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ProbeSetData

Tags

  • assigned: pjotrp
  • status: unclear
  • priority: medium
  • type: enhancement
  • keywords: database, mariadb, innodb

Description

This is by far the largest table (~200Gb). I need to add disk space to be able to host it on the NVME and move stuff around. Final move is GN2 code and we have over 400Gb free.

This time I failed porting to InnoDB. Next time:

  • [ ] Move database to large drive
  • [ ] Run second instance of mariadb, upgrade too
  • [ ] Export a small version of ISAM to ISAM
  • [ ] Try different sizes of innodb exports
  • [ ] Make (ordered) conversion and test performance
  • [ ] Muck out ibdata1 and transaction logs

I disabled these and they need to be restored:

  • [X] binary log
  • [X] backup script
  • [ ] flush db - leave that off for now
  • [X] cron system-check
  • [X] systemd MYSQLD_OPTS setting

The following fetches the data to be used for mapping:

SELECT
                            Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2
                    FROM
                            (ProbeSetData, ProbeSetFreeze,
                             Strain, ProbeSet, ProbeSetXRef)
                    left join ProbeSetSE on
                            (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
                    left join NStrain on
                            (NStrain.DataId = ProbeSetData.Id AND
                            NStrain.StrainId = ProbeSetData.StrainId)
                    WHERE
                            ProbeSet.Name = '4336695' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
                            ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
                            ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA' AND
                            ProbeSetXRef.DataId = ProbeSetData.Id AND
                            ProbeSetData.StrainId = Strain.Id
                    Order BY
                            Strain.Name;

Prototocol from

Every table update has to follow the template:

Reboot Tux01 and Tux02

Table upgrade

Check recent backups

  • [X] ascertain there is a backup
  • [X] copy original files

Make temporary table

mysql 1.5K Jun 27  2021 ProbeSetData.frm
mysql  63G Dec  4 22:15 ProbeSetData.MYD
mysql 118G Dec 28 08:52 ProbeSetData.MYI
mysql 1.5K Jan  1 20:45 mytest.frm
mysql  20G Jan  1 21:34 mytest.ibd

If you have enough space, you can create a copy of the actual table and do the work on that:

Original:

| ProbeSetData | CREATE TABLE 'ProbeSetData' (
  'Id' int(10) unsigned NOT NULL DEFAULT 0,
  'StrainId' int(20) NOT NULL,
  'value' float NOT NULL,
  UNIQUE KEY 'DataId' ('Id','StrainId'),
  KEY 'strainid' ('StrainId')
) ENGINE=MyISAM DEFAULT CHARSET=latin1 |

New:

DROP table mytest2;
CREATE table mytest2(
  Id INT unsigned NOT NULL DEFAULT 0,
  StrainId MEDIUMINT unsigned NOT NULL DEFAULT 0,
  value float NOT NULL,
  primary key(Id,StrainId),
  key (StrainId)) CHARACTER SET utf8mb4 ;

Note loading latin1 is slower than utf8! I tried.

And fill it killing quite a few birds with one stone :). You may want to disable the binary logger before running:

INSERT INTO mytest2 (Id,StrainId,value) SELECT Id,StrainId,value FROM ProbeSetData LIMIT 51631478;

Makes a table at 1% of size - a table of 2.3GB. I wonder why the full thing took up 330Gb before we ran out of disk space.

Show progress

SELECT TABLE_SCHEMA,TABLE_NAME,DATA_LENGTH,AVG_ROW_LENGTH,TABLE_ROWS FROM information_schema.TABLE
S WHERE DATA_LENGTH>1000000000 order by data_length;

May add order by Id,StrainID next time.

Once the process is done, you can rename the tables:

DROP ProbeSetData;
RENAME TABLE tbl_name TO new_tbl_name, tbl_name2 TO ProbeSetData;

Check table structure

SHOW CREATE TABLE ProbeSetData;

This is a really simple table

| ProbeSetData | CREATE TABLE 'ProbeSetData' (
  'Id' int(10) unsigned NOT NULL DEFAULT 0,
  'StrainId' int(20) NOT NULL,
  'value' float NOT NULL,
  UNIQUE KEY 'DataId' ('Id','StrainId'),
  KEY 'strainid' ('StrainId')
) ENGINE=MyISAM DEFAULT CHARSET=latin1 |
MariaDB [db_webqtl]> select * from ProbeSetData limit 2;
+----+----------+-------+
| Id | StrainId | value |
+----+----------+-------+
|  1 |        1 | 5.742 |
|  1 |        2 | 5.006 |
+----+----------+-------+
2 rows in set (0.000 sec)

But large

MariaDB [db_webqtl]> select count(*) from ProbeSetData;
+------------+
| count(*)   |
+------------+
| 5141631478 |
+------------+
1 row in set (0.000 sec)

This parses the full table (MYISAM version)

MariaDB [db_webqtl]> select count(distinct id) from ProbeSetData;
+--------------------+
| count(distinct id) |
+--------------------+
|           48119047 |
+--------------------+
1 row in set (4 min 40.035 sec)

Do this also on Penguin2.

| ProbeSetData | CREATE TABLE 'ProbeSetData' (
  'Id' int(10) unsigned NOT NULL DEFAULT 0,
  'StrainId' smallint(5) unsigned NOT NULL DEFAULT 0,
  'value' float NOT NULL,
  UNIQUE KEY 'DataId' ('Id','StrainId')
) ENGINE=InnoDB DEFAULT CHARSET=latin1 |

The table layout is a bit puzzling.

MariaDB [db_webqtl]> select max(StrainId) from ProbeSetData;
+---------------+
| max(StrainId) |
+---------------+
|         65777 |
+---------------+
MariaDB [db_webqtl]> select max(Id) from ProbeSetData;
+----------+
| max(Id)  |
+----------+
| 91406791 |
+----------+

For StrainID MediumInt is a better fit with unsigned range is 0 to 16777215 and Id should be a INT (instead of BIGINT for the time being). That will make the table+indices smaller and faster. Note that MediumInt does not save RAM, just disk space. But that can impact IO performance by 25%.

When a value overflows MariaDB will throw an error. Therefore it is safe to pick the smallest possible size. So even if we grow out of values we can quickly resize the table in, say, 10 years. That is, if we are still using SQL.

Check GN1,2,3 code for use of table

rg ProbeSetData --color=always |less -R
rg ProbeSetData --type=py -l|fzf --preview="rg --color=always -A 20 ProbeSetData {}" --preview-window=right:85%:wrap

No surprises from the code scan.

Create test

Some select statement and maybe a page of GN2.

The tests we can share from ProbeSetXRef.

Page of GN2 is the mapping page, e.g.

Create primary key

ALTER TABLE ProbeSetData
  ADD PRIMARY KEY(Id,StrainId);

(no quotes for column names)

Create indices

SHOW INDEX FROM ProbeSetData;
DROP INDEX ProbeSetId ON ProbeSetData;

Convert to innodb

ALTER TABLE ProbeSetData ENGINE = InnoDB;

Change charset

ALTER TABLE ProbeSetSE CONVERT TO CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci;

Update fulltext

For those cases see bottom of move-to-innodb.gmi.

Run optimiser

OPTIMIZE NO_WRITE_TO_BINLOG TABLE ProbeSetData;

After running the optimiser rename the tables

RENAME TABLE orig TO orig_old, mytest TO orig;

Check test

Notes

I found it is a bad idea to remove large .ibd files by hand because mariadb wants to recreate them to play the transaction log.


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