSE.MYD + 11G Aug 27 2019 ProbeData.MYD + 63G Dec 4 22:15 ProbeSetData.MYD
(note each is about double that size because of indexes)
ProbeSetSE is done. So ProbeData and ProbeSetData are the main candidates right now.
Note I set buffers to 16GB for now
+innodb_buffer_pool_size=16G +innodb_ft_min_token_size=3 +# innodb_use_sys_malloc=0 +innodb_file_per_table=ON
time mysqlcheck -c -u webqtlout -pwebqtlout db_webqtl
To check one single table Probe
root@tux01:/var/lib/mysql/db_webqtl# mysqlcheck -c db_webqtl -u webqtlout -pwebqtlout Probe db_webqtl.Probe OK
Make sure we have not a FULLTEXT column we do not know about (note it needs backquotes around ls):
root@tux01:/var/lib/mysql/db_webqtl# for x in ls -1 *.MYD|sed -e 's,\.MYD,,' ; do echo $x ; mysql -u webqtlout -pwebqtlout db_webqtl -e "select group_concat(distinct column_name) from information_schema.STATISTICS where table_schema = 'db_webqtl' and table_name = '$x' and index_type = 'FULLTEXT'" ; done|less GeneRIF_BASIC ProbeSet pubmedsearch
still the same.
Start with ProbeSetSE
-rw-rw---- 1 mysql mysql 8.1G Dec 28 08:39 ProbeSetSE.MYI -rw-rw---- 1 mysql mysql 7.1G Nov 2 05:07 ProbeSetSE.MYD -rw-rw---- 1 mysql mysql 8.5K Feb 3 2021 ProbeSetSE.frm
MariaDB [db_webqtl]> select * from ProbeSetSE limit 2; +--------+----------+----------+ | DataId | StrainId | error | +--------+----------+----------+ | 1 | 1 | 0.681091 | | 1 | 2 | 0.361151 | +--------+----------+----------+ 2 rows in set (0.001 sec) MariaDB [db_webqtl]> select count(*) from ProbeSetSE limit 2; +-----------+ | count(*) | +-----------+ | 688744613 | +-----------+ 1 row in set (0.000 sec)
MariaDB [db_webqtl]> flush tables ProbeSetSE; Query OK, 0 rows affected (0.002 sec)
MariaDB [db_webqtl]> select count(*) from ProbeSetSE where error<0.36; +-----------+ | count(*) | +-----------+ | 601603553 | +-----------+ 1 row in set (1 min 1.189 sec)
Some testing shows strainid and error are not indexed. Test query on myisam:
MariaDB [db_webqtl]> select count(*) from ProbeSetSE where strainid<20 and error<0.10; +----------+ | count(*) | +----------+ | 61625074 | +----------+ 1 row in set (58.301 sec)
Check index and primary key (PK):
SHOW CREATE TABLE ProbeSetSE;
| ProbeSetSE | CREATE TABLE "ProbeSetSE" (
"DataId" int(10) unsigned NOT NULL DEFAULT 0,
"StrainId" smallint(5) unsigned NOT NULL DEFAULT 0,
"error" float NOT NULL,
UNIQUE KEY "DataId" ("DataId","StrainId")
) ENGINE=MyISAM DEFAULT CHARSET=latin1 |
Note the latin1 we don't need. Also innodb needs a primary key.
The mapping page retrieves SE through a call to
retrieve_sample_data(this_trait, dataset)
we also have an API endpoint
@app.route("/api/v_{}/sample_data/<path:dataset_name>".format(version))
@app.route("/api/v_{}/sample_data/<path:dataset_name>.<path:file_format>".format(version))
def all_sample_data(dataset_name, file_format="csv"):
But I can't get it to work for a trait.
curl "http://genenetwork.org/api/v_pre1/sample_data/1427571_at"
so, instead, I exported the CSV from
It took the server 2.02924s seconds to process this page. It took your browser 1.577 second(s) to render this page.
This is our test 'setup'.
On Tux01 the database is hosted on a drive with 111 GB free. Not enough for all conversions. There should be an extra drive in there which requires configuration with reboot. But first we can convert this small table. Backups we have already automated. But I'll add
tar cvzf /home/wrk/ProbeSetSE.tgz ProbeSetSE*
To convert to InnoDB we should:
For ProbeSetSE note the UNIQUE key was already defined. So set a primary key:
ALTER TABLE ProbeSetSE ADD PRIMARY KEY(DataId,StrainId); Query OK, 688744613 rows affected (15 min 13.830 sec) Records: 688744613 Duplicates: 0 Warnings: 0
Unsurprisingly the index grew
-rw-rw---- 1 mysql mysql 16G Dec 28 11:06 ProbeSetSE.MYI
MariaDB [db_webqtl]> SHOW CHARACTER SET LIKE 'utf8mb4'; +---------+---------------+--------------------+--------+ | Charset | Description | Default collation | Maxlen | +---------+---------------+--------------------+--------+ | utf8mb4 | UTF-8 Unicode | utf8mb4_general_ci | 4 | +---------+---------------+--------------------+--------+ 1 row in set (0.000 sec)
MariaDB [db_webqtl]> ALTER TABLE ProbeSetSE CONVERT TO CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci; Stage: 2 of 2 'Enabling keys' 0% of stage done Query OK, 688744613 rows affected (15 min 14.380 sec) Records: 688744613 Duplicates: 0 Warnings: 0
For this table it has no effect since there are not text fields. Still this looks good:
SHOW CREATE TABLE ProbeSetSE;
| ProbeSetSE | CREATE TABLE "ProbeSetSE" (
"DataId" int(10) unsigned NOT NULL DEFAULT 0,
"StrainId" smallint(5) unsigned NOT NULL DEFAULT 0,
"error" float NOT NULL,
PRIMARY KEY ("DataId","StrainId"),
UNIQUE KEY "DataId" ("DataId","StrainId")
) ENGINE=MyISAM DEFAULT CHARSET=utf8mb4 |
Looking good! Now there are two indexes which are the same to
MariaDB [db_webqtl]> DROP INDEX DataId ON ProbeSetSE;
MariaDB [db_webqtl]> show index from ProbeSetSE; 2 rows in set (0.000 sec)
So, on to converting to innodb
Unfortunately we can't swith to 4k page tables because we have existing tables. We'll do that later some day in a controlled fashion.
MariaDB [db_webqtl]> ALTER TABLE ProbeSetSE ENGINE = InnoDB; Query OK, 688744613 rows affected (1 hour 51 min 36.273 sec) Records: 688744613 Duplicates: 0 Warnings: 0
2 hours for a lousy table conversion!
The new file sizes are:
-rw-rw---- 1 mysql mysql 1.5K Dec 28 11:33 ProbeSetSE.frm -rw-rw---- 1 mysql mysql 51G Dec 28 13:25 ProbeSetSE.ibd
So the has tripled (including a new index) and during conversion it has both the old and the new on disk. I'll need to make space for this baby.
Let's try OPTIMIZE
OPTIMIZE NO_WRITE_TO_BINLOG TABLE ProbeSetSE;
Ah, now the size is similar to myisam and loading the mapping page is slighty faster.
What about performance?
MariaDB [db_webqtl]> select count(*) from ProbeSetSE where strainid<20 and error<0.10; +----------+ | count(*) | +----------+ | 61625074 | +----------+ 1 row in set (3 min 22.958 sec)
Whoah. 3 times slower - which makes sense if you know the physical size of the data. Full table scans should be rare, but we need to make sure we don't slow them down that much!
Again I exported the CSV from
It took the server 1.46351s seconds to process this page. It took your browser 2.119 second(s) to render this page
and it shows practically the same results.
Prototocol from
Every table update has to follow the template:
If you have enough space, you can create a copy of the actual table and do the work on that:
CREATE TABLE new_tbl [AS] SELECT * FROM MYTABLE;
Then you can change the column as desired:
ALTER TABLE tbl_name MODIFY COLUMN col_name BIGINT AUTO_INCREMENT;
Once the process is done, you can rename the tables:
DROP MYTABLE; RENAME TABLE tbl_name TO new_tbl_name, tbl_name2 TO MYTABLE;
SHOW CREATE TABLE MYTABLE;
select * from MYTABLE limit 2;
select count(*) from MYTABLE;
Do this also on Penguin2.
rg MYTABLE --color=always |less -R
rg MYTABLE --type=py -l|fzf --preview="rg --color=always -A 20 MYTABLE {}" --preview-window=right:85%:wrap
Some select statement and maybe a page of GN2.
ALTER TABLE MYTABLE ADD PRIMARY KEY(col1,col2);
SHOW INDEX FROM MYTABLE; DROP INDEX ProbeSetId ON MYTABLE;
ALTER TABLE MYTABLE ENGINE = InnoDB;
ALTER TABLE ProbeSetSE CONVERT TO CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci;
For those cases see bottom of move-to-innodb.gmi.
OPTIMIZE NO_WRITE_TO_BINLOG TABLE MYTABLE;
After running the optimiser rename the tables
RENAME TABLE orig TO orig_old, mytest TO orig;
In an earlier track I wrote how to deal with Fulltext fields
pjotrp 16 Oct 2019 at 10:47
Fulltext
To list fulltext info for one table do:
select group_concat(distinct column_name) from information_schema.STATISTICS where table_schema = 'db_webqtl' and table_name = 'Probeset' and index_type = 'FULLTEXT';
Or
SHOW CREATE TABLE ProbeSet;
FULLTEXT KEY 'SEARCH_GENE_IDX' ('Symbol','alias'),
FULLTEXT KEY 'SEARCH_FULL_IDX' ('Name','description','Symbol','alias','GenbankId','UniGeneId','Probe_Target_Description'),
FULLTEXT KEY 'RefSeq_FULL_IDX' ('RefSeq_TranscriptId')
ENGINE=MyISAM AUTO_INCREMENT=12806592 DEFAULT CHARSET=latin1
To see all:
root@tux02:/var/lib/mysql/db_webqtl# for x in ls -1 *.MYD|sed -e 's,\.MYD,,' ; do echo $x ; mysql -u webqtlout -pwebqtlout db_webqtl -e "select group_concat(distinct column_name) from information_schema.STATISTICS where table_schema = 'db_webqtl' and table_name = '$x' and index_type = 'FULLTEXT'" ; done
So we have to fix only
ProbeSet GeneRIF_BASIC pubmedsearch
REPAIR TABLE ProbeSet QUICK; REPAIR TABLE GeneRIF_BASIC QUICK; REPAIR TABLE pubmedsearch QUICK;
Note that GN1 search only appears to use ProbeSet. Reindexing takes about 10 minutes on Tux02.
ALTER TABLE ProbeSet ENGINE = InnoDB;
After updating to ProbeSet to innodb the following query failed
SELECT distinct ProbeSet.Name as TNAME, 0 as thistable, ProbeSetXRef.Mean as TMEAN, ProbeSetXRef.LRS as TLRS, ProbeSetXRef.PVALUE as TPVALUE, ProbeSet.Chr_num as TCHR_NUM, ProbeSet.Mb as TMB, ProbeSet.Symbol as TSYMBOL, ProbeSet.name_num as TNAME_NUM FROM ProbeSetXRef, ProbeSet WHERE ((MATCH (ProbeSet.Name, ProbeSet.description, ProbeSet.symbol, alias, GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('shh' IN BOOLEAN MODE)) or (MATCH (ProbeSet.symbol) AGAINST ('"Hx" "ShhNC" "9530036O11Rik" "Dsh" "Hhg1" "Hxl3" "M100081"' IN BOOLEAN MODE))) and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = 112 ORDER BY ProbeSet.symbol ASC;
with
ERROR 1191 (HY000): Can't find FULLTEXT index matching the column list
The shorter version works
SELECT distinct ProbeSet.Name as TNAME, 0 as thistable, ProbeSetXRef.Mean as TMEAN, ProbeSetXRef.LRS as TLRS, ProbeSetXRef.PVALUE as TPVALUE, ProbeSet.Chr_num as TCHR_NUM, ProbeSet.Mb as TMB, ProbeSet.Symbol as TSYMBOL, ProbeSet.name_num as TNAME_NUM FROM ProbeSetXRef, ProbeSet WHERE ((MATCH (ProbeSet.Name, ProbeSet.description, ProbeSet.symbol, alias, GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('"Shh" "ShhNC" "9530036O11Rik" "Dsh" "Hhg1"' IN BOOLEAN MODE))) and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = 112;
when you remove any column in the MATCH statement we get this error. Which kinda makes sense I suppose. We need to add an index for the single ProbeSet.symbol match. Create it with
CREATE FULLTEXT INDEX ft_ProbeSet_Symbol ON ProbeSet(Symbol);
Now we have
PRIMARY KEY ('Id'),
UNIQUE KEY 'ProbeSetId' ('ChipId','Name'),
KEY 'Name_IDX' ('Name'),
KEY 'symbol_IDX' ('Symbol'),
KEY 'RefSeq_TranscriptId' ('RefSeq_TranscriptId'),
KEY 'GENBANK_IDX' ('GenbankId'),
KEY 'TargetId' ('TargetId'),
KEY 'Position' ('Chr'),
KEY 'GeneId_IDX' ('GeneId'),
FULLTEXT KEY 'SEARCH_GENE_IDX' ('Symbol','alias'),
FULLTEXT KEY 'RefSeq_FULL_IDX' ('RefSeq_TranscriptId'),
FULLTEXT KEY 'SEARCH_FULL_IDX' ('Name','description','Symbol','alias','GenbankId','UniGeneId','Probe_Target_Description'),
FULLTEXT KEY 'ft_ProbeSet_Symbol' ('Symbol')
and the query works.
Converting to unicode I was getting
Specified key was too long; max key length is 3072 bytes
Turned out simple utf8 worked:
ALTER TABLE ProbeSet CONVERT TO CHARACTER SET utf8 COLLATE utf8_general_ci;
and utf8mb3 is not recommended. We'll need fix that FIXME. See
Full text search is the least straightforward, see
and
Now for ProbeSet - one of the critical locked tables we need this.
time mysqlcheck -c -u webqtlout -pwebqtlout db_webqtl db_webqtl.Docs warning : 1 client is using or hasn't closed the table properly status : OK real 16m52.567s
The largest tables are
1.6G Aug 27 2019 Probe.MYD 2.1G Aug 27 2019 LCorrRamin3.MYD 2.1G Dec 4 22:15 ProbeSetXRef.MYD 2.3G Dec 18 14:56 ProbeSet.MYD 2.6G Aug 27 2019 ProbeSE.MYD 7.1G Nov 2 05:07 ProbeSetSE.MYD 8.3G Aug 28 2019 SnpPattern.MYD 11G Aug 27 2019 ProbeData.MYD 11G May 22 2020 GenoData.MYD 11G Aug 27 2019 SnpAll.MYD 63G Dec 4 22:15 ProbeSetData.MYD
On Penguin2 we are already runing ProbeSetData as
238G Jul 10 2020 ProbeSetData.ibd
which is pretty massive! It includes the index, which is 180G, so the difference is not that great. Also we should try a 4kb page size. Also make sure to enable innodb_file_per_table.
With a recent update the following tables appeared to lock up: ProbeSet, ProbeSetFreeze, ProbeSetXRef. All of them small, so let's move them to innodb.
select count(*) from ProbeSetFreeze limit 2;
+----------+
| count(*) |
+----------+
| 931 |
+----------+
SHOW CREATE TABLE ProbeSetFreeze;
CREATE TABLE 'ProbeSetFreeze' (
'Id' smallint(5) unsigned NOT NULL AUTO_INCREMENT,
'ProbeFreezeId' smallint(5) unsigned NOT NULL DEFAULT 0,
'AvgID' smallint(5) unsigned NOT NULL DEFAULT 0,
'Name' varchar(40) DEFAULT NULL,
'Name2' varchar(100) NOT NULL DEFAULT '',
'FullName' varchar(100) NOT NULL DEFAULT '',
'ShortName' varchar(100) NOT NULL DEFAULT '',
'CreateTime' date NOT NULL DEFAULT '0000-00-00',
'OrderList' int(5) DEFAULT NULL,
'public' tinyint(4) NOT NULL DEFAULT 0,
'confidentiality' tinyint(4) NOT NULL DEFAULT 0,
'AuthorisedUsers' varchar(300) NOT NULL,
'DataScale' varchar(20) NOT NULL DEFAULT 'log2',
PRIMARY KEY ('Id'),
UNIQUE KEY 'FullName' ('FullName'),
UNIQUE KEY 'Name' ('Name'),
KEY 'NameIndex' ('Name2')
) ENGINE=MyISAM AUTO_INCREMENT=1054 DEFAULT CHARSET=latin1
There is a primary key. Good.
ALTER TABLE ProbeSetSE ADD PRIMARY KEY(DataId,StrainId); Query OK, 688744613 rows affected (15 min 13.830 sec) Records: 688744613 Duplicates: 0 Warnings: 0
Unsurprisingly the index grew
-rw-rw---- 1 mysql mysql 16G Dec 28 11:06 ProbeSetSE.MYI
MariaDB [db_webqtl]> SHOW CHARACTER SET LIKE 'utf8mb4'; +---------+---------------+--------------------+--------+ | Charset | Description | Default collation | Maxlen | +---------+---------------+--------------------+--------+ | utf8mb4 | UTF-8 Unicode | utf8mb4_general_ci | 4 | +---------+---------------+--------------------+--------+ 1 row in set (0.000 sec)
To properly convert a table with broken characters, first convet the table to BINARY format and thereafter convert to utf8mb1. Here's an example of doing that with the Investigators table:
ALTER TABLE Investigators CONVERT TO CHARACTER SET BINARY; ALTER TABLE Investigators CONVERT TO CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci;
You can read more here:
With the ProbeSetSE table:
MariaDB [db_webqtl]> ALTER TABLE ProbeSetSE CONVERT TO CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci; Stage: 2 of 2 'Enabling keys' 0% of stage done Query OK, 688744613 rows affected (15 min 14.380 sec) Records: 688744613 Duplicates: 0 Warnings: 0
For this table it has no effect since there are not text fields. Still this looks good:
SHOW CREATE TABLE ProbeSetSE;
| ProbeSetSE | CREATE TABLE "ProbeSetSE" (
"DataId" int(10) unsigned NOT NULL DEFAULT 0,
"StrainId" smallint(5) unsigned NOT NULL DEFAULT 0,
"error" float NOT NULL,
PRIMARY KEY ("DataId","StrainId"),
UNIQUE KEY "DataId" ("DataId","StrainId")
) ENGINE=MyISAM DEFAULT CHARSET=utf8mb4 |
Looking good! Now there are two indexes which are the same to
MariaDB [db_webqtl]> DROP INDEX DataId ON ProbeSetSE;
MariaDB [db_webqtl]> show index from ProbeSetSE; 2 rows in set (0.000 sec)
So, on to converting to innodb
Unfortunately we can't swith to 4k page tables because we have existing tables. We'll do that later some day in a controlled fashion.
MariaDB [db_webqtl]> ALTER TABLE ProbeSetSE ENGINE = InnoDB; Query OK, 688744613 rows affected (1 hour 51 min 36.273 sec) Records: 688744613 Duplicates: 0 Warnings: 0
2 hours for a lousy table conversion!
The new file sizes are:
-rw-rw---- 1 mysql mysql 1.5K Dec 28 11:33 ProbeSetSE.frm -rw-rw---- 1 mysql mysql 51G Dec 28 13:25 ProbeSetSE.ibd
So the has tripled (including a new index) and during conversion it has both the old and the new on disk. I'll need to make space for this baby.
Let's try OPTIMIZE
OPTIMIZE NO_WRITE_TO_BINLOG TABLE ProbeSetSE;
Ah, now the size is similar to myisam and loading the mapping page is slighty faster.
What about performance?
MariaDB [db_webqtl]> select count(*) from ProbeSetSE where strainid<20 and error<0.10; +----------+ | count(*) | +----------+ | 61625074 | +----------+ 1 row in set (3 min 22.958 sec)
Whoah. 3 times slower - which makes sense if you know the physical size of the data. Full table scans should be rare, but we need to make sure we don't slow them down that much!
Again I exported the CSV from
It took the server 1.46351s seconds to process this page. It took your browser 2.119 second(s) to render this page
and it shows practically the same results.
Prototocol from
Every table update has to follow the template:
If you have enough space, you can create a copy of the actual table and do the work on that:
CREATE TABLE new_tbl [AS] SELECT * FROM MYTABLE;
Then you can change the column as desired:
ALTER TABLE tbl_name MODIFY COLUMN col_name BIGINT AUTO_INCREMENT;
Once the process is done, you can rename the tables:
DROP MYTABLE; RENAME TABLE tbl_name TO new_tbl_name, tbl_name2 TO MYTABLE;
SHOW CREATE TABLE MYTABLE;
select * from MYTABLE limit 2;
select count(*) from MYTABLE;
Do this also on Penguin2.
rg MYTABLE --color=always |less -R
rg MYTABLE --type=py -l|fzf --preview="rg --color=always -A 20 MYTABLE {}" --preview-window=right:85%:wrap
Some select statement and maybe a page of GN2.
ALTER TABLE MYTABLE ADD PRIMARY KEY(Id);
SHOW INDEX FROM MYTABLE; DROP INDEX ProbeSetId ON MYTABLE;
ALTER TABLE MYTABLE ENGINE = InnoDB;
ALTER TABLE ProbeSetSE CONVERT TO CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci;
For those cases see bottom of move-to-innodb.gmi.
OPTIMIZE NO_WRITE_TO_BINLOG TABLE MYTABLE;
After running the optimiser rename the tables
RENAME TABLE orig TO orig_old, mytest TO orig;
In an earlier track I wrote how to deal with Fulltext fields
pjotrp 16 Oct 2019 at 10:47
Fulltext
To list fulltext info for one table do:
select group_concat(distinct column_name) from information_schema.STATISTICS where table_schema = 'db_webqtl' and table_name = 'Probeset' and index_type = 'FULLTEXT';
Or
SHOW CREATE TABLE ProbeSet;
E.g.
FULLTEXT KEY 'SEARCH_GENE_IDX' ('Symbol','alias'),
FULLTEXT KEY 'SEARCH_FULL_IDX' ('Name','description','Symbol','alias','GenbankId','UniGeneId','Probe_Target_Description'),
FULLTEXT KEY 'RefSeq_FULL_IDX' ('RefSeq_TranscriptId')
To see all:
root@tux02:/var/lib/mysql/db_webqtl# for x in ls -1 *.MYD|sed -e 's,\.MYD,,' ; do echo $x ; mysql -u webqtlout -pwebqtlout db_webqtl -e "select group_concat(distinct column_name) from information_schema.STATISTICS where table_schema = 'db_webqtl' and table_name = '$x' and index_type = 'FULLTEXT'" ; done
So we have to fix only
ProbeSet GeneRIF_BASIC pubmedsearch
(probably should not try the following)
REPAIR TABLE ProbeSet QUICK; REPAIR TABLE GeneRIF_BASIC QUICK; REPAIR TABLE pubmedsearch QUICK;
after a repair I had to
root@tux01:/var/lib/mysql/db_webqtl# myisamchk ProbeSet -r - recovering (with sort) MyISAM-table 'ProbeSet' Data records: 0 - Fixing index 1 - Fixing index 2 - Fixing index 3 etc
Note that GN1 search only appears to use ProbeSet. Reindexing takes about 10 minutes on Tux02.
After updating to ProbeSet to innodb the following query failed
SELECT distinct ProbeSet.Name as TNAME, 0 as thistable, ProbeSetXRef.Mean as TMEAN, ProbeSetXRef.LRS as TLRS, ProbeSetXRef.PVALUE as TPVALUE, ProbeSet.Chr_num as TCHR_NUM, ProbeSet.Mb as TMB, ProbeSet.Symbol as TSYMBOL, ProbeSet.name_num as TNAME_NUM FROM ProbeSetXRef, ProbeSet WHERE ((MATCH (ProbeSet.Name, ProbeSet.description, ProbeSet.symbol, alias, GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('shh' IN BOOLEAN MODE)) or (MATCH (ProbeSet.symbol) AGAINST ('"Hx" "ShhNC" "9530036O11Rik" "Dsh" "Hhg1" "Hxl3" "M100081"' IN BOOLEAN MODE))) and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = 112 ORDER BY ProbeSet.symbol ASC;
with
ERROR 1191 (HY000): Can't find FULLTEXT index matching the column list
The shorter version works
SELECT distinct ProbeSet.Name as TNAME, 0 as thistable, ProbeSetXRef.Mean as TMEAN, ProbeSetXRef.LRS as TLRS, ProbeSetXRef.PVALUE as TPVALUE, ProbeSet.Chr_num as TCHR_NUM, ProbeSet.Mb as TMB, ProbeSet.Symbol as TSYMBOL, ProbeSet.name_num as TNAME_NUM FROM ProbeSetXRef, ProbeSet WHERE ((MATCH (ProbeSet.Name, ProbeSet.description, ProbeSet.symbol, alias, GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('"Shh" "ShhNC" "9530036O11Rik" "Dsh" "Hhg1"' IN BOOLEAN MODE))) and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = 112;
when you remove any column in the MATCH statement we get this error. Which kinda makes sense I suppose. We need to add an index for the single ProbeSet.symbol match. Create it with
CREATE FULLTEXT INDEX ft_ProbeSet_Symbol ON ProbeSet(Symbol);
Now we have
FULLTEXT KEY 'SEARCH_GENE_IDX' ('Symbol','alias'),
FULLTEXT KEY 'SEARCH_FULL_IDX' ('Name','description','Symbol','alias','GenbankId','UniGeneId','Probe_Target_Description'),
FULLTEXT KEY 'RefSeq_FULL_IDX' ('RefSeq_TranscriptId'),
FULLTEXT KEY 'ft_ProbeSet_Symbol' ('Symbol')
and the query works.
pjotrp 16 Oct 2019 at 09:24 (edited)
Full text search is the least straightforward, see
and
Now for ProbeSet - one of the critical locked tables we need this.
pjotrp 15 Oct 2019 at 16:38 (edited)
time mysqlcheck -c -u webqtlout -pwebqtlout db_webqtl db_webqtl.Docs warning : 1 client is using or hasn't closed the table properly status : OK real 16m52.567s
The largest tables are
1.6G Aug 27 2019 Probe.MYD 2.1G Aug 27 2019 LCorrRamin3.MYD 2.1G Dec 4 22:15 ProbeSetXRef.MYD 2.3G Dec 18 14:56 ProbeSet.MYD 2.6G Aug 27 2019 ProbeSE.MYD 7.1G Nov 2 05:07 ProbeSetSE.MYD 8.3G Aug 28 2019 SnpPattern.MYD 11G Aug 27 2019 ProbeData.MYD 11G May 22 2020 GenoData.MYD 11G Aug 27 2019 SnpAll.MYD 63G Dec 4 22:15 ProbeSetData.MYD
On Penguin2 we are already runing ProbeSetData as
238G Jul 10 2020 ProbeSetData.ibd
which is pretty massive! It includes the index, which is 180G, so the difference is not that great. Also we should try a 4kb page size. Also make sure to enable innodb_file_per_table.
With a recent update the following tables appeared to lock up: ProbeSet, ProbeSetFreeze, ProbeSetXRef. All of them small, so let's move them to innodb.
select count(*) from ProbeSetFreeze limit 2;
+----------+
| count(*) |
+----------+
| 931 |
+----------+
SHOW CREATE TABLE ProbeSetFreeze;
CREATE TABLE 'ProbeSetFreeze' (
'Id' smallint(5) unsigned NOT NULL AUTO_INCREMENT,
'ProbeFreezeId' smallint(5) unsigned NOT NULL DEFAULT 0,
'AvgID' smallint(5) unsigned NOT NULL DEFAULT 0,
'Name' varchar(40) DEFAULT NULL,
'Name2' varchar(100) NOT NULL DEFAULT '',
'FullName' varchar(100) NOT NULL DEFAULT '',
'ShortName' varchar(100) NOT NULL DEFAULT '',
'CreateTime' date NOT NULL DEFAULT '0000-00-00',
'OrderList' int(5) DEFAULT NULL,
'public' tinyint(4) NOT NULL DEFAULT 0,
'confidentiality' tinyint(4) NOT NULL DEFAULT 0,
'AuthorisedUsers' varchar(300) NOT NULL,
'DataScale' varchar(20) NOT NULL DEFAULT 'log2',
PRIMARY KEY ('Id'),
UNIQUE KEY 'FullName' ('FullName'),
UNIQUE KEY 'Name' ('Name'),
KEY 'NameIndex' ('Name2')
) ENGINE=MyISAM AUTO_INCREMENT=1054 DEFAULT CHARSET=latin1
There is a primary key. Good. You might want to check
mysql -uwebqtlout -pwebqtlout db_webqtl SHOW FULL PROCESSLIST; flush tables; ALTER TABLE ProbeSetFreeze CONVERT TO CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci;
This makes GN a bit snappier, it appears. Next to fix is the AccessLog because Gn1 writes to it.
So:
show create table TempData; ALTER TABLE TempData ENGINE = InnoDB; ALTER TABLE TempData CONVERT TO CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci; alter table TempData add primary key (Id); show create table TempData;
Some tables showed problems with AUTO_INCREMENT. Simply redefine the column without the attribute:
ALTER TABLE Chr_Length CHANGE Id Id smallint(5) UNSIGNED NOT NULL;
I needed more disk space to move the largest tables note the new SSD disk is twice as slow as the old SSD:
/dev/nvme0n1p2: Timing buffered disk reads: 364 MB in 3.00 seconds = 121.23 MB/sec /dev/nvme2n1p6: Timing buffered disk reads: 760 MB in 3.00 seconds = 253.27 MB/sec
This is due to the caddy interface. Copying mariadb data is really slow. Meanwhile rsync shows a sustained 50Mbs to the new drive.